Ploidy level and caffeine content in leaves of Coffea Ploidia e conteúdo de cafeína em folhas de Coffea

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Maria Bernadete Silvarolla

1999-07-01

Full Text Available Several species of Coffea and varieties of C. arabica differing in chromosome number had their caffeine content determined in the leaves. For Coffea arabica var. "Angustifolia", var. "Caturra" and var. "Icatu", it was observed caffeine decrease from the haploid (2n = 22 to tetraploid leaves (2n = 44. Caffeine in the tetraploid "Angustifolia" was decreased by 50% when compared to the haploid. Caffeine reduction was also observed in leaves of C. canephora var. "Kouilou" as chromosome number was increased (2n = 22 ® 2n = 44. In this case, caffeine in the leaves of the diploid genotype was close to 4 times higher than in the tetraploid. On the other hand it was observed an increase of the alkaloid when the chromosome number was doubled in the C. canephora var. "Robusta".Variedades e espécies de café (Coffea que diferem quanto ao número de cromossomos tiveram o conteúdo de cafeína determinado em suas folhas. Para as variedades "Angustifolia", "Caturra" e "Icatu" de Coffea arabica foi observada redução no teor de cafeína de folhas haplóides (2n = 22 em relação a tetraplóides (2n = 44. Cafeína na forma tetraplóide da var. "Angustifolia" foi reduzida em 50% quando comparada com a forma haplóide. Redução de cafeína também foi observada em folhas de C. canephora var. "Kouilou" quando o número de cromossomos aumentou (2n = 22 ® 2n = 44. Neste caso, a cafeína nas folhas do genótipo diplóide foi cerca de quatro vezes maior que no tetraplóide. Por outro lado, foi observado aumento desse alcalóide quando o número de cromossomos foi duplicado em C. canephora var. "Robusta".

Inter-genomic DNA Exchanges and Homeologous Gene Silencing Shaped the Nascent Allopolyploid Coffee Genome (Coffea arabica L.

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Philippe Lashermes

2016-09-01

Full Text Available Allopolyploidization is a biological process that has played a major role in plant speciation and evolution. Genomic changes are common consequences of polyploidization, but their dynamics over time are still poorly understood. Coffea arabica, a recently formed allotetraploid, was chosen to study genetic changes that accompany allopolyploid formation. Both RNA-seq and DNA-seq data were generated from two genetically distant C. arabica accessions. Genomic structural variation was investigated using C. canephora, one of its diploid progenitors, as reference genome. The fate of 9047 duplicate homeologous genes was inferred and compared between the accessions. The pattern of SNP density along the reference genome was consistent with the allopolyploid structure. Large genomic duplications or deletions were not detected. Two homeologous copies were retained and expressed in 96% of the genes analyzed. Nevertheless, duplicated genes were found to be affected by various genomic changes leading to homeolog loss or silencing. Genetic and epigenetic changes were evidenced that could have played a major role in the stabilization of the unique ancestral allotetraploid and its subsequent diversification. While the early evolution of C. arabica mainly involved homeologous crossover exchanges, the later stage appears to have relied on more gradual evolution involving gene conversion and homeolog silencing.

Comportamiento productivo de clones de café robusta (Coffea Canephora p en Manglaralto, Ecuador.

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Mercedes Arzube Mayorga

2017-05-01

Abstract The research was carried out in the experimental farm Manglaralto, owned by the Peninsula State University of Santa Elena, located at the coordinates UTM 528944m E and 9796468m S zone 17M datum WGS-84 at 12 msnm, with topography of less than 1%, research (Coffea canephora P., high productivity in the agroecological conditions of Manglaralto Ecuador. For the establishment of the trial, 23 clones of robust coffee, selected by COFENAC in the Amazon region of northern Ecuador, were used. The clones were arranged randomly, each clone is an experimental unit represented by 20 plants, planted at a distance of 3 x 3 meters. Preliminary results were submitted to the descriptive statistics analysis, determining measures of central tendency and mean arithmetic dispersion, standard deviation, coefficient of variation, between clones and within the clones. However, in the fourth year, clones 1, 4, 5, 6, 14, 15, 16 and 18 stand out as promising in production. The productive behavior is very encouraging considering that clone 1 obtained production of 61 quintals and the clone 15 reached 39.3 quintals of gold coffee per hectare, the other clones enunciated obtain average production of 42 quintals.

Estimating biophysical properties of coffee (Coffea canephora) plants with above-canopy field measurements, using CropSpec®

Science.gov (United States)

Putra, Bayu T. Widjaja; Soni, Peeyush; Morimoto, Eiji; Pujiyanto, Pujiyanto

2018-04-01

Remote sensing technologies have been applied to many crops, but tree crops like Robusta coffee (Coffea canephora) under shade conditions require additional attention while making above-canopy measurements. The objective of this study was to determine how well chlorophyll and nitrogen status of Robusta coffee plants can be estimated with the laser-based (CropSpec®) active sensor. This study also identified appropriate vegetation indices for estimating Nitrogen content by above-canopy measurement, using near-infra red and red-edge bands. Varying light intensity and different background of the plants were considered in developing the indices. Field experiments were conducted involving different non-destructive tools (CropSpec® and SPAD-502 chlorophyll meter). Subsequently, Kjeldahl laboratory analyses were performed to determine the actual Nitrogen content of the plants with different ages and field conditions used in the non-destructive previous stage. Measurements were undertaken for assessing the biophysical properties of tree plant. The usefulness of near-infrared and red-edge bands from these sensors in measuring critical nitrogen levels of coffee plants by above-canopy measurement are investigated in this study.

Galactinol synthase transcriptional profile in two genotypes of Coffea canephora with contrasting tolerance to drought

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Tiago Benedito Dos Santos

2015-06-01

Full Text Available Increased synthesis of galactinol and raffinose family oligosaccharides (RFOs has been reported in vegetative tissues in response to a range of abiotic stresses. In this work, we evaluated the transcriptional profile of a Coffea canephora galactinol synthase gene (CcGolS1 in two clones that differed in tolerance to water deficit in order to assess the contribution of this gene to drought tolerance. The expression of CcGolS1 in leaves was differentially regulated by water deficit, depending on the intensity of stress and the genotype. In clone 109A (drought-susceptible, the abundance of CcGolS1 transcripts decreased upon exposure to drought, reaching minimum values during recovery from severe water deficit and stress. In contrast, CcGolS1 gene expression in clone 14 (drought-tolerant was stimulated by water deficit. Changes in galactinol and RFO content did not correlate with variation in the steady-state transcript level. However, the magnitude of increase in RFO accumulation was higher in the tolerant cultivar, mainly under severe water deficit. The finding that the drought-tolerant coffee clone showed enhanced accumulation of CcGolS1 transcripts and RFOs under water deficit suggests the possibility of using this gene to improve drought tolerance in this important crop.

Cinética da secagem de clones de café (Coffea canephora Pierre em terreiro de chão batido Kinetics of coffee berry clones drying (Coffea canephora Pierre in ground pavement

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Osvaldo Resende

2010-01-01

Full Text Available Objetivou-se com o presente trabalho estudar a cinética da secagem de quatro clones de café da espécie Coffea canephora submetidos à secagem em terreiro de chão batido, bem como ajustar diferentes modelos matemáticos aos valores experimentais selecionando aquele que melhor representa o fenômeno em estudo. Foram utilizados frutos de café dos clones: Cpafro 194, Cpafro 193, Cpafro 167 e Cpafro180, colhidos com os teores de água iniciais de 1,20; 1,32; 1,51 e 1,46 (decimal base seca (b.s., respectivamente. A secagem prosseguiu em terreiro de chão batido até que o produto atingisse o teor de água de 0,137; 0,133; 0,142 e 0,140 (decimal b.s. respectivamente para os clones Cpafro 194, Cpafro 193, Cpafro 167 e Cpafro 180. Aos dados experimentais foram ajustados dez modelos matemáticos citados na literatura específica e utilizados para representação do processo de secagem de produtos agrícolas. Baseando-se em parâmetros estatísticos, conclui-se que os modelos Verma, Dois Termos e Aproximação da Difusão foram adequados para representação da secagem dos quatro clones de café analisados, e além destes, para o clone Cpafro 167, os modelos Thompson, Page, Newton, Logarítmico, Henderson e Pabis e Exponencial de Dois Termos também se mostraram satisfatórios na descrição do fenômeno; já o tempo necessário para a secagem em terreiro de chão batido dos clones de café Cpafro 194, Cpafro 193, Cpafro 167 e Cpafro 180 foi de 189,5 h.The objective of this work was to study the drying kinetics of four coffee berry clones Coffea canephora species dried in ground pavement and to fit different mathematical models to different experimental data selecting the one that best represents the phenomenon. Have been used coffee berry of clones: Cpafro 194, Cpafro 193, Cpafro 167 and Cpafro 180, harvested at moisture content of 1.20; 1.32; 1.51 e 1.46 (decimal d.b., respectively. The drying continued in ground pavement until achieved the moisture

Biomass production by Coffea canephora Pierre ex Froehner in two productives cycles

International Nuclear Information System (INIS)

Bustamante González, Carlos; Rodríguez, Maritza I.; Pérez Díaz, Alberto; Viñals, Rolando; Martín Alonso, Gloria M.; Rivera, Ramón

2015-01-01

In areas of the Estación Central de Investigaciones de Café y Cacao located in La Mandarina, Tercer Frente municipality, Santiago de Cuba province, and La Alcarraza, municipality Sagua de Tánamo, Holguín province, the biomass production of Coffea canephora Pierre ex Froehner var. Robusta was assessed from planting until the fourth year in both locations and after pruning until the fourth year in Alcarraza. The coffee trees were planted at 3 x 1,5 m in Cambisol under Samanea saman Jerr shade in the first town and Leucaena leucocephala Lam de Wit in the second. The biomass was separated into: leaves, branches, stems, fruits and roots. From 24 months and one year after pruning, leaflitter was collected monthly. For the study of the root system soil blocks of 25 x 25 x 25 cm were extracted, in an area formed by 1,5 m (distance to the street) and 0,75 m (between plants), centered relative to the coffee plant and up to a meter deep. The extracted soil represented ¼ of the volume occupied by the plant. The dry mass of each organ was determined. Dry matter production reached values of 25 t dry mass ha-1 regardless of the stage of the plantation. Until the fourth year the root system dominated the biomass, followed by the leaves and then the stems. The participation of the fruits in the biomass increased in the crop stage and when concluding the experiment the coffees had dedicated for its formation among the 16-20 % of the total dry mass, independently of the development cycle. (author)

Caracterización de genotipos élite de Coffea canephora por su tolerancia a sequía.

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Ana Odetth Quintana-Escobar

2016-12-01

Full Text Available El objetivo del presente trabajo fue identi car el grado de tolerancia a sequía en diferentes genotipos élite de Coffea canephora P. var. Robusta. El estudio se realizó del 2013 al 2015 en Tuxtla Chico, Chiapas, México. De cada genotipo (INIFAP P9, INIFAP P4, INIFAP P5, INIFAP P7, INIFAP P8 se utilizaron veinte plantas, excepto para el INIFAP P9 con doce; un grupo con la mitad de plantas de cada genotipo se mantuvo en condiciones de capacidad de campo (CC y la otra mitad en punto de marchitez permanente (PMP. Al nalizar la etapa de estrés y después del riego de recuperación, se evaluaron variables morfológicas y siológicas, tales como parámetros de crecimiento, contenido relativo de agua, acumulación de prolina, índice y densidad estomática e índice de tolerancia a sequía. Los genotipos de C. canephora presentaron entre ellos diferente grado de tolerancia al dé cit hídrico, pero compartieron entre sí la detención de sus funciones y activación de diferentes rutas para tolerar la sequía, como disminución en el contenido relativo de agua y aumento de prolina durante el periodo de estrés. Al determinar el índice de tolerancia a sequía, el genotipo más tolerante fue el INIFAP P5 de acuerdo con las variables número de hojas retenidas y totales, tasa de crecimiento relativo, número de pares de ramas plagiotrópicas y nudos totales; mientras que el INIFAP P4 se identi có como uno de los más susceptibles de acuerdo con la tasa de crecimiento relativo y el número de nudos totales, en las cuales presentó los valores más bajos.

Developing core collections to optimize the management and the exploitation of diversity of the coffee Coffea canephora.

Science.gov (United States)

Leroy, Thierry; De Bellis, Fabien; Legnate, Hyacinthe; Musoli, Pascal; Kalonji, Adrien; Loor Solórzano, Rey Gastón; Cubry, Philippe

2014-06-01

The management of diversity for conservation and breeding is of great importance for all plant species and is particularly true in perennial species, such as the coffee Coffea canephora. This species exhibits a large genetic and phenotypic diversity with six different diversity groups. Large field collections are available in the Ivory Coast, Uganda and other Asian, American and African countries but are very expensive and time consuming to establish and maintain in large areas. We propose to improve coffee germplasm management through the construction of genetic core collections derived from a set of 565 accessions that are characterized with 13 microsatellite markers. Core collections of 12, 24 and 48 accessions were defined using two methods aimed to maximize the allelic diversity (Maximization strategy) or genetic distance (Maximum-Length Sub-Tree method). A composite core collection of 77 accessions is proposed for both objectives of an optimal management of diversity and breeding. This core collection presents a gene diversity value of 0.8 and exhibits the totality of the major alleles (i.e., 184) that are present in the initial set. The seven proposed core collections constitute a valuable tool for diversity management and a foundation for breeding programs. The use of these collections for collection management in research centers and breeding perspectives for coffee improvement are discussed.

Selection of Coffea canephora parents from the botanical varieties Conilon and Robusta for the production of intervarietal hybrids

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Leilane Nicolino Lamarão de Oliveira

2018-04-01

Full Text Available ABSTRACT: The objective of this research was to quantify the genetic divergence of potential Coffea canephora parents, with the goal of developing progenies that associate the best traits of the Conilon and Robusta botanical varieties for hybrid vigor expression. Thus, 10 morphological and productive characteristics of 130 clones of Conilon and Robusta botanical varieties and their intervarietal hybrids were evaluated over 2 years. The experiment was conducted in a randomized block design with four replicates of four plants per plot. For selection of parents, the main component analysis was used to associate values with reference points obtained from the average of each botanical variety. The first two principal components allowed for the separation of the botanical varieties representing the variability contained in the original data with 76% for the first year and 69% for the second year. Although, the genotype × years interaction had significant effects, there were minor differences in the grouping from one year to the next, which is associated with the higher repeatability estimates observed in this study. It was observed that crosses with the 16-1-81I, 9-1-82L, and 13-1-61I parents of the botanical variety Robusta and the 167I, 890E, and 130I parents of the Conilon botanical variety presented greater potential for obtaining selection gains.

Etude de l’hybridation inter-spécifique entre espèces du genre Coffea en Nouvelle-Calédonie : distribution des niches favorables et structuration de la diversité

OpenAIRE

Gomez , Céline

2009-01-01

Coffee trees are originated from inter-tropical forests of Africa and Madagascar and their diversification origin areas are highly threatened. Among the 103 species of the Coffea genus, only three are cultivated: C. arabica, C. canephora and C. liberica. C. canephora has the widest natural distribution in tropical African forests, and its genetic diversity is structured in five distinct groups. The study of the genetic diversity structuring has revealed a particular importance of the Dahomey ...

The Greater Phenotypic Homeostasis of the Allopolyploid Coffea arabica Improved the Transcriptional Homeostasis Over that of Both Diploid Parents.

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Bertrand, Benoît; Bardil, Amélie; Baraille, Hélène; Dussert, Stéphane; Doulbeau, Sylvie; Dubois, Emeric; Severac, Dany; Dereeper, Alexis; Etienne, Hervé

2015-10-01

Polyploidy impacts the diversity of plant species, giving rise to novel phenotypes and leading to ecological diversification. In order to observe adaptive and evolutionary capacities of polyploids, we compared the growth, primary metabolism and transcriptomic expression level in the leaves of the newly formed allotetraploid Coffea arabica species compared with its two diploid parental species (Coffea eugenioides and Coffea canephora), exposed to four thermal regimes (TRs; 18-14, 23-19, 28-24 and 33-29°C). The growth rate of the allopolyploid C. arabica was similar to that of C. canephora under the hottest TR and that of C. eugenioides under the coldest TR. For metabolite contents measured at the hottest TR, the allopolyploid showed similar behavior to C. canephora, the parent which tolerates higher growth temperatures in the natural environment. However, at the coldest TR, the allopolyploid displayed higher sucrose, raffinose and ABA contents than those of its two parents and similar linolenic acid leaf composition and Chl content to those of C. eugenioides. At the gene expression level, few differences between the allopolyploid and its parents were observed for studied genes linked to photosynthesis, respiration and the circadian clock, whereas genes linked to redox activity showed a greater capacity of the allopolyploid for homeostasis. Finally, we found that the overall transcriptional response to TRs of the allopolyploid was more homeostatic compared with its parents. This better transcriptional homeostasis of the allopolyploid C. arabica afforded a greater phenotypic homeostasis when faced with environments that are unsuited to the diploid parental species. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Effects of gamma radiation of Cobalt-60 on arabica and conillon seeds coffea: physic-chemistry evaluation

International Nuclear Information System (INIS)

Silva, Marcus Henriques da

2012-01-01

Brazil is the largest producer and exporter of coffee in the world. The coffee bean is one of the main products of the Brazilian trade balance. Two species of coffee are the most economically important: the Coffea arabica L. and Coffea canephora Pierre is the largest representative of the Coffea canephora Pierre is the coffea conillon. Food irradiation is an area of research that aims to increase the shelf life of foods and controlling pests. This study aimed to verify the physicochemical variables of Arabica coffee and conillon were affected when exposed to doses of gamma radiation from cobalt-60. The samples were provided by Polo in Coffee Quality Technology, Federal University of Lavras - UFLA. The coffee samples were subjected to irradiation doses: 0 (control), 5 kGy and 10 kGy, a multipurpose irradiator of IPEN - Research Institute of Nuclear Energy and the University of São Paulo, at a rate of 7.5 kGy / hour. For irradiation the samples were vacuum-packed in appropriate packaging aluminised. After the process of irradiation the samples were stored at a temperature of 15 ± 1 deg C and relative humidity of 17 ± 1%. The following analyzes were performed: levels of total sugars, glucose, sucrose, caffeine, humidity, pH, total acidity, electrical conductivity and fibers. Analyses were performed 1, 30, 60 and 90 days after irradiation, and the results were submitted to analysis of variance and means were compared by Tukey test at 5%. It was observed that the analysis results of the samples irradiated with 5 kGy and 10 kGy showed values similar to the control. It was concluded that irradiation did not induce deleterious effects on arabica coffee seeds and conillon irradiated with 5 kGy and 10 kGy to 90 days after irradiation. (author)

Amélioration génétique de Coffea canephora Pierre par hybridation ...

African Journals Online (AJOL)

Le café représente l\\'un des produits échangés les plus importants dans le monde. La culture du caféier C. canephora (robusta) constitue une importante source de revenus pour les pays producteurs. En Côte d\\'Ivoire, le café et le cacao représentent 20 % du Produit Intérieur Brut, plus de 50 % des exportations et près de ...

Browse Title Index

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2006), Amélioration génétique de Coffea canephora Pierre par hybridation interspécifique : étude de descendances de première génération de Coffea canephora Pierre x Coffea congensis Froenhner, Abstract PDF. AS N'Guetta, KB Kouamanan, ...

Meta-analysis for heritability of estimates development and production traits of Coffea canephora PierreMeta-análise para estimativas de herdabilidade de características do desenvolvimento e produção do Coffea canephora Pierre

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Telde Natel Custódio

2012-12-01

Full Text Available Heritability of estimates related to development and production traits of coffee (C. canephora are widely used informations in genetic improvement programs. However, because of the great number of scientific papers published in the recent years, conflicting conclusions are observed. Thus, to summarize such information has become a necessity. In this context, a meta-analysis was conducted with the objective of summarizing the heritability estimates of traits related to the development and production of C. canephora. Heritability estimates were appraised regarding the following traits: plant height, diameter of the canopy, fruit size, maturation cycle, bean production (kg ha-1, maturation uniformity, flat bean percentage, empty bean percentage, peaberry percentage, moisture percentage of the bean at harvest, cherry coffee and coffee coconut ratio, cherry coffee and benefited coffee ratio, coffee coconut and benefited coffee ratio, percentage of medium sieve and yield. The data regarding the heritability estimates are from scientific articles published in national and international journals, congress annals, and post-graduation thesis and dissertations. The most of the appraised traits, except the diameter of the canopy and of the yield, are highly inherited, reflecting the high genetic variety of coffee plants, and possible for satisfactory genetic gains to be reached in improvement programs in which those traits are evaluated. The use of techniques of meta-analysis shows to be efficient to synthesize the results of studies of estimation of heritability obtained in experiments evaluating the characteristics related to development and production C. canephora.Estimativas de herdabilidade de características relacionadas ao desenvolvimento e produção de cafeeiros (C. canephora são informações muito utilizadas em programas de melhoramento genético, no entanto, em virtude do grande número de trabalhos científicos publicados nos últimos anos

Coffee seed physiology

NARCIS (Netherlands)

Eira, M.T.S.; Silva, da E.A.A.; Castro, de R.D.; Dussert, S.; Walters, C.; Bewley, J.D.; Hilhorst, H.W.M.

2006-01-01

Coffee is a member of the Rubiaceae family and the genus Coffea. There are more than 70 species of coffee but only two are economically important: Coffea arabica L. and Coffea canephora Pierre; 70 % of the coffee traded in the world is arabica and 30 % is robusta (C. canephora). Other species such

Agronomie Africaine - Vol 18, No 3 (2006)

African Journals Online (AJOL)

Amélioration génétique de Coffea canephora Pierre par hybridation interspécifique : étude de descendances de première génération de Coffea canephora Pierre x Coffea congensis Froenhner · EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT. AS N'Guetta, KB ...

Biochemical and molecular characterization of the antioxidative system of Coffea sp. under cold conditions in genotypes with contrasting tolerance.

Science.gov (United States)

Fortunato, Ana S; Lidon, Fernando C; Batista-Santos, Paula; Leitão, António Eduardo; Pais, Isabel P; Ribeiro, Ana I; Ramalho, José Cochicho

2010-03-15

Low positive temperature (chilling) is frequently linked to the promotion of oxidative stress conditions, and is of particular importance in the coffee plant due to its severe impact on growth, development, photosynthesis and production. Nevertheless, some acclimation ability has been reported within the Coffea genus, and is possibly related to oxidative stress control. Using an integrated biochemical and molecular approach, the characterization of the antioxidative system of genotypes with different cold acclimation abilities was performed. Experiments were carried out using 1.5-year-old coffee seedlings of Coffea canephora cv. Apoatã, C. arabica cv. Catuaí, C. dewevrei and 2 hybrids, Icatu (C. arabicaxC. canephora) and Piatã (C. dewevreixC. arabica) subjected to a gradual cold treatment and a recovery period. Icatu showed the greatest ability to control oxidative stress, as reflected by the enhancement of several antioxidative components (Cu,Zn-SOD and APX activities; ascorbate, alpha-tocopherol and chlorogenic acids (CGAs) contents) and lower reactive oxygen species contents (H(2)O(2) and OH). Gene expression studies show that GRed, DHAR and class III and IV chitinases might also be involved in the cold acclimation ability of Icatu. Catuaí showed intermediate acclimation ability through the reinforcement of some antioxidative molecules, usually to a lesser extent than that observed in Icatu. On the other hand, C. dewevrei showed the poorest response in terms of antioxidant accumulation, and also showed the greatest increase in OH values. The difference in the triggering of antioxidative traits supports the hypothesis of its importance to cold (and photoinhibition) tolerance in Coffea sp. and could provide a useful probe to identify tolerant genotypes. Copyright 2009 Elsevier GmbH. All rights reserved.

The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae.

Science.gov (United States)

Sabir, Jamal S M; Jansen, Robert K; Arasappan, Dhivya; Calderon, Virginie; Noutahi, Emmanuel; Zheng, Chunfang; Park, Seongjun; Sabir, Meshaal J; Baeshen, Mohammed N; Hajrah, Nahid H; Khiyami, Mohammad A; Baeshen, Nabih A; Obaid, Abdullah Y; Al-Malki, Abdulrahman L; Sankoff, David; El-Mabrouk, Nadia; Ruhlman, Tracey A

2016-09-22

Alkaloid accumulation in plants is activated in response to stress, is limited in distribution and specific alkaloid repertoires are variable across taxa. Rauvolfioideae (Apocynaceae, Gentianales) represents a major center of structural expansion in the monoterpenoid indole alkaloids (MIAs) yielding thousands of unique molecules including highly valuable chemotherapeutics. The paucity of genome-level data for Apocynaceae precludes a deeper understanding of MIA pathway evolution hindering the elucidation of remaining pathway enzymes and the improvement of MIA availability in planta or in vitro. We sequenced the nuclear genome of Rhazya stricta (Apocynaceae, Rauvolfioideae) and present this high quality assembly in comparison with that of coffee (Rubiaceae, Coffea canephora, Gentianales) and others to investigate the evolution of genome-scale features. The annotated Rhazya genome was used to develop the community resource, RhaCyc, a metabolic pathway database. Gene family trees were constructed to identify homologs of MIA pathway genes and to examine their evolutionary history. We found that, unlike Coffea, the Rhazya lineage has experienced many structural rearrangements. Gene tree analyses suggest recent, lineage-specific expansion and diversification among homologs encoding MIA pathway genes in Gentianales and provide candidate sequences with the potential to close gaps in characterized pathways and support prospecting for new MIA production avenues.

Potencial de Formigas (Hymenoptera: Formicidae como Agentes Anti-herbívoros em Cultivo de Café (Coffea canephora Pierre e Feijão Guandu [Cajanus cajans (L. Millsp

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Leandro Chevalier

2013-07-01

Abstract. This study analyzed the role of ants as anti-herbivore agents in Coffee (Coffea canephora Pierre and Pigeon Pea [Cajanus cajans (L. Millsp] plants in agroecosystem under organic management. In these plants we used artificial eggs and sugar solution in experiments that simulated the presence of herbivore insects. Coffee plants did not possess any natural attractive that could intensify foraging activity of ants, but pigeon pea plants were infested by treehoppers which attracted ants. Activity of ants was surveyed after sugar solution application and artificial eggs removal was measured 24 and 48 h after start of the experiments. Sugar solution sprinkled on plants foliage increased significantly the activity of ants on coffee and pigeon pea plants. The removal of artificial eggs was significantly greater in branch with ants than without ants for pigeon pea plants. The sugar solution addiction resulted in greater artificial eggs removal in pigeon pea plants, but not in coffee plants. The treatment with sugar solution and presence of treehoppers had similar effects on the activity of ants on the plants. This study showed that the application of sugar solution can be used to increase activity of ants on plants as well as the potential of ants as anti-herbivore agents can be evaluated in experiments that simulate the presence of insects on the plants.

Simple Sequence Repeat Analysis of Selected NSIC-registered Coffee Varieties in the Philippines

OpenAIRE

Daisy May C. Santos; Carla Francesca F. Besa; Angelo Joshua A. Victoria

2016-01-01

Coffee (Coffea sp.) is an important commercial crop worldwide. Three species of coffee are used as beverage, namely Coffea arabica, C. canephora, and C. liberica. Coffea arabica L. is the most cultivated among the three coffee species due to its taste quality, rich aroma, and low caffeine content. Despite its inferior taste and aroma, C. canephora Pierre ex A. Froehner, which has the highest caffeine content, is the second most widely cultivated because of its resistance to coffee diseases. O...

Effects of gamma radiation of Cobalt-60 on arabica and conillon seeds coffea: physic-chemistry evaluation; Efeitos da radiacao gama do Cobalto-60 em sementes de cafe arabica e conillon: avaliacao fisico-quimica

Energy Technology Data Exchange (ETDEWEB)

Silva, Marcus Henriques da

2012-07-01

Brazil is the largest producer and exporter of coffee in the world. The coffee bean is one of the main products of the Brazilian trade balance. Two species of coffee are the most economically important: the Coffea arabica L. and Coffea canephora Pierre is the largest representative of the Coffea canephora Pierre is the coffea conillon. Food irradiation is an area of research that aims to increase the shelf life of foods and controlling pests. This study aimed to verify the physicochemical variables of Arabica coffee and conillon were affected when exposed to doses of gamma radiation from cobalt-60. The samples were provided by Polo in Coffee Quality Technology, Federal University of Lavras - UFLA. The coffee samples were subjected to irradiation doses: 0 (control), 5 kGy and 10 kGy, a multipurpose irradiator of IPEN - Research Institute of Nuclear Energy and the University of São Paulo, at a rate of 7.5 kGy / hour. For irradiation the samples were vacuum-packed in appropriate packaging aluminised. After the process of irradiation the samples were stored at a temperature of 15 ± 1 deg C and relative humidity of 17 ± 1%. The following analyzes were performed: levels of total sugars, glucose, sucrose, caffeine, humidity, pH, total acidity, electrical conductivity and fibers. Analyses were performed 1, 30, 60 and 90 days after irradiation, and the results were submitted to analysis of variance and means were compared by Tukey test at 5%. It was observed that the analysis results of the samples irradiated with 5 kGy and 10 kGy showed values similar to the control. It was concluded that irradiation did not induce deleterious effects on arabica coffee seeds and conillon irradiated with 5 kGy and 10 kGy to 90 days after irradiation. (author)

New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination.

Science.gov (United States)

Jacques, Marie-Agnès; Denancé, Nicolas; Legendre, Bruno; Morel, Emmanuelle; Briand, Martial; Mississipi, Stelly; Durand, Karine; Olivier, Valérie; Portier, Perrine; Poliakoff, Françoise; Crouzillat, Dominique

2015-12-28

Xylella fastidiosa is a xylem-limited phytopathogenic bacterium endemic to the Americas that has recently emerged in Asia and Europe. Although this bacterium is classified as a quarantine organism in the European Union, importation of plant material from contaminated areas and latent infection in asymptomatic plants have engendered its inevitable introduction. In 2012, four coffee plants (Coffea arabica and Coffea canephora) with leaf scorch symptoms growing in a confined greenhouse were detected and intercepted in France. After identification of the causal agent, this outbreak was eradicated. Three X. fastidiosa strains were isolated from these plants, confirming a preliminary identification based on immunology. The strains were characterized by multiplex PCR and by multilocus sequence analysis/typing (MLSA-MLST) based on seven housekeeping genes. One strain, CFBP 8073, isolated from C. canephora imported from Mexico, was assigned to X. fastidiosa subsp. fastidiosa/X. fastidiosa subsp. sandyi. This strain harbors a novel sequence type (ST) with novel alleles at two loci. The two other strains, CFBP 8072 and CFBP 8074, isolated from Coffea arabica imported from Ecuador, were allocated to X. fastidiosa subsp. pauca. These two strains shared a novel ST with novel alleles at two loci. These MLST profiles showed evidence of recombination events. We provide genome sequences for CFBP 8072 and CFBP 8073 strains. Comparative genomic analyses of these two genome sequences with publicly available X. fastidiosa genomes, including the Italian strain CoDiRO, confirmed these phylogenetic positions and provided candidate alleles for coffee plant adaptation. This study demonstrates the global diversity of X. fastidiosa and highlights the diversity of strains isolated from coffee plants. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Coffea canephora Pierre

African Journals Online (AJOL)

Uganda has been hampered by logistics. These clonal ... confirmed that it is highly profitable to apply nitrogen to robusta coffee. The differences ..... cost of in yield over due to response profit"'. /ha/year {kg}"1. Nitrogen zero level {kg) to ...

Identification and chromosomal distribution of copia-like retrotransposon sequences in the coffee (Coffea L. genome

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Juan-Carlos Herrera

2013-12-01

Full Text Available The presence of copia-like transposable elements in seven coffee (Coffea sp. species, including the cultivated Coffea arabica, was investigated. The highly conserved domains of the reverse transcriptase (RT present in the copia retrotransposons were amplified by PCR using degenerated primers. Fragments of roughly 300 bp were obtained and the nucleotide sequence was determined for 36 clones, 19 of which showed good quality. The deduced amino acid sequences were compared by multiple alignment analysis. The data suggested two distinct coffee RT groups, designated as CRTG1 and CRTG2. The sequence identities among the groups ranged from 52 to 60% for CRTG1 and 74 to 85% for CRTG2. The multiple alignment analysis revealed that some of the clones in CRTG1 were closely related to the representative elements present in other plant species such as Brassica napus, Populus ciliata and Picea abis. Furthermore, the chromosomal localization of the RT domains in C. arabica and their putative ancestors was investigated by fluorescence in situ hybridization (FISH analysis. FISH signals were observed throughout the chromosomes following a similar dispersed pattern with some localized regions exhibiting higher concentrations of those elements, providing new evidence of their relative conservation and stability in the coffee genome

Fumonisin B2 production by Aspergillus niger in Thai coffee beans

NARCIS (Netherlands)

Noonim, P.; Mahakarnchanakul, W.; Nielsen, K.F.; Frisvad, J.C.; Samson, R.A.

2009-01-01

During 2006 and 2007, a total of 64 Thai dried coffee bean samples (Coffea arabica) from two growing sites in Chiangmai Province and 32 Thai dried coffee bean samples (Coffea canephora) from two growing sites in Chumporn Province, Thailand, were collected and assessed for fumonisin contamination by

Absorção, translocação e utilização de zinco, cobre e manganês por mudas enxertadas de Coffea arabica Absorption, translocation and utilization of zinc, copper and manganese in grafted seedlings of Coffea arabica

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Marcelo Antonio Tomaz

2006-04-01

Full Text Available Comparativamente ao pé-franco, a combinação enxerto/porta-enxerto altera os complexos mecanismos de "feedback" entre parte aérea e raízes, afetando de maneira positiva ou negativa a eficiência nutricional da planta. Este trabalho teve como objetivo avaliar, em cultivo hidropônico, a eficiência da absorção, translocação e utilização de Zn, Cu e Mn por mudas de Coffea arabica L., de acordo com o porta-enxerto utilizado. O experimento foi realizado em casa de vegetação, por um período de 170 dias, em vasos que continham areia como substrato, recebendo solução nutritiva circulante. Utilizaram-se, como enxerto, quatro genótipos de C. arabica: os cultivares Catuaí Vermelho IAC 15 e Oeiras MG 6851 e os híbridos 'H 419-10-3-1-5' e 'H 514-5-5-3' , e, como porta-enxerto, quatro genótipos, sendo três de Coffea canephora Pierre ex Froenher: Apoatã LC 2258, Conilon Muriaé-1 e RC EMCAPA 8141 (recombinação entre clones da variedade Robustão Capixaba - EMCAPA 8141 e uma linhagem de Coffea arabica L.: Mundo Novo IAC 376-4, além de quatro pés-francos. O delineamento experimental utilizado foi em blocos casualizados com 20 tratamentos, quatro repetições e uma planta por parcela. A eficiência nutricional das mudas quanto ao Zn, Cu e Mn variou de acordo com a combinação enxerto/porta-enxerto. A progênie 'H 514-5-5-3' foi mais eficiente quanto à utilização de Zn, Cu e Mn e produção de matéria seca, quando combinada com os porta-enxertos Apoatã LC 2258 e Mundo Novo IAC 376-4. O Catuaí Vermelho IAC 15 foi mais eficiente na utilização de Cu e Mn quando combinado com Apoatã LC 2258.There are complexes feedback mechanisms involving the relationship rootstock/scion, whick can positively or negatively affect the plant nutrient efficiency use. The goal of the present work was to evaluate the efficiency of uptake, translocation and utilization of Zn, Cu and Mn in coffee seedlings. The experiment was carried out in a greenhouse

Glomus halonatum Rose & Trappe (Glomeromycota in South America: comments on the morphological characteristics of the species Glomus halonatum Rose & Trappe (Glomeromycota na América do Sul: comentários sobre a morfologia das espécies

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Bruno Tomio Goto

2009-12-01

Full Text Available Ornamented glomerospores of an arbuscular mycorrhizal fungus were collected from an area of Atlantic Forest in Goiana (Pernambuco, Brazil. The area had been cultivated with Coffea canephora Pierre ex. Froehner [=Coffea robusta (L. Linden] and Bixa orellana L., then left fallow and today is covered by herbaceous raider species. After taxonomic analysis using current descriptive and terminological criteria, the species was identified as Glomus halonatum. A description, illustrations and comments about the species are presented.Glomerosporos ornamentados de um fungo micorrízico arbuscular foram coletados em uma área de Floresta Atlântica em Goiana (Pernambuco, Brasil. A área tinha sido cultivada com Coffea canephora Pierre ex. Froehner [=Coffea robusta (L. Linden] e Bixa orellana L., abandonada, e hoje está coberta por espécies herbáceas invasoras. Após análise taxonômica usando critérios descritivos e terminológicos atuais, a espécie foi identificada como Glomus halonatum. São apresentados descrição, ilustrações e comentários sobre a espécie.

Variation of Potential Yield of Hybrid Population of Robusta coffee (Coffea canepor

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Novie Pranata Erdiansyah

2014-08-01

Full Text Available The low yield of Robusta coffee in Indonesia may be due to the use of planting materials derived from seeds. The research objective was to determine the variation of Robusta coffee yield wich local propagated by using seeds. The study was conducted in Kaliwining experimental Station of ICCRI (Indonesian Coffee andCocoa Research Institute. There were two populations observed. Number of progeny used in this study were 186 genotypes consisting of two groups from crossesBP 409 x Q 121 with 89 progenies and BP 961 x BP 409 with 81 progenies. The results showed that planting materials from seeds exhibit properties mixed results.Progeny that have the best results (yield more than 2 ton/ha not more than 5% of the total population. In both populations there is a big difference between the progenythat has high and low yield. Highest yield B population could reach 2,500 kg/ha and the C population reached 2,200 kg/ha. The lowest yield can only produce coffee270 kg/ha in populations B and 120 kg/ha in population C.Key words: Coffea canephora, hybrid, variation, yield

Simple Sequence Repeat Analysis of Selected NSIC-registered Coffee Varieties in the Philippines

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Daisy May C. Santos

2016-06-01

Full Text Available Coffee (Coffea sp. is an important commercial crop worldwide. Three species of coffee are used as beverage, namely Coffea arabica, C. canephora, and C. liberica. Coffea arabica L. is the most cultivated among the three coffee species due to its taste quality, rich aroma, and low caffeine content. Despite its inferior taste and aroma, C. canephora Pierre ex A. Froehner, which has the highest caffeine content, is the second most widely cultivated because of its resistance to coffee diseases. On the other hand, C. liberica W.Bull ex Hierncomes is characterized by its very strong taste and flavor. The Philippines used to be a leading exporter of coffee until coffee rust destroyed the farms in Batangas, home of the famous Kapeng Barako. The country has been attempting to revive the coffee industry by focusing on the production of specialty coffee with registered varieties on the National Seed Industry Council (NSIC. Correct identification and isolation of pure coffee beans are the main factors that determine coffee’s market value. Local farms usually misidentify and mix coffee beans of different varieties, leading to the depreciation of their value. This study used simple sequence repeat (SSR markers to evaluate and distinguish Philippine NSIC-registered coffee species and varieties. The neighbor-joining tree generated using PAUP showed high bootstrap support, separating C. arabica, C. canephora, and C. liberica from each other. Among the twenty primer pairs used, seven were able to distinguish C. arabica, nine for C. liberica, and one for C. canephora.

Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content.

Science.gov (United States)

Tran, Hue T M; Ramaraj, Thiruvarangan; Furtado, Agnelo; Lee, Leonard Slade; Henry, Robert J

2018-03-07

Arabica coffee (Coffea arabica) has a small gene pool limiting genetic improvement. Selection for caffeine content within this gene pool would be assisted by identification of the genes controlling this important trait. Sequencing of DNA bulks from 18 genotypes with extreme high- or low-caffeine content from a population of 232 genotypes was used to identify linked polymorphisms. To obtain a reference genome, a whole genome assembly of arabica coffee (variety K7) was achieved by sequencing using short read (Illumina) and long-read (PacBio) technology. Assembly was performed using a range of assembly tools resulting in 76 409 scaffolds with a scaffold N50 of 54 544 bp and a total scaffold length of 1448 Mb. Validation of the genome assembly using different tools showed high completeness of the genome. More than 99% of transcriptome sequences mapped to the C. arabica draft genome, and 89% of BUSCOs were present. The assembled genome annotated using AUGUSTUS yielded 99 829 gene models. Using the draft arabica genome as reference in mapping and variant calling allowed the detection of 1444 nonsynonymous single nucleotide polymorphisms (SNPs) associated with caffeine content. Based on Kyoto Encyclopaedia of Genes and Genomes pathway-based analysis, 65 caffeine-associated SNPs were discovered, among which 11 SNPs were associated with genes encoding enzymes involved in the conversion of substrates, which participate in the caffeine biosynthesis pathways. This analysis demonstrated the complex genetic control of this key trait in coffee. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits.

Science.gov (United States)

Privat, Isabelle; Bardil, Amélie; Gomez, Aureliano Bombarely; Severac, Dany; Dantec, Christelle; Fuentes, Ivanna; Mueller, Lukas; Joët, Thierry; Pot, David; Foucrier, Séverine; Dussert, Stéphane; Leroy, Thierry; Journot, Laurent; de Kochko, Alexandre; Campa, Claudine; Combes, Marie-Christine; Lashermes, Philippe; Bertrand, Benoit

2011-01-05

Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics. The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta). Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers) in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica). Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study. We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics). This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research.

The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits

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Leroy Thierry

2011-01-01

Full Text Available Abstract Background Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics. Results The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta. Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica. Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study. Conclusion We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics. This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid, drastically enlarging its impact for high-throughput gene expression in the community of coffee research.

Qualidade da bebida em espécies e populações derivadas de híbridos interespecíficos de Coffea Cupping quality of coffee species and interspecific hybrids

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Alcides Carvalho

1990-01-01

Full Text Available Avaliou-se, em dois experimentos, a qualidade da bebida das espécies Coffea canephora e C. congensis e derivados de híbridações interespecíficas [C. canephora duplicado (dp x C. arabica, C. canephora x C. eugenioides, C. arabica x C. dewevrei dp e C. racemosa x C. arabica]. Por tratar-se de análise de bebida de cafés pouco conhecidos, avaliou-se a eficiência de uma escala de 1 a 10 pontos em comparação à escala de 0 a 5 pontos utilizada para C. arabica. Foram, também, acrescentadas pelos provadores indicações relacionadas ao gosto da bebida. A escala de 6 pontos mostrou-se pouco eficaz na discriminação dos tratamentos e a de 10 pontos, utilizada alternativamente, revelou-se mais eficiente nos dois experimentos. No primeiro, verificou-se, quanto à qualidade, uma superioridade dos grupos C arabica x C. dewevrei dp e C. canephora dp x C. arabica pelas duas escalas. No segundo experimento, o grupo C. racemosa x C. arabica apresentou a maior média, apesar de não diferir, pela escala 1, dos demais grupos. Pela escala 2, superou, no entanto, os grupos C. canephora e C. congensis. Gostos incomuns foram observados nas amostras com relação à bebida. Atribuem-se à grande diversidade do material analisado e a falta de familiarização dos provadores com espécies bem diferentes de C. arabica, certas discrepâncias com relação à determinação desses defeitos nas amostras analisadas.Investigations on coffee cupping quality of the species C. canephora, C. congensis and several populations derived from interespecific crosses (C. canephora dp x C. arabica, C. canephora x C. eugenioides, C. arabica x C. dewevrei dp and C. racemosa x C. arabica were undertaken in two trials, in order to guide breeding programs using this germoplasm. Two grading systems were used for classification of the cupping quality, the normal six points scale used for C. arabica samples and a new one with 10 points, 1 for the lowest and 10 for the highest quality

Crescimento, fotossíntese e composição mineral em genótipos de Coffea com potencial para utilização como porta-enxerto Growth, photosynthesis and mineral composition of Coffea germplasm with potential as rootstock

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Eduardo Lauriano Alfonsi

2005-01-01

Full Text Available Foi estudado o desenvolvimento da parte aérea e das raízes, as trocas gasosas fotossintéticas e a composição mineral nos genótipos de Coffea, Apoatã IAC 2258 (C. canephora; Bangelan IAC col. 5 (C. congensis X C. canephora; Catuaí IAC 144 (C. arabica; Excelsa (C. liberica, var. dewevrei e Piatã (IAC 387 (C. arabica X C. liberica, var. dewevrei, visando conhecer seus potenciais para utilização como porta-enxerto em C. arabica. Utilizaram-se plantas jovens cultivadas em terra, contida em saco plástico e em tubos de PVC sob telado, e no campo em plantas de quatro anos de idade. Em 'Bangelan' observaram-se maior comprimento da raiz pivotante e mais quantidade de raízes secundárias do que em 'Catuaí' e 'Piatã'. Os teores foliares de potássio do 'Piatã', 'Apoatã' e 'Bangelan' foram maiores aos observados para 'Catuaí' e 'Excelsa'. No campo, com baixa disponibilidade de água e nutrientes, os teores foliares de fósforo em 'Apoatã' e 'Piatã' foram maiores que em 'Catuaí' e 'Excelsa'. Em 'Catuaí,' notou-se maior eficiência na absorção de todos os micronutrientes (B, Cu, Mn e Zn, exceto ferro. A taxa fotossintética, condutância estomática e transpiração decresceram à tarde em todos os genótipos. Sob défice hídrico no solo, houve quedas significativas nas taxas fotossintéticas, condutância estomática e transpiração, sendo mais pronunciadas em 'Apoatã' e 'Excelsa', e menos em 'Catuaí' e 'Piatã', em relação aos valores observados sem restrição hídrica. A taxa fotossintética do 'Apoatã' foi menos influenciada pelo teor de água no solo em relação aos demais genótipos, que mostraram quedas acentuadas no período da tarde. Verificaram-se em 'Bangelan' e 'Apoatã' características favoráveis para a utilização como porta-enxerto em C. arabica.The development of shoot and roots, photosynthetic gas exchange and mineral composition of Coffea plants were studied in 'Apoatã' IAC 2258 (C. canephora, 'Bangelan

Sustained photosynthetic performance of Coffea spp. under long-term enhanced [CO2].

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José C Ramalho

Full Text Available Coffee is one of the world's most traded agricultural products. Modeling studies have predicted that climate change will have a strong impact on the suitability of current cultivation areas, but these studies have not anticipated possible mitigating effects of the elevated atmospheric [CO2] because no information exists for the coffee plant. Potted plants from two genotypes of Coffea arabica and one of C. canephora were grown under controlled conditions of irradiance (800 μmol m(-2 s(-1, RH (75% and 380 or 700 μL CO2 L(-1 for 1 year, without water, nutrient or root development restrictions. In all genotypes, the high [CO2] treatment promoted opposite trends for stomatal density and size, which decreased and increased, respectively. Regardless of the genotype or the growth [CO2], the net rate of CO2 assimilation increased (34-49% when measured at 700 than at 380 μL CO2 L(-1. This result, together with the almost unchanged stomatal conductance, led to an instantaneous water use efficiency increase. The results also showed a reinforcement of photosynthetic (and respiratory components, namely thylakoid electron transport and the activities of RuBisCo, ribulose 5-phosphate kinase, malate dehydrogenase and pyruvate kinase, what may have contributed to the enhancements in the maximum rates of electron transport, carboxylation and photosynthetic capacity under elevated [CO2], although these responses were genotype dependent. The photosystem II efficiency, energy driven to photochemical events, non-structural carbohydrates, photosynthetic pigment and membrane permeability did not respond to [CO2] supply. Some alterations in total fatty acid content and the unsaturation level of the chloroplast membranes were noted but, apparently, did not affect photosynthetic functioning. Despite some differences among the genotypes, no clear species-dependent responses to elevated [CO2] were observed. Overall, as no apparent sign of photosynthetic down

Sustained Photosynthetic Performance of Coffea spp. under Long-Term Enhanced [CO2

Science.gov (United States)

Ramalho, José C.; Rodrigues, Ana P.; Semedo, José N.; Pais, Isabel P.; Martins, Lima D.; Simões-Costa, Maria C.; Leitão, António E.; Fortunato, Ana S.; Batista-Santos, Paula; Palos, Isabel M.; Tomaz, Marcelo A.; Scotti-Campos, Paula; Lidon, Fernando C.; DaMatta, Fábio M.

2013-01-01

Coffee is one of the world’s most traded agricultural products. Modeling studies have predicted that climate change will have a strong impact on the suitability of current cultivation areas, but these studies have not anticipated possible mitigating effects of the elevated atmospheric [CO2] because no information exists for the coffee plant. Potted plants from two genotypes of Coffea arabica and one of C. canephora were grown under controlled conditions of irradiance (800 μmol m-2 s-1), RH (75%) and 380 or 700 μL CO2 L-1 for 1 year, without water, nutrient or root development restrictions. In all genotypes, the high [CO2] treatment promoted opposite trends for stomatal density and size, which decreased and increased, respectively. Regardless of the genotype or the growth [CO2], the net rate of CO2 assimilation increased (34-49%) when measured at 700 than at 380 μL CO2 L-1. This result, together with the almost unchanged stomatal conductance, led to an instantaneous water use efficiency increase. The results also showed a reinforcement of photosynthetic (and respiratory) components, namely thylakoid electron transport and the activities of RuBisCo, ribulose 5-phosphate kinase, malate dehydrogenase and pyruvate kinase, what may have contributed to the enhancements in the maximum rates of electron transport, carboxylation and photosynthetic capacity under elevated [CO2], although these responses were genotype dependent. The photosystem II efficiency, energy driven to photochemical events, non-structural carbohydrates, photosynthetic pigment and membrane permeability did not respond to [CO2] supply. Some alterations in total fatty acid content and the unsaturation level of the chloroplast membranes were noted but, apparently, did not affect photosynthetic functioning. Despite some differences among the genotypes, no clear species-dependent responses to elevated [CO2] were observed. Overall, as no apparent sign of photosynthetic down-regulation was found, our data

Climate-based statistical regression models for crop yield forecasting of coffee in humid tropical Kerala, India

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Jayakumar, M.; Rajavel, M.; Surendran, U.

2016-12-01

A study on the variability of coffee yield of both Coffea arabica and Coffea canephora as influenced by climate parameters (rainfall (RF), maximum temperature (Tmax), minimum temperature (Tmin), and mean relative humidity (RH)) was undertaken at Regional Coffee Research Station, Chundale, Wayanad, Kerala State, India. The result on the coffee yield data of 30 years (1980 to 2009) revealed that the yield of coffee is fluctuating with the variations in climatic parameters. Among the species, productivity was higher for C. canephora coffee than C. arabica in most of the years. Maximum yield of C. canephora (2040 kg ha-1) was recorded in 2003-2004 and there was declining trend of yield noticed in the recent years. Similarly, the maximum yield of C. arabica (1745 kg ha-1) was recorded in 1988-1989 and decreased yield was noticed in the subsequent years till 1997-1998 due to year to year variability in climate. The highest correlation coefficient was found between the yield of C. arabica coffee and maximum temperature during January (0.7) and between C. arabica coffee yield and RH during July (0.4). Yield of C. canephora coffee had highest correlation with maximum temperature, RH and rainfall during February. Statistical regression model between selected climatic parameters and yield of C. arabica and C. canephora coffee was developed to forecast the yield of coffee in Wayanad district in Kerala. The model was validated for years 2010, 2011, and 2012 with the coffee yield data obtained during the years and the prediction was found to be good.

Avaliação de genótipos de cafeeiros Arabica e Robusta no estado do Acre Evaluation of Arabica and Robusta coffee genotypes in the state of Acre

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Celso Luis Bergo

2008-02-01

Full Text Available Conduziu-se este trabalho, com o objetivo de introduzir e avaliar 40 genótipos de cafeeiros das espécies Coffea arabica e Coffea canephora nas condições edafoclimáticas do Estado do Acre, visando disponibilizar aos cafeicultores acreanos, cultivares com melhor potencial produtivo. Da espécie C. arabica foram avaliados genótipos das cultivares Icatu, Bourbon, Mundo Novo, Catuaí, Obatã e Catimor. Da espécie C. canephora foram avaliadas as cultivares Conilon e Robusta, caracterizadas como Grupo Robusta. Os genótipos utilizados foram provenientes do Instituto Agronômico de Campinas (IAC e da Embrapa Rondônia. O experimento foi conduzido no Campo Experimental da Embrapa Acre, Rio Branco, AC, no período de 1995 a 2004. O delineamento experimental foi em blocos casualizados com cinco repetições. As características avaliadas foram: produtividade, altura, diâmetro da copa e vigor. Da espécie C. arabica, grupo Icatu, destacou-se Icatu-PR-182039-1(IAC H 4782-7-788 com produtividade média de café beneficiado de 34 sc/ ha, Icatu IAC-4041; Icatu IAC-2945; Icatu IAC-2944-MT; Icatu IAC-4040 e Icatu IAC-4046 com produtividade variando de 20 a 26 sacas. Para o grupo Catuaí os melhores genótipos foram Obatã IAC 4275, Obatã IAC 1169 e Catimor IAC 4466 com produtividade média de café beneficiado de 49, 45 e 37 sacas por hectare respectivamente. Na espécie C. canephora foram avaliados 8 genótipos das cultivares Conilon e Robusta e quanto à produtividade não houve diferença estatística, observou-se incremento de 7 sacas/ha para a variedade Conilon IAC 66-3 quando comparado ao Conilon plantado na região. Nesta espécie os genótipos apresentaram sintomas de deficiência hídrica na época seca (julho/agosto.This work aimed to introduce and evaluate 40 coffee genotypes of Coffea arabica e Coffea canephora species in soil and weather conditions of Acre and had as main goal to provide cultivars to coffee producers with better potential of

Development of an instant coffee enriched with chlorogenic acids.

Science.gov (United States)

Corso, Marinês Paula; Vignoli, Josiane Alessandra; Benassi, Marta de Toledo

2016-03-01

The objective of this study was to present possible formulations for an instant coffee product enriched with chlorogenic acids for the Brazilian market. Formulations were prepared with different concentrations of freeze dried extracts of green Coffea canephora beans (G) added to freeze dried extracts of roasted Coffea arabica (A) and Coffea canephora (C). Medium (M) and dark (D) roasting degrees instant coffee were produced (AM, AD, CM and CD) to obtain four formulations with green extract addition (AMG, ADG, CMG and CDG). Chlorogenic acids were determined by HPLC, with average contents of 7.2 %. Roasted extracts and formulations were evaluated for 5-CQA and caffeine contents (by HPLC), browned compounds (absorbance 420 nm), and antioxidant activity (ABTS and Folin). Coffee brews of the four formulations were also assessed in a lab-scale test by 42 consumers for acceptance of the color, aroma, flavor and body, overall acceptance and purchase intent, using a 10 cm hybrid scale. The formulations obtained acceptance scores of 6.6 and 7.7 for all attributes, thus they were equally acceptable. Greater purchase intent was observed for ADG, CDG and CMG (6.9) in comparison to AMG (6.1). The formulations had, on average, 2.5 times more 5-CQA than the average obtained from conventional commercial instant coffees. In addition to being more economically viable, the formulations developed with C. canephora (CDG and CMG) showed greater antioxidant potential (32.5 g of Trolox/100 g and 13.8 g of gallic acid equivalent/100 g) due to a balance in the amount of bioactive compounds.

A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms.

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Christiane Noronha Fernandes-Brum

Full Text Available microRNAs (miRNAs are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs are derived from double-stranded RNA (dsRNA or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL in processing the smallRNAs (sRNAs and ARGONAUTE (AGO as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR, Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover. We aimed to unravel the components and functions of the RNA-guided silencing pathway in a non-model plant species of worldwide economic relevance. The sRNA-guided silencing complex members have been identified in the Coffea canephora genome, and they have been characterized at the structural, functional, and evolutionary levels by computational analyses. Eleven AGO proteins, nine DCL proteins (which include a DCL1-like protein that was not previously annotated, and eight RDR proteins were identified. Another 48 proteins implicated in smallRNA (sRNA pathways were also identified. Furthermore, we identified 235 miRNA precursors and 317 mature miRNAs from 113 MIR families, and we characterized ccp-MIR156, ccp-MIR172, and ccp-MIR390. Target prediction and gene ontology analyses of 2239 putative targets showed that significant pathways in coffee are targeted by miRNAs. We provide evidence of the expansion of the loci related to sRNA pathways, insights into the activities of these proteins by domain and catalytic site analyses, and gene expression analysis. The number of MIR loci and their targeted pathways highlight the importance of miRNAs in coffee. We identified several roles of sRNAs in C. canephora, which offers substantial insight into better understanding the transcriptional and post-transcriptional regulation of this major crop.

Evaluation naturelle de l'impact de Beauveria bassiana ...

African Journals Online (AJOL)

A study of finding out natural enemies of the coffee cherry borer beetle Coffea canephora, Hypothenemus hampei (Ferrari) (Coleoptera, Scolytidae) was carried out at two ecologically different sites of Cameroon: Nkoemvone in the South region of the country and Nkolbisson around Yaoundé in the central region. For six ...

Coffee vs. Cacao: A Case Study from the Vietnamese Central Highlands

Science.gov (United States)

Ha, Dang Thanh; Shively, Gerald

2005-01-01

Mr. Nam, the vice chair of a village in Dak Lak province of Vietnam, was keen to protect farmers in his village from the sharp decline in prices of coffee ("Coffea canephora" Pierre ex Froehner). He did this by encouraging farmers in his village to plant cacao ("Theobroma cacao" L. subsp. "cacao"). Cacao was suitable…

Alpha-amylase inhibitor-1 gene from Phaseolus vulgaris expressed in Coffea arabica plants inhibits alpha-amylases from the coffee berry borer pest.

Science.gov (United States)

Barbosa, Aulus E A D; Albuquerque, Erika V S; Silva, Maria C M; Souza, Djair S L; Oliveira-Neto, Osmundo B; Valencia, Arnubio; Rocha, Thales L; Grossi-de-Sa, Maria F

2010-06-17

Coffee is an important crop and is crucial to the economy of many developing countries, generating around US$70 billion per year. There are 115 species in the Coffea genus, but only two, C. arabica and C. canephora, are commercially cultivated. Coffee plants are attacked by many pathogens and insect-pests, which affect not only the production of coffee but also its grain quality, reducing the commercial value of the product. The main insect-pest, the coffee berry borer (Hypotheneumus hampei), is responsible for worldwide annual losses of around US$500 million. The coffee berry borer exclusively damages the coffee berries, and it is mainly controlled by organochlorine insecticides that are both toxic and carcinogenic. Unfortunately, natural resistance in the genus Coffea to H. hampei has not been documented. To overcome these problems, biotechnological strategies can be used to introduce an alpha-amylase inhibitor gene (alpha-AI1), which confers resistance against the coffee berry borer insect-pest, into C. arabica plants. We transformed C. arabica with the alpha-amylase inhibitor-1 gene (alpha-AI1) from the common bean, Phaseolus vulgaris, under control of the seed-specific phytohemagglutinin promoter (PHA-L). The presence of the alpha-AI1 gene in six regenerated transgenic T1 coffee plants was identified by PCR and Southern blotting. Immunoblotting and ELISA experiments using antibodies against alpha-AI1 inhibitor showed a maximum alpha-AI1 concentration of 0.29% in crude seed extracts. Inhibitory in vitro assays of the alpha-AI1 protein against H. hampei alpha-amylases in transgenic seed extracts showed up to 88% inhibition of enzyme activity. This is the first report showing the production of transgenic coffee plants with the biotechnological potential to control the coffee berry borer, the most important insect-pest of crop coffee.

α-Amylase inhibitor-1 gene from Phaseolus vulgaris expressed in Coffea arabica plants inhibits α-amylases from the coffee berry borer pest

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Oliveira-Neto Osmundo B

2010-06-01

Full Text Available Abstract Background Coffee is an important crop and is crucial to the economy of many developing countries, generating around US$70 billion per year. There are 115 species in the Coffea genus, but only two, C. arabica and C. canephora, are commercially cultivated. Coffee plants are attacked by many pathogens and insect-pests, which affect not only the production of coffee but also its grain quality, reducing the commercial value of the product. The main insect-pest, the coffee berry borer (Hypotheneumus hampei, is responsible for worldwide annual losses of around US$500 million. The coffee berry borer exclusively damages the coffee berries, and it is mainly controlled by organochlorine insecticides that are both toxic and carcinogenic. Unfortunately, natural resistance in the genus Coffea to H. hampei has not been documented. To overcome these problems, biotechnological strategies can be used to introduce an α-amylase inhibitor gene (α-AI1, which confers resistance against the coffee berry borer insect-pest, into C. arabica plants. Results We transformed C. arabica with the α-amylase inhibitor-1 gene (α-AI1 from the common bean, Phaseolus vulgaris, under control of the seed-specific phytohemagglutinin promoter (PHA-L. The presence of the α-AI1 gene in six regenerated transgenic T1 coffee plants was identified by PCR and Southern blotting. Immunoblotting and ELISA experiments using antibodies against α-AI1 inhibitor showed a maximum α-AI1 concentration of 0.29% in crude seed extracts. Inhibitory in vitro assays of the α-AI1 protein against H. hampei α-amylases in transgenic seed extracts showed up to 88% inhibition of enzyme activity. Conclusions This is the first report showing the production of transgenic coffee plants with the biotechnological potential to control the coffee berry borer, the most important insect-pest of crop coffee.

Recent Advances in the Genetic Transformation of Coffee

Science.gov (United States)

Mishra, M. K.; Slater, A.

2012-01-01

Coffee is one of the most important plantation crops, grown in about 80 countries across the world. The genus Coffea comprises approximately 100 species of which only two species, that is, Coffea arabica (commonly known as arabica coffee) and Coffea canephora (known as robusta coffee), are commercially cultivated. Genetic improvement of coffee through traditional breeding is slow due to the perennial nature of the plant. Genetic transformation has tremendous potential in developing improved coffee varieties with desired agronomic traits, which are otherwise difficult to achieve through traditional breeding. During the last twenty years, significant progress has been made in coffee biotechnology, particularly in the area of transgenic technology. This paper provides a detailed account of the advances made in the genetic transformation of coffee and their potential applications. PMID:22970380

PENGARUH PEMBERIAN LIMBAH KULIT KOPI (Coffea robusta L. TERHADAP PERTUMBUHAN CABAI KERITING (Capsicum annum L.

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Zainal Berlian

2015-08-01

Full Text Available Curly chili (Capsicum annum L. is a kind of vegetable commodities which very demand among the Indonesian because of its spicy taste that can be used as a flavoring dishes and has a high economic value. The goal of this study is to determine the effect of bark compost coffee (Coffea robusta in growing media on the growth and development of plants curly chili (Capsicum annum L. and severe skin compost coffee (Coffea robusta which gives the maximum growth of the plant curly chili (Capsicum annum L.. This research is conducted in the Laboratory Science UIN Raden Fatah Palembang by using experimental methods and completely randomized design (CRD consisting of 4 treatments and 6 replications treatment namely: P0 = Without the addition of compost the coffee (Coffea robusta (control, P1= Adding compost the coffee (Coffea robusta 30 grams, P2= Adding compost the coffee (Coffea robusta 60 grams , P3 = Addition of compost skin (Coffea robusta coffee 90 grams. Data are analyzed by F test followed by a test BJND (Difference Distance Real Duncan. The parameters of this study are plant height, number of leaves (pieces, the amount of fruit, and fruit weight. The results show that the addition of compost the coffee (Coffea robusta 90 grams (treatment P3 gives a very real effect on the growth of plant height, number of leaves, number of fruits, and also fruit weight. The conclusion is compost the coffee (Coffea robusta gives effect to the addition of compost and bark coffee (Coffea robusta 90 grams provides maximum growth and development of the plant curly chili (Capsicum annum L..

Estudo cariométrico dos poliplóides de Coffea

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Giorgio Schreiber

1946-01-01

Full Text Available Foi estudado o volume nuclear de uma série de plantas de café com 22-44-66-88 cromossômios: C. congensis, C. arabica var. monosperma, C. arabica var. typica e C. arabica var. bullata e pelo método estatístico cariométrico. Das curvas de frequência (que não são "normais", foi calculado o valor normal (modo para cada número de cromossômios. Com êstes valores modais e os respectivos números de cromossômios foi calculada a equação de regressão, o êrro de estimação e o coeficiente de correlação. A correlação é perfeita, sendo, porém, a espécie C. congensis discordante dos demais elementos da série por ter um valor volumétrico correspondente a 33 cromossômios apesar dos 22 encontrados nas metáfases somáticas. Êste resultado é apontado para ulteriores investigações citogenéticas sôbre esta espécie. O resultado geral destas pesquisas mostra a perfeita correlação entre o número de genomas haplóides e o volume nuclear ; deve ser considerado, porém, válido somente no confronto entre núcleos que se encontram na mesma fase do ciclo de crescimento interfásico.Caryometric researches on Coffea polyploids. General discussion of the problem and preliminary results. A series of polyploid plant of Coffea with 22, 44, 66, and 88 chromosomes (C. congensis, C. arabica var. monosperma, C. arabica var. typica, C. arabica var. bullata have been studied with caryometric statistical method. The chromosome numbers have been plotted again,st the modal value of the frequency curves of nuclear volume and the regression equation, standard error of estimation and correlation coefficent have been calculated. The correlation results perfect between the chromosome number and the nuclear volume for all the elements of the polyploid series of Coffea arabica. Coffea congensis, althought with 22 chromosomes, has a nuclear volume exactly correspondent to that of C. arabica with 33 chromosomes. This fact is appointed for further

Characterization of Coffee ringspot virus-Lavras: A model for an emerging threat to coffee production and quality

Energy Technology Data Exchange (ETDEWEB)

Ramalho, T.O.; Figueira, A.R.; Sotero, A.J. [Universidade Federal de Lavras, Departamento de Fitopatologia, Caixa Postal 3037, CEP 37200-000 Lavras, MG (Brazil); Wang, R. [Department of Plant Pathology, University of Kentucky, Lexington, KY 40546 (United States); Geraldino Duarte, P.S. [Universidade Federal de Lavras, Departamento de Fitopatologia, Caixa Postal 3037, CEP 37200-000 Lavras, MG (Brazil); Farman, M. [Department of Plant Pathology, University of Kentucky, Lexington, KY 40546 (United States); Goodin, M.M., E-mail: mgoodin@uky.edu [Department of Plant Pathology, University of Kentucky, Lexington, KY 40546 (United States)

2014-09-15

The emergence of viruses in Coffee (Coffea arabica and Coffea canephora), the most widely traded agricultural commodity in the world, is of critical concern. The RNA1 (6552 nt) of Coffee ringspot virus is organized into five open reading frames (ORFs) capable of encoding the viral nucleocapsid (ORF1p), phosphoprotein (ORF2p), putative cell-to-cell movement protein (ORF3p), matrix protein (ORF4p) and glycoprotein (ORF5p). Each ORF is separated by a conserved intergenic junction. RNA2 (5945 nt), which completes the bipartite genome, encodes a single protein (ORF6p) with homology to RNA-dependent RNA polymerases. Phylogenetic analysis of L protein sequences firmly establishes CoRSV as a member of the recently proposed Dichorhavirus genus. Predictive algorithms, in planta protein expression, and a yeast-based nuclear import assay were used to determine the nucleophillic character of five CoRSV proteins. Finally, the temperature-dependent ability of CoRSV to establish systemic infections in an initially local lesion host was quantified. - Highlights: • We report genome sequence determination for Coffee ringspot virus (CoRSV). • CoRSV should be considered a member of the proposed Dichorhavirus genus. • We report temperature-dependent systemic infection of an initially local lesion host. • We report in planta protein and localization data for five CoRSV proteins. • In silico predictions of the CoRSV proteins were validated using in vivo assays.

Characterization of Coffee ringspot virus-Lavras: A model for an emerging threat to coffee production and quality

International Nuclear Information System (INIS)

Ramalho, T.O.; Figueira, A.R.; Sotero, A.J.; Wang, R.; Geraldino Duarte, P.S.; Farman, M.; Goodin, M.M.

2014-01-01

The emergence of viruses in Coffee (Coffea arabica and Coffea canephora), the most widely traded agricultural commodity in the world, is of critical concern. The RNA1 (6552 nt) of Coffee ringspot virus is organized into five open reading frames (ORFs) capable of encoding the viral nucleocapsid (ORF1p), phosphoprotein (ORF2p), putative cell-to-cell movement protein (ORF3p), matrix protein (ORF4p) and glycoprotein (ORF5p). Each ORF is separated by a conserved intergenic junction. RNA2 (5945 nt), which completes the bipartite genome, encodes a single protein (ORF6p) with homology to RNA-dependent RNA polymerases. Phylogenetic analysis of L protein sequences firmly establishes CoRSV as a member of the recently proposed Dichorhavirus genus. Predictive algorithms, in planta protein expression, and a yeast-based nuclear import assay were used to determine the nucleophillic character of five CoRSV proteins. Finally, the temperature-dependent ability of CoRSV to establish systemic infections in an initially local lesion host was quantified. - Highlights: • We report genome sequence determination for Coffee ringspot virus (CoRSV). • CoRSV should be considered a member of the proposed Dichorhavirus genus. • We report temperature-dependent systemic infection of an initially local lesion host. • We report in planta protein and localization data for five CoRSV proteins. • In silico predictions of the CoRSV proteins were validated using in vivo assays

Análises quali- e quantitativa de cafés comerciais via ressonância magnética nuclear

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Tavares Leila Aley

2006-01-01

Full Text Available Coffee is one of the beverages most widely consumed in the world and the "cafezinho" is normally prepared from a blend of roasted powder of two species, Coffea arabica and Coffea canephora. Each one exhibits differences in their taste and in the chemical composition, especially in the caffeine percentage. There are several procedures proposed in the literature for caffeine determination in different samples like soft drinks, coffee, medicines, etc but most of them need a sample workup which involves at least one step of purification. This work describes the quantitative analysis of caffeine using ¹H NMR and the identification of the major components in commercial coffee samples using 1D and 2D NMR techniques without any sample pre-treatment.

Quali- and quantitative analysis of commercial coffee by NMR

International Nuclear Information System (INIS)

Tavares, Leila Aley; Ferreira, Antonio Gilberto

2006-01-01

Coffee is one of the beverages most widely consumed in the world and the 'cafezinho' is normally prepared from a blend of roasted powder of two species, Coffea arabica and Coffea canephora. Each one exhibits differences in their taste and in the chemical composition, especially in the caffeine percentage. There are several procedures proposed in the literature for caffeine determination in different samples like soft drinks, coffee, medicines, etc but most of them need a sample workup which involves at least one step of purification. This work describes the quantitative analysis of caffeine using 1 H NMR and the identification of the major components in commercial coffee samples using 1D and 2D NMR techniques without any sample pre-treatment. (author)

Collimated scanning LS-INAA for testing trace elements homogeneity in Brazilian coffee beans

International Nuclear Information System (INIS)

Tagliaferro, F.S.; Nadai Fernandes de, E.A.; Bode, P.; Baas, H.W.

2008-01-01

The degree of homogeneity is normally assessed by the variability of the results of independent analyses of several (e.g., 15) normal-scale replicates. Large sample instrumental neutron activation analysis (LS-INAA) with a collimated Ge detector allows inspecting the degree of homogeneity of the initial batch material, using a kilogram-size sample. The test is based on the spatial distributions of induced radioactivity. Such test was applied to samples of Brazilian whole (green) coffee beans (Coffea arabica and Coffea canephora) of approximately 1 kg in the frame of development of a coffee reference material. Results indicated that the material do not contain significant element composition inhomogeneities between batches of approximately 30-50 g, masses typically forming the starting base of a reference material. (author)

Consequences of Stoichiometric Error on Nuclear DNA Content Evaluation in Coffea liberica var. dewevrei using DAPI and Propidium Iodide

OpenAIRE

NOIROT, MICHEL; BARRE, PHILIPPE; LOUARN, JACQUES; DUPERRAY, CHRISTOPHE; HAMON, SERGE

2002-01-01

The genome size of coffee trees (Coffea sp.) was assessed using flow cytometry. Nuclear DNA was stained with two dyes [4′,6‐diamino‐2‐phenylindole dihydrochloride hydrate (DAPI) and propidium iodide (PI)]. Fluorescence in coffee tree nuclei (C‐PI or C‐DAPI) was compared with that of the standard, petunia (P‐PI or P‐DAPI). If there is no stoichiometric error, then the ratio between fluorescence of the target nuclei and that of the standard nuclei (R‐PI or R‐DAPI) is expected to be proportional...

Quality of the surface of Coffea arabica wood

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Pedro Paulo de Carvalho Braga

2014-03-01

Full Text Available The wood of Coffea arabica L. is considered a a residue of the coffee industry and is widely used as a source of energy. Few studies have shown other destinations such as the manufacture of small objects and furniture with rustic design. The objective of this work was to find the best fit in cutting speed during machining planer trowel the wood of Coffea arabica, taking into consideration the quality of the machined surface. The wood from the Coffea arabica came from an 15 years planting, spacing 3 x 2 m, of the municipality of Machado / MG. The tree was pruned, unfolded and flattened, in order for getting cut-proof of 30 mm thick, with variables length and width. The machining tests were performed at the Laboratory of Wood Machining (DCF / UFLA, varying the cutting speed in plane trowel. The qualification of the machined surface was performed by the feed per tooth (fz, visual analysis (ASTM D 1666-87 and roughness Ra and Rz. It was used a completely randomized design with 30 repetitions. We conducted the analysis of variance test and the average of Scott-Knott, at 5% significance level. It was calculated the percentage of marks obtained for the feed per tooth. The results showed that the quality of machined surface with cutting speeds of 19 and 21 m∙s-1 and forward speed of 6 m∙min-1 were satisfactory with small surveys of fiber and low values of feed per tooth ( fz and roughness Ra and Rz.

Influence of integral and decaffeinated coffee brews on metabolic parameters of rats fed with hiperlipidemic diets

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Júlia Ariana de Souza Gomes

2013-10-01

Full Text Available The objective of this study was to evaluate the influence of integral and decaffeinated coffee brews (Coffea arabica L and C. canephora Pierre on the metabolic parameters of rats fed with hyperlipidemic diet. Thirty male Wistar rats (initial weight of 270 g ± 20 g were used in the study, which were divided into six groups five each. The treatments were normal diet, hyperlipidemic diet, hyperlipidemic diet associated with integral coffee arabica or canephora brews (7.2 mL/kg/day and hyperlipidemic diet associated to decaffeinated arabica, or canephora brews, using the same dosage. After 41 days, performance analyses were conducted.The rats were then euthanized and the carcasses were used for the analysis of dried ether extract and crude protein. Fractions of adipose tissue were processed for histological analysis. There was a reduction in weight gain and accumulation of lipids in the carcasses, lower diameter of adipocytes and a lower relative weight of the liver and kidneys of rats fed with hyperlipidemic diet associated with integral coffee brew. Integral coffee brew reduced the obesity in the rats receiving hyperlipidemic diet, but the same effect did not occur with the decaffeinated types.

Genetic variation in Coffea canephora L. (Var. Robusta) accessions ...

African Journals Online (AJOL)

STORAGESEVER

2009-02-04

Feb 4, 2009 ... in the world. Most genetic diversity of robusta coffee accessions conserved in ex situ collections has ... to coffee production and emphasis is now being directed to ...... and Production of Beans and Beverage, Croom Helm., London, pp. 13-47. ... sequence repeat primers used in polymerase chain reaction.

Isolation, identification and toxigenic potential of ochratoxin A-producing Aspergillus species from coffee beans grown in two regions of Thailand

DEFF Research Database (Denmark)

Noonim, P.; Mahakarnchanakul, W.; Nielsen, Kristian Fog

2008-01-01

In 2006 and 2007, 32 Thai dried coffee bean samples (Coffea arabica) from two growing sites of Chiang Mai Province, and 32 Thai dried coffee bean samples (Coffea canephora var. robusta) from two growing sites of Chumphon Province, Thailand, were collected and assessed for the distribution of fungi...... with the potential to produce ochratoxin A (OTA). The overall percentage of fungal contamination in coffee was 98% and reduced to 60% after surface disinfection. There were remarkable ecological differences in the composition of ochratoxigenic species present in these two regions. Arabica coffee bean samples from...... the North had an average of 78% incidence of colonization with Aspergillus of section Circumdati with Aspergillus westerdijkiae and A. melleus as the predominant species. Aspergillus spp. of section Nigri were found in 75% of the samples whereas A. ochraceus was not detected. Robusta coffee beans from...

Incidência de microorganismos em sementes de café robusta durante o armazenamento

OpenAIRE

BRACCINI,ALESSANDRO DE LUCCA E; SCAPIM,CARLOS ALBERTO; BRACCINI,MARIA DO CARMO LANA; ANDRADE,CARLOS ALBERTO DE BASTOS; VIDIGAL FILHO,PEDRO SOARES

1999-01-01

Foi realizado um trabalho com o objetivo de isolar e identificar os microrganismos presentes em sementes de café robusta (Coffea canephora Pierre ex Froehner) no decorrer do armazenamento. Para tanto, sementes de café do cultivar Conillon, acondicionadas em diferentes embalagens (saco de polietileno transparente, saco de papel kraft e saco de algodão) e com graus de umidade iniciais distintos (25 e 35%) foram submetidas a cinco períodos de armazenamento (0, 3, 6, 9 e 12 meses), em condições c...

Incidência de microorganismos em sementes de café robusta durante o armazenamento Incidence of microorganisms in robusta coffee seeds during the storage

OpenAIRE

ALESSANDRO DE LUCCA E BRACCINI; CARLOS ALBERTO SCAPIM; MARIA DO CARMO LANA BRACCINI; CARLOS ALBERTO DE BASTOS ANDRADE; PEDRO SOARES VIDIGAL FILHO

1999-01-01

Foi realizado um trabalho com o objetivo de isolar e identificar os microrganismos presentes em sementes de café robusta (Coffea canephora Pierre ex Froehner) no decorrer do armazenamento. Para tanto, sementes de café do cultivar Conillon, acondicionadas em diferentes embalagens (saco de polietileno transparente, saco de papel kraft e saco de algodão) e com graus de umidade iniciais distintos (25 e 35%) foram submetidas a cinco períodos de armazenamento (0, 3, 6, 9 e 12 meses), em condições c...

The economic value of coffee (Coffea arabica) genetic resources

NARCIS (Netherlands)

Hein, L.G.; Gatzweiler, F.

2006-01-01

Whereas the economic value of genetic diversity is widely recognized there are, to date, relatively few experiences with the actual valuation of genetic resources. This paper presents an analysis of the economic value of Coffea arabica genetic resources contained in Ethiopian highland forests. The

Ecosystem Service of Shade Trees on Nutrient Cycling and Productivity of Coffee Agro-ecosystems

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Rusdi Evizal

2009-05-01

Full Text Available Shade trees are significant in certification scheme of sustainable coffee production. They play an importance role on ecosystem functioning. This research is aimed to study ecosystem service of shade trees in some coffee agro-ecosystems particularly on nutrient cycling and land productivity. Four agro-ecosys tems of Robusta coffee (Coffea canephora, namely sun coffee (without shade trees, coffee shaded by Michelia champaca, coffee shaded by Gliricidia sepium, and coffee shaded by Erythrina indica are evaluated during 2007—2008. Smallholder coffee plantation in Sumberjaya Subdistrict, West Lampung, which managed under local standard were employed using Randomized Complete Block Design with 3 replications. The result showed that litter fall dynamic from shade trees and from coffee trees was influenced by rainfall. Shade trees decreased weed biomass while increased litter fall production. In dry season, shade trees decreased litter fall from coffee shaded by M. champaca. G. sepium and E. indica shaded coffee showed higher yield than sun coffee and M. champaca shaded coffee. Except for M. champaca shaded coffee, yield had positive correlation (r = 0.99 with litter fall production and had negative correlation (r = —0.82 with weed biomass production. Biomass production (litter fall + weed of sun coffee and shaded coffee was not significantly different. Litter fall of shade trees had significance on nutrient cycle mainly to balance the lost of nitrogen in coffee bean harvesting.Key Words: Coffea canephora, Michelia champaca, Gliricidia sepium, Erythrina indica, litter production, nutrient cycle, coffee yield.

Can Coffee Chemical Compounds and Insecticidal Plants Be Harnessed for Control of Major Coffee Pests?

Science.gov (United States)

Green, Paul W C; Davis, Aaron P; Cossé, Allard A; Vega, Fernando E

2015-11-04

Pests and pathogens threaten coffee production worldwide and are difficult to control using conventional methods, such as insecticides. We review the literature on the chemistry of coffee, concentrating on compounds most commonly reported from Coffea arabica and Coffea canephora. Differences in chemistry can distinguish coffee species and varieties, and plants grown under different biogeographic conditions exhibit different chemotypes. A number of chemical groups, such as alkaloids and caffeoylquinic acids, are known to be insecticidal, but most studies have investigated their effects on coffee quality and flavor. More research is required to bridge this gap in knowledge, so that coffee can be bred to be more resistant to pests. Furthermore, we report on some pesticidal plants that have been used for control of coffee pests. Locally sourced pesticidal plants have been underutilized and offer a sustainable alternative to conventional insecticides and could be used to augment breeding for resilience of coffee plants.

Fumonisin B2 production by Aspergillus niger in Thai coffee beans

DEFF Research Database (Denmark)

Noonim, P.; Mahakarnchanaku, W.; Nielsen, Kristian Fog

2009-01-01

During 2006 and 2007, a total of 64 Thai dried coffee bean samples (Coffea arabica) from two growing sites in Chiangmai Province and 32 Thai dried coffee bean samples (Coffea canephora) from two growing sites in Chumporn Province, Thailand, were collected and assessed for fumonisin contamination...... by black Aspergilli. No Fusarium species known to produce fumonisin were detected, but black Aspergilli had high incidences on both Arabica and Robusta Thai coffee beans. Liquid chromatography (LC) with high-resolution mass spectrometric (HRMS) detection showed that 67% of Aspergillus niger isolates from...... coffee beans were capable of producing fumonisins B2 (FB2) and B4 when grown on Czapek Yeast Agar with 5% NaCl. Small amounts (1-9.7 ng g-1) of FB2 were detected in seven of 12 selected coffee samples after ion-exchange purification and LC-MS/MS detection. Two samples also contained FB4...

Climate Change Impacts on Worldwide Coffee Production

Science.gov (United States)

Foreman, T.; Rising, J. A.

2015-12-01

Coffee (Coffea arabica and Coffea canephora) plays a vital role in many countries' economies, providing necessary income to 25 million members of tropical countries, and supporting a $81 billion industry, making it one of the most valuable commodities in the world. At the same time, coffee is at the center of many issues of sustainability. It is vulnerable to climate change, with disease outbreaks becoming more common and suitable regions beginning to shift. We develop a statistical production model for coffee which incorporates temperature, precipitation, frost, and humidity effects using a new database of worldwide coffee production. We then use this model to project coffee yields and production into the future based on a variety of climate forecasts. This model can then be used together with a market model to forecast the locations of future coffee production as well as future prices, supply, and demand.

Agroclimatic zoning of robusta coffee in the State of Paraná and impacts of climate changeZoneamento agroclimático de café robusta no Estado do Paraná e impactos das mudanças climáticas

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Cristiane de Conti Medina

2012-08-01

Full Text Available The aim of the study was the agroclimatic zoning of robusta coffee (Coffea canephora Pierre ex Froehner in the state of Paraná, and to verify changes caused by temperature rise related to global warming, as predictions for the next 100 years reported by the IPCC (Intergovernmental Panel on Climate Change. An alternative to keep coffee production in the state of Paraná will be the introduction of robusta coffee, original from Africa, adapted to areas with annual mean temperatures between 22 and 26oC. We used the historical weather database from IAPAR (Agronomic Institute of Paraná and considered as apt for cropping the areas within the following conditions: risk of annual frost lower than 25% of probability, annual mean temperature between 22 and 26 °C, and annual water deficiency below 150 mm. The spatial analyzes were based on the Shuttle Radar Topography Mission (SRTM and crossed into the environment of a Geographic Information System (GIS, generating maps of the agroclimatic zoning of Coffea canephora for the current climate and scenarios of climate change with the addition of 1.8 and 4 °C in the mean temperature. The zoning for the current weather indicated that parts of northwestern and western regions of Paraná are suitable for cultivation. Under climate change scenarios, considering the rainfall regime unchanged, the area suitable for cultivation expands, justifying studies on this species in the state of Paraná. O objetivo do trabalho foi realizar o zoneamento agroclimático de café robusta (Coffea canephora Pierre ex Froehner no estado do Paraná e verificar as alterações causadas neste, pelo incremento de temperatura, provocado pelo aquecimento global, conforme prognósticos para os próximos 100 anos divulgados pelo IPCC (Intergovernmental Panel on Climate Change. Uma alternativa para manter a produção cafeeira no estado do Paraná poderá ser a introdução do café robusta, originário da África, adaptado a regiões com

Pengaruh Bionematisida Berbahan Aktif Jamur Paecilomyces lilacinus Strain 251 terhadap Serangan Pratylenchus coffeae pada Kopi Robusta

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Soekadar Wiryadiputra

2002-07-01

Full Text Available Experiment on the effect of P. lilacinus on the infestation of P. coffeae on robusta coffee was conducted in Sumber Asin Experimental Garden, Malang. The treatments were dosages of bionematicide i.e. : 0 (control, 0.25, 0.50, 1.00, 2.00, and 4.00 g; carbofuran (3 % active ingredient 50 g/plant and organic soil treatment (OST at 100 g/plant. Each treatment was replicated four times, and each replication consists of five coffee trees. The results in second year observation revealed that the population of P. coffeae in the roots on PL 251 treatments was not significantly different compared to the control, whereas in soil samples the population of both P. coffeae and Rotylenchulus reniformis inclined to be lower than the control, although they were not statistically significant. The lowest infestation was observed on PL 251 treatment at a dosage level of 4.00 g/tree. On nematode infestation, no significant difference on treatments of carbofuran and OST compared to the control. The yield of green coffee (market coffee was the highest on the treatment of PL 251 at a dosage of 4.00 g/tree and significantly higher than the control and carbofuran treatments, with increasing levels of 225.3 and 198.9%, respectively. Keywords: bionematicide Paecilomyces lilacinus strain 251 (PL 251, Pratylenchus coffeae, Rotylenchulus reniformis

Contribuição do porta-enxerto, no teor de cafeína em grãos de café Contribution of the root-stock on the caffeine content of the coffee grains

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M. Melo

1976-01-01

Full Text Available A contribuição do porta-enxerto no teor de cafeína dos grãos de café foi investigada nos cultivares mundo novo e laurina de Coffea arabica e no robusta de C. canephora, os quais diferem marcadamente no teor desse alcalóide. Os resultados obtidos indicam que o porta-enxerto, independentemente de seu genótipo, não exerce efeito mensurável sobre o teor de cafeína nos grãos. Variações individuais foram verificadas no teor de cafeína no robusta, devido à sua variabilidade genética, indicando a possibilidade de seleção para essa característica dentro desse material. Do ponto de vista agrícola o robusta poderia ser usado como porta-enxerto para as seleções de C. arabica, sem qualquer efeito no produto final.The contribution of the root-stock on the caffeine content of the coffee grains was studied in the Mundo Novo and Laurina cultivais of Coffea arabica and in the Rubosta cultivar of C. canephora which markedly differ in the alkaloid content. The results indicate that the root-stock, independently of its genotype, does not influence the caffeine content of the grains. Individual variation in caffeine content was found in the Robusta due to its genetic variability, pointing out to the possibility of selection for this characteristics in this material. It was also concluded that Robusta cultivars can be used as root-stock for Arabica selections without affecting the final product.

Covering the different steps of the coffee processing: Can headspace VOC emissions be exploited to successfully distinguish between Arabica and Robusta?

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Colzi, Ilaria; Taiti, Cosimo; Marone, Elettra; Magnelli, Susanna; Gonnelli, Cristina; Mancuso, Stefano

2017-12-15

This work was performed to evaluate the possible application of PTR-ToF-MS technique in distinguishing between Coffea arabica (Arabica) and Coffea canephora var. robusta (Robusta) commercial stocks in each step of the processing chain (green beans, roasted beans, ground coffee, brews). volatile organic compounds (VOC) spectra from coffee samples of 7 Arabica and 6 Robusta commercial stocks were recorded and submitted to multivariate statistical analysis. Results clearly showed that, in each stage of the coffee processing, the volatile composition of coffee is highly influenced by the species. Actually, with the exception of green beans, PTR-ToF-MS technique was able to correctly recognize Arabica and Robusta samples. Particularly, among 134 tentatively identified VOCs, some masses (16 for roasted coffee, 12 for ground coffee and 12 for brewed coffee) were found to significantly discriminate the two species. Therefore, headspace VOC analyses was showed to represent a valuable tool to distinguish between Arabica and Robusta. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantification of the Robusta fraction in a coffee blend via Raman spectroscopy: proof of principle.

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Wermelinger, Thomas; D'Ambrosio, Lucio; Klopprogge, Babette; Yeretzian, Chahan

2011-09-14

Among the 100 different known Coffea species, Coffea arabica L. (Arabica) and Coffea canephora Pierre (Robusta) are the only two of commercial interest. They differ in a range of agronomic, genetic, and chemical properties. Due to the significant price difference between Arabica and Robusta, there is an economic incentive to illicitly replace Arabica with Robusta. Therefore, it is crucial to have accurate methods to determine the Robusta-to-Arabica-ratio in blends. This paper presents the proof of principle of a new and fast approach to determine the Robusta fraction in a blend based on Raman spectroscopy. The oils of two references (a pure Robusta and pure Arabica coffee) and six blends thereof consisting of different Robusta and Arabica fractions were extracted using a Soxhlet system. The solutes were analyzed by means of Raman spectroscopy without further workup. Using the intensity ratio between two Raman peaks, one characteristic for kahweol and one characteristic for fatty acids, allowed determinination of the Robusta content in a given mixture. The intensity ratio is linearly dependent on the Robusta content of the compound. Above a Robusta content of 75 wt %, kahweol was not detectable. The Raman data are in agreement with results obtained from the very time-consuming multistep DIN 10777 procedures based on HPLC.

Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves.

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de Sousa, Leandro Pio de; da Silva, Marcio José da; Mondego, Jorge Maurício

2018-05-17

Coffee is one of the most valuable agricultural commodities and the plants' leaves are the primary site of infection for most coffee diseases, such as the devastating coffee leaf rust. Therefore, the use of bacterial microbiota that inhabits coffee leaves to fight infections could be an alternative agricultural method to protect against coffee diseases. Here, we report the leaf-associated bacteria in three coffee genotypes over the course of a year, with the aim to determine the diversity of bacterial microbiota. The results indicate a prevalence of Enterobacteriales in Coffea canephora, Pseudomonadales in C. arabica 'Obatã', and an intriguing lack of bacterial dominance in C. arabica 'Catuaí'. Using PERMANOVA analyses, we assessed the association between bacterial abundance in the coffee genotypes and environmental parameters such as temperature, precipitation, and mineral nutrients in the leaves. We detected a close relationship between the amount of Mn and the abundance of Pseudomonadales in 'Obatã' and the amount of Ca and the abundance of Enterobacteriales in C. canephora. We suggest that mineral nutrients can be key drivers that shape leaf microbial communities.

Susceptibility of the Parasitoid Phymastichus coffea LaSalle (Hymenoptera: Eulophidae) to Beauveria bassiana under laboratory conditions; Susceptibilidad del parasitoide Phymastichus coffea LaSalle (Hymenoptera:Eulophidae) a Beauveria bassiana en condiciones de laboratorio

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Castillo, Alfredo; Gomez, Jaime; Infante, Francisco [El Colegio de la Frontera Sur (ECOSUR), Chiapas (Mexico). Dept. de Entomologia Tropical], e-mail: acastill@ecosur.mx, e-mail: jgomez@ecosur.mx, e-mail: finfante@ecosur.mx; Vega, Fernando E. [United States Department of Agriculture (USDA), Beltsville, MD (United States). Agricultural Research Service. Sustainable Perennial Crops Lab.], e-mail: fernando.vega@ars.usda.gov

2009-09-15

The coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae), is the most important coffee pest worldwide. Beauveria bassiana is a generalist entomopathogenic fungus widely used by coffee farmers to control this pest and Phymastichus coffea LaSalle (Hymenoptera: Eulophidae) is an African endo parasitoid of H. hampei adults, recently imported to several Latin American and Caribbean countries to aid in the coffee berry borer control. The objective of this study was to determine if B. bassiana is detrimental to P. coffea. The susceptibility of the parasitoid was evaluated in terms of adult survivorship, mean lethal concentration (LC{sub 50}), mean lethal time (LT{sub 50}), reproduction and immature mortality. The main effect of the fungus resulted in reduction of adult longevity and mortality of 100% for immature stages of this parasitoid. The LC{sub 50} for adults was 0.11% equivalent to 9.53 x 10{sup 7} conidia/ml of B. bassiana and a LT{sub 50} of 29.4 h, equivalent to reduction of 22% of its normal longevity as an adult. P. coffea was capable of disseminating spores of B. bassiana to non-infected H. hampei adults, which could indirectly cause the death of its own progeny. These results could be valuable when considering the use of both organisms in the field, especially in an integrated pest management program. (author)

Evolutionary Expansion of WRKY Gene Family in Banana and Its Expression Profile during the Infection of Root Lesion Nematode, Pratylenchus coffeae

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Suthanthiram, Backiyarani; Subbaraya, Uma; Marimuthu Somasundram, Saraswathi; Muthu, Mayilvaganan

2016-01-01

The WRKY family of transcription factors orchestrate the reprogrammed expression of the complex network of defense genes at various biotic and abiotic stresses. Within the last 96 million years, three rounds of Musa polyploidization events had occurred from selective pressure causing duplication of MusaWRKYs with new activities. Here, we identified a total of 153 WRKY transcription factors available from the DH Pahang genome. Based on their phylogenetic relationship, the MusaWRKYs available with complete gene sequence were classified into the seven common WRKY sub-groups. Synteny analyses data revealed paralogous relationships, with 17 MusaWRKY gene pairs originating from the duplication events that had occurred within the Musa lineage. We also found 15 other MusaWRKY gene pairs originating from much older duplication events that had occurred along Arecales and Poales lineage of commelinids. Based on the synonymous and nonsynonymous substitution rates, the fate of duplicated MusaWRKY genes was predicted to have undergone sub-functionalization in which the duplicated gene copies retain a subset of the ancestral gene function. Also, to understand the regulatory roles of MusaWRKY during a biotic stress, Illumina sequencing was performed on resistant and susceptible cultivars during the infection of root lesion nematode, Pratylenchus coffeae. The differential WRKY gene expression analysis in nematode resistant and susceptible cultivars during challenged and unchallenged conditions had distinguished: 1) MusaWRKYs participating in general banana defense mechanism against P.coffeae common to both susceptible and resistant cultivars, 2) MusaWRKYs that may aid in the pathogen survival as suppressors of plant triggered immunity, 3) MusaWRKYs that may aid in the host defense as activators of plant triggered immunity and 4) cultivar specific MusaWRKY regulation. Mainly, MusaWRKY52, -69 and -92 are found to be P.coffeae specific and can act as activators or repressors in a

Evolutionary Expansion of WRKY Gene Family in Banana and Its Expression Profile during the Infection of Root Lesion Nematode, Pratylenchus coffeae.

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Raja Kaliyappan

Full Text Available The WRKY family of transcription factors orchestrate the reprogrammed expression of the complex network of defense genes at various biotic and abiotic stresses. Within the last 96 million years, three rounds of Musa polyploidization events had occurred from selective pressure causing duplication of MusaWRKYs with new activities. Here, we identified a total of 153 WRKY transcription factors available from the DH Pahang genome. Based on their phylogenetic relationship, the MusaWRKYs available with complete gene sequence were classified into the seven common WRKY sub-groups. Synteny analyses data revealed paralogous relationships, with 17 MusaWRKY gene pairs originating from the duplication events that had occurred within the Musa lineage. We also found 15 other MusaWRKY gene pairs originating from much older duplication events that had occurred along Arecales and Poales lineage of commelinids. Based on the synonymous and nonsynonymous substitution rates, the fate of duplicated MusaWRKY genes was predicted to have undergone sub-functionalization in which the duplicated gene copies retain a subset of the ancestral gene function. Also, to understand the regulatory roles of MusaWRKY during a biotic stress, Illumina sequencing was performed on resistant and susceptible cultivars during the infection of root lesion nematode, Pratylenchus coffeae. The differential WRKY gene expression analysis in nematode resistant and susceptible cultivars during challenged and unchallenged conditions had distinguished: 1 MusaWRKYs participating in general banana defense mechanism against P.coffeae common to both susceptible and resistant cultivars, 2 MusaWRKYs that may aid in the pathogen survival as suppressors of plant triggered immunity, 3 MusaWRKYs that may aid in the host defense as activators of plant triggered immunity and 4 cultivar specific MusaWRKY regulation. Mainly, MusaWRKY52, -69 and -92 are found to be P.coffeae specific and can act as activators or

Uma nova forma de Coffea

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C. A. Krug

1950-01-01

Full Text Available Nos extensos trabalhos de melhoramento do cafeeiro, há 18 anos em realização na Subdivisão de Genética do Instituto Agronômico, tem-se dedicado especial atenção à espécie C. arabica L., pelo fato de todos os nossos cafèzais pertencerem a esta espécie que, sem dúvida, fornece o produto de melhor qualidade. Nas regiões de terras extremamente cansadas, um dos principais fatôres levados em consideração no melhoramento é a rusticidade, caráter êsse, entretanto, encontrado de preferência em outras espécies, tais como o C. canephora e C. Dewevrei, cujos cafés são de má qualidade. A hibridação interespecífica, que poderia reunir em uma só planta caraterísticos de rusticidade e boa qualidade de bebida, tem o inconveniente de dar origem a plantas triplóides, que são estéreis. Daí se deduz que a obtenção artificial de formas que combinassem êsses caraterísticos constitui problema, cuja solução é extremamente demorada. No presente trabalho, apresentam-se os caracteres de uma nova forma de Coffea, encontrada em cafèzal da Fazenda Itaporã, em Terra Roxa, município de Viradouro, que, com algumas ressalvas, oferece a desejada combinação de caracteres. Trata-se, provàvelmente, de um híbrido espontâneo entre C. arabica e C. Dewevrei, com 2n = 44 cromosômios, extremamente rústico e produtivo, cujas sementes fornecem uma bebida que pode ser classificada como boa. Apenas apresenta, como principal defeito, uma auto-esterilidade quase completa. Os seus caraterísticos botânicos são descritos em detalhe. Devido ao seu porte elevado, ramos abundantes e folhas grandes e coriáceas, esse cafeeiro se assemelha ao C. Dewevrei. Os frutos são oval-elípticos, de um vermelho bem escuro quando maduros, e as sementes oblongas, constatan-do-se elevada percentagem do tipo "moca" e "chocha". Quanto à constituição citológica, as pesquisas conduziram à hipótese de este cafeeiro possuir 22 cromosômios de C. arabica e 22 (n

Dinâmica dos micronutrientes em cafeeiros enxertados Dynamics of micronutrient in grafted coffee

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André Dominghetti Ferreira

2013-04-01

Full Text Available As respostas à disponibilidade dos nutrientes variam entre espécies distintas dentro de um mesmo gênero, por causa, principalmente, das exigências nutricionais variáveis, capacidade de absorção, translocação e utilização dos nutrientes. O objetivo deste trabalho foi avaliar a eficiência de absorção, translocação e uso dos micronutrientes por diferentes cultivares de Coffea arabica L., enxertados em Apoatã IAC 2258 (Coffea canephora. O experimento foi instalado em casa de vegetação, utilizando-se o método de cultivo em solução nutritiva. Foi utilizado um fatorial 7 x 3 + 2, sendo sete cultivares de Coffea arabica L. (Palma II, Catucaí 2 SL, Oeiras MG 6851, Obatã IAC 1669-20, Acauã, Topázio MG 1190 e Paraíso MG H 419-1, três tipos de mudas (pé franco, autoenxertada e enxertada sobre o cultivar Apoatã IAC 2258 e duas testemunhas (Apoatã autoenxertado e Apoatã pé franco. O porta-enxerto utilizado influenciou negativamente na absorção de boro, ferro e manganês. A translocação dos micronutrientes boro e cobre obteve maiores índices nas mudas enxertadas. O cultivar Palma II, quando enxertado, apresentou o maior índice de utilização dos nutrientes, mostrando-se passível de ser enxertado. O porta-enxerto utilizado mostrou-se apto para a enxertia, por não sofrer influência negativa, tanto pela enxertia, quanto pelos cultivares utilizados.Responses to availability of nutrients vary between different species within the same genus, mainly because the different nutritional requirements, absorption capacity, translocation and use of nutrients, The purpose of this study was to evaluate the efficiency of absorption, translocation and use of micronutrients by different cultivars of Coffea arabica L. grafted into Apoatã IAC 2258 (Coffea canephora. The experiment was conducted in a greenhouse using cultivation in nutrient solution in a 7 x 3 + 2 factorial design: seven cultivars of Coffea arabica L. (Palma II, Catuca

Antioxidant effect of Arabian coffee ( Coffea arabica L) blended with ...

African Journals Online (AJOL)

Purpose: To investigate the antioxidant activity of Coffea Arabica L in high-fat diet (HFD)-fed C57BL/6J mice. Methods: A decoction of Arabian coffee blended with or without cardamom or cloves was orally administered to HFD-fed C57BL/6J mice for a period of 60 days. At the end of the treatment, blood and tissue samples ...

Anatomical and chemical properties and density of Coffea arabica L. wood

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Marisa Aparecida Pereira

2014-09-01

Full Text Available The state of Minas Gerais is the largest producer of coffee in Brazil and the amount of residue in crops seems adequate to support production of solid wood products of Coffea arabica L., which is currently used for energy purposes or remains in the area. This activity adds insignificant value the coffee products and release CO2, which has harmful effects to the environment. This study was conducted with the aim of characterizing technologically Coffea arabica L. wood to enhance its use in furniture, to characterize its anatomical, chemical and wood basic density. The density showed an average of 0.608g.cm-3. The anatomical analysis showed distinct growth layers, semiporosos vessels with simple perforation plates. The axial parenchyma is apotracheal and diffuse in the aggregate with heterogeneous rays, not laminated and fiber libriformes not septate with bordered pits distinct. The chemical content of extract in hot and cold water were respectively 6.1% and 9.6%. The ash content was found to be 0.68%. Data were comparable to those of mahogany (Swietenia macrophylla and Piptadenia peregrina Benth, (angico-vermelho used for the production of furniture.

Pest Management Strategies Against the Coffee Berry Borer (Coleoptera: Curculionidae: Scolytinae).

Science.gov (United States)

Infante, Francisco

2018-03-22

Coffee ( Coffea arabica and C. canephora) is one of the most widely traded agricultural commodities and the main cash crop in ∼80 tropical countries. Among the factors that limit coffee production, the coffee berry borer, Hypothenemus hampei (Ferrari) has been considered the main insect pest, causing losses of over U.S. $500 million dollars annually. Control of this pest has been hindered by two main factors: the cryptic nature of the insect (i.e., protected inside the coffee berry) and the availability of coffee berries in the field allowing the survival of the pest from one generation to the next. Coffee berry borer control has primarily been based on the use of synthetic insecticides. Management strategies have focused on the use of African parasitoids ( Cephalonomia stephanoderis, Prorops nasuta, and Phymastichus coffea), fungal entomopathogens ( Beauveria bassiana), and insect traps. These approaches have had mixed results. Recent work on the basic biology of the insect has provided novel insights that might be useful in developing novel pest management strategies. For example, the discovery of symbiotic bacteria responsible for caffeine breakdown as part of the coffee berry borer microbiome opens new possibilities for pest management via the disruption of these bacteria. Some chemicals with repellent propieties have been identified, and these have a high potential for field implementation. Finally, the publication of the CBB genome has provided insights on the biology of the insect that will help us to understand why it has been so successful at exploiting the coffee plant. Here I discuss the tools we now have against the CBB and likely control strategies that may be useful in the near future.

Genética de coffea VI: independência dos fatores xc xc (xanthocarpa e br br (bronze em coffea arabica L.

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C. A. Krug

1942-01-01

Full Text Available Em artigos anteriores (1, 2 os autores demonstraram que a cor amarela dos frutos e a coloração bronzeada das folhas novas são, em Coffea arabica L, controladas, cada uma, por um único par de fatores genéticos (respectivamente xc xc e Br Br. Os híbridos F1 no primeiro caso com plantas de frutos vermelhos, e no segundo com plantas de folhas novas verdes, demonstraram tratar-se de casos em que há dominância incompleta nesta geração, os frutos híbridos possuindo uma coloração vermelho clara e as folhas novas se apresentando com uma tonalidade bronze clara. Como algumas das hibridações realizadas envolviam, ao mesmo tempo, os dois caracteres em questão, apresentou-se a oportunidade para constatar se havia ou não independência entre os dois pares de fatores que controlam estes caracteres. Neste artigo apresentam-se os resultados das observações realizadas, tanto em diversas populações de F2 como também em dois back-crosses. Os dados confirmam plenamente a hipótese estabelecida, isto é, da independência entre os dois pares de fatores em questão (xc xc e Br Br. Este fato era esperado à vista do número relativamente elevado de cromosômios nas variedades cruzadas (2n = 44.In two previous publications (1,2 the authors demonstrated that in Coffea arabica L. yellow fruit color and bronze color of young leaves are each controled by one pair of genes (respectively xc xc and Br Br. The F1 hybrids, in the first instance between plants with yellow and red fruits and in the second instance between plants with bronze and green colored young leaves, showed incomplete dominance of both characters, the F1 fruits being of a light red color and the F1 young leaves of a light bronze one. As some of the crosses involved both pairs of genes, it was possible to find out wether they are linked or independent. In the present article the authors are publishing the results obtained with several F2 populations and also with 2 types of back crosses

Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves

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Leandro Pio de Sousa

2018-05-01

Full Text Available Abstract Coffee is one of the most valuable agricultural commodities and the plants’ leaves are the primary site of infection for most coffee diseases, such as the devastating coffee leaf rust. Therefore, the use of bacterial microbiota that inhabits coffee leaves to fight infections could be an alternative agricultural method to protect against coffee diseases. Here, we report the leaf-associated bacteria in three coffee genotypes over the course of a year, with the aim to determine the diversity of bacterial microbiota. The results indicate a prevalence of Enterobacteriales in Coffea canephora, Pseudomonadales in C. arabica ‘Obatã’, and an intriguing lack of bacterial dominance in C. arabica ‘Catuaí’. Using PERMANOVA analyses, we assessed the association between bacterial abundance in the coffee genotypes and environmental parameters such as temperature, precipitation, and mineral nutrients in the leaves. We detected a close relationship between the amount of Mn and the abundance of Pseudomonadales in ‘Obatã’ and the amount of Ca and the abundance of Enterobacteriales in C. canephora. We suggest that mineral nutrients can be key drivers that shape leaf microbial communities.

Susceptibility of the Parasitoid Phymastichus coffea LaSalle (Hymenoptera: Eulophidae) to Beauveria bassiana under laboratory conditions

International Nuclear Information System (INIS)

Castillo, Alfredo; Gomez, Jaime; Infante, Francisco; Vega, Fernando E.

2009-01-01

The coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae), is the most important coffee pest worldwide. Beauveria bassiana is a generalist entomopathogenic fungus widely used by coffee farmers to control this pest and Phymastichus coffea LaSalle (Hymenoptera: Eulophidae) is an African endo parasitoid of H. hampei adults, recently imported to several Latin American and Caribbean countries to aid in the coffee berry borer control. The objective of this study was to determine if B. bassiana is detrimental to P. coffea. The susceptibility of the parasitoid was evaluated in terms of adult survivorship, mean lethal concentration (LC 50 ), mean lethal time (LT 50 ), reproduction and immature mortality. The main effect of the fungus resulted in reduction of adult longevity and mortality of 100% for immature stages of this parasitoid. The LC 50 for adults was 0.11% equivalent to 9.53 x 10 7 conidia/ml of B. bassiana and a LT 50 of 29.4 h, equivalent to reduction of 22% of its normal longevity as an adult. P. coffea was capable of disseminating spores of B. bassiana to non-infected H. hampei adults, which could indirectly cause the death of its own progeny. These results could be valuable when considering the use of both organisms in the field, especially in an integrated pest management program. (author)

Homostachydrine (pipecolic acid betaine) as authentication marker of roasted blends of Coffea arabica and Coffea canephora (Robusta) beans.

Science.gov (United States)

Servillo, Luigi; Giovane, Alfonso; Casale, Rosario; Cautela, Domenico; D'Onofrio, Nunzia; Balestrieri, Maria Luisa; Castaldo, Domenico

2016-08-15

The occurrence of pipecolic acid betaine (homostachydrine) and its biosynthetic precursor N-methylpipecolic acid was detected for the first time in green coffee beans of Robusta and Arabica species. The analyses were conducted by HPLC-ESI tandem mass spectrometry and the metabolites identified by product ion spectra and comparison with authentic standards. N-methylpipecolic acid was found at similar levels in green coffee beans of Robusta and Arabica, whereas a noticeable difference of homostachydrine content was observed between the two green coffee bean species. Interestingly, homostachydrine content was found to be unaffected by coffee bean roasting treatment because of a noticeable heat stability, a feature that makes this compound a candidate marker to determine the content of Robusta and Arabica species in roasted coffee blends. To this end, a number of certified pure Arabica and Robusta green beans were analyzed for their homostachydrine content. Results showed that homostachydrine content was 1.5±0.5mg/kg in Arabica beans and 31.0±10.0mg/kg in Robusta beans. Finally, to further support the suitability of homostachydrine as quality marker of roasted blends of Arabica and Robusta coffee beans, commercial samples of roasted ground coffee blends were analyzed and the correspondence between the derived percentages of Arabica and Robusta beans with those declared on packages by manufacturers was verified. Copyright © 2016 Elsevier Ltd. All rights reserved.

Study on the determination of coffea arabic radio sensibility curve

International Nuclear Information System (INIS)

Robleda, D.; Velazquez, R.

1993-01-01

The radiosensitivity curve of Coffea Arabic submitted to gamma irradiation from a 60C o source at the MRX-1500 with a dose power of 105 Gy/min was determined. For that study,. coffee seeds were irradiated at doses of 10,40,80 and 120 Gy, with a 40% of relative humidity; percentage of germination, height decrease, number and size of leaves, number and length of modes. As result of this analysis, GR50 and GR20 doses for searching genetic variability related to plant size reduction

Microbial inputs in coffee (Coffea arabica L.) production systems, southwestern Ethiopia

OpenAIRE

Muleta, Diriba

2007-01-01

Arabica coffee is the key cash crop and top mainstay of the Ethiopian economy and requires sustainable production methods. Southwestern natural forests, the site of this study, are believed to be the centre of origin and diversity for Coffea arabica and still harbour wild Arabica coffee that may serve as an important gene pool for future breeding. Cost reductions, sustainability and quality improvement are now the major priorities in coffee production systems and require organic growing of co...

PERBANDINGAN KARAKTERISTIK KIMIA DAN NILAI SENSORI ANTARA KOPI LUWAK DAN KOPI BIASA DARI VARIETAS ARABICA (Cafeea arabica. L) DAN ROBUSTA (Cafeea canephora. L)

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Mahendradatta, Meta; Zainal; Israyanti; Abu Bakar, Tawali

2012-01-01

"Luwak??? coffee is well known as an extraordinary coffee due to its taste and high sell price. Special taste and odor of ???luwak??? coffee are caused by the change of protein, fat and caffeine content. This research aimed to know the comparison of caffein content, proximate analysis (protein and fat), taste and odor between ???luwak??? coffee and original coffee from arabika (Caffea arabica L) and robusta (Caffea canephora L) varieties. The treatments were robusta ???luwak???, arabica ???lu...

Effects of roasting temperatures and gamma irradiation on the content of chlorogenic acid, caffeic acid and soluble carbohydrates of coffee

International Nuclear Information System (INIS)

Deshpande, S.N.; Aguilar, A.A.

1975-01-01

Two varieties of Puerto Rican coffee, Coffea canephora L. var. Robusta, and Coffea arabica L. var. Borbon, were subjected to four different doses of radiation and roasted at two different temperatures. Aqueous extracts of the ground coffee beans were analyzed for chlorogenic acid and caffeic acid at 324 nm and 360 nm wavelength settings, respectively. Samples subjected to the roasting treatments in conjuction with irradiation treatments were treated with basic lead acetate prior to the colorimetric analyses in order to eliminate interfering substances. The total carbohydrate content was also determined by colorimetric techniques with anthrone reagent. The total nitrogen content of the pulverized samples were determined by the micro-Kjeldahl method. While roasting treatments caused a reduction in the concentrations of the chlorogenic acid, caffeic acid, and the carbohydrates, the radiation treatments increased the concentrations of soluble carbohydrates without affecting the concentrations of chlorogenic acid or caffeic acid. It therefore appears that radiation treatments seem to cause degradation of the acid-polysaccharide complexes liberating soluble sugars. There were no noticable changes in the total content of nitrogen caused by roasting or the radiation treatments as indicated by the statistical analysis employing the split plot design. (author)

Efecto de la dieta artificial MP sobre la emergencia y relacion de sexos de Phymastichus coffea (Hymenoptera:Eulophidae) mantenido sobre su hueped, Hypothenemus hampei (Coleoptera: Scloytidae)a traves de generaciones contin

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Phymastichus coffea La Salle (Hymenoptera: Eulophidae) is an endoparasitoid that attacks the adult coffee berry borer, Hypothenemus hampei Ferrari (Coleoptera: Scolytidae). The MP diet developed by Portilla and Streett is the only reported diet that allows cultures of P. coffea to develop and repr...

Aplicación de una técnica de Cromatografía de Exclusión molecular para la purificación de ADN en plantas de Coffea sp. APPLICATION OF A TECHNIQUE OF MOLECULAR EXCLUSION CHROMATOGRAPHY FOR THE PURIFICATION OF DNA FROM Coffea sp. PLANTS

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Ana María García Cepero

2006-12-01

Full Text Available Uno de los mayores inconvenientes en la extracción y purificación de biomoléculas a partir de plantas del género Coffea, es un alto contenido de polifenoles y compuestos tánicos. En el presente artículo se describe una metodología que permite obtener ADN de alta pureza. La extracción del ADN del homogeneizado de tejido foliar en siete genotipos de Coffea sp., se realizó mediante la técnica citada por Chaparro (1993 y su purificación se logró mediante cromatografía de exclusión molecular sobre una fase estacionaria de Sephacryl S-1000. Los resultados muestran que la alta eficiencia de separación de ARN degradado, proteínas, pigmentos y compuestos que absorben entre 220 y 300 nm, permiten obtener un ADN de alta pureza a juzgar por los datos espectrofotométricos y electroforéticos.One of the greatest difficulties in extracting and purifying biomolecules from plants in the genus Coffea is the high polyphenol and tannin contents. In this study a methodology is described that allows obtaining high purity DNA from leaf tissues of seven genotypes of Coffea sp. by means of the technique desribed by Chaparro (1993 and its further purification was achieved by molecular exclusion chromatography on Sephacryl S-1000 (Pharmacia. The results showed that the high separation efficiency of degraded RNA, proteins, pigments, and other compounds that absorb between 220 and 300 nm allowed obtaining high purity DNA as judged by the spectophometric and electroforetic data.

Cold induced changes on sugar contents and respiratory enzyme activities in coffee genotypes Alterações dos teores de açúcares e da atividade de enzimas do metabolismo respiratório em genótipos de café submetidos ao frio

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Fábio Luiz Partelli

2010-04-01

Full Text Available The present research aimed to characterize some biochemical responses of Coffea canephora (clones 02 and 153 and C. arabica (Catucaí IPR 102 genotypes subjected to low positive temperatures, helping to elucidate the mechanisms involved in cold tolerance. For that, one year old plants were subjected successively to 1 a temperature decrease (0.5°C a day from 25/20°C to 13/8°C (acclimation period, 2 a three day chilling cycle (3x13/4°C and to 3 a recovery period of 14 days (25/20°C. In Catucaí (less cold sensitive when compared to clone 02 there was an increased activity in the respiratory enzymes malate dehydrogenase and pyruvate kinase. Furthermore, Catucaí showed significant increases along the cold imposition and the higher absolute values after chilling exposure of the soluble sugars (sucrose, glucose, fructose, raffinose, arabinose and mannitol that are frequently involved in osmoregulation and membrane stabilization/protection. The analysis of respiratory enzymes and of soluble sugar balance may give valuable information about the cold acclimation/tolerance mechanisms, contributing to a correct selection and breeding of Coffea sp. genotypes.A pesquisa teve por objetivo caracterizar respostas bioquímicas de genótipos de Coffea canephora (clones 02 and 153 e C. arabica (Catucaí IPR 102 submetidos a baixas temperaturas positivas, ajudando a elucidar os mecanismos envolvidos na tolerância ao frio. Plantas com um ano de idade foram submetidas sucessivamente a 1 decréscimo da temperatura (0,5°C por dia desde 25/20°C até 13/8°C (período de aclimatização, 2 um ciclo de três dias a 13/4°C e 3 14 dias de recuperação (25/20°C. Em Catucaí, genótipo menos sensível ao frio quando comparado com o clone 02, observou-se um aumento das atividades das enzimas malato desidrogenase e piruvate cinase, relacionadas com a respiração. Nesse genótipo, os níveis de açúcares solúveis sacarose, glucose, frutose, rafinose, arabinose e

Exogenous gibberellins inhibit coffee (Coffea arabica cv. Rubi) seed germination and cause cell death in the embryo

NARCIS (Netherlands)

Silva, Da E.A.A.; Toorop, P.E.; Nijsse, J.; Bewley, J.D.; Hilhorst, H.W.M.

2005-01-01

The mechanism of inhibition of coffee (Coffea arabica cv. Rubi) seed germination by exogenous gibberellins (GAs) and the requirement of germination for endogenous GA were studied. Exogenous GA4+7 inhibited coffee seed germination. The response to GA4+7 showed two sensitivity thresholds: a lower one

Adaptabilidade e estabilidade via regressão não paramétrica em genótipos de café Adaptability and stability based on nonparametric regression in coffee genotypes

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Moysés Nascimento

2010-01-01

Full Text Available O objetivo deste trabalho foi avaliar uma metodologia de análise de adaptabilidade e estabilidade fenotípica de genótipos de café baseada em regressão não paramétrica. A técnica utilizada difere das demais, pois reduz a influência na estimação do parâmetro de adaptabilidade de algum ponto extremo, ocasionado pela presença de genótipos com respostas demasiadamente diferenciadas a determinado ambiente. Foram utilizados dados provenientes de um experimento sobre produtividade média de grãos de 40 genótipos de café (Coffea canephora, com delineamento em blocos ao acaso, com seis repetições. Os genótipos foram avaliados em cinco anos (1996, 1998, 1999, 2000 e 2001, em dois locais (Sooretama e Marilândia, ES no total de dez ambientes. A metodologia proposta demonstrou ser adequada e eficiente, pois extingue os efeitos impróprios induzidos pela presença de pontos extremos e evita a recomendação incorreta de genótipos quanto à adaptabilidade.The objective of this work was to evaluate a methodology of phenotypic adaptability and stability analyses of coffee genotypes based on nonparametric regression. The technique used differs from other techniques because it reduces the influence of extreme points resulting from the presence of genotypes whose answers to a certain environment are too different on the estimation of the adaptability parameter. Data from an experiment studying the average yield of 40 coffee (Coffea canephora genotypes in a randomized block design with six replicates were used to evaluate the method. The genotypes were evaluated along five years (1996, 1998, 1999, 2000 and 2001 in two locations (Sooretama and Marilândia, ES, Brazil, in a total of ten environments. The methodology proposed proved adequate and efficient, since it eliminates the disproportionate effects induced by the presence of extreme points and avoids misleading recommendations of genotypes in terms of adaptability.

Redistribution of the solar radiation and the rain inside of coffee plantations (Arabic Coffea L.)

International Nuclear Information System (INIS)

Jaramillo Robledo, Alvaro

2005-01-01

The following review presents a series of studies on microclimates of non-shaded and shaded conditions of coffee plantations (Coffea arabica L.) in Colombia. Likewise, The redistribution of solar radiation and the temperature, as well as the energy balance, of the coffee plant and the crop are described. The results on the components of water balance and transport of nutrients within the coffee plantations are reported

O dimorfismo dos ramos em Coffea arabica L.

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A. Carvalho

1950-06-01

Full Text Available O dimorfismo dos ramos tem sido observado em vários gêneros de plantas, tais como Gossypium, Theobroma, Hedera, Musa, Araucária, Castilla, bem como em Coffea. Tal fenômeno se carateriza por uma diferenciação somática, que, na maioria dos casos, é permanente, podendo-se propagar as diferentes formas pela reprodução vegetativa. Como acontece nos representantes de Coffea, tal dimorfismo se carateriza por diferenças no hábito de crescimento, isto é, na direção dos ramos. Assim, a extremidade de um ramo ponteiro (ortotrópico reproduz, quando enxertada, uma planta normal, ao passo que a de um ramo lateral (plagiotrópico somente dará origem a ramos laterais. Em se tratando de um fenômeno tanto de interesse teórico como de importância prática (para a propagação vegetativa, resolveu-se fazer uma série de investigações em tôrno dêsse assunto, cujos primeiros resultados os autores relatam no presente trabalho. Apresentaram-se, em primeiro lugar, as observações feitas com referência à natureza das gemas existentes nas axilas das fôlhas de plantas novas, tanto na haste principal, como nos ramos laterais. Verificou-se que: a no eixo hipocotiledonar não há indícios da existência de gemas ; b na axila das fôlhas cotiledonares há um grupo de gemas dormentes, que são despertadas, dando origem a ramos ortotrópicos, quando o eixo epicotiledonar é cortado abaixo do primeiro par de fôlhas primárias; c o aparecimento de gemas, que dão ramos laterais (plagiotrópicos, só ocorre pela primeira vez, nas axilas do oitavo ao décimo primeiro par de folhas ; observou-se que certas estruturas genéticas impedem a formação de ramos plagiotrópicos mesmo até o trigésimo terceiro par de fôlhas ; d nas axilas da haste principal, possuidoras de gemas que dão origem a ramos plagiotrópicos, ocorrem também duas e, mais raramente, três outras, que produzem ramos ortotrópicos, e que se desenvolvem quando se suprime o eixo

Produtividade do cafeeiro Mundo Novo enxertado e submetido à adubação verde antes e após recepa da lavoura Productivity of grafted coffee during intercropping with five leguminous species in the western region of São Paulo State, Brazil

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Edison Martins Paulo

2006-01-01

Full Text Available Estudaram-se a produção e o crescimento do cafeeiro Mundo Novo (Coffea arabica L. enxertado sobre o Apoatã IAC 2258 (Coffea canephora Pierre ex Froehner submetido à adubação verde com as seguintes espécies leguminosas: crotalária espectábilis (Crotalaria spectabilis Roth., crotalária júncea (Crotalaria juncea L., guandu [Cajanus cajan (L. Millsp.], mucuna anã (Stizolobium deeringeanum Bort. e soja IAC 9 [Glycine max (L. Merril] e um tratamento testemunha sem plantas leguminosas. As leguminosas foram semeadas a 50 cm da projeção da copa dos cafeeiros e incorporadas no florescimento. O experimento foi desenvolvido no Pólo Regional de Desenvolvimento Tecnológico dos Agronegócios da Alta Paulista, em Adamantina, no período de 1989 a 1995. Adotou-se o delineamento estatístico de blocos ao acaso com seis tratamentos e cinco repetições. Os adubos verdes crotalária espectábilis, crotalária júncea, mucuna anã e soja, durante o período experimental, e a crotalária espectábilis após a recepa, não diminuíram a produção do cafeeiro. O guandu, embora tenha aumentado o teor de matéria orgânica do solo, foi a única leguminosa que diminuiu a produção e o diâmetro do caule dos cafeeiros. O guandu e a crotalária júncea, respectivamente, produziram as maiores quantidades de fitomassa seca. A produção do café se correlacionou inversamente com a fitomassa seca das leguminosas e positivamente com altura e diâmetro do caule do cafeeiro.Yield of arabica coffee (Coffea arabica of grafted onto robusta coffee (Coffea canephora Pierre ex Froehner Apoatã IAC 2258 was evaluated during six years of intercropping with five leguminous species: sunn hemp (Crotalaria juncea L., Crotalaria spectabilis Roth., dwarf velvet bean (Stizolobium deeringeanum Bort., soybean Glycine max (L. Merryl] and pigeon pea [Cajanus cajan (L. Millsp.] in the Western region of São Paulo State, Brazil, from 1989 to 1995. Leguminous species were sown 50 cm

Genética de coffea VII: hereditariedade dos caracteres de coffea arabica L. var. maragogipe hort ex froehner

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C. A. Krug

1942-01-01

Full Text Available A variedade maragogipe do Coffea arabica L. foi encontrada pela primeira vez por Crisógono José Fernandes, em 1870, no município baiano de Maragogipe onde, provavelmente, se originou por mutação. Desde 1933 esta variedade vem sendo estudada pela Secção de Genética do Instituto Agronômico do Estado de São Paulo, em Campinas, com o fim de se determinar a sua constituição genética. Muitas autofecundações, cruzamentos e back-crosses foram, então, realizados. Grande parte das plantas obtidas só puderam ser classificadas após a colheita do ano de 1940. Todas foram examinadas quanto à forma e dimensões das folhas e um grande número ainda quanto à forma e dimensões das flores, frutos e sementes. Verificou-se que o caráter maragogipe mostra dominância quase completa em F1, não sendo possivel uma separação das ciasses maragogipe puro e híbrido. Em F2, e nos back-crosses com as formas normais, obtiveram-se, respectivamente, relações de 3:1 e 1:1 entre plantas maragogipe e plantas normais, relações essas que demonstram que os caracteres do maragogipe são controlados por um único par de fatores genéticos dominantes, para os quais se propõe o símbolo Mg-Mg, derivado do próprio nome desta variedade.In the present article the results of the genetical analysis of the characters of the maragogipe variety of Coffea arabica L are presented. This variety which originated as a mutation from C. arabica L. var. typica Cramer, in 1870, in the State of Baía in North Brazil, represents a gigas form of that variety, having larger leaves, flowers and fruits, its plants being also taller; it is also known for its low productivity. Since 1933 a genetical analysis of this variety was undertaken, many of its plants being selfed and crossed with other maragogipe plants and also with individuals of the typica and bourbon varieties of C. arabica; two generations have been studied, including F2's and several back-crosses. It was concluded

Inhibitory effect of Coffea arabica bean in testosterone induced prostatic hyperplasia in Sprague-Dawley rats

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Kristian Alfonso G. Cueto

2016-05-01

Full Text Available Benign prostatic hyperplasia (BPH has been described as the uncontrolled prostate gland growth which leads to difficulty in urination. One of the treatment of BPH is saw palmetto lipid extracts which has been shown to inhibit prostate 5 α-reductase and some of its components (lauric acid, myristic acid and oleic acid also inhibit the enzyme. Coffee was also rich in fatty acids namely linoleic acid, oleic acid and palmitic acid. The aim of this research is to investigate whether coffee is effective in preventing testosterone-induced prostatic hyperplasia in rats using testosterone propionate and estradiol valerate. After and before the induction, the rats were tested for prostate specific antigen (PSA . The condition of the prostate gland of the test animals were correlated with the results of the said test and in the histopathologic results. After 14 days of experimentation, animals in the test group significantly decreased their PSA levels as compared to the BPH group. The histomorphology showed that Coffea arabica bean oil inhibited testosterone propionate while estradiol valerate induced prostatic hyperplasia. These findings indicate that Coffee arabica bean oil effectively inhibited the development of BPH. With the proven safety of coffee oil, these findings strongly support the feasibility of using Coffea arabica bean oil therapeutically in treating BPH.

Impacts of leaf age and heat stress duration on photosynthetic gas exchange and foliar nonstructural carbohydrates in Coffea arabica

Science.gov (United States)

Danielle E. Marias; Frederick C. Meinzer; Christopher Still

2017-01-01

Given future climate predictions of increased temperature, and frequency and intensity of heat waves in the tropics, suitable habitat to grow ecologically, economically, and socially valuable Coffea arabica is severely threatened. We investigated how leaf age and heat stress duration impact recovery from heat stress in C. arabica...

Dinâmica dos micronutrientes em cafeeiros enxertados

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André Dominghetti Ferreira

2013-04-01

Full Text Available As respostas à disponibilidade dos nutrientes variam entre espécies distintas dentro de um mesmo gênero, por causa, principalmente, das exigências nutricionais variáveis, capacidade de absorção, translocação e utilização dos nutrientes. O objetivo deste trabalho foi avaliar a eficiência de absorção, translocação e uso dos micronutrientes por diferentes cultivares de Coffea arabica L., enxertados em Apoatã IAC 2258 (Coffea canephora. O experimento foi instalado em casa de vegetação, utilizando-se o método de cultivo em solução nutritiva. Foi utilizado um fatorial 7 x 3 + 2, sendo sete cultivares de Coffea arabica L. (Palma II, Catucaí 2 SL, Oeiras MG 6851, Obatã IAC 1669-20, Acauã, Topázio MG 1190 e Paraíso MG H 419-1, três tipos de mudas (pé franco, autoenxertada e enxertada sobre o cultivar Apoatã IAC 2258 e duas testemunhas (Apoatã autoenxertado e Apoatã pé franco. O porta-enxerto utilizado influenciou negativamente na absorção de boro, ferro e manganês. A translocação dos micronutrientes boro e cobre obteve maiores índices nas mudas enxertadas. O cultivar Palma II, quando enxertado, apresentou o maior índice de utilização dos nutrientes, mostrando-se passível de ser enxertado. O porta-enxerto utilizado mostrou-se apto para a enxertia, por não sofrer influência negativa, tanto pela enxertia, quanto pelos cultivares utilizados.

Detection of enterotoxins produced by B. cereus through PCR analysis of ground and roasted coffee samples in Rio de Janeiro, Brazil

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Cyllene de Matos Ornelas da Cunha Corrêa de Souza

2011-06-01

Full Text Available Coffee is one of the most appreciated drinks in the world. Coffee ground is obtained from the fruit of a small plant that belongs to the genus Coffea. Coffea arabica and Coffea canephora robusta are the two most commercially important species. They are more commonly known as arabica and robusta, respectively. Two-thirds of Coffea arabica plants are grown in South and Central America, and Eastern Africa - the place of origin for this coffee species. Contamination by microorganisms has been a major matter affecting coffee quality in Brazil, mainly due to the harvesting method adopted. Brazilian harvests are based on fruits collected from the ground mixed with those that fall on collection cloths. As the Bacillus cereus bacterium frequently uses the soil as its environmental reservoir, it is easily capable of becoming a contaminant. This study aimed to evaluate the contamination and potential of B. cereus enterotoxin genes encoding the HBL and NHE complexes, which were observed in strains of ground and roasted coffee samples sold in Rio de Janeiro. The PCR (Polymerase Chain Reaction results revealed high potential of enterotoxin production in the samples. The method described by Speck (1984 was used for the isolation of contaminants. The investigation of the potential production of enterotoxins through isolates of the microorganism was performed using the B. cereus enterotoxin Reverse Passive Latex Agglutination test-kit (BCET-RPLA, Oxoid, according to the manufacturer's instructions. The potential of enterotoxin production was investigated using polymerase chain reaction (PCR methods for hblA, hblD and hblC genes (encoding hemolysin HBL and for nheA, nheB and nheC genes (encoding non-hemolytic enterotoxin - NHE. Of all the 17 strains, 100% were positive for at least 1 enterotoxin gene; 52.9% (9/17 were positive for the 3 genes encoding the HBL complex; 35.3% (6/17 were positive for the three NHE encoding genes; and 29.4% (5/17 were positive for

Effect of the inoculation density in Coffea arabica L. cv. `Caturra rojo' somatic embryos germination in RITA® Temporary Immersion System

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Raúl Barbon

2014-04-01

Full Text Available The development of somatic embryogenesis of coffee (Coffea spp. in liquid culture medium is a viable alternative for the propagation of these species. The use of liquid culture medium and temporary immersion systems could increase the germination of somatic embryos and improve the quality of plants. The objective of this work was to determine the effect of inoculation density on germination of somatic embryos of Coffea arabica L. cv. `Caturra rojo' in temporary immersion systems RITA®. It were used as inoculum densities 40, 50, 60, 70 and 80 somatic embryos per RITA®. After 90 days of culture the number of somatic embryos germinated, hyperhydricity symptoms, number of true leaves, length and root development was quantified. With inoculum density of 70 somatic embryos per RITA®, it was obtained a highest germination percentage (60% with good leaf development and length of the plants. Key words: hyperhydricity, liquid culture medium, partial germination, total germination, somatic embryogenesis

Field-cage evaluation of the parasitoid Phymastichus coffea LaSalle (Hymenoptera: Eulophidae) as a natural enemy of the coffee berry borer

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Phymastichus coffea (Hymenoptera: Eulophidae) is an African parasitoid that has been imported to Mexico and other Latin American countries for the biological control of the coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae: Scolytinae). As a part of the evaluation of this ...

Productivity of coffee crop (Coffea arabica L.) in conversion to the organic production system

OpenAIRE

Malta, Marcelo Ribeiro; Empresa de Pesquisa Agropecuária de Minas Gerais - EPAMIG; Pereira, Rosemary Gualberto Fonseca Alvarenga; Universidade Federal de Lavras - UFLA; Chagas, Sílvio Júlio de Rezende; Empresa de Pesquisa Agropecuária de Minas Gerais - EPAMIG; Guimarães, Rubens José; Universidade Federal de Lavras - UFLA

2008-01-01

This experiment was carried out in Lavras, MG, to verify the productivity of coffee crop (Coffea arabica L.) in conversion to the organic production system. The experiment was set in a six-year old coffee crop of the cultivar Catuaí Amarelo IAC 86, with spacing of 4,0 x 0,6 m, previously cultivated under the conventional system. In the organic treatments a 4 x 4 balanced lattice design with 5 replications in a 3 x 2 x 2 factorial scheme was used, besides 4 additional treatments. The f...

The coffee agroforestry system. Its importance for the agro-alimentary and nutritional security in Ecuador

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Luciano Abelardo Ponce Vaca

2018-01-01

Full Text Available In the context of coffee growing, Ecuador is characterized by planting two main commercial species of Coffea arabica L. (Arabica coffee, and Coffea canephora Pierre ex Froehner (Robusta coffee, where small production units and agroforestry systems predominate. To overcome the low national production, which constitutes the central problem of coffee growing in the country, the Ministry of Agriculture and Livestock of Ecuador, promoted the project «Reactivation of the Ecuadorian coffee industry», which contributes to food security and nutrition with integral approach. In these circumstances, the objective of this paper is to analyze the importance of coffee agroforestry systems for agro-alimentary and nutritional security in Ecuador. The proposal is born from the agro-economic diagnosis «case study», from the situation of the Coffee Production Units, from the Association of Peasants «Juntos Lucharemos» from the La Unión parish of the Jipijapa county, province of Manabí, in which they settled Main contributions to the agro-alimentary and nutritional security coming from the coffee agroforestry systems, this allowed to analyze characteristics related to the object of study. Based on the research results, gaps in national consumption needs were detected. This proposal contributed to articulate and promote the reactivation of coffee growing on agroecological bases, in harmony with the dimensions of sustainability in order to protect and conserve biodiversity and the coffee forest.

Genetic Diversity of Arabica Coffee (Coffea arabica L. in Nicaragua as Estimated by Simple Sequence Repeat Markers

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Mulatu Geleta

2012-01-01

Full Text Available Coffea arabica L. (arabica coffee, the only tetraploid species in the genus Coffea, represents the majority of the world’s coffee production and has a significant contribution to Nicaragua’s economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei’s gene diversity (HT and the within-population gene diversity (HS were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST=0.13; P<0.001. The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved through ex situ conservation of a low number of populations from each variety.

Physiological Dose-Response of Coffee (Coffea arabica L. Plants to Glyphosate Depends on Growth Stage Respuesta Fisiológica de Plantas de Café (Coffea arabica L. a Glifosato Depende de la Etapa de Crecimiento

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Leonardo Bianco de Carvalho

2012-06-01

Full Text Available Glyphosate is the main herbicide used in coffee (Coffea arabica L. plantations in Brazil. Problems with herbicide drift commonly occur in orchard fields due to non-adequate spraying conditions. A series of experiments was carried out aiming to evaluate physiological dose-response of C. arabica plants submitted to exposure to simulated glyphosate drift in two distinct plant growth stages. Glyphosate was applied at 0, 180, 360, and 720 g acid equivalent (AE ha-1 directly on coffee plants with 10 and 45 d after transplanting (DAT. Glyphosate doses in a range of 180-360 g AE ha-1 increased photosynthesis, transpiration and stomatal conductance in 10 DAT-plants up to 14 d after application (DAA while, in 45 DAT-plants, an increase was observed only up to 2 DAA, but this pattern was not persistent afterwards so that no difference in gas exchange was observed at 60 DAA in both plants. Macronutrient content was not affected by glyphosate application in both plants. Plant DM accumulation was not affected by glyphosate application at 10 DAT-plants, but an increase in plant growth was observed when glyphosate was applied in a range of 360-720 g AE ha-1 in 45 DAT-plants. Coffea arabica cv. Catuaí Vermelho IAC-144 responded differentially to glyphosate drift depending on plant growth stage, regarding on photosynthesis, transpiration, stomatal conductance, and plant growth, in spite of macronutrient nutrition was not affected.Glifosato es el principal herbicida utilizado en las plantaciones de café (Coffea arabica L. en Brasil. Problemas con la deriva de herbicidas comúnmente ocurren en los campos de cultivo debido a condiciones no adecuadas de pulverización. Una serie de experimentos se llevó a cabo con el objetivo de evaluar la relación dosis-respuesta fisiológica de plantas de C. arabica expuestas a situaciones simuladas de exposición a deriva de glifosato en dos etapas distintas de crecimiento de las plantas. El glifosato se aplicó en dosis de 0

ALTERNATIVAS DE APLICAÇÃO DO "DRIS" À CULTURA DE CAFÉ CONILON (Coffea canephora Pierre

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Wadt Paulo Guilherme Salvador

1999-01-01

Full Text Available O sistema integrado de diagnose e recomendação (DRIS tem sido indicado como alternativa para a avaliação nutricional das plantas, em relação ao método tradicional de interpretação da concentração dos teores foliares pelo critério do nível crítico. Esse trabalho objetivou avaliar a aplicação de diferentes métodos do DRIS (de Jones, de Elwali & Gascho e de Rathfon & Burger em dados oriundos de lavouras comerciais cafeeiras, do estado do Espírito Santo, nos anos agrícolas de 1986/87, 1987/88 e 1988/89. Adicionalmente, avaliou-se a validade da adoção do teste F na seleção das relações para o cálculo desses índices. A adoção do teste F mostrou-se promissora, pois melhorou a capacidade do DRIS em discriminar as lavouras nutricionalmente balanceadas daquelas desbalanceadas. Quanto as diferentes fórmulas de cálculo dos índices DRIS, embora tenha havido diferenças elas, os diagnósticos tenderam a ser consistentes entre si, com pouca dependência quanto ao tipo de fórmula utilizada. Os resultados sugeriram, ainda, que o manejo da adubação nitrogenada foi adequado, pois observou-se que a maioria das lavouras não apresentaram deficiência de N; enquanto que, para P, Ca, B e K houve indicações de que esses nutrientes poderiam estar ocorrendo com maior número de casos como limitantes da produtividade cafeeira no estado do Espírito Santo.

Post-harvest practices linked with ochratoxin A contamination of coffee in three provinces of Cordillera Administrative Region, Philippines.

Science.gov (United States)

Barcelo, Jonathan M; Barcelo, Racquel C

2018-02-01

One of the emerging concerns in the Cordillera Administrative Region, Philippines is ochratoxin A (OTA) contamination in coffee. During 2015 to 2016, a total of 51 Arabica (Coffea arabica) coffee samples from Benguet province and 71 Robusta (Coffea canephora var. Robusta) coffee samples from the provinces of Ifugao and Kalinga were analysed for OTA contamination. The OTA-producing fungal contaminants during drying and storage of Arabica and Robusta coffee were Aspergillus niger and Aspergillus ochraceus. Ochratoxin A was more commonly detected in Robusta coffee (36.6%) than in Arabica coffee (21.6%). Among the contaminated samples, Robusta coffee cherries in the drying yard had the highest mean OTA level (120.2 μg kg -1 , n = 10) while roasted Robusta coffee beans had the lowest mean level (4.8 μg kg -1 , n = 9). The onset of contamination of Arabica coffee occurred during storage, with a mean OTA level of 46.7 μg kg -1 (n = 9). Roasted coffee had lower OTA content although five samples had levels >5.0 μg kg -1 . Pearson Chi-square analysis (χ 2 ) and Fisher's exact test revealed that several post-harvest practices involving non-removal of the husk or hull and mixing of defective coffee were significantly associated with the occurrence of OTA during drying and storage (p coffee in all stages of post-harvest and rapid reduction of moisture content particularly during drying.

Sensorial analysis of irradiated coffee (Coffea arabica L.) by electron beam

International Nuclear Information System (INIS)

Rodrigues, Flavio T.; Fanaro, Gustavo B.; Koike, Amanda C.R.; Villavicencio, Anna Lucia C.H.; Silva, Maria E.M. Pinto e

2013-01-01

Coffee is an important commodity and it is one of the most widely consumed beverages in the world. The acceptance of coffee by consumers depends mainly on the sensory characteristics of the beverage, that is its flavor, body, color, acidity and aroma. Food irradiation is processing technology environmental friendly and safety which aimed at the improvement of food quality. Depending on the absorbed radiation dose various effects can be achieved resulting in increase the shelf life, disinfestation, microorganism load reduction, without causing sensory changes to the food. Sensory analysis is the examination of a food through the evaluation of the attributes sensorial of product. The objective this paper was to evaluate the sensory properties, acceptance and purchase intent by the consumer of coffee (Coffea arabica L.) after the irradiation process with doses 6.0, 12.0 and 18.0kGy by electron beam. (author)

Sensorial analysis of irradiated coffee (Coffea arabica L.) by electron beam

Energy Technology Data Exchange (ETDEWEB)

Rodrigues, Flavio T.; Fanaro, Gustavo B.; Koike, Amanda C.R.; Villavicencio, Anna Lucia C.H., E-mail: flaviot@ymail.com [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Silva, Maria E.M. Pinto e [Universidade de Sao Paulo (USP), Sao Paulo, SP (Brazil). Fac. de Saude Publica. Dept. de Nutricao

2013-07-01

Coffee is an important commodity and it is one of the most widely consumed beverages in the world. The acceptance of coffee by consumers depends mainly on the sensory characteristics of the beverage, that is its flavor, body, color, acidity and aroma. Food irradiation is processing technology environmental friendly and safety which aimed at the improvement of food quality. Depending on the absorbed radiation dose various effects can be achieved resulting in increase the shelf life, disinfestation, microorganism load reduction, without causing sensory changes to the food. Sensory analysis is the examination of a food through the evaluation of the attributes sensorial of product. The objective this paper was to evaluate the sensory properties, acceptance and purchase intent by the consumer of coffee (Coffea arabica L.) after the irradiation process with doses 6.0, 12.0 and 18.0kGy by electron beam. (author)

Arbuscular mycorrhizal fungi associated with shade trees and Coffea arabica L. in a coffee-based agroforestry system in Bonga, Southwestern Ethiopia

OpenAIRE

Sewnet ,Tadesse Chanie; Tuju, Fassil Assefa

2013-01-01

In a first step to understand the interactions between Coffea arabica L. trees and mycorrhizae in Ethio¬pia, an investigation of the current mycorrhizal colonization status of roots was undertaken. We sampled 14 shade tree species occurring in coffee populations in Bonga forest, Ethiopia. Milletia fer¬ruginea, Schefflera abyssinica, Croton macrostachyus, Ficus vasta, F. sur, Albizia gummifera, Olea capensis, Cordia africana, Ehretia abyssinica, Pouteria adolfi-friederici, Pavetta oliveriana, ...

Perfil sensorial da bebida café (Coffea arabica L. determinado por análise tempo-intensidade Sensorial profile of beverage coffee (Coffea arabica L. determined by analysis time-intensity

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Marlene A. M. Monteiro

2005-12-01

Full Text Available O presente trabalho teve como objetivo avaliar o gosto amargo, sabor fermentado e sabor queimado de nove amostras (mole/clara, dura/clara, rio/clara, mole/expresso, dura/expresso, rio/expresso, mole/escura, dura/escura e rio/escura da bebida café (Coffea arabica L. por meio da análise Tempo-Intensidade (TI. Foram avaliados seis parâmetros da curva: tempo para atingir a intensidade máxima (TImáx, intensidade máxima do estímulo (Imáx, tempo correspondente ao ponto onde a intensidade máxima começa a declinar (Td, tempo de duração da intensidade máxima (Platô, área sob a curva (Área e tempo total de duração do estímulo (Ttot. A análise demonstrou que as amostras de torra escura tiveram maior intensidade máxima (Imáx e tempo de duração do estímulo (Ttot para gosto amargo e sabor queimado, sendo que as amostras de torra clara apresentaram menor intensidade destes estímulos. Em relação ao sabor fermentado, a amostra rio/expresso foi a que apresentou maior intensidade.The present work had as objective to evaluate the bitter taste, fermented flavor and burned flavor of nine samples (soft/light, hard/light, rio/light, soft/express, hard/express, rio/express, soft/dark, hard/dark and rio/dark of the drink coffee (Coffea arabica L. through the analysis Time-Intensity (TI. Six parameters of the curve were evaluated: time to reach the maximum intensity (TImáx, maximum intensity of the incentive (Imáx, time corresponding to the point where the maximum intensity begins to refuse (Td, time of duration of the maximum intensity (Plateau, area under the curve (Área and total time of duration of the incentive (Ttot. The analysis demonstrated that the samples of dark toast had larger maximum intensity (Imáx and time of duration of the incentive (Ttot for bitter taste and burned flavor, while the samples of light toast presented smaller intensity of these stimulus. For the fermented flavor, the sample rio/express was the one that

Somatic Embryogenesis in Coffee: The Evolution of Biotechnology and the Integration of Omics Technologies Offer Great Opportunities.

Science.gov (United States)

Campos, Nádia A; Panis, Bart; Carpentier, Sebastien C

2017-01-01

One of the most important crops cultivated around the world is coffee. There are two main cultivated species, Coffea arabica and C. canephora. Both species are difficult to improve through conventional breeding, taking at least 20 years to produce a new cultivar. Biotechnological tools such as genetic transformation, micropropagation and somatic embryogenesis (SE) have been extensively studied in order to provide practical results for coffee improvement. While genetic transformation got many attention in the past and is booming with the CRISPR technology, micropropagation and SE are still the major bottle neck and urgently need more attention. The methodologies to induce SE and the further development of the embryos are genotype-dependent, what leads to an almost empirical development of specific protocols for each cultivar or clone. This is a serious limitation and excludes a general comprehensive understanding of the process as a whole. The aim of this review is to provide an overview of which achievements and molecular insights have been gained in (coffee) somatic embryogenesis and encourage researchers to invest further in the in vitro technology and combine it with the latest omics techniques (genomics, transcriptomics, proteomics, metabolomics, and phenomics). We conclude that the evolution of biotechnology and the integration of omics technologies offer great opportunities to (i) optimize the production process of SE and the subsequent conversion into rooted plantlets and (ii) to screen for possible somaclonal variation. However, currently the usage of the latest biotechnology did not pass the stage beyond proof of potential and needs to further improve.

CARACTERIZACIÓN FENOTÍPICA DEL GERMOPLASMA DE Coffea canephora Pierre BASE PARA SU MEJORAMIENTO EN ECUADOR

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Luis Fernando Plaza Avellán

2015-06-01

Full Text Available La diversidad agroecológica en la que se desarrolla la producción cafetalera del Ecuador, ayuda a realizar trabajos de investigación que permiten identificar genotipos superiores para zonas específicas de producción. Bajo esta premisa, el presente trabajo tuvo como objetivo central determinar el comportamiento agronómico, productivo y sanitario de los genotipos que conforman el banco de germoplasma de café robusta de la EETP-INIAP; para identificar y seleccionar individuos superiores en las condiciones ambientales del trópico húmedo, en condiciones de secano. Se aplicaron técnicas estadísticas que permitieron identificar genotipos superiores, para seleccionar “cabezas de clon”, dentro y entre accesiones genéticamente diversas y con características de interés comercial. Los resultados obtenidos mostraron correlación positiva (P<0,05 entre la producción y los caracteres de diámetro del tallo, ramas total, ramas productivas, longitud de rama y número de nudos. El COF-001 resultó similar a NP 3018; NP-3056 tiene pocas diferencias con NP-3018 y COF-001; NP-2024 es similar a COF-005; COF 004 es parecido al COF-005; COF-002 y NP-2044 son distintos a los demás materiales. Un total de cuatro genotipos fueron seleccionados para su recomendación comercial bajo un sistema de siembra policlonal: árbol 15 del COF-004, árbol 10 de NP-2024, árbol 15 del COF-003 y árbol 4 de NP-4024, los cuales, reportan rendimientos promedios de 70 qq de café oro/ ha-1, buenas características agronómicas y tolerancia a plagas y enfermedades.

Spatial estimation of foliar phosphorus in different species of the genus Coffea based on soil properties

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Samuel de Assis Silva

2014-10-01

Full Text Available Information underlying analyses of coffee fertilization systems should consider both the soil and the nutritional status of plants. This study investigated the spatial relationship between phosphorus (P levels in coffee plant tissues and soil chemical and physical properties. The study was performed using two arabica and one canephora coffee variety. Sampling grids were established in the areas, and the points georeferenced. The assessed properties of the soil were levels of available phosphorus (P-Mehlich, remaining phosphorus (P-rem and particle size, and of the plant tissue, phosphorus levels (foliar P. The data were subjected to descriptive statistical analysis, correlation analysis, cluster analysis, and probability tests. Geostatistical and trend analyses were only performed for pairs of variables with significant linear correlation. The spatial variability for foliar P content was high for the variety Catuai and medium for the other evaluated plants. Unlike P-Mehlich, the variability in P-rem of the soil indicated the nutritional status of this nutrient in the plant.

Interações entre auxinas e ácido bórico, no enraizamento de estacas caulinares de Coffea arabica L. cv. Mundo Novo Interactions between auxins and boric acid in the rooting of stem cuttings Coffea arabica L. cv. "Mundo Novo"

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E.O. Ono

1992-01-01

Full Text Available O presente trabalho teve como finalidade, estudar o efeito de auxinas e do boro no enraizamento de estacas caulinares de Coffea arabica L. cv. "Mundo Novo". As estacas foram retiradas de ramos ortotrópicos semi-lenhosos de cafeeiro, as quais foram tratadas durante 24 horas com soluções de IBA ou NAA e boro, e a mistura das três substâncias, resultando um total de 14 tratamentos. Para a avaliação do objetivo em questão, foram realizadas as seguintes observações, mediante coleta após 90 dias de plantio: número de estacas enraizadas e número de estacas com calos. Através dos resultados obtidos, pode-se concluir que, para obter um maior número de estacas enraizadas, é conveniente o tratamento com NAA à 100 ou 200 ppm mais boro.The present research had as purpose to study auxin and boron effects on rooting of Coffea arábica L. cv. "Mundo Novo" stem cuttings. The cuttings were taken from orthotropous semi-hardwood branches of coffee-tree, which were treated during 24 hours with IBA or NAA and boron solutions, and the mixture of the three substances, resulting a total of 14 treatments. The following observations were realized, taking the cuttings 90 days after planting: number of rooted cuttings and "callus" formation per cutting. It can be concluded that to obtain a higher number of rooted cuttings, the treatment with NAA at 100 or 200 ppm plus boron is the most suitable.

Perdas causadas por Coccus viridis (Hemiptera: Coccidae em mudas de Coffea arabica L.

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Flávio Lemes Fernandes

2009-08-01

Full Text Available Coccus viridis (Green danifica plantas jovens e adultas de Coffea arabica Linnaeu. No entanto, nada se sabe sobre a magnitude dos danos causados por esta praga. Assim, este trabalho teve por objetivo estudar as relações entre o ataque de C. viridis e as perdas causadas por este inseto a C. arabica. Este trabalho foi conduzido em casa de vegetação na Universidade Federal de Viçosa. Foram utilizadas sementes da linhagem IAC 15 da variedade “Catuaí vermelho” de café (C. arabica. Para a confecção dos tratamentos esta praga foi criada em casa de vegetação separada do experimento. Os tratamentos foram: plantas infestadas e não infestadas por adultos e ninfas da cochonilha verde. As plantas foram nutridas com solução nutritiva. Durante 110 dias foram avaliados: números de adultos e de ninfas de primeiro, segundo e terceiro ínstares, área foliar, diâmetro do caule, altura das plantas em todas repetições. No final do experimento avaliou-se o peso das raízes, caule, folhas e total. Os pesos das raízes, matéria seca total, área foliar e diâmetro do caule de plantas não atacadas por C. viridis superaram em 1,31; 1,41; 1,50 e 8,93 vezes, respectivamente o peso de plantas atacadas. As variáveis selecionadas foram: diâmetro do caule (cm, área foliar (cm², peso de raízes (g, ninfas, adultos e total das cochonilhas. Concluindo que a planta de C. arabica é afetada de forma diferente entre seus órgãos e que a ninfa de terceiro ínstar e adultos são as fases que mais causam danos a C. arabica.Losses Caused by Coccus viridis (Green (Hemiptera: Coccidae on Seedlings of Coffea arabica L.Abstract. Coccus viridis (Green cause losses on seedling and old plants of Coffea arabica (Green. However, nothing is known about of the damages caused by this pest. Thus, the objective of this work was to evaluate the relations between atack of C. viridis and the losses caused by this insect. on C. arabica. This work was conduced in greenhouse at

Application of RNAi to confirm theobromine as the major intermediate for caffeine biosynthesis in coffee plants with potential for construction of decaffeinated varieties.

Science.gov (United States)

Ogita, Shinjiro; Uefuji, Hirotaka; Morimoto, Masayuki; Sano, Hiroshi

2004-04-01

The caffeine biosynthetic pathway in coffee plants has been proposed to involve three distinct N -methyltransferases, xanthosine methyltransferase (XMT), 7- N -methylxanthine methyltransferase (MXMT; theobromine synthase), and 3,7-dimethylxanthine methyltransferase (DXMT; caffeine synthase). We previously isolated all corresponding cDNAs designated as CaXMT1 , CaMXMT1 , CaMXMT2 and CaDXMT1 , respectively, and showed that caffeine was indeed synthesized in vitro by the combination of their gene products. In order to regulate caffeine biosynthesis in planta , we suppressed expression of CaMXMT1 by the double stranded RNA interference (RNAi) method. For this purpose, we first established a protocol for efficient somatic embryogenesis of Coffea arabica and C. canephora , and then Agrobacterium -mediated transformation techniques. The RNAi transgenic lines of embryogenic tissues derived from C. arabica and transgenic plantlets of C. canephora demonstrated a clear reduction in transcripts for CaMXMT1 in comparison with the control plants. Transcripts for CaXMT1 and CaDXMT1 were also reduced in the most cases. Both embryonic tissues and plantlets exhibited a concomitant reduction of theobromine and caffeine contents to a range between 30% and 50% of that of the control. These results suggest that the CaMXMT1 -RNAi sequence affected expression of not only CaMXMT1 itself, but also CaXMT1 and CaDXMT1 , and that, since the reduction in theobromine content was proportional to that for caffeine, it is involved in the major synthetic pathway in coffee plants. The results also indicate that the method can be practically applied to produce decaffeinated coffee plants.

An endoplasmic reticulum-localized Coffea arabica BURP domain-containing protein affects the response of transgenic Arabidopsis plants to diverse abiotic stresses.

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Dinh, Sy Nguyen; Kang, Hunseung

2017-11-01

The Coffea arabica BURP domain-containing gene plays an important role in the response of transgenic Arabidopsis plants to abiotic stresses via regulating the level of diverse proteins. Although the functions of plant-specific BURP domain-containing proteins (BDP) have been determined for a few plants, their roles in the growth, development, and stress responses of most plant species, including coffee plant (Coffea arabica), are largely unknown. In this study, the function of a C. arabica BDP, designated CaBDP1, was investigated in transgenic Arabidopsis plants. The expression of CaBDP1 was highly modulated in coffee plants subjected to drought, cold, salt, or ABA. Confocal analysis of CaBDP1-GFP fusion proteins revealed that CaBDP1 is localized in the endoplasmic reticulum. The ectopic expression of CaBDP1 in Arabidopsis resulted in delayed germination of the transgenic plants under abiotic stress and in the presence of ABA. Cotyledon greening and seedling growth of the transgenic plants were inhibited in the presence of ABA due to the upregulation of ABA signaling-related genes like ABI3, ABI4, and ABI5. Proteome analysis revealed that the levels of several proteins are modulated in CaBDP1-expressing transgenic plants. The results of this study underscore the importance of BURP domain proteins in plant responses to diverse abiotic stresses.

Alterações morfofisiológicas em folhas de Coffea arabica L. cv. "Oeiras" sob influência do sombreamento por Acacia mangium Willd Morphophysiological alterations in leaves of Coffea arabica L. cv. 'Oeiras' shaded by Acacia mangium Willd

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Inês Angélica Cordeiro Gomes

2008-02-01

Full Text Available Diferenças na disponibilidade de radiação podem causar modificações na estrutura e função das folhas do cafeeiro, que podem responder de maneira diferencial à radiação por alterações morfológicas, anatômicas, de crescimento e na taxa fotossintética. O objetivo deste trabalho foi avaliar características morfofisiológicas de cafeeiros (Coffea arabica L. cv. "Oeiras" sombreados por acácia (Acacia mangium Willd. na época seca e chuvosa no sul de Minas Gerais. As maiores taxas fotossintéticas e maiores espessuras da epiderme adaxial foram observadas na estação chuvosa nas linhas de cafeeiros a pleno sol. O sombreamento influenciou em menor espessura das folhas e em espaços intercelulares maiores no tecido esponjoso. Foi também verificada mudança na forma dos cloroplastos, os quais apresentaram-se mais alongados em folhas de cafeeiros a pleno sol quando relacionados aos arborizados.Light availability is one of the most important environmental factors affecting leaf structure and functions in coffee plants that can respond differently to radiation by changes in leaf anatomy, morphology, growth and photosynthetic rate. The objective of this research was evaluate some morphophysiological aspects in leaves of coffee (Coffea arabica L. cv. 'Oeiras' cropped under shelter trees in the south of Minas Gerais during the rainy and dry season. The shade caused lower leaves thickness and higher intercellular spaces in spongious tissue. There was also verified a change in chloroplast shape, which showed more elongated in coffee tree kept at full sunlight in relation to that ones maintained on shading.

Microclimate and development of 'Conilon' coffee intercropped with rubber trees

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Fábio Luiz Partelli

2014-11-01

Full Text Available The objective of this work was to evaluate the influence of intercropping 'Conilon' coffee (Coffea canephora with rubber trees on coffee tree microclimate, nutrition, growth, and yield. Rubber trees were planted in two double rows 33 m apart, with 4x2.3 m spacing between plants. Treatments consisted of the distances from the coffee plants to the rubber trees: 3, 6, 9, 12, and 15 m. Measurements of atmospheric variables (temperature, irradiance, and relative humidity, leaf nutrient concentration, internode length of plagiotropic and orthotropic branches, individual leaf area, chlorophyll content, and yield were performed. Intercropping promotes changes in the microclimatic conditions of coffee plants close to rubber trees, with reduction of temperature and irradiance level and increase in air relative humidity. The proximity of the coffee tree to the rubber trees promotes the elongation of the plagiotropic and orthotropic branches and increases the individual leaf area; however, it does not affect leaf concentrations of N, K, Mg, Fe, Zn, and B in 'Conilon' coffee and does not have a negative impact on yield.

Morphological Characterization and Identification of Coffea liberica Callus of Somatic Embryogenesis Propagation.

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Fitria Ardiyani

2015-08-01

Full Text Available Compared with other types of coffee, Liberica coffee is more difficult to be propagates using clonal methods. Meanwhile, demand for planting materials and consumption of this type of coffee is increasing lately. The objective of this paper is to present results of the work on morpological characterization of Liberica coffee (Coffea liberica callus produced by somatic embryogenesis propagation. This research used C. liberica Arruminensis clone. This clone was one of Liberica coffee clones which had superior taste. Main activitis carried out in this experiment were explant sterilization, explant induction and histological analysis on the callus produced. The result of this research showed that non embryogenic callus was higher (72% than embryogenic callus (28%. The callus description can be used to identify type and characteristic of the callus. Therefore, it can be a parameter to choose type of callus for propagation material. This is important because choosing the right callus is determine of the succesfully process of Liberica somatic embryogenesis. Keywords: somatic embryogenesis, Liberica, embryogenic, non-embryogenic

Meta-analysis for heritability estimates of vegetative and reproductive traits of Coffea arabica L.Meta-análise para estimativas de herdabilidade de caracteres vegetativos e reprodutivos de Coffea arabica L.

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Danielle Pereira Baliza

2012-08-01

Full Text Available The compilation of informations resulting from independent studies has been difficulted in almost all scientific fields, mainly due to the great number of scientific papers published in recent years. As a result, summarizing information became a need. In this context, a meta-analysis was conducted with the objective of summarizing the estimates for the heritability for vegetative and reproductive traits of coffee (Coffea arabica L.. Heritability estimates were appraised regarding the following traits: average height of plant, average diameter of the canopy, vegetative vigor, production of processed coffee, yield and rust. The data regarding the heritability estimates are from scientific articles published in national and international journals, congress annals, PhD thesis and Master dissertations. The technique of meta-analysis summarized the estimates heritability from different studies and made possible to conclude that all of the appraised traits are highly inherited, reflecting the great genetic variety of coffee plants, and that is possible to reach satisfactory genetic gains in improvement programs in which those traits are evaluated. A compilação de informações advindas de estudos independentes tem sido dificultada em quase todos os campos da ciência, devido principalmente, ao grande número de trabalhos científicos publicados nos últimos anos. Assim, sumarizar informações tornou-se uma necessidade. Neste contexto, uma meta-análise foi conduzida com o objetivo de sistematizar as estimativas para a herdabilidade de caracteres vegetativos e reprodutivos de cafeeiros (Coffea arabica L.. Foram avaliadas as estimativas de herdabilidade referentes aos seguintes caracteres: altura média da planta, diâmetro médio da copa, vigor vegetativo, produção de café beneficiado, rendimento e resistência a ferrugem. Os dados referentes às estimativas de herdabilidade são provenientes de artigos científicos publicados em revistas

An efficient immunodetection method for histone modifications in plants.

Science.gov (United States)

Nic-Can, Geovanny; Hernández-Castellano, Sara; Kú-González, Angela; Loyola-Vargas, Víctor M; De-la-Peña, Clelia

2013-12-16

Epigenetic mechanisms can be highly dynamic, but the cross-talk among them and with the genome is still poorly understood. Many of these mechanisms work at different places in the cell and at different times of organism development. Covalent histone modifications are one of the most complex and studied epigenetic mechanisms involved in cellular reprogramming and development in plants. Therefore, the knowledge of the spatial distribution of histone methylation in different tissues is important to understand their behavior on specific cells. Based on the importance of epigenetic marks for biology, we present a simplified, inexpensive and efficient protocol for in situ immunolocalization on different tissues such as flowers, buds, callus, somatic embryo and meristematic tissue from several plants of agronomical and biological importance. Here, we fully describe all the steps to perform the localization of histone modifications. Using this method, we were able to visualize the distribution of H3K4me3 and H3K9me2 without loss of histological integrity of tissues from several plants, including Agave tequilana, Capsicum chinense, Coffea canephora and Cedrela odorata, as well as Arabidopsis thaliana. There are many protocols to study chromatin modifications; however, most of them are expensive, difficult and require sophisticated equipment. Here, we provide an efficient protocol for in situ localization of histone methylation that dispenses with the use of expensive and sensitive enzymes. The present method can be used to investigate the cellular distribution and localization of a wide array of proteins, which could help to clarify the biological role that they play at specific times and places in different tissues of various plant species.

Crescimento vegetativo e produtividade de cafeeiros Conilon propagados por estacas em tubetes Vegetative growth and productivity of Conilon coffee-trees proceeding from seedlings produced of deep-rooted cuttings in plastic tubes

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José Augusto Teixeira do Amaral

2007-12-01

Full Text Available Objetivou-se neste trabalho avaliar o crescimento vegetativo e a produtividade de cafeeiros conilon (Coffea canephora Pierre ex Froehner, oriundos de mudas produzidas por estacas plantadas inicialmente em tubetes plásticos de 50 cm³ de capacidade. O experimento foi constituído de cinco tratamentos, que corresponderam aos tempos de permanência das estacas nos tubetes: 0; 15; 30; 45 e 60 dias. Transcorridos esses tempos as mudas foram, sucessivamente, transplantadas para sacos de polietileno, contendo mistura de terra, esterco de curral e adubo químico, enviveiradas em um viveiro coberto com sombrite (50%, provido de micro aspersão automática. As mudas permaneceram no viveiro com micro aspersão automática por 150 dias, quando então foram transferidas para o viveiro de aclimatação, onde ficaram por mais 30 dias. Após esse período, em setembro de 1999, as mudas foram plantadas em condições de campo, na área experimental do CCA-UFES, em Alegre, Sul do Estado do Espírito Santo. Foram feitas as seguintes medições: crescimento de ramos ortotrópicos e plagiotrópicos no segundo ano após o plantio e as quatro primeiras colheitas. A produção inicial de mudas de café conilon em tubetes não afetou o crescimento vegetativo, tampouco a produção de frutos.The objective of this work was to evaluate the vegetative growth and productivity of conilon coffee-tree (Coffea canephora Pierre ex Froehner, proceeding from seedlings produced of deep-rooted cuttings initially in plastic tubes with capacity of 50 cm³. The treatments were constituted of permanence period in plastic tube for 0; 15; 30; 45 and 60 days. After these periods the plants were transplanted for polyethylene bags filled with substrate (soil + sand + manure bovine and chemical fertilization maintained on the greenhouse with environment under shading canvas (50% and automatic micro aspersion during 150 days. After this time the plants were maintained during 30 days in

Progresso genético da produtividade de café beneficiado com a seleção de clones de cafeeiro 'Conilon'

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André Rostand Ramalho

2016-09-01

Full Text Available RESUMO A espécie Coffea canephora Pierre ex Froehner possui ampla distribuição geográfica, com ocorrência em regiões tropicais de diversos continentes. Aproximadamente 30% da produção brasileira de café é proveniente do cultivo dessa espécie, sendo que o Estado de Rondónia se destaca como seu segundo maior produtor. Este trabalho teve como objetivo estimar os parâmetros genéticos com a seleção de clones de C. canephora, da variedade botânica 'Conilon', visando caracterizar a variabilidade genética e estimar o progresso genético da produtividade de café beneficiado. A análise de variância da produção de café beneficiado evidenciou que a fonte de variação "clones" foi significativa nas safras avaliadas, de acordo com o teste F a 1% de significância. A predominância do componente genético na expressão dessa característica, associado a uma boa precisão experimental, indica a possibilidade de obtenção de ganhos com a seleção de plantas. O progresso genético da produção de café beneficiado com o plantio dos clones selecionados foi de 57,85%, que equivale a um aumento na média em quatro anos de 44,75 sacas ha-1, para 70,64 sacas ha-1. Além do incremento na produtividade de grãos, os clones de ciclo intermediário selecionados favorecem a concentração da colheita e a redução dos custos operacionais.

Teste de condutividade elétrica individual na avaliação da qualidade fisiológica de sementes de café (Coffea arabica L. Individual electrical conductivity test for evaluation of the physiological quality of coffee seeds (Coffea arabica L.

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Paula de Souza Cabral Costa

2006-02-01

Full Text Available O teste de condutividade elétrica é usado para medir os exsudatos das sementes, que certamente refletem a integridade do sistema de membranas. O teste é rápido e de operação simples, mas a metodologia necessita ser testada para cada espécie individualmente para obter uma melhor precisão e exatidão dos resultados. Este trabalho foi conduzido visando determinar o ponto de partição na realização do teste de condutividade elétrica em sementes de café. Dez lotes de sementes de Coffea arabica sem pergaminho, cultivar Acaiá foram usados nesse estudo. Para a avaliação do ponto de partição as sementes foram embebidas por 96 horas e submetidas ao teste de germinação, correlacionando os valores de condutividade observados com os valores obtidos no teste de germinação. O ponto de partição é de 120,5µS.cm-1, considerando 70% de germinação.The conductivity test is used to measure the leaches from the seeds, which certaintily reflect the membrane system integrity. The test is rapid and it is of simple operation, but the methodology needs to be tested for each individual species in order to reach a better precision and accuracy. This work was conducted to determinate the partition point for the realization of electrical conductivity test in coffee seeds. Ten seed lots of Coffea arabica, cultivar Acaiá, without parchment, were used in this study. For the evaluation of the partition point, seeds were imbibed for 96 hours and submitted to the germination test, with the correlation between the conductivity values and those obtained in the germination test being evaluated. The partition point is 120,5µS.cm-1, considering 70% of germination.

SELECCIÓN DE “CABEZAS DE CLON” EN CAFÉ ROBUSTA (Coffea canephora EN EL TRÓPICO SECO, ECUADOR

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Luis Alberto Duicela Guambi

2016-06-01

Full Text Available La investigación se ejecutó de junio 2007 a diciembre 2012, en el Centro Experimental de café robusta ubicado en el Recinto Las Mercedes, cantón Isidro Ayora, provincia del Guayas, donde prevalece la zona de vida “Bosque muy seco tropical”. El objetivo fue seleccionar árboles “Cabezas de clon” de alto valor genético para impulsar la caficultura en el trópico seco del litoral ecuatoriano. Se evaluaron 32 accesiones de distinto origen, cada una conformada de 20 cafetos. En una primera etapa, se evaluaron los caracteres morfológicos y productivos de las accesiones y en una segunda etapa se incluyeron los atributos organolépticos e industriales de los árboles promisorios. El análisis estadístico incluyó el cálculo de estadígrafos, análisis de varianza, componentes principales y conglomerados jerárquicos. Los resultados permitieron identificar y seleccionar dos accesiones tipo conilón y siete tipo robusta. Las “cabezas de clon” seleccionadas fueron: CONERB-01-Planta 13-14-17-20, CON-ETP-01-Planta 11, COF-01-Plantas 02 y 04, COF-02-Plantas 15 y 17, COF-04-Planta 18, COF-05-Planta 2, COF-06-Plantas 3-15-17, NP-4024-Planta 15 y NP-2024-Planta 10. El potencial productivo de los árboles seleccionados varía de 2,5 a 3,9 t ha-1, por tanto, se infiere que existen genotipos de alta productividad, adaptados al trópico seco y al manejo intensivo con riego.

A High-Throughput Molecular Pipeline Reveals the Diversity in Prevalence and Abundance of Pratylenchus and Meloidogyne Species in Coffee Plantations.

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Bell, Christopher A; Atkinson, Howard J; Andrade, Alan C; Nguyen, Hoa X; Swibawa, I Gede; Lilley, Catherine J; McCarthy, James; Urwin, P E

2018-05-01

Coffee yields are adversely affected by plant-parasitic nematodes and the pathogens are largely underreported because a simple and reliable identification method is not available. We describe a polymerase chain reaction-based approach to rapidly detect and quantify the major Pratylenchus and Meloidogyne nematode species that are capable of parasitizing coffee. The procedure was applied to soil samples obtained from a number of coffee farms in Brazil, Vietnam, and Indonesia to assess the prevalence of these species associated both with coffee (Coffea arabica and C. canephora) and its intercropped species Musa acuminata (banana) and Piper nigrum (black pepper). Pratylenchus coffeae and P. brachyurus were associated with coffee in all three countries but there were distinct profiles of Meloidogyne spp. Meloidogyne incognita, M. exigua, and M. paranaensis were identified in samples from Brazil and M. incognita and M. hapla were detected around the roots of coffee in Vietnam. No Meloidogyne spp. were detected in samples from Indonesia. There was a high abundance of Meloidogyne spp. in soil samples in which Pratylenchus spp. were low or not detected, suggesting that the success of one genus may deter another. Meloidogyne spp. in Vietnam and Pratylenchus spp. in Indonesia were more numerous around intercropped plants than in association with coffee. The data suggest a widespread but differential nematode problem associated with coffee production across the regions studied. The issue is compounded by the current choice of intercrops that support large nematode populations. Wider application of the approach would elucidate the true global scale of the nematode problem and the cost to coffee production. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Looking into individual coffee beans during the roasting process: direct micro-probe sampling on-line photo-ionisation mass spectrometric analysis of coffee roasting gases.

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Hertz-Schünemann, Romy; Streibel, Thorsten; Ehlert, Sven; Zimmermann, Ralf

2013-09-01

A micro-probe (μ-probe) gas sampling device for on-line analysis of gases evolving in confined, small objects by single-photon ionisation time-of-flight mass spectrometry (SPI-TOFMS) was developed. The technique is applied for the first time in a feasibility study to record the formation of volatile and flavour compounds during the roasting process within (inside) or in the direct vicinity (outside) of individual coffee beans. A real-time on-line analysis of evolving volatile and semi-volatile organic compounds (VOC and SVOC) as they are formed under the mild pyrolytic conditions of the roasting process was performed. The soft-ionisation mass spectra depict a molecular ion signature, which is well corresponding with the existing knowledge of coffee roasting and evolving compounds. Additionally, thereby it is possible to discriminate between Coffea arabica (Arabica) and Coffea canephora (Robusta). The recognized differences in the roasting gas profiles reflect the differences in the precursor composition of the coffee cultivars very well. Furthermore, a well-known set of marker compounds for Arabica and Robusta, namely the lipids kahweol and cafestol (detected in their dehydrated form at m/z 296 and m/z 298, respectively) were observed. If the variation in time of different compounds is observed, distinctly different evolution behaviours were detected. Here, phenol (m/z 94) and caffeine (m/z 194) are exemplary chosen, whereas phenol shows very sharp emission peaks, caffeine do not have this highly transient behaviour. Finally, the changes of the chemical signature as a function of the roasting time, the influence of sampling position (inside, outside) and cultivar (Arabica, Robusta) is investigated by multivariate statistics (PCA). In summary, this pilot study demonstrates the high potential of the measurement technique to enhance the fundamental knowledge of the formation processes of volatile and semi-volatile flavour compounds inside the individual coffee bean.

Producing diversity: Agroforests Sustain Avian Richness and Abundance in India's Western Ghats

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Krithi K Karanth

2016-09-01

Full Text Available Globally, protected areas have long been the corner stone of biodiversity conservation efforts. In India’s Western Ghats, small and isolated protected areas are embedded in a matrix of multiple land-uses, most of which include agroforests. These agroforests are being increasingly recognized for their supplementary role in conserving wildlife. We examined bird species richness and densities in areca (Areca catechu, coffee (Coffea arabica and Coffea canephora and rubber (Hevea brasiliensis agroforests in the Western Ghats. We developed a priori hypotheses, predicting that bird species richness and guild density would be highest in coffee, followed by areca and rubber agroforests. We carried out 551 point-count surveys involving 386 hours of sampling in 187 agroforests across a 29,634 km2 area of the Ghats. We observed 204 bird species, of which 170 were residents. The average estimated richness per agroforest was higher in coffee (60.5 compared to rubber (45.4 and areca (34.1. We modeled species richness as a function of relevant biogeographic and environmental covariates. The most influential factors were tree cover, tree density and rainfall in all agroforests, but the strength of these effects varied. Coffee supported higher densities in all four habitat and three feeding guilds compared to areca and rubber. We integrated extensive field sampling with modeling that accounted for imperfect detection, while assessing bird richness and densities across multiple agroforest types. We establish that coffee agroforests are substantially richer in birds than rubber and areca, but all three agroforests play an important role in providing subsidiary habitats for birds in the Ghats. Policy decisions and markets must incorporate such biodiversity values and services provided by these agroforests to sustain and facilitate long-term biodiversity conservation.

Agrobacterium-mediated genetic transformation of Coffea arabica (L.) is greatly enhanced by using established embryogenic callus cultures

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2011-01-01

Background Following genome sequencing of crop plants, one of the main challenges today is determining the function of all the predicted genes. When gene validation approaches are used for woody species, the main obstacle is the low recovery rate of transgenic plants from elite or commercial cultivars. Embryogenic calli have frequently been the target tissue for transformation, but the difficulty in producing or maintaining embryogenic tissues is one of the main problems encountered in genetic transformation of many woody plants, including Coffea arabica. Results We identified the conditions required for successful long-term proliferation of embryogenic cultures in C. arabica and designed a highly efficient and reliable Agrobacterium tumefaciens-mediated transformation method based on these conditions. The transformation protocol with LBA1119 harboring pBin 35S GFP was established by evaluating the effect of different parameters on transformation efficiency by GFP detection. Using embryogenic callus cultures, co-cultivation with LBA1119 OD600 = 0.6 for five days at 20 °C enabled reproducible transformation. The maintenance conditions for the embryogenic callus cultures, particularly a high auxin to cytokinin ratio, the age of the culture (optimum for 7-10 months of proliferation) and the use of a yellow callus phenotype, were the most important factors for achieving highly efficient transformation (> 90%). At the histological level, successful transformation was related to the number of proembryogenic masses present. All the selected plants were proved to be transformed by PCR and Southern blot hybridization. Conclusion Most progress in increasing transformation efficiency in coffee has been achieved by optimizing the production conditions of embryogenic cultures used as target tissues for transformation. This is the first time that a strong positive effect of the age of the culture on transformation efficiency was demonstrated. Our results make Agrobacterium

Agrobacterium-mediated genetic transformation of Coffea arabica (L. is greatly enhanced by using established embryogenic callus cultures

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Lashermes Philippe

2011-05-01

Full Text Available Abstract Background Following genome sequencing of crop plants, one of the main challenges today is determining the function of all the predicted genes. When gene validation approaches are used for woody species, the main obstacle is the low recovery rate of transgenic plants from elite or commercial cultivars. Embryogenic calli have frequently been the target tissue for transformation, but the difficulty in producing or maintaining embryogenic tissues is one of the main problems encountered in genetic transformation of many woody plants, including Coffea arabica. Results We identified the conditions required for successful long-term proliferation of embryogenic cultures in C. arabica and designed a highly efficient and reliable Agrobacterium tumefaciens-mediated transformation method based on these conditions. The transformation protocol with LBA1119 harboring pBin 35S GFP was established by evaluating the effect of different parameters on transformation efficiency by GFP detection. Using embryogenic callus cultures, co-cultivation with LBA1119 OD600 = 0.6 for five days at 20 °C enabled reproducible transformation. The maintenance conditions for the embryogenic callus cultures, particularly a high auxin to cytokinin ratio, the age of the culture (optimum for 7-10 months of proliferation and the use of a yellow callus phenotype, were the most important factors for achieving highly efficient transformation (> 90%. At the histological level, successful transformation was related to the number of proembryogenic masses present. All the selected plants were proved to be transformed by PCR and Southern blot hybridization. Conclusion Most progress in increasing transformation efficiency in coffee has been achieved by optimizing the production conditions of embryogenic cultures used as target tissues for transformation. This is the first time that a strong positive effect of the age of the culture on transformation efficiency was demonstrated. Our

Genetic diversity among 16 genotypes of Coffea arabica in the Brazilian cerrado.

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Machado, C M S; Pimentel, N S; Golynsk, A; Ferreira, A; Vieira, H D; Partelli, F L

2017-09-21

For the selection of coffee plants that have favorable characteristics, it is necessary to evaluate variables related to production. Knowledge of the genetic divergence of arabica coffee is of extreme importance, as this knowledge can be associated with plant breeding programs in order to combine genetic divergence with good productive performance. The objective of this study was to evaluate the genetic divergence among 16 genotypes of Coffea arabica with the purpose of identifying the most dissimilar genotypes for the establishment of breeding programs and adaptation to the Brazilian cerrado. The genetic divergence was evaluated using multivariate procedures, the analysis of the average grouping unweighted pair group method with arithmetic mean (UPGMA) and main components in 2013 and 2014. Eight characters were evaluated in an experiment conducted in Morrinhos, Goiás. The presence of genetic divergence among the 16 C. arabica genotypes under cerrado conditions was recorded. The formation of UPGMA groups for the evaluated characteristics was pertinent due to the number of genotypes. The first three major components accounted for 81.77% of the total variance. The genotype H-419-3-4-4-13(C-241) of low size was the most divergent, followed by Catucaí 2 SL and Catiguá MG2, according to the main components.

Inoculación de Consorcios Micorrícicos Arbusculares en Coffea arabica, Variedad Caturra en la Región San Martín

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Del Aguila, Karen M.; Vallejos-Torres, Geomar; Arévalo, Luis A.; Becerra, Alejandra G.

2018-01-01

Resumen El objetivo del presente estudio fue determinar el efecto de nueve consorcios micorrícicos arbusculares y la inoculación a plántulas de café Coffea arabica, variedad Caturra, comparados con un control (sin inoculación), durante siete meses en vivero. El cultivo de café en la Región San Martín es una de las actividades agrícolas económicas más importantes. Una alternativa para incrementar la producción consiste en la aplicación de hongos micorrizas. Se empleó un Diseño Completamente al...

High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection.

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Florez, Juan Carlos; Mofatto, Luciana Souto; do Livramento Freitas-Lopes, Rejane; Ferreira, Sávio Siqueira; Zambolim, Eunize Maciel; Carazzolle, Marcelo Falsarella; Zambolim, Laércio; Caixeta, Eveline Teixeira

2017-12-01

We provide a transcriptional profile of coffee rust interaction and identified putative up regulated resistant genes Coffee rust disease, caused by the fungus Hemileia vastatrix, is one of the major diseases in coffee throughout the world. The use of resistant cultivars is considered to be the most effective control strategy for this disease. To identify candidate genes related to different mechanism defense in coffee, we present a time-course comparative gene expression profile of Caturra (susceptible) and Híbrido de Timor (HdT, resistant) in response to H. vastatrix race XXXIII infection. The main objectives were to obtain a global overview of transcriptome in both interaction, compatible and incompatible, and, specially, analyze up-regulated HdT specific genes with inducible resistant and defense signaling pathways. Using both Coffea canephora as a reference genome and de novo assembly, we obtained 43,159 transcripts. At early infection events (12 and 24 h after infection), HdT responded to the attack of H. vastatrix with a larger number of up-regulated genes than Caturra, which was related to prehaustorial resistance. The genes found in HdT at early hours were involved in receptor-like kinases, response ion fluxes, production of reactive oxygen species, protein phosphorylation, ethylene biosynthesis and callose deposition. We selected 13 up-regulated HdT-exclusive genes to validate by real-time qPCR, which most of them confirmed their higher expression in HdT than in Caturra at early stage of infection. These genes have the potential to assist the development of new coffee rust control strategies. Collectively, our results provide understanding of expression profiles in coffee-H. vastatrix interaction over a time course in susceptible and resistant coffee plants.

Anatomia e desenvolvimento ontogenético de Coffea arabica L. var. typica Cramer Anatomy and ontogenetical development of Coffea arabica L. var. typica Cramer

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D. M. Dedecca

1957-01-01

Full Text Available O presente estudo anatômico de Coffea arabica L. var. typica Cramer tem por finalidade fornecer informações básicas necessárias ao estudo da anatomia comparada das principais espécies e variedades de cafeeiros, cultivadas no Estado de São Paulo. Nesta primeira contribuição o autor realiza o estudo anatômico detalhado dos órgãos vegetativos e reprodutivos da variedade typica, não se limitando apenas à anatomia descritiva dos diversos órgãos, mas também, sempre que possível, discutindo o desenvolvimento ontogenético das diversas partes do cafeeiro. No estudo da raíz e do caule procurou-se estabelecer a duração do desenvolvimento primário, assinalando o local de aparecimento, primeiramente do câmbio vascular e, posteriormente, do felógeno ou câmbio suberoso. Na discussão da anatonia das folhas mereceu especial atenção o estudo das domácias, sua morfologia e possível função. As flores são estudadas detalhadamente nos seus diversos elementos. Nos capítulos referentes à anatomia do fruto e da semente, além do estudo puramente descritivo das suas estruturas são ainda discutidas as diversas modificações verificadas durante o desenvolvimento do ovário e dos óvulos, respectivamente em fruto e sementes.The knowledge of the anatomy of Coffea arabica L. var. typica Cramer should be considered as a basic contribution to the comparative study of the anatomy of coffee species and varieties cultivated in the State of São Paulo, Brazil. The detailed investigations carried out on the vegetative and reproductive organs of the coffee plant revealed the following. The roots at the end of the primary growth present a protostelic, poliarch (6, 7, 8, 9, 11 primary xylem bundles, and exarch structure, the following tissues or zone of tissues being visible: root cap, epidermis, exodermis, cortex, endodermis, pericycle, primary phloem and primary xylem. This primary growth has a very short duration and is very soon followed by the

Avaliação da suscetibilidade à Xylella fastidiosa em diferentes espécies de cafeeiro Susceptibity valuation to Xylella fastidiosa in different coffee species

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Rachel Benetti Queiroz-Voltan

2005-01-01

Full Text Available A bactéria Xylella fastidiosa Wells et al. foi detectada pela primeira vez em cafeeiro no Brasil, em 1995, entretanto acredita-se que a cultura foi infectada por essa bactéria há muitos anos, embora os sintomas fossem atribuídos a um estresse nutricional. Até o momento têm sido realizados estudos principalmente com espécies de C. arabica e C. canephora, porém, em outras espécies do gênero, somente foi detectada sua presença. Neste trabalho, objetivou-se avaliar a proporção de elementos de vaso do xilema obstruídos, total e parcialmente, pela X. fastidiosa, naturalmente infectadas, em diferentes espécies de cafeeiro do Banco de Germoplasma do IAC, visando identificar material resistente a essa bactéria para ser utilizado no programa de melhoramento genético. Os acessos estudados foram: C. canephora (progenitora da 'Guarini', C. liberica var. liberica, os quatro acessos de C. liberica var. dewevrei (Ugandae, Dibowskii, Abeokutae, Excelsa e o híbrido interespecífico Piatã (C. arabica X C. liberica var. dewevrei. Todos eles mostraram-se menos suscetíveis à X. fastidiosa. A porcentagem de obstrução dos elementos de vasos na folha não foi maior que 0,6% na maioria dos acessos, com exceção de Excelsa e do híbrido Piatã com até 2% de obstrução, sendo bem menos suscetíveis a essa bactéria do que as cultivares de C. arabica. Trata-se, portanto, de materiais genéticos importantes para serem utilizados no programa de melhoramento do cafeeiro visando à resistência ao agente dessa doença.Xylella fastidiosa Wells et al. bacteria was firstly detected in coffee plants in Brazil in 1995. However it is believed to be attacking this crop this time. Disease symptoms have been attributed mostly to nutritional unbalances. Up to date studies have comprised only the species C. arabica and C. canephora. However X. fastidiosa was also detected in other Coffea species, but without disease symptoms. Aiming to identify in the IAC

Observações citológicas em Coffea: XV - Microsporogênese em Coffea arabica L.

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A. J. T. Mendes

1950-03-01

Full Text Available No presente trabalho são apresentadas as observações realizadas sôbre a microsporogênese nas variedades semperflorens e caturra, de Coffea arabica L. Notou-se que, no início da prófase, os cromossômios se colorem muito mal, não permitindo observações sôbre a sua morfologia; em paquitene, os cromossômios se apresentam com várias secções heteropicnóticas separadas por secções muito finas, que se colorem mal; o centrômero é bastante nítido e se acha ladeado de zonas bem heteropicnóticas; as extremidades dos braços dos cromossômios se colorem mal e se perdem no meio do citoplasma ; o nucléolo é bastante visível e a êle se acham ligados alguns cromossômios. É difícil determinar o número exato de cromossômios ligados ao nucléolo, tendo-se encontrado de 1 a 4. De paquitene a metáfase I, as fases se sucedem rapidamente. Em diplotene, os cromossômios são curtos, não mais se percebendo o centrômero. Em diaquinese os 22 pares de cromossômios se repelem pela sua parte mais colorida, onde se encontra o centrômero, e se unem pela parte clara, onde se notam os quiasmas ; o número de quiasmas, por célula, varia de 29 a 43 ; a média por bivalente é de 1,67, em semperjlorens, e 1,75, em caturra. Em metáfase I, o número médio de quiasmas, por bivalente,. é de 1,69, em semperjlorens, e 1,67, em caturra. Em anáfase I, os 22 pares de cromossômios se separam normalmente. Em telófase I, os cromossômios se colorem mal. Não há, praticamente, intercinese; os cromossômios contraem-se de novo e entram em anáfase II. A formação dos micrósporos é normal. Depois de soltos, ocorre a divisão nuclear, dando origem a dois núcleos com 22 cromossômios. Isto ocorre três a quatro dias antes da abertura das flores; o núcleo vegetativo é grande, esférico e homogêneo, colo-rindo-se mal; o núcleo reprodutivo é menor, reticulado, colore-se bem e se localiza na periferia da célula; ao seu redor se destaca uma por

Estimation of leaf area in coffee leaves (Coffea arabica L. of the Castillo® variety

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Carlos Andrés Unigarro-Muñoz

2015-01-01

Full Text Available Allometric models based on measurements of single leaf dimensions or a combination there are useful tools for determining individual leaf area (LA because they are non-destructive, precise, simple and economical methods. The present study was carried out at the Central Station Naranjal of Cenicafé, located in the Department of Caldas (Colombia, four models were defined using the variables length (L and/or width (W to estimate LA in coffee leaves of the Castillo® variety (Coffea arabica L.. Estimation of regression coefficients was performed using information recorded from 6,441 leaves (group 1, and their validation was performed using records from another 992 leaves (group 2. Leaves were collected from all strata of the canopy and ranged from 0.76 to 140 cm2 in LA. In addition to exhibiting coefficients of variation differing from zero based on t-tests at 1%, the evaluated models possess coefficients of determination between 0.93 and 0.99. Four expressions have developed and adjusted to estimate leaf area in individual leaves, based on the measurement of simple variables and non-destructive.

Qualidade da matéria orgânica e distribuição do fósforo no solo de lavouras orgânicas de café Conilon Organic matter quality and phosphorus distribution in soils under organic Conilon coffee

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Fábio Luiz Partelli

2009-10-01

Full Text Available O cultivo de café orgânico utiliza fontes não solúveis de fósforo e grande quantidade e variedade de material orgânico em seu manejo. Assim, o objetivo do trabalho foi avaliar as frações que compõem a matéria orgânica e distribuição do fósforo no solo de cafeeiros Coffea canephora da cultivar 'Conilon' cultivados sob diferentes sistemas de manejos de produção orgânica. O solo foi coletado na projeção da copa do cafeeiro, na camada de 0 a 20cm. Determinaram-se as características químicas e granulométricas do solo em procedimentos de rotina e as frações de fósforo e da material orgânica. Na maioria das lavouras, o fósforo orgânico constituiu a maior parte do fósforo lábil, e a fração humina constituiu a maior parte da matéria orgânica. Houve maior presença de fósforo inorgânico nos solos das lavouras com maiores concentrações de fósforo total e lábil. O conteúdo total de Pi + Po nos solos avaliados apresentou valores elevados, variando de 426,9 até 910,4mg dm-3 de solo. A fração humina constituiu a maior parte da matéria orgânica. As frações que compõem a distribuição do fósforo no solo apresentaram discrepâncias entre os sistemas de manejos de produção orgânica.The organic management in coffee uses insoluble phosphorus sources and a large quantity and variety of organic material. Thus, the objective of this research was to evaluate organic matter composition and phosphorus distribution on soils from Coffea canephora cv. 'Conilon' crops, under different organic management production systems. Soil under the coffee tree canopy was collected from 0 to 20cm depth. Chemical and soil texture characteristics were determined by routine analysis as well as phosphorus and organic matter constitution. On the average crops organic phosphorus was the main part of the labile phosphorus and carbon humine. There was a higher content of inorganic phosphorus on soils from the crops with the highest

Relationship between aluminum stress and caffeine biosynthesis in suspension cells of Coffea arabica L.

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Pech-Kú, Roberto; Muñoz-Sánchez, J Armando; Monforte-González, Miriam; Vázquez-Flota, Felipe; Rodas-Junco, Beatriz A; González-Mendoza, Víctor M; Hernández-Sotomayor, S M Teresa

2018-04-01

Toxicity by aluminum is a growth-limiting factor in plants cultivated in acidic soils. This metal also promotes signal transduction pathways leading to the biosynthesis of defense compounds, including secondary metabolites. In this study, we observed that Coffea arabica L. cells that were kept in the dark did not produce detectable levels of caffeine. However, irradiation with light and supplementation of the culture medium with theobromine were the best conditions for cell maintenance to investigate the role of aluminum in caffeine biosynthesis. The addition of theobromine to the cells did not cause any changes to cell growth and was useful for the bioconversion of theobromine to caffeine. During a short-term AlCl 3 -treatment (500μM) of C. arabica cells kept under light irradiation, increases in the caffeine levels in samples that were recovered from both the cells and culture media were evident. This augmentation coincided with increases in the enzyme activity of caffeine synthase (CS) and the transcript level of the gene encoding this enzyme (CS). Together, these results suggest that actions by Al and theobromine on the same pathway lead to the induction of caffeine biosynthesis. Copyright © 2017 Elsevier Inc. All rights reserved.

Vegetation classification of Coffea on Hawaii Island using WorldView-2 satellite imagery

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Gaertner, Julie; Genovese, Vanessa Brooks; Potter, Christopher; Sewake, Kelvin; Manoukis, Nicholas C.

2017-10-01

Coffee is an important crop in tropical regions of the world; about 125 million people depend on coffee agriculture for their livelihoods. Understanding the spatial extent of coffee fields is useful for management and control of coffee pests such as Hypothenemus hampei and other pests that use coffee fruit as a host for immature stages such as the Mediterranean fruit fly, for economic planning, and for following changes in coffee agroecosystems over time. We present two methods for detecting Coffea arabica fields using remote sensing and geospatial technologies on WorldView-2 high-resolution spectral data of the Kona region of Hawaii Island. The first method, a pixel-based method using a maximum likelihood algorithm, attained 72% producer accuracy and 69% user accuracy (68% overall accuracy) based on analysis of 104 ground truth testing polygons. The second method, an object-based image analysis (OBIA) method, considered both spectral and textural information and improved accuracy, resulting in 76% producer accuracy and 94% user accuracy (81% overall accuracy) for the same testing areas. We conclude that the OBIA method is useful for detecting coffee fields grown in the open and use it to estimate the distribution of about 1050 hectares under coffee agriculture in the Kona region in 2012.

A flórula invasora da cultura do café (Coffea arabica L. no Estado de Minas Gerais, Brasil Weeds in coffee (Coffea arabica L. plantations in the state of Minas Gerais, Brazil

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Manuel Losada Gavilanes

1988-01-01

Full Text Available Nas áreas de cultura de café (Coffea arábica L., no Estado de Minas Gerais, foram coletadas e identificadas 388 espécies de plantas invasoras (= plantas daninhas, pertencentes a 51 famílias botânicas, representando 182 gêneros, sendo que as famílias Compositae, Gramineae, Leguminosae, Malvaceae, Solanaceae, Euphorbiaceae, Rubiaceae, Amaranthaceae, Convolvulaceae e Verbenaceae, são as mais importantes em relação à cultura. As plantas coletadas, devidamente etiquetadas e identificadas, foram anexadas, parte delas no PAMG (Herbário da EPAMIG, Belo Horizonte, MG e, a outra parte, no Herbarium ESAL (Herbário do Departamento de Biologia da Escola Superior de Agricultura de Lavras - ESAL, Lavras - MG.A survey in the cultivation area of coffee in the State of Minas Gerais, Brazil, has resulted in the determination of 388 weed species, of 182 genera belonging to 51 families; the families presenting a greater number of espécies are: Compositae, Leguminosae, Gramineae, Malvaceae, Solanaceae, Rubiaceae, Convolvulaceae, Euphorbiaceae, Amaranthaceae and Verbenaceae with 65, 48, 42, 30, 19, 17, 16, 14, 12, 10 species, respectively.

The Effect of Bacteria Colony Pseudomonas fluorescens (UB_Pf1 and Bacillus subtilis (UB_Bs1 on the Mortality of Pratylenchus coffeae (Tylenchida: Pratylenchidae

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Presti Mardiyani Purwaningtyas

2016-11-01

Full Text Available Parasitic Root-Lession nematode of Pratylenchus coffeae can reduce the Indonesian coffee plants productivity. Several studies reported that Pseudomonas fluorescens and Bacillus subtilis endophytic bacteria were antagonistic bacteria to nematode. The objective of this research was to reveal the effectiveness of bacterial colonies density of P. fluorescens (UB_Pf1, B.subtilis (UB BS1, and a combination of both bacteria on nematode mortality using median lethal concentration (LC50 and median lethal time 50 (LT50. The densities of bacteria used in this study were 107, 109, 1011 and 1013 cfu/ml. 35 testing nematodes were used and the mortality was counted at 6, 12, 24, 36, and 48 hours after treatments. The results showed that LC50 values of P. fluorescens was (UB_Pf1 was 4,3x108 cfu/ml, LC50 B. subtilis (UB_Bs1 was 1,9x109cfu/ ml, and LC50 combination of both bacteria was, 8x107 cfu/ml. It implies that the application of the combination of both bacteria are more pathogenic than single bacterial treatment. The results also showed that the highest LT50 value was 13.21  hours combination of bacterial colonies with a density of 1013 cfu/ml and the lowest LT50 value was 52.00 hours on P. fluorescens (UB_Pf1 treatment with colonies density of 107 cfu/ml.How to CitePurwaningtyas, P. M., Rahardjo, B. T., & Tarno, H. (2016. The Effect of Bacteria Colony Pseudomonas fluorescens (UB_Pf1 and Bacillus subtilis (UB_Bs1 on the Mortality of Pratylenchus coffeae (Tylenchida: Pratylenchidae. Biosaintifika: Journal of Biology & Biology Education, 8(3, 286-293. 

Influence of the fungi population on the physicochemical and chemical composition of coffee (Coffea arabica L.

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Liliana Auxiliadora Avelar Pereira Pasin

2011-09-01

Full Text Available The influence of fungi associated with coffee fruits was verified regarding the chemical and physicochemical composition of Coffea arabica L. raw grains. The fruits were harvested at EPAMIG Experimental farm in Lavras, State of Minas Gerais - making up the different samples here analyzed. After processing and drying, the grains were incubated in wet chamber for fungal exteriorization through the blotter test method and submitted to the following analyses: polyphenoloxidase, total reducing and non-reducing sugars, clorogenic acid, titrable acidity, potassium leaching, electric conductivity and caffeine. The occurrence of the P. variable, P. rugulosum, P. funiculosum, F. equiseti, F. semitectum, A.alutaceus, A. niger and C. cladosporioides fungi in the different samples was detected. From the analysis of the results obtained, it was observed that the presence of the Aspergillus alutaceus fungus reduces the activity of the enzyme polyphenoloxidase and increases the values of potassium leaching, electric conductivity and chlorogenic acid. The incidence of the Cladosporium cladosporioides fungus influenced the average values of potassium leaching and electric conductivity.

Rust and Thinning Management Effect on Cup Quality and Plant Performance for Two Cultivars of Coffea arabica L.

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Echeverria-Beirute, Fabian; Murray, Seth C; Klein, Patricia; Kerth, Chris; Miller, Rhonda; Bertrand, Benoit

2018-05-30

Beverage quality is a complex attribute of coffee ( Coffea arabica L.). Genotype (G), environment (E), management (M), postharvest processing, and roasting are all involved. However, little is known about how G × M interactions influence beverage quality. We investigated how yield and coffee leaf rust (CLR) disease (caused by Hemileia vastatrix Berk. et Br.) management affect cup quality and plant performance, in two coffee cultivars. Sensory and chemical analyses revealed that 10 of 70 attributes and 18 of 154 chemical volatile compounds were significantly affected by G and M. Remarkably, acetaminophen was found for the first time in roasted coffee and in higher concentrations under more stressful conditions. A principal component analysis described 87% of the variation in quality and plant overall performance. This study is a first step in understanding the complexity of the physiological, metabolic, and molecular changes in coffee production, which will be useful for the improvement of coffee cultivars.

DIRECT AND INDIRECT SOMATIC EMBRYOGENESIS ON ARABICA COFFEE (Coffea arabica

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Meynarti Sari Dewi Ibrahim

2013-10-01

Full Text Available Propagation of Coffea arabica L. through direct and indirect somatic embryogenesis technique is promising for producing large number of coffee seedlings. The objectives of the research were to evaluate methods for direct and indirect somatic embryo-genesis induction of C. arabica var. Kartika. The explants were the youngest fully expanded leaves of arabica coffee. The evalu-ated medium was modified Murashige and Skoog (MS medium supplemented with a combination of 2.26 µM 2,4-D + 4.54 or 9.08 µM thidiazuron; 4.52 µM 2,4-D + 4.54 or 9.08 µM thidiazuron; or 9.04 µM 2,4-D + 9.08 µM thidiazuron. Both calli (100 mg and pre-embryos developed from the edge of leaf explants were subcultured into regeneration medium (half strength MS with modified vitamin, supplemented with kinetine 9.30 µM and adenine sulfate 40 mg L-1. The results showed coffee leaf explant cultured on medium containing 2.26 µM 2,4-D + 4.54 or 9.08 µM thidiazuron to induce direct somatic embriogenesis from explant, while that of 4.52 or 9.04 µM 2,4-D + 9.08 µM thidiazuron to induced indirect somatic embrio-genesis. The medium for calli induction from coffee by explants was medium supplemented with 4.52 or 9.04 µM 2,4-D in combination with 9.08 µM thidiazuron. On the other hand, the best medium for activation of induction of somatic embryos was MS medium supplemented with 9.04 µM 2,4-D + 9.08 µM thidiazuron. Based on this results, the first step for developing micropropagation for coffee has been resolved. The subsequent studies will be directed to evaluate agronomic performance of the derived planting materials.

Survivability of Vibrio cholerae O1 in Cooked Rice, Coffee, and Tea

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Tang, John Yew Huat; Izenty, Bariah Ibrahim; Nur' Izzati, Ahmad Juanda; Masran, Siti Rahmah; Yeo, Chew Chieng; Roslan, Arshad; Abu Bakar, Che Abdullah

2013-01-01

This study aimed to investigate the survival of Vibrio cholerae O1 in 3 types of preparation for cooked rice, Oryza sativa L., (plain rice, rice with coconut milk, and rice with ginger); coffee, Coffea canephora, (plain coffee, coffee with sugar, and coffee with sweetened condensed milk); and tea, Camellia sinensis, (plain tea, tea with sugar, and tea with sweetened condensed milk) held at room temperature (27°C). The survival of V. cholerae O1 was determined by spread plate method on TCBS agar. Initial cultures of 8.00 log CFU/mL were inoculated into each food sample. After 6 h incubation, significant growth was only detected in rice with coconut milk (9.67 log CFU/mL; P < 0.05). However, all 3 types of rice preparation showed significant growth of V. cholerae after 24 h (P < 0.05). For coffee and tea preparations, V. cholerae survived up to 6 h in tea with condensed milk (4.72 log CFU/mL) but not in similar preparation of coffee. This study showed evidence for the survivability of V. cholerae in rice, coffee, and tea. Thus, holding these food and beverages for an extended period of time at room temperature should be avoided. PMID:26904604

Survivability of Vibrio cholerae O1 in Cooked Rice, Coffee, and Tea

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John Yew Huat Tang

2013-01-01

Full Text Available This study aimed to investigate the survival of Vibrio cholerae O1 in 3 types of preparation for cooked rice, Oryza sativa L., (plain rice, rice with coconut milk, and rice with ginger; coffee, Coffea canephora, (plain coffee, coffee with sugar, and coffee with sweetened condensed milk; and tea, Camellia sinensis, (plain tea, tea with sugar, and tea with sweetened condensed milk held at room temperature (27°C. The survival of V. cholerae O1 was determined by spread plate method on TCBS agar. Initial cultures of 8.00 log CFU/mL were inoculated into each food sample. After 6 h incubation, significant growth was only detected in rice with coconut milk (9.67 log CFU/mL; P<0.05. However, all 3 types of rice preparation showed significant growth of V. cholerae after 24 h (P<0.05. For coffee and tea preparations, V. cholerae survived up to 6 h in tea with condensed milk (4.72 log CFU/mL but not in similar preparation of coffee. This study showed evidence for the survivability of V. cholerae in rice, coffee, and tea. Thus, holding these food and beverages for an extended period of time at room temperature should be avoided.

Estudio preliminar de la comunidad de hongos endófitos en hojas de café (Coffea arabica

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Mónica Milena Morales Valencia

2006-01-01

Full Text Available Los endófitos son organismos que viven asintomáticamente dentro de tejidos vegetales vivos. Este grupo no está restringido a los hongos sino que también se pueden encontrar bacterias e incluso invertebrados. Hasta el momento han sido poco estudiados, sobre todo en zonas tropicales. En el presente trabajo se hizo un estudio preliminar de la diversidad de la comunidad de hongos endófitos presentes en hojas de café (Coffea arabica en tres sitios del departamento de Cundinamarca, Colombia. Se muestrearon fragmentos foliares que representaron un área total de 2.700 mm2, procedentes de 15 árboles, en los cuales se encontraron 279 individuos de 38 morfotipos diferentes. El taxón más abundante fue Colletotrichum, el cual estuvo representado por el 47% de todos los individuos encontrados. Las comunidades de hongos endófitos estudiadas se ajustaron al modelo de distribución logarítmica normal, es decir, muchas especies raras y pocas abundantes.

Genetic molecular analysis of Coffea arabica (Rubiaceae hybrids using SRAP markers

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Manoj Kumar Mishra

2011-06-01

Full Text Available In Coffea arabica (arabica coffee, the phenotypic as well as genetic variability has been found low because of the narrow genetic basis and self fertile nature of the species. Because of high similarity in phenotypic appearance among the majority of arabica collections, selection of parental lines for inter-varietals hybridization and identification of resultant hybrids at an early stage of plant growth is difficult. DNA markers are known to be reliable in identifying closely related cultivars and hybrids. Sequence Related Amplified Polymorphism (SRAP is a new molecular marker technology developed based on PCR. In this paper, sixty arabica-hybrid progenies belonging to six crosses were analyzed using 31 highly polymorphic SRAP markers. The analysis revealed seven types of SRAP marker profiles which are useful in discriminating the parents and hybrids. The number of bands amplified per primer pair ranges from 6.13 to 8.58 with average number of seven bands. Among six hybrid combinations, percentage of bands shared between hybrids and their parents ranged from 66.29% to 85.71% with polymorphic bands varied from 27.64% to 60.0%. Percentage of hybrid specific fragments obtained in various hybrid combinations ranged from 0.71% to 10.86% and ascribed to the consequence of meiotic recombination. Based on the similarity index calculation, it was observed that F1 hybrids share maximum number of bands with the female parent compared to male parent. The results obtained in the present study revealed the effectiveness of SRAP technique in cultivar identification and hybrid analysis in this coffee species. Rev. Biol. Trop. 59 (2: 607-617. Epub 2011 June 01.

Transferência do fator caturra para o cultivar Mundo Novo de Coffea arabica Transfer of the CT gene to Mundo Novo cultivar

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A. Carvalho

1972-01-01

Full Text Available No presente trabalho são relatados os estudos realizados visando à introdução do gene Ct (caturra que contribui para reduzir a altura da planta, no cultivar Mundo" Novo de Coffea arabica.Estudaram-se, em ensaios de produtividade, as populações Fv F.,, F3 e F4. Nessas populações e principalmente entre os descendentes dos "caféeiros H 2077-2-5 e H 2077-2-12, foram selecionadas plantas homozigotas para os alelos Ct e também para os alelos responsáveis pela cor do fruto xc ou Xc. Essas combinações foram denominadas 'Catuaí Amarelo' e 'Catuaí Vermelho', respectivamente, e suas características são apresentadas. Os novos cultivares vêm-se mostrando de interesse econômico para as regiões cafeeiras não somente pelo porte pequeno, mas também pela produtividade, pelo vigor vegetativo e pela precocidade.The successful transfer of the Ct gene for short internode to the tall cultivar of Coffea arábica'Mundo Novo' is reported. Individual selections were carried out in the F1, F2, F3 and F4 generations. It was found that early selection in the F2 generation was quite effective. A remarkably good correlation was found between productitivity of F2 plants and the yield of the F3 and F4 generations. Plants of the F4 generation have shown reasonable uniformity and high yield in several trials. The new selections showed to be early producers. Two new cultivars were released namely 'Catuaí Amarelo' and 'Catuaí Vermelho'. The former has yellow fruits whereas the latter has red fruits. The plants are much shorter that the ones of Mundo Novo. The new cultivars have a very strong secondary and tertiary branching. Because of these characteristics Catuaí Amarelo and Catuaí Vermelho are being planted in large scale replacing the tall cultivars.

Contribution to the study of 14C-acetate as the precursor of aminoacids in detached leaves of coffee (Coffea arabica cv. Mundo Novo)

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Brasil, O.G.

1975-01-01

Labelled acetates with 14 C were used as the forerunner of aminoacids in leaves of coffee (Coffea arabica cv Mundo Novo). Leaves with the labelled acetates were incubated and released CO 2 was retained in paper discs with hiamine for further radioactivity detection. Separated proteins furnished 13 amino-acids through acid hidrolysis, all of them were identified by bidimensional filter paper chromatography. Through the obtained results it is possible to conclude that acetates are metabolized by the leafs and are related to the processes of leaf synthesis. It was possible to show that an utilization of acetate for energetical production via Krebs cycle was donne. The obtained conclusions show too that methylic carbon was more incorporated than carboxylic carbon [pt

Mortalidade de Coccus viridis (Hemiptera: Coccidae por Lecanicillium spp. em diferentes órgãos de Coffea arabica

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Flávio Lemes Fernandes

2009-04-01

Full Text Available Objetivou-se neste trabalho avaliar a mortalidade de Coccus viridis por Lecanicillium spp. em folhas e ramos de Coffea arabica. O trabalho foi realizado na casa de vegetação na Universidade Federal de Viçosa, entre fevereiro de 2005 a junho de 2006. Foram utilizadas sementes da variedade Catuaí vermelho de café (C. arabica. A solução nutritiva utilizada foi composta por 3,0 mmol/L de N, 9,0 mmol/L de K, 1,0 mmol/L de P, 4,0 mmol/L de Ca, 2,1 mmol/L de S, 46 µmol/L de B, 0,3 µmol/L de Cu, 60,0 µmol/L de Fe, 2,0 µmol/L de Mg, 0,5 µmol/L de Mo e 36,0 µmol/L de Mn. As cochonilhas e o fungo foram coletados de folhas de café em lavouras comerciais de Viçosa, MG e foram mantidos em gaiolas em Casa de Vegetação. As plantas foram infestadas com oito meses de idade. A infestação foi realizada por contato de C. viridis infectadas com o fungo sobre as cochonilhas sadias. As densidades de C. viridis viva e morta nas folhas e nos ramos foram avaliadas aos 0, 15, 30, 35, 45, 60 e 75 dias após a infestação. Usou-se análise de variância, teste de média de Skott-Knott e análise de regressão linear simples a p<0,05. O fungo Lecanicillium spp. causou mortalidade em todos os estádios de C. viridis. De forma geral, a maior mortalidade ocorreu no terceiro ínstar. Além disso, o fungo causou maior mortalidade nesse inseto praga na face abaxial da folha de café. Mortality of Coccus viridis (Hemiptera: Coccidae by Lecanicillium spp. in differents Coffea arabica organs in greenhouseAbstract. The objective of this work was to evaluate the mortality of Coccus viridis by Lecanicillium spp. on faces of the leaves, and branches of Coffea arabica. This work was conducted in greenhouse at UFV. The experiment was carried out from February 2005 to June 2006. Seeds of the lineage IAC 15 from the variety “Catuaí Vermelho” coffee (C. arabica were used. The nutritive solution utilized was composed for 3. 0 mmol/L of N, 9. 0 mmol/L of K, 1. 0 mmol

Effect of Robusta coffee beans ointment on full thickness wound healing

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Yorinta Putri Kenisa

2012-03-01

Full Text Available Background: Traumatic lesions, whether chemical, physical, or thermal in nature, are among the most common lesion in the mouth. Wound healing is essential for the maintenance of normal structure, function, and survival of organisms. Experiments of Robusta coffee powder on rat-induced alloxan incision wound, clinically demonstrated similar healing rate with the povidone iodine 10%. No studies that look directly the effect of coffee extract in ointment form when viewed in terms of histopathology. Robusta coffee bean (Coffea canephora consists of chlorogenic acid (CGA and caffeic acid which are belived to act as antioxidant and take part in wound healing process. Purpose: The aim of this study was to identify the enhancement of healing process of full-thickness skin wound after Robusta coffee beans extract ointment application. Methods: Sample consisted of 20 Cavia cabaya treated with full-thickness with wounds and was given Robusta coffee beans extract ointment concentration range of 22.5%, 45%, and 90% except the control group which was given ointment base material. Animals were then harvested on the fourth day and made for histopathological preparations. Data were calculated and compared by one-way ANOVA test and LSD test. Results: The study showed that Robusta coffee bean extract ointment can increase the number of lymphocytes, plasma cells, macrophages, fibroblasts, and blood vessels by the presence of chlorogenic acid (CGA and Caffeic acid. Conclusion: In conclusion Robusta coffee bean extract ointment enhance the healing process of fullthickness skin wound of Cavia cabaya.Latar belakang: Lesi traumatik, baik akibat rangsang kimia, fisik, atau termal, merupakan lesi yang paling umum terjadi di dalam rongga mulut. Penyembuhan luka yang terjadi ini penting untuk pemeliharaan struktur normal, fungsi, dan kelangsungan hidup organisme. Percobaan pemberian bubuk kopi Robusta terhadap luka sayatan pada tikus yang diinduksi aloksan, secara klinis

Melhoramento do cafeeiro: V - Melhoramento por hibridação

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C. A. Krug

1952-06-01

Full Text Available A hibridação como método de melhoramento do cafeeiro, oferece amplas possibilidades que ainda se acham pouco exploradas. Para o caso da espécie C. arabica, a hibridação entre suas variedades, além de fornecer dados seguros sôbre a constituição genética, permite também a verificação de ocorrência da heterose, o melhoramento sem mudança dos caracteres das variedades, ou sintetização de estruturas genéticas novas. Os cruzamentos interespecíficos poderão contribuir decisivamente para a solução do problema da melhoria da qualidade do produto e dar indicações a respeito das relações das várias espécies e da reação dos fatôres genéticos de uma espécie em ambientes genéticos diversos. Cêrca de 2500 híbridos se acham em estudo na Secção de Genética, envolvendo plantas da mesma variedade, plantas de variedades diferentes e cafeeiros pertencentes a espécies distintas. As diversas possibilidades dêsses cruzamentos no melhoramento do cafeeiro são indicadas, chamando-se especial atenção para os híbridos interespecíficos, principalmente aquêles que envolvem a espécie tetraplóide C. arabica e outras espécies diplóides, como C. canephora, C. Dewevrei e C. congensis. Êstes híbridos triplóides, após duplicação do número de cromosômios, poderão constituir fonte de novas formas de Coffea, permitindo a expansão do cultivo do café era São Paulo.Artificial hybridization in coffee breeding offers possibilities that are still unexplored. Inter-varietal hybridization has been used in Coffea arabica in order to get information about the genetic constitution of the varieties, and occurrence of heterosis, to breed without changing the morphological characters of the varieties and also to synthesize new genetic types of economic value. Inter-specific hybridization has been employed for improvement of cup quality and to furnish data about the relationship of various coffee species and the behaviour of known

Resposta fisiológica de clone de café Conilon sensível à deficiência hídrica enxertado em porta-enxerto tolerante Physiological response of Conilon coffee clone sensitive to drought grafted onto tolerant rootstock

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Vânia Aparecida Silva

2010-05-01

Full Text Available O objetivo deste trabalho foi determinar alterações fisiológicas e de tolerância à seca em clones de café Conilon (Coffea canephora contrastantes quanto à sensibilidade ao deficit hídrico. Foram avaliadas as enxertias recíprocas entre os clones 109A, sensível ao deficit hídrico, e 120, tolerante - 120/109A, 120/120, 109A/120, 109A/109A -, além de seus respectivos pés-francos. As plantas foram cultivadas em vasos de 12 L em casa de vegetação. Após seis meses, metade das plantas foi submetida ao deficit hídrico por meio da suspensão da irrigação, até que as folhas atingissem o potencial hídrico de antemanhã de -3,0 MPa. Quando o clone 120 foi usado como porta-enxerto, as plantas apresentaram sistema radicular mais profundo, mas com menor massa, retardaram por mais tempo a desidratação celular das folhas e apresentaram maior eficiência no uso da água. Sob seca severa, os teores de amido e sacarose decresceram em todos os tratamentos, enquanto os teores de glicose, frutose, aminoácidos totais e prolina aumentaram, particularmente nos tratamentos 109A pé-franco, 109A/109A e 120/109A. Essas plantas apresentaram menor eficiência no uso da água. O acúmulo de solutos não foi associado à tolerância à seca. O uso de porta-enxertos tolerantes à seca contribui para a maior tolerância das plantas ao deficit hídrico.The objective of this work was to determine alterations in physiology and those due to drought tolerance on Conilon coffee (Coffea canephora contrasting clones regarding the sensitivity to hydric stress. The reciprocal grafting between clones 109A, drought sensitive, and 120, drought tolerant, - 120/109A, 120/120, 109A/120, 109A/109A - along with their ungrafted control plants (109A and 120 were evaluated. Plants were cultivated in 12-L vases in greenhouse. Six months after grafting, half of the plants was subjected to water deficit, by suspending irrigation until leaves reached the hydric potential of -3

Furan in roasted, ground and brewed coffee

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Gruczyńska, Eliza; Kowalska, Dorota; Kozłowska, Mariola; Majewska, Ewa; Tarnowska, Katarzyna

2018-01-01

Coffee is the most popular hot beverage in the world. The annual coffee production in 2010, 2014 and 2016 was 8.1, 9.0 and 9.3 million tons respectively. There are more than 100 coffee species, but only two of them: Arabica (Coffea arabica) and Robusta (Coffea canephora) have gained commercial importance. During roasting of green coffee beans not only desirable compounds are formed, that exert positive influence on the taste and flavour of coffee, but also small quantities of undesirable ones. Furan (C4H4O) is one of the latter. Furan is a volatile compound (boiling temp. of 31.4 oC) formed during thermal processing of food. The toxicity of furan has been well documented and it is classified as “possible human carcinogen” (Group 2B) by the International Agency for Research on Cancer. Various pathways have been reported for furan formation during food processing. It can be formed from carbohydrates, amino acids by their thermal degradation or thermal re-arrangement and by oxidation of ascorbic acid and polyunsaturated acids and carotenoids. High concentrations of furan have been reported in coffee, baked and roasted food and in food subjected to preserving in cans and jars. Furan levels in brewed coffee are typically near or below 120 μg/L, but it can approach thousands μg/kg in roasted whole beans or ground coffee. The highest concentration of furan in roasted coffee reaches the level of 7000 μg/kg. Taking into account that coffee is the most popular hot drink, it becomes the main contributor to furan exposure from dietary sources for adults. In this article the published scientific papers concerned with the presence of furan in roasted non-brewed and brewed coffee have been reviewed. The formation mechanisms and occurrence of furan in coffee and the harmful influence of furan on the consumer health have been discussed.

EFEITO DE Ilex paraguariensis St. Hil. e Coffea arabica L. SOBRE O CRESCIMENTO DE Fonsecaea pedrosoi ATCC 46428

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Maria Lucia Scroferneker

2007-12-01

Full Text Available Este trabalho avaliou o efeito de extratos aquosos de Ilex paraguariensis (erva-mate e Coffea arabica (café em ágar Sabouraud dextrose no crescimento de Fonsecaea pedrosoi ATCC 46428. F. pedrosoi foi cultivada em placas de Petri contendo ágar Sabouraud dextrose suplementado com extratos aquosos derivados de 0,5; 1; 2; 3; 4 e 5g de pó de erva-mate ou de café fervidos em 100ml de água destilada por 30 min. Os diâmetros das colônias do fungo foram determinados após 7 dias. A incorporação dos extratos de erva-mate ou café no meio de crescimento não causou diferenças significativas no crescimento radial de F. pedrosoi ATCC 46428 comparado ao controle. Entretanto, estudos sobre o requerimento nutricional são importantes na sistematização do perfil bioquímico, o que pode contribuir na elucidação da bioquímica funcional do microrganismo.

Avaliação da fertilidade dos solos de sistemas agroflorestais com cafeeiro (Coffea arabica L. em Lavras-MG Evaluation of soil fertility in agroforest systems with coffee trees (Coffea arabica L. in Lavras-MG

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Bruno Grandi Salgado

2006-06-01

Full Text Available Com o objetivo de avaliar a fertilidade dos solos em um sistema agroflorestal composto por cafeeiros (Coffea arábica L. - Mundo Novo, ingazeiros (Inga vera Willd e grevíleas (Grevilea robusta A. Cunn, situado em Lavras, Minas Gerais, foi instalado o presente experimento. Usou-se um delineamento experimental inteiramente casualizado com três tratamentos e sete repetições. Os tratamentos foram: a cafeeiros a pleno sol, b cafeeiros consorciados com ingazeiros e c cafeeiros consociados com grevílea. Os espaçamentos dos cafeeiros nos três sistemas foi 4 x 1 m, para o ingazeiro 8 m x 15 m e para a grevílea 12 m x 10 m. Aos 15 anos de idade do cafeeiro e do ingazeiro e aos 9 anos da grevílea foram avaliadas as seguintes características dos solos, pH, acidez potencial (H+Al, alumínio trocável (Al+3, bases trocáveis (Ca+2 e Mg+2, potássio disponível (K+, fósforo disponível(P, enxofre (S, CTC efetiva (T, soma de bases (SB, saturação de bases (V e matéria orgânica (MO. Os resultados foram submetidos à analise de variância e as médias, comparadas pelo teste de Scott-Knott. Após a análise dos dados, concluiu-se que, embora tenha havido diferenças entre alguns elementos estudados, as características químicas dos solos nos três sistemas não foram severamente afetadas.The objective of this wark was to evaluat e the soil fertility in an agroforest system using coffee trees (Coffea arabica L - Mundo Novo, inga trees (Inga vera Wild and grevillea trees (Grevillea robusta A Cunn situated in Lavras, Minas Geris. A completely randomized experimental design with tree treatments and seven replicates was utilized. The treatments were : a coffee trees in full sunshine; b coffee trees mixed with inga trees and c coffee trees mixed with grevillea trees. Tree spacings in the three systems were 4 x 1m for coffee, 8 m x 15 m for inga and 12 x 10 m for grevillea. With coffee and inga trees at 15 years of age and grevillea trees at 9 years of age

Proteolytic activities of bacteria, yeasts and filamentous fungi isolated from coffee fruit (Coffea arabica L. = Atividade proteolítica de bactérias, leveduras e fungos filamentosos presentes em grãos de café (Coffea arabica L.

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Mirian Pereira Rodarte

2011-07-01

Full Text Available One hundred forty-four microorganisms previously isolated from coffee fruit (Coffea arabica were grown on casein agar to evaluate their proteolytic activities. Fifty percent of filamentous fungi, 52.5% of bacteria and 2.6% of yeasts were able to secrete proteases. Positiveisolates were further examined in liquid culture for their protease activities by hydrolysis of casein at different pH values (5.0, 7.0 and 9.0 at 30 oC. Bacillus megaterium, B. subtilis, Enterobacteragglomerans, Kurthia sp, Pseudomonas paucimobilis and Tatumella ptyseos demonstrated the highest proteolytic activities at pH 9.0. One yeast isolate, Citeromyces matritensis, had a proteolytic activityof 2.40 U at pH 5.0. Aspergillus dimorphicus, A. ochraceus, Fusarium moniliforme, F. solani, Penicillium fellutanum and P. waksmanii showed the highest activities. Of the bacterial isolates, the highestenzyme activities were observed in B. subtilis 333 (27.1 U, Tatumella ptyseos (27.0 U and B. megaterium 817 (26.2 U. Of the filamentous fungi, Aspergillus ochraceus (48.7 U, Fusarium moniliforme 221 (37.5 U and F. solani 359 (37.4 U had the highest activities at pH 9.0. Este trabalho teve por objetivos avaliar a capacidade de secreção de proteases extracelulares por 144 microrganismos, previamente isoladosde grãos de café (Coffea arabica durante fermentação por via seca, e determinar a atividade das enzimas produzidas. Os microrganismos foram cultivados em ágar-caseína para avaliação da produção de enzimas proteolíticas. Dos 40 isolados de bactéria presentes na amostra, 52,5% apresentaram resultado positivo para o teste. Considerando os 66 isolados de fungos filamentosos, 50% foram capazes de secretar proteases, enquanto que dos 38 isolados de leveduras, apenas 2,6% conseguiram promover a hidrólise da caseína do meio. Os isolados que apresentaram capacidade de secreção de proteases foram, posteriormente, cultivados em meio líquido para a determinação da atividade

Disposable Bioreactors for Plant Micropropagation and Mass Plant Cell Culture

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Ducos, Jean-Paul; Terrier, Bénédicte; Courtois, Didier

Different types of bioreactors are used at Nestlé R&D Centre - Tours for mass propagation of selected plant varieties by somatic embryogenesis and for large scale culture of plants cells to produce metabolites or recombinant proteins. Recent studies have been directed to cut down the production costs of these two processes by developing disposable cell culture systems. Vegetative propagation of elite plant varieties is achieved through somatic embryogenesis in liquid medium. A pilot scale process has recently been set up for the industrial propagation of Coffea canephora (Robusta coffee). The current production capacity is 3.0 million embryos per year. The pre-germination of the embryos was previously conducted by temporary immersion in liquid medium in 10-L glass bioreactors. An improved process has been developed using a 10-L disposable bioreactor consisting of a bag containing a rigid plastic box ('Box-in-Bag' bioreactor), insuring, amongst other advantages, a higher light transmittance to the biomass due to its horizontal design. For large scale cell culture, two novel flexible plastic-based disposable bioreactors have been developed from 10 to 100 L working volumes, validated with several plant species ('Wave and Undertow' and 'Slug Bubble' bioreactors). The advantages and the limits of these new types of bioreactor are discussed, based mainly on our own experience on coffee somatic embryogenesis and mass cell culture of soya and tobacco.

Evaluation of genetic divergence among clones of conilon coffee after scheduled cycle pruning.

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Dalcomo, J M; Vieira, H D; Ferreira, A; Lima, W L; Ferrão, R G; Fonseca, A F A; Ferrão, M A G; Partelli, F L

2015-11-30

Coffea canephora genotypes from the breeding program of Instituto Capixaba de Pesquisa e Extensão Rural were evaluated, and genetic diversity was estimated with the aim of future improvement strategies. From an initial group of 55 genotypes, 18 from the region of Castelo, ES, were selected, and three clones of the cultivars "Vitória" and "robusta tropical." Upon completion of the scheduled cycle pruning, 17 morphoagronomic traits were measured in the 22 genotypes selected. The principal components method was used to evaluate the contributions relative to the traits. The genetic dissimilarity matrix was obtained through Mahalanobis generalized distance, and genotypes were grouped using the hierarchical method based on the mean of the distances. The most promising clones of Avaliação Castelo were AC02, AC03, AC12, AC13, AC22, AC24, AC26, AC27, AC28, AC29, AC30, AC35, AC36, AC37, AC39, AC40, AC43, and AC46. These methods detected high genetic variability, grouping, by similarity, the genotypes in five groups. The trait that contributed the least to genetic divergence was the number of leaves in plagiotropic branches; however, this was not eliminated, because discarding it altered the groups. There are superior genotypes with potential for use in the next stages of the breeding program, aimed at both the composition of clonal variety and hybridizations.

CARACTHERIZATION OF BIOMASS ENERGY AND CARBONIZATION OF COFFEE GRAINS (Coffea arabica, L AND (Cedrelinga catenaeformis, DUKE WOOD RESIDUES

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Ailton Teixeira do Vale

2007-12-01

Full Text Available Brazil produces annually two million tons of coffee s husks from farms or industrial processing units. This wastematerial can be used for energy production; currently it is mainly used in agricultural practices as field straw cover up. This paperdeals with coffee s (Coffea arabica, L husks biomass energy characteristics, including wood carbonization. As a reference, the samestudy was performed with a wood species regularly used for building construction named Cedrorana (Cedrelinga catenaeformis,Duke. Coffee s husks was obtained from a farm 150 km far from Brasilia city and cedrorana sawdust from a local saw mill. Thispaper presents results from energy and biomass variables like moisture content, bulk density, lower and superior heating power, ashcontent, fixed carbon, volatile matter and volumetric energy. It has also studied carbonization, charcoal, pyroligneous licqor and noncondensablegases. A comparison between Coffee s husk with 0% moisture content and Cedrorana sawdust portrays the followingresults: bulk density 144.41 kg/m3, fixed carbon 10.31%, superior heating power 4.57 kWh (or 16.46 MJ or 3.933 Mcal/kg, charcoalcontent 40,64% and heating value per cubic meter 2,179 MJ/m3

Allelopathic effects of two cover crops Commelina diffusa Burm. F. and Tradescantia zebrina Shunltz on Coffea arabica L.

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Georgina Berroa Navarro

2016-03-01

Full Text Available Allelopathic effect of the cover crops Tradescantia zebrina Shunltz (cucaracha and Commelina diffusa Burm. F. (canutillo were evaluated on Coffea arabica Lin. seeds Caturra Rojo variety. Germination tests were carried out “in vitro” and it was evaluated the root longitude, percentage of total germination and period of germination, as well as the height of the plant and the emergency percentage for the incorporation tests to the soil. It was also carried out, to both over crops, the preliminary chemical qualitative characterization. The results showed that the extracts of T. zebrina and of C. diffusa stimulated the “in vitro” germination and growth of C. arabica at different concentration levels. The incorporation to the soil of the extracts of C. diffusa stimulated the development of the plants of C. arabica, in a significant way, that supposes a considerable advantage in that concerns to the employment of these cover crops, when not implying noxious effects beside all the benefits implied when using cover crops. These last ones go from the protection and improvement of the properties of the soil, to the control of the spontaneous flora in the coffee agroecosystems.

Bacillus species (BT42) isolated from Coffea arabica L. rhizosphere antagonizes Colletotrichum gloeosporioides and Fusarium oxysporum and also exhibits multiple plant growth promoting activity.

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Kejela, Tekalign; Thakkar, Vasudev R; Thakor, Parth

2016-11-18

Colletotrichum and Fusarium species are among pathogenic fungi widely affecting Coffea arabica L., resulting in major yield loss. In the present study, we aimed to isolate bacteria from root rhizosphere of the same plant that is capable of antagonizing Colletotrichum gloeosporioides and Fusarium oxysporum as well as promotes plant growth. A total of 42 Bacillus species were isolated, one of the isolates named BT42 showed maximum radial mycelial growth inhibition against Colletotrichum gloeosporioides (78%) and Fusarium oxysporum (86%). BT42 increased germination of Coffee arabica L. seeds by 38.89%, decreased disease incidence due to infection of Colletotrichum gloeosporioides to 2.77% and due to infection of Fusarium oxysporum to 0 (p Fusarium oxysporum. The mechanism of action of inhibition of the pathogenic fungi found to be synergistic effects of secondary metabolites, lytic enzymes, and siderophores. The major inhibitory secondary metabolite identified as harmine (β-carboline alkaloids).

[Establisment of a genetic transformation method of coffee (Coffea arabica cv. Catimor) and incorporation of bar gene for ammonium glufosinate resistance].

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Fernández Da Silva, Rafael

2003-01-01

In order to establish a successful method of genetic transformation in Coffea arabica cv. Catimor, different conditions of generation and electroporation were evaluated on different plant tissues. Cell suspension system was improved using one hormone only (BA), obtaining high yields of primary and secondary somatic embryo production. For selection of viable and potentially transformed cells, MTT (1%) method and ammonium glufosinate concentration (1 mg/L in leaf, callus and embryos; and 5 mg/L in cells) were established. Different conditions were evaluated to electroporate different explants (embryogenic callus, vitroplants leaves, globular and torpedo embryos). The highest gus gene expression percentage by explant were found on enzymatic treated tissues at 375 V/cm in callus, and at 625 V/cm in leaves and embryos. Torpedo embryos cultured on liquid medium were the only type of tissue that could regenerate into plants, where secondary somatic embryos were obtained. Those embryos were positive to the gus gene histochemical test and to the gus and bar genes amplification on a PCR reaction.

Observações anatômicas em plantas de Coffea arabica L. obtidas por enraizamento de estacas

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Adriana Madeira Santos Jesus

2010-04-01

Full Text Available Uma forma para se obter diminuição significativa de tempo e recursos despendidos nos programas de melhoramento de Coffea arabica L. é a clonagem de híbridos F1 por meio de estacas caulinares. Alguns estudos, em diferentes instituições, foram realizados buscando-se definir um método eficiente para esse tipo de clonagem. Com o objetivo de verificar-se a presença de barreiras anatômicas ao enraizamento de estacas caulinares do cafeeiro e a origem das raízes adventícias, bem como compara-las às raízes provenientes de plantas obtidas por semeadura, foram realizadas análises anatômicas no Departamento de Biologia da Universidade Federal de Lavras (UFLA, Lavras, MG. Utilizaram-se estacas caulinares de cafeeiro dos cultivares Acaiá e Rubi e mudas obtidas por semeadura direta e por estaquia. Os cortes realizados nas estacas caulinares mostraram não existirem barreiras anatômicas ao enraizamento adventício. Nas estacas enraizadas, a origem do primórdio radicular foi próxima aos tecidos vasculares. Cortes histológicos nas raízes formadas nas estacas e nas raízes de mudas obtidas por semeadura confirmaram que elas apresentam as mesmas estruturas primárias.

A hibridação interespecífica no melhoramento do cafeeiro

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A. J. Teixeira Mendes

1951-12-01

Full Text Available The cultivation of coffee in the American coffee producing countries is not faced with any serious handicap. The future can not be far distant, however, when it will be necessary to establish new plantations back on the high-priced old exploited lands. Need will be felt for improved varieties. At the same time, it is not known if in a near future the American coffee growers will not be in trouble with diseases as terrible as Hemileia, which the present age of transport cannot restrict to non-American areas. In the program of coffee improvement, interspecific crosses are expected to take a very important place. The introducing of desired characteristics of other species into Coffea arabica by hybridization is made difficult by the fact that, while C. arabica is self-fertile, the other species are self-sterile. It is known, also, that the high cup quality C. arabica species, with 44 somatic chromosomes, gives sterile triploid hybrids (2n = 33 when crossed to the leaf disease resistant Coffea canephora and other diploid (2n = 22 species. Very seldom, however, do the triploids produce seed, as a result of back-cross to C. arabica either through open or controlled pollination. The cytological constitution of the plants obtained from these seeds is variable ; some triploids give rise to seedlings having mostly a chromosome number around 44 ; the progeny plants from other hybrids have this number mostly around 55. Numerous aneuploids have been found among these progenies. Attention has been given to the plants derived from the hybrids as to their developmental and production characteristics. At least two 44-chromosome plants have shown to be interesting in these respects and one of them, productive and self-fertile, showed up characteristics very similar to the maragogipe variety of C. arabica. More detailed comparative observations are necessary ; however, the obtaining of such a plant proves that the triploids are a permanent source of new

CONSTRUCCIÓN DE UNA BIBLIOTECA GENÓMICA DE Coffea Arabica Var. COLOMBIA Y EVALUACIÓN CON UNA SECUENCIA HOMÓLOGA A UBIQUITINA

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Elsa Leonor Álvarez Méndez 1, 2,

2004-06-01

Full Text Available Con el fin de buscar secuencias de interés en el genoma de Coffea arabica var. Colombia, se construyó una biblioteca genómica en el vector Lambda FIX II (Stratagene con un tamaño promedio de inserto de 15Kb y con un título de 1,33x106 ufp/ml que representa aproximadamente 3,7 veces el genoma haploide.La biblioteca fue evaluada utilizando como sonda un producto de PCR amplificado con la combinación de iniciadores InhF - R631 y que presenta alta homología con secuencias tipo ubiquitinas de Arabidopsis thaliana y Oriza sativa. Se identificaron dos clones recombinantes (cof-ubi1 y cof-ubi2 que hibridizaron con la sonda tipo ubiquitina. Los resultados obtenidos indican que la biblioteca genómica es adecuada para la identificación de secuencias de interés, mapeo genético y estudios sobre regulación de la expresión de genes.

Genética de Coffea. XVIII - Variegação no cafeeiro Leaf variegation in coffee plants

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A. Carvalho

1954-01-01

Full Text Available A variegação das fôlhas do cafeeiro tanto em plantas novas como em plantas adultas tem sido freqüentemente observada. Plantas variegadas podem ocorrer espontaneamente nas progénies das diversas variedades de Coffea arabica L., motivo porque não devem constituir variedade distinta dessa espécie, como foi proposto por Cramer. As plantas variegadas em estudo puderam ser agrupadas em duas categorias, isto é, aquelas em que a variegação não se acha associada com anomalias na forma e textura das folhas e aquelas nas quais a variegação é acompanhada dessas anomalias. No primeiro grupo o padrão de variegação não é uniforme para tôdas as fôlhas, enquanto no segundo grupo o padrão é semelhante para tôda a planta. Usualmente apenas alguns ramos das plantas do primeiro grupo são variegados. Observou-se algumas vezes que as duas fôlhas do mesmo verticilo têm padrões semelhantes de variegação. Encontraram-se também fôlhas variegadas nas quais a metade da lâmina é variegada ou mesmo albina, enquanto a outra metade apresenta a côr verde normal. Os dados genéticos obtidos, embora preliminares para a maioria das plantas variegadas em investigação, permitiram concluir que o padrão de variegação da planta 180, pertencente ao primeiro grupo, é herdado pelo citoplasma e não é transmitido pelo pólen. O padrão de variegação da planta 253-21, pertencente ao segundo grupo, no entanto, parece ser transmitido pelo polen.Leaf variegation in coffee plants is a relatively common abnormality, and variegated seedlings have been found to occur spontaneously in progenies of most varieties of Coffea arabica L. For this reason it is thought that variegated types should not be described as distinct varieties, as it was done before by Cramer. Variegated coffee plants can be grouped in two categories : first, those in which variegated leaves are normal in shape and texture, but do not show a uniform variegation pattern; and second, those

Xylella fastidiosa CoDiRO strain associated with the olive quick decline syndrome in southern Italy belongs to a clonal complex of the subspecies pauca that evolved in Central America.

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Marcelletti, Simone; Scortichini, Marco

2016-12-01

Xylella fastidiosa, a xylem-limited bacterium transmitted by xylem-fluid-feeding Hemiptera insects, causes economic losses of both woody and herbaceous plant species. A Xyl. fastidiosa subsp. pauca strain, namely CoDiRO, was recently found to be associated with the 'olive quick decline syndrome' in southern Italy (i.e. Apulia region). Recently, some Xyl. fastidiosa strains intercepted in France from Coffea spp. plant cuttings imported from Central and South America were characterized. The introduction of infected plant material from Central America in Apulia was also postulated even though an ad hoc study to confirm this hypothesis is lacking. In the present study, we assessed the complete and draft genome of 27 Xyl. fastidiosa strains. Through a genome-wide approach, we confirmed the occurrence of three subspecies within Xyl. fastidiosa, namely fastidiosa, multiplex and pauca, and demonstrated the occurrence of a genetic clonal complex of four Xyl. fastidiosa strains belonging to subspecies pauca which evolved in Central America. The CoDiRO strain displayed 13 SNPs when compared with a strain isolated in Costa Rica from Coffea sp. and 32 SNPs when compared with two strains obtained from Nerium oleander in Costa Rica. These results support the close relationships of the two strains. The four strains in the clonal complex contain prophage-like genes in their genomes. This study strongly supports the possibility of the introduction of Xyl. fastidiosa in southern Italy via coffee plants grown in Central America. The data also stress how the current global circulation of agricultural commodities potentially threatens the agrosystems worldwide.

Evaluación de la incidencia de la aplicación foliar de ácido giberélico en la floración de árboles de coffea arabica l. y su impacto frente al cambio climático

OpenAIRE

Zapata Restrepo, Leidy Natalia

2013-01-01

Tesis (Maestría en Desarrollo Sostenible y Medio Ambiente). Universidad de Manizales. Facultad de Ciencias Contables, Económicas y Administrativas, 2013 La giberelina es conocida como una fitohormona que participa activamente en el control de la floración de varias especies. En el presente estudio se evaluó la aplicación exógena de ácido giberélico (0.1% y 0.5%) a 2959 plantas de Coffea arabica L., variedad Castillo cultivar Rosario con el Objetivo de establecer la relación existente entr...

Application of thermography for monitoring stomatal conductance of Coffea arabica under different shading systems.

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Craparo, A C W; Steppe, K; Van Asten, P J A; Läderach, P; Jassogne, L T P; Grab, S W

2017-12-31

Stomatal regulation is a key process in the physiology of Coffea arabica (C. arabica). Intrinsically linked to photosynthesis and water relations, it provides insights into the plant's adaptive capacity, survival and growth. The ability to rapidly quantify this parameter for C. arabica under different agroecological systems would be an indispensable tool. Using a Flir E6 MIR Camera, an index that is equivalent to stomatal conductance (I g ) was compared with stomatal conductance measurements (g s ) in a mature coffee plantation. In order to account for varying meteorological conditions between days, the methods were also compared under stable meteorological conditions in a laboratory and I g was also converted to absolute stomatal conductance values (g 1 ). In contrast to typical plant-thermography methods which measure indices once per day over an extended time period, we used high resolution hourly measurements over daily time series with 9 sun and 9 shade replicates. Eight daily time series showed a strong correlation between methods, while the remaining 10 were not significant. Including several other meteorological parameters in the calculation of g 1 did not contribute to any stronger correlation between methods. Total pooled data (combined daily series) resulted in a correlation of ρ=0.66 (P≤2.2e-16), indicating that our approach is particularly useful for situations where absolute values of stomatal conductance are not required, such as for comparative purposes, screening or trend analysis. We use the findings to advance the protocol for a more accurate methodology which may assist in quantifying advantageous microenvironment designs for coffee, considering the current and future climates of coffee growing regions. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Composition of the root mycorrhizal community associated with Coffea arabica in Fifa Mountains (Jazan region, Saudi Arabia).

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Mahdhi, Mosbah; Tounekti, Taieb; Al-Turki, Turki Ali; Khemira, Habib

2017-08-01

Arbuscular mycorrhizal fungi (AMF) constitute a key functional group of soil biota that can greatly contribute to crop productivity and ecosystem sustainability. They improve nutrient uptake and enhance the ability of plants to cope with abiotic stresses. The presence of AMF in coffee (Coffea arabica L.) plant roots have been reported in several locations but not in Saudi Arabia despite the fact that coffee has been in cultivation here since ancient times. The objective of the present study was to investigate the diversity of AMF communities colonizing the roots of coffee trees growing in two sites of Fifa Mountains (south-west Saudi Arabia): site 1 at 700 m altitude and site 2 at 1400 m. The AMF large subunit rDNA regions (LSU) were subjected to nested PCR, cloning, sequencing, and phylogenetic analysis. Microscopic observations indicated higher mycorrhizal intensity (24.3%) and spore density (256 spores/100 g of soil) in site 2 (higher altitude). Phylogenetic analysis revealed 10 phylotypes, six belonging to the family Glomeraceae, two to Claroideoglomercea, one to Acaulosporaceae and one to Gigasporaceae family. Glomus was the dominant genus at both sites and the genus Gigaspora was detected only at site 2. This is the first study reporting the presence of AMF in coffee roots and the composition of this particular mycorrhizal community in Saudi Arabia. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Study of Allelopathy of Some Shade Trees to Coffea arabicaL. Seedlings

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Adi Prawoto

2006-05-01

recommended as shade trees or intercrops with Arabica coffee and for D. zibethinusits cropping pattern must be arranged so the mineral competition could be maintained minimum. Key words: Allelopathy, Coffea arabica, Macadamia integrifolia, Cinnamomum burmani, Cassia siamea, Cassia spectabilis, mineral.

The Complete Plastid Genome Sequence of Madagascar Periwinkle Catharanthus roseus (L.) G. Don: Plastid Genome Evolution, Molecular Marker Identification, and Phylogenetic Implications in Asterids

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Ku, Chuan; Chung, Wan-Chia; Chen, Ling-Ling; Kuo, Chih-Horng

2013-01-01

The Madagascar periwinkle ( Catharanthus roseus in the family Apocynaceae) is an important medicinal plant and is the source of several widely marketed chemotherapeutic drugs. It is also commonly grown for its ornamental values and, due to ease of infection and distinctiveness of symptoms, is often used as the host for studies on phytoplasmas, an important group of uncultivated plant pathogens. To gain insights into the characteristics of apocynaceous plastid genomes (plastomes), we used a reference-assisted approach to assemble the complete plastome of C . roseus , which could be applied to other C . roseus -related studies. The C . roseus plastome is the second completely sequenced plastome in the asterid order Gentianales. We performed comparative analyses with two other representative sequences in the same order, including the complete plastome of Coffea arabica (from the basal Gentianales family Rubiaceae) and the nearly complete plastome of Asclepias syriaca (Apocynaceae). The results demonstrated considerable variations in gene content and plastome organization within Apocynaceae, including the presence/absence of three essential genes (i.e., accD, clpP, and ycf1) and large size changes in non-coding regions (e.g., rps2-rpoC2 and IRb-ndhF). To find plastome markers of potential utility for Catharanthus breeding and phylogenetic analyses, we identified 41 C . roseus -specific simple sequence repeats. Furthermore, five intergenic regions with high divergence between C . roseus and three other euasterids I taxa were identified as candidate markers. To resolve the euasterids I interordinal relationships, 82 plastome genes were used for phylogenetic inference. With the addition of representatives from Apocynaceae and sampling of most other asterid orders, a sister relationship between Gentianales and Solanales is supported. PMID:23825699

Sensory Description of Cultivars (Coffea Arabica L. Resistant to Rust and Its Correlation with Caffeine, Trigonelline, and Chlorogenic Acid Compounds

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Larissa de Oliveira Fassio

2016-01-01

Full Text Available Considering the importance of the chemical compounds in Arabica coffee beans in the definition of the drink sensory quality and authentication of coffee regions, the aim of this study was to evaluate, from principal component analysis—PCA—if there is a relation between the caffeine, trigonelline, and chlorogenic acid (5-CQA content and the sensory attributes of the drink, and in this context, enabling the differentiation of cultivars in two coffee-producing regions of Brazil. We evaluated seven rust-resistant Coffea arabica cultivars, and two rust-susceptible cultivars in two cultivation environments: Lavras, in the southern region of Minas Gerais state, and Patrocinio in the Cerrado region of Minas Gerais. The flavor and acidity were determinant for differentiation of the cultivars and their interaction with the evaluated environments. Cultivars Araponga MG1, Catigua MG2, and Catigua MG1 are the most suitable for the production of specialty coffee in the state of Minas Gerais. A poor correlation was found between caffeine, trigonelline, 5-CQA contents, and fragrance, flavor, acidity, body, and final score attributes. However, these compounds enabled the differentiation of the environments. The PCA indicated superiority in the sensory quality of cultivars resistant to rust, compared to the control, Bourbon Amarelo, and Topázio MG1190.

Divergência genética entre progênies de café robusta Genetic divergence among robusta coffe progenies

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Milana Gonçalves Ivoglo

2008-12-01

Full Text Available Estudou-se a divergência genética de 21 progênies de meios-irmãos - 19 do grupo Congolês e duas do grupo Guineano - de introduções do germoplasma de café robusta (Coffea canephora do IAC. O estudo baseou-se em análises multivariadas de 14 características morfo-agronômicas, com o propósito de selecionar as progênies mais divergentes, visando à definição de população-base para posterior seleção e produção de híbridos. Avaliou-se também a importância das características discriminantes para análises de divergência, visando ao descarte das variáveis, segundo suas contribuições relativas. O experimento foi plantado e desenvolvido em campo experimental localizado no Pólo Regional do Nordeste Paulista, Mococa (SP, em blocos casualizados, com 21 tratamentos e 24 repetições. O agrupamento dos genótipos foi realizado com base nos métodos de Tocher e UPGMA. A matriz de dissimilaridade genética foi obtida por meio da distância generalizada de Mahalanobis, que serviu de base para a formação dos grupos. Os métodos empregados foram eficientes em detectar ampla variabilidade genética entre as progênies avaliadas. Vários grupos dissimilares foram identificados. As progênies IAC 2262, IAC 2290, IAC 2286, IAC 2292 e IAC 2291 são indicadas para compor programas de intercruzamentos, por terem sido consideradas as mais promissoras na obtenção de populações segregantes ou híbridos heteróticos. As características que menos contribuíram para a divergência genética foram, hierarquicamente: diâmetro da copa antes da poda, altura da planta antes da poda e área foliar.It was studied genetic divergence of 21 half-sib progenies, being 19 of the Congolês group and two of the Guineano group, introductions of germoplasma robust (Coffea canephora, based in 14 morpho-agronomic traits and multivariate procedures. It's aims to select the lineages most divergent for definition of population-base for posterior reciprocal

EVALUACIÓN DE CUATRO ESPECIES FORESTALES ASOCIADAS CON CAFÉ (Coffea Arabica L. Y EN MONOCULTIVO EN EL LITORAL ECUATORIANO

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Pedro Suatunce Cunuhay

2009-12-01

Full Text Available Se implantó un ensayo de sistema agroforestal con café (Coffea arabica L. en el área del cantón Quevedo, en la Finca Experimental “La Represa”, en el año de 1997. Se plantaron cuatro especies forestales en asociación con café (C. arabica L., y también se establecieron parcelas de árboles y café en monocultivo, en parcelas contiguas. Las especies forestales utilizadas fueron el guayacán blanco (Cybistax donnell-smithii Rose, laurel prieto (Cordia megalantha Chadat, fernansánchez (Triplaris cumingiana Wedd y teca (Tectona grandis L. F.. El objetivo fue comparar la producción de madera y café bajo los sistemas agroforestales y en los sistemas de plantación en monocultivo tanto de los árboles como del café. La producción por hectárea de café fue mayor en monocultivo. La incidencia (% del minador del café (Perileucoptera coffeella Green fue baja en los dos sistemas, además no hubo diferencias significativas entre los cafetales asociados y en monocultivo. El volumen de las especies forestales fue mayor en los sistemas agroforestales. Según la evaluación del uso eficiente de la tierra, cualquiera de los sistemas agroforestales evaluados es mejor que los cultivos puros de estas especies.

Effect of CO2 on somatic embryos development Coffea arabica L. cv. ‘Caturra rojo’ and Clematis tangutica K.

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Raúl Barbon

2016-07-01

Full Text Available Studies to optimize somatic embryogenesis have traditionally focused on the components of the culture medium but little other in vitro environment factors have been analyzed such as the composition of the gaseous atmosphere. The objective of this work was to determine the influence of CO2 on the development of the somatic embryo during the transition from the globular to the torpedo stage. The research was carried out on two model species for somatic embryogenesis that they are developed in different climatic zones: Coffea arabica L. cv. ‘Caturra rojo’ and Clematis tangutica K. Three CO2 concentrations (2.5, 5.0 and 10.0% combined with 21% O2 and two controls (passive exchange and forced ventilation were used. The effect of CO2 on the differentiation of somatic embryos from globular to torpedo stage in coffee and clematis was demonstrated, since in the treatments with passive exchange, where there was accumulation of CO2, the differentiation of somatic embryos was superior to treatments with forced ventilation. With 5.0% CO2 the process of differentiation of the embryos in the globular stage was stimulated, because in the treatment with this concentration of CO2 for coffee and clematis the highest proportion of embryos in torpedo stages and low levels of malformation were obtained.   Keywords: carbon dioxide, differentiation, in vitro environment, somatic embryogenesis

Characterization of Fatty Acid, Amino Acid and Volatile Compound Compositions and Bioactive Components of Seven Coffee (Coffea robusta Cultivars Grown in Hainan Province, China

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Wenjiang Dong

2015-09-01

Full Text Available Compositions of fatty acid, amino acids, and volatile compound were investigated in green coffee beans of seven cultivars of Coffea robusta grown in Hainan Province, China. The chlorogenic acids, trigonelline, caffeine, total lipid, and total protein contents as well as color parameters were measured. Chemometric techniques, principal component analysis (PCA, hierarchical cluster analysis (HCA, and analysis of one-way variance (ANOVA were performed on the complete data set to reveal chemical differences among all cultivars and identify markers characteristic of a particular botanical origin of the coffee. The major fatty acids of coffee were linoleic acid, palmitic acid, oleic acid, and arachic acid. Leucine (0.84 g/100 g DW, lysine (0.63 g/100 g DW, and arginine (0.61 g/100 g DW were the predominant essential amino acids (EAAs in the coffee samples. Seventy-nine volatile compounds were identified and semi-quantified by HS-SPME/GC-MS. PCA of the complete data matrix demonstrated that there were significant differences among all cultivars, HCA supported the results of PCA and achieved a satisfactory classification performance.

Taxonomia de Coffea arabica L. VI: caracteres morfológicos dos haplóides

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A. Carvalho

1952-06-01

Full Text Available No decorrer dos trabalhos de melhoramento do café em execução no Instituto Agronômico de Campinas, plantas haplóides foram encontradas nas variedades typica, bourbon, maragogipe, semperflorens, laurina, erecta, caturra e San Ramon, da espécie Coffea arabica. Todos os haplóides apresentam porte menor e fôlhas mais estreitas e mais finas do que as variedades que lhes deram origem. Apesar de as flores serem completas, nota-se esterilidade muito acentuada. Raramente se formam alguns frutos, e êstes são providos de uma única semente, motivo pelo qual as plantas haplóides são denominadas "monosperma". Os fatôres genéticos dominantes maragogipe (Mg, erecta (Er, caturra (Ct e San Ramon, bem como os gens recessivos semperflorens (sf, e laurina (lr, das variedades estudadas, manifestam-se nas plantas haplóides, de modo semelhante ao que ocorre nas plantas diplóides correspondentes. O fator para coloração bronze dos brotos novos tem dominância incompleta e, na condição heterozigota (Brbr, mostra intensidade intermediária de côr. Nas plantas haplóides contendo um só alelo Br, a côr dos brotos novos é bronze-clara. Uma única dose do fator Na, que também apresenta dominância incompleta, dando, na forma heterozigota (Nana e na presença de tt, o fenótipo conhecido por murta, manifesta-se, na forma haplóide, dando plantas semelhantes às homozigotas ttNaNa, apenas com fôlhas mais estreitas e mais finas. Chamou-se atenção para as linhas puras de café obtidas pela duplicação do número de cromosômios dos haplóides e sua aplicação nos ensaios de linhagens e na determinação das taxas de mutação. As observações realizadas na meiose da espécie C. arabica, bem como os dados das análises genéticas e as observações feitas nesses haplóides parecem indicar que, se essa espécie fôr alotetraplóide, tal origem deve ser bem antiga, comportando-se hoje a espécie C. arábica, como um diplóide normal. As plantas

Ochratoxigenic fungi associated with green coffee beans (Coffea arabica L.) in conventional and organic cultivation in Brazil.

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de Fátima Rezende, Elisângela; Borges, Josiane Gonçalves; Cirillo, Marcelo Ângelo; Prado, Guilherme; Paiva, Leandro Carlos; Batista, Luís Roberto

2013-01-01

The genera Aspergillus comprises species that produce mycotoxins such as aflatoxins, ochratoxins and patulin. These are cosmopolitan species, natural contaminants of agricultural products. In coffee grains, the most important Aspergillus species in terms of the risk of presenting mycotoxins belong to the genera Aspergillus Section Circumdati and Section Nigri. The purpose of this study was to assess the occurrence of isolated ochratoxigenic fungi of coffee grains from organic and conventional cultivation from the South of Minas Gerais, Brazil, as well as to evaluate which farming system presents higher contamination risk by ochratoxin A (OTA) produced by fungi. Thirty samples of coffee grains (Coffea arabica L.) were analysed, being 20 of them of conventional coffee grains and 10 of them organic. The microbiological analysis was done with the Direct Plating Technique in a Dichloran Rose Bengal Chloramphenicol Agar (DRBC) media. The identification was done based on the macro and micro morphological characteristics and on the toxigenic potential with the Plug Agar technique. From the 30 samples analysed, 480 filamentous fungi of the genera Aspergillus of the Circumdati and Nigri Sections were isolated. The ochratoxigenic species identified were: Aspergillus auricoumus, A. ochraceus, A. ostianus, A. niger and A. niger Aggregate. The most frequent species which produces ochratoxin A among the isolated ones was A. ochraceus, corresponding to 89.55%. There was no significant difference regarding the presence of ochratoxigenic A. ochreceus between the conventional and organic cultivation systems, which suggests that the contamination risk is similar for both cultivation systems.

Influence of the in vitro environment on the germination of somatic embryos of Coffea arabica L. cv. 'Caturra rojo' and Clematis tangutica K.

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Raúl Barbon

2017-07-01

Full Text Available The in vitro environment is a factor that in recent years has begun to investigate, because gases such as oxygen, carbon dioxide and ethylene play an important role in the morphogenesis of somatic embryos and their development in plants. The objective of this work was to determine the effect of the CO2 on the germination of coffee somatic embryos (Coffea arabica L. cv. 'Caturra rojo' and clematis (Clematis tangutica K.. Three gas mixtures composed of CO2 concentrations (2.5, 5.0 and 10.0% combined with 21% O2 and two controls (passive exchange and forced ventilation were used. A positive effect of CO2 on the germination of somatic embryos in the torpedo stage in coffee and clematis was obtained, because in the treatments with passive exchange, where there was CO2 accumulation, germination of the somatic embryos was superior to the treatments with Forced ventilation. With 2.5% and 5.0% CO2, the germination process is stimulated while with 10.0% CO2 there is an inhibition of germination with the appearance of malformations and hyperhydricity.   Keywords: gaseous atmosphere, carbon dioxide, somatic embryogenesis, secondary embryogenesis, hyperhydricity

Morphometric and Productive Characterization of Nineteen Genotypes from the Colombian Coffea Collection / Caracterización Morfométrica y Productiva de Diecinueve Genotipos de la Colección Colombiana del Género Coffea

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Jhon Wilson Mejía Montoya

2013-12-01

Full Text Available Nineteen genotypes of the Colombian Coffee (Coffeaarabica L. Collection were characterized through features related to productivity, crown architecture and light interception. The results revealed significant differences among genotypes. Branches and leaves were found to be dominantly plagiophyl. Leaf area (LA and Leaf area index (LAI made accession CU1812 (which correspondsto variety Castillo® stand out for its photosynthetically activeradiation (PAR interception and coffee bean production. Likewise, a PAR based cluster analysis allowed dividing the genotypes in three groups. Because of their higher yield, the most outstanding genotypes were Caturra, CU-1812 and Harrar R2. This factor showed correlation with PAR absorption. The current results are useful for future works in coffee breeding programs. / Se caracterizaron 19 genotipos de la Colección Colombiana de Café (Coffea arabica L.; para ello se estudiaron aspectos relacionados con la arquitectura del dosel, la interceptación de la radiación y la producción. Los resultados mostraron diferencias significativas entre los genotipos, predominando en las ramas la distribución plagiofila; una disposición similar se observóen las hojas. El área foliar (AF y el índice de área foliar (IAF,contribuyeron a que la introducción CU1812, componente de la variedad Castillo®, se destacara por presentar los mayores valores de interceptación de radiación fotosintéticamente activa (RFA y producción de café cereza. Así mismo, el análisis de agrupamiento con base en la RFA, permitió ordenar los genotipos en tres grupos,destacándose Caturra, CU-1812 y Harrar R2 por su mayorrendimiento, factor que mostró correlación con la RFA captadapor el dosel. Los resultados obtenidos en esta investigación son de utilidad en futuros trabajos de mejoramiento genético en café.

CARACTERIZACIÓN AGROFORESTAL EN SISTEMAS DE CAFÉ TRADICIONAL Y RÚSTICO, EN SAN MIGUEL, VERACRUZ, MÉXICO

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Luis Villavicencio-Enríquez

2013-01-01

Full Text Available Se realizaron caracterizaciones agroforestales en cafetales de tipo tradicional y rústico en la comunidad de San Miguel, Amatlán de los Reyes, Veracruz, México, con el objetivo de analizarlos y compararlos entre sí. Los resultados indican que ambos sistemas obtienen beneficios económicos similares aunque la composición de especies del dosel y los productos obtenidos son distintos. El principal producto económico son los árboles maderables (Cedrela odorata, Robinsonella mirandae y Mastichodendron capirii, seguido del café (Coffea arabica y C. canephora y las palmas Chamaedorae tepejilote y Chamaedorae elegans. La relación beneficio/costo obtenida para la venta de los productos forestales y agrícolas indica una mayor ganancia económica para el sistema rústico de café ($ 20,784.00·año-1·ha-1 respecto al sistema tradicional de café ($ 19,236.00·año-1·ha-1. Aunque las ganancias en ambos sistemas son relativamente buenas, el efecto que este tipo de explotación tiene sobre los recursos forestales puede ser poco sustentable a través del tiempo, ya que en el sistema rústico no existen labores de reforestación. El sistema tradicional de café se encuentra en una mejor condición de sustentabilidad y producción a largo plazo, ya que los elementos utilizados para la comercialización de árboles maderables y para combustible son reforestados por la importancia comercial que éstos tienen.

Natural Antimicrobials and Oral Microorganisms: A Systematic Review on Herbal Interventions for the Eradication of Multispecies Oral Biofilms.

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Karygianni, Lamprini; Al-Ahmad, Ali; Argyropoulou, Aikaterini; Hellwig, Elmar; Anderson, Annette C; Skaltsounis, Alexios L

2015-01-01

Oral diseases such as caries and periodontitis are mainly caused by microbial biofilms. Antibiotic therapy has reached its limits with regard to antimicrobial resistance, and new therapeutic measures utilizing natural phytochemicals are currently a focus of research. Hence, this systematic review provides a critical presentation of the antimicrobial effects of various medicinal herbs against in vitro, ex vivo, and in situ formed multispecies oral biofilms. Searches were performed in three English databases (PubMed, EMBASE, CAMbase) and the electronic archives of five German journals from the times of their establishment until October 10th, 2014, with the search terms "(plant extracts OR herbal extracts OR plant OR herb) AND (oral biofilm OR dental biofilm OR dental plaque OR oral disease OR dental disease)." The pooled data were assessed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PRISMA). Initially, 1848 articles were identified, out of which 585 full-text articles were screened, 149 articles were reevaluated for eligibility and finally, 14 articles met all inclusion criteria. The data of 14 reports disclosed enhanced antiadhesive and antibiofilm activity by the plant extracts obtained from Vitis vinifera, Pinus spp., Coffea canephora, Camellia sinensis, Vaccinium macrocarpon, Galla chinensis, Caesalpinia ferrea Martius, Psidium cattleianum, representative Brazilian plants and manuka honey. Overall, a positive correlation was revealed between herb-based therapies and elimination rates of all types of multispecies oral biofilms. In that context, integrating or even replacing conventional dental therapy protocols with herbal-inspired treatments can allow effective antimicrobial control of oral biofilms and thus, dental diseases.

Natural antimicrobials and oral microorganisms: A systematic review on herbal interventions for the eradication of multispecies oral biofilms.

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Lamprini eKarygianni

2016-01-01

Full Text Available Oral diseases such as caries and periodontitis are mainly caused by microbial biofilms. Antibiotic therapy has reached its limits with regard to antimicrobial resistance, and new therapeutic measures utilizing natural phytochemicals are currently a focus of research. Hence, this systematic review provides a critical presentation of the antimicrobial effects of various medicinal herbs against in vitro, ex vivo and in situ formed multispecies oral biofilms. Searches were performed in three English databases (PubMed, EMBASE, CAMbase and the electronic archives of five German journals from the times of their establishment until October 10th, 2014, with the search terms (plant extracts OR herbal extracts OR plant OR herb AND (oral biofilm OR dental biofilm OR dental plaque OR oral disease OR dental disease. The pooled data were assessed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Initially, 1,848 articles were identified, out of which 585 full-text articles were screened, 149 articles were reevaluated for eligibility and finally, 14 articles met all inclusion criteria. The data of 14 reports disclosed enhanced antiadhesive and antibiofilm activity by the plant extracts obtained from Vitis vinifera, Pinus spp., Coffea canephora, Camellia sinensis, Vaccinium macrocarpon, Galla chinensis, Caesalpinia ferrea Martius, Psidium cattleianum, representative Brazilian plants and manuka honey. Overall, a positive correlation was revealed between herb-based therapies and elimination rates of all types of multispecies oral biofilms. In that context, integrating or even replacing conventional dental therapy protocols with herbal-inspired treatments can allow effective antimicrobial control of oral biofilms and thus, dental diseases.

Melhoramento do cafeeiro: XXXVIII. Observações sobre progênies do cultivar Mundo-Novo de Coffea arabica na estação experimental de Mococa Coffee breeding: XXXVIII-observation on progenies of the Mundo-Novo cultivars of Coffea arabica in the Mococa experimental station

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Túlio R. Rocha

1980-01-01

Full Text Available Os dados analisados no experimento localizado em Mococa sobre a produtividade de 112 progênies dos cultivares Mundo-Novo S1 e S2, Bourbon-Amarelo, BourbonVermelho e Caturra-Vermelho de Coffea arabica no período de 1955 a 1971, indicaram que as de Mundo-Novo S1, de prefixos MP 474, MP 502, MP 469, MP 492 e MP 475, revelaram-se como as mais produtivas, assemelhando-se a algumas progênies 'Mundo--Novo' S2. Dentre estas, destacou-se a de prefixo MP 388-6, que atingiu o nível mais elevado de produção do experimento. As progênies de 'Mundo-Novo', em conjunto, produziram 44% a mais do que as de Bourbon-Amarelo e, estas, 60% a mais do que as de Bourbon-Vermelho e Caturra-Vermelho. A altura e o diâmetro da copa atingiram valores médios mais elevados para as progênies de 'Mundo-Novo'. Verificaram-se correlações positivas e altamente significativas entre altura média da planta e diâmetro médio da copa com a produção das progênies. As progênies mais produtivas revelaram rendimento (relação entre peso de café maduro e beneficiado de aproximadamente 6,0 e porcentagem de sementes normais, do tipo chato, acima de 80. Quanto ao tamanho das sementes do tipo chato, duas progênies 'Mundo-Novo' S1, MP 474 e MP 452, apresentaram peneira média maior, permi-tindo seleção de plantas com essa característica e com elevada produção.Coffee progenies of the Mundo-Novo cultivars of Coffea arabica were studied in an experiment located at the Mococa Experimental Station of the Instituto Agronômico in comparison with Bourbon-Amarelo, Bourbon-Vermelho and Caturra-Vermelho cultivars of the same species. During a period of 17 consecutive cropping years (1955-1971, Mundo-Novo yielded approximately 44% more than Bourbon-Amarelo and this cultivars yielded 60% more than Bourbon-Vermelho and Caturra-Vermelho. Among the 89 S1 'Mundo-Novo' progenies, MP 474, MP 502, MP 469, MP 492 and MP 475 yielded as much as the two best 'Mundo-Novo' S2 progenies. Greater

Crescimento vegetativo e produção de cafeeiros (Coffea arabica L. recepados em duas épocas, conduzidos em espaçamentos crescentes Vegetative growth and yield of coffee plants (Coffea arabica L. in two different pruning times, conducted at different spacings

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Sérgio Parreiras Pereira

2007-06-01

Full Text Available O experimento foi instalado na Fazenda Experimental da Empresa de Pesquisa Agropecuária de Minas Gerais - EPAMIG em Machado, Sul de Minas Gerais, em 1992, com o objetivo de avaliar as conseqüências da redução dos espaçamentos entre as linhas e entre as plantas na linha de plantio sobre a produção e a fenologia do cafeeiro(Coffea arabica L.. O delineamento experimental foi o blocos casualizados - DBC, em um arranjo fatorial 4 x 3 com parcela subdividida, sendo quatro distâncias entre as linhas (2,0; 2,5; 3,0 e 3,5 m e três distâncias entre as plantas na linha de plantio (0,5; 0,75; 1,0 m, e duas épocas de poda (uma precoce feita logo após a colheita em de julho 2002 e a outra tardia em de janeiro de 2003, totalizando 24 tratamentos com três repetições. Em julho de 2002 e em janeiro de 2003 foi realizada a poda tipo "recepa", na qual foram conduzidas duas brotações por planta. Em agosto de 2004, avaliou-se o crescimento dos componentes vegetativos e a produção das parcelas. Os espaçamentos adotados não influenciaram o crescimento de nenhum dos componentes vegetativos das brotações no período avaliado. Todas as características vegetativas foram influenciadas positivamente pela adoção da poda precoce, assim como a produtividade da primeira colheita realizada após a poda, que foi também influenciada positivamente pela adoção de espaçamentos mais adensados. Os cafeeiros que foram submetidos à poda tardia não produziram, em julho de 2004, como aqueles podados precocemente.The experiment was established in the Empresa de Pesquisa Agropecuária de Minas Gerais - Epamig Experiment Station, located in the city of Machado, south of the Minas Gerais state, Brazil, in the year of 1992, with the objective of evaluating the consequences of the reduction on planting spaces among rows and among plants, upon beans yield and plant phenology (Coffea arabica L.. The experimental design used was a 4x 3 factorial with split plot at

Use of coffee (Coffea arabica pulp for the production of briquettes and pellets for heat generation

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Robert Cubero-Abarca

2014-10-01

Full Text Available Coffee bean (Coffea arabica processing generates high amount of residues that are sources of environmental pollution. Therefore, an appropriate solution is needed. The objective of this study was to determine the potential of coffee pulp to produce briquettes and pellets. The study included pulp drying (using air, solar and hot air methods; the production of briquettes and pellets; the evaluation of their energy, physical and mechanical properties; and the evaluation of pellet quality using X-ray densitometry. The results showed that the pulp presented an initial moisture content of 90%, resulting in drying times of 699, 308 and 55 hours for air, solar and hot air drying, respectively, and the calorific values of the pellets and briquettes were 12,501 kJ kg-1 and 11,591 kJ kg-1, respectively. The ash content was 8.68% for the briquettes and 6.74% for the pellets. The density of the briquettes was 1,110 kg m-3, compared with 1,300 kg m-3 for the pellets. The apparent densities were 1,000 kg m-3 and 600 kg m-3 for the briquettes and pellets, respectively, and the water absorptions by the briquettes were 7.90% and 8.10% by the pellets. The maximum horizontal compression effort was 26.86 kg cm-2, measured in the pellets, compared with 4.52 kg cm-2 in the briquettes. The maximum horizontal load was 93.24 kg, measured in the briquettes, compared with 33.50 kg in the pellets. The value of the pellet durability test was 75.54%. X-ray densitometry showed that the pellet was uniform and a few cracks were observed on the pellet surface.

Optimization of coffee (Coffea arabica transformation parameters using uidA and hpt genes: effect of osmotic pre-treatment, helium pressure and target distance

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Andrés M Gatica

2009-11-01

Full Text Available The aim of this work was to optimize the biolistic delivery parameters that affect the DNA delivery and stable expression of marker genes into coffee tissues (Coffea arabica. L. cvs. Caturra and Catuaí. The effect of osmotic preculture length, osmotic concentration of medium, Helium pressure and target distance on transient expression of the uidA gene in coffee leaves and somatic embryos were tested. The highest transient uidA expression was obtained when Caturra (18.3±2.8 and Catuaí (6.8±2.0 leaves and Catuaí embryos (80.0±7.4 were cultured for 5h on Yasuda medium complemented with 0.5M Mannitol +0.5M Sorbitol. The combination of 1100psi and a target distance of 9cm resulted in the highest number of blue spots per Caturra leaf segment (23.6±3.9, whereas for the Catuaí variety the combination of 1100psi and a target distance of six (10.2±1.9 and nine (8.2±1.9 cm gave the highest number of blue spots per leaf segment. The optimized protocol was tested with pCAMBIA 1 301 (uidA gene and the hpt gene, pCAMBIA 1 305.2 (uidA version GUSPlus ™ and the hpt gene and pCAMBIA 1 301-BAR (uidA gene and the bar gene. The highest number of blue spots was obtained when Caturra (54.6±5.7 and Catuaí (28.9±4.3 leaves were bombarded with pCAMBIA 1 305.2. Selection of bombarded coffee tissues with 100mg/l hygromicyn caused the oxidation of tissues. Rev. Biol. Trop. 57 (Suppl. 1: 151-160. Epub 2009 November 30.La presente investigación tuvo como objetivo optimizar los parámetros que afectan la incorporación y expresión de genes marcadores mediante biobalística en segmentos de hoja y embriones somáticos de café (Coffea arabica. L. cvs. Caturra y Catuaí. La mayor expresión transitoria del gen uidA en segmentos de hoja de Caturra (18.3±2.8 y Catuaí (6.8±2.0 y embriones somáticos de Catuaí (80.0±7.4 se obtuvo al cultivar los explantes por cinco horas previo al bombardeo en el medio Yasuda complementado con 0.5M mannitol+0.5M sorbitol

Phytochemical Profile and in vitro Assessment of the Cytotoxicity of Green and Roasted Coffee Oils (Coffea arabica L. and their Polar Fractions

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Ana Paula Lorenzen Voytena

2018-03-01

Full Text Available Green Coffea arabica L. seed oil (GCO has been used as an active cosmetic ingredient in many skin care products, due to its composition and balance of fatty acids. On the other hand, while roasted coffee oil (RCO is mainly used for imparting aroma in the food industry, there is no data available to suggest its safety in cell-based model systems. In this context, the present study aims to evaluate the chemical composition of GCO, RCO, and their correspondent polar fractions (PFs; and assess their cytotoxicity and antioxidant potential in vitro. RCO and RCO PF exhibited significantly higher amounts of phenolic compounds, when compared to both GCO and GCO PF. In the DPPH assay, after 5 min of incubation, RCO inhibited about 80% of radicals, while GCO only achieved half of this activity. Similar results were also obtained for their PFs. Upon exposure to GCO, no cytotoxic effects were observed, in fact, there were slight increments in cell proliferation. Nevertheless, cell exposure to RCO led to significant decreases in cell viability. Increases in the concentration of coffee oil PFs were associated with correspondent relevant increased cytotoxicity. Upon hydrogen peroxide-induced oxidative stress, neither GCO nor RCO treatment were effective in protecting cells.

Proteomic analysis of apoplastic fluid of Coffea arabica leaves highlights novel biomarkers for resistance against Hemileia vastatrix

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Leonor eGuerra-Guimarães

2015-06-01

Full Text Available A proteomic analysis of the apoplastic fluid (APF of coffee leaves was conducted to investigate the cellular processes associated with incompatible (resistant and compatible (susceptible Coffea arabica-Hemileia vastatrix interactions, during the 24-96 hai period. The APF proteins were extracted by leaf vacuum infiltration and protein profiles were obtained by 2-DE. The comparative analysis of the gels revealed 210 polypeptide spots whose volume changed in abundance between samples (control, resistant and susceptible during the 24-96 hai period. The proteins identified were involved mainly in protein degradation, cell wall metabolism and stress/defense responses, most of them being hydrolases (around 70%, particularly sugar hydrolases and peptidases/proteases. The changes in the APF proteome along the infection process revealed two distinct phases of defense responses, an initial/basal one (24-48 hai and a late/specific one (72-96 hai. Compared to susceptibility, resistance was associated with a higher number of proteins, which was more evident in the late/specific phase. Proteins involved in the resistance response were mainly, glycohydrolases of the cell wall, serine proteases and pathogen related-like proteins (PR-proteins, suggesting that some of these proteins could be putative candidates for resistant markers of coffee to H. vastatrix. Antibodies were produced against chitinase, pectin methylesterase, serine carboxypeptidase, reticuline oxidase and subtilase and by an immunodetection assay it was observed an increase of these proteins in the resistant sample. With this methodology we have identified proteins that are candidate markers of resistance and that will be useful in coffee breeding programs to assist in the selection of cultivars with resistance to H. vastatrix.

Adição de Zn e absorção, translocação e utilização de Zn e P por cultivares de cafeeiro

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Reis Jr. Roberto dos Anjos

2002-01-01

Full Text Available A crescente exigência de nutrientes, especialmente micronutrientes, pelos cultivares de café vem exigindo uma melhor compreensão da dinâmica desses nutrientes no sistema solo-planta. Com o objetivo de avaliar o efeito de concentrações de Zn (0,4 ; 1,3 e 2,3 mimol Zn L-1 na solução nutritiva sobre o crescimento, produção de matéria seca, eficiência de absorção, translocação e utilização de Zn e P em dois cultivares de café (Coffea arabica cv. Catuaí e Coffea canephora cv. Conilon, foi realizado um experimento sob delineamento inteiramente casualizado com esquema fatorial 3 × 2 (três doses de Zn e dois cultivares com três repetições. Plantas de café dos dois cultivares estudados foram cultivadas em casa de vegetação, com solução nutritiva completa por 50 dias, após os quais receberam solução nutritiva modificada com três doses de Zn. Aos 114 dias após a transferência para a solução nutritiva modificada, as plantas foram coletadas e separadas em folhas superiores, inferiores, caule e raízes. Foram avaliadas altura do caule, número de ramificações laterais, área foliar, produção de matéria seca e conteúdos de P e Zn nas diversas partes da planta, além das eficiências de absorção, translocação e utilização de P e Zn. A dose 2,3 mimol Zn L-1 proporcionou os maiores valores para as características de crescimento avaliadas, tanto para o cultivar Catuaí, quanto para Conilon. Os maiores conteúdos de Zn observados no Catuaí indicam que este é mais exigente em Zn que o Conilon na fase de mudas. O Conilon apresentou menores eficiências de absorção e translocação e maior eficiência de utilização de Zn, refletindo sua menor demanda por este nutriente. As concentrações de Zn empregadas neste experimento não promoveram interação Zn-P.

Ensembl Genomes 2016: more genomes, more complexity.

Science.gov (United States)

Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

2016-01-04

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

High-throughput metabolic profiling of diverse green Coffea arabica beans identified tryptophan as a universal discrimination factor for immature beans.

Science.gov (United States)

Setoyama, Daiki; Iwasa, Keiko; Seta, Harumichi; Shimizu, Hiroaki; Fujimura, Yoshinori; Miura, Daisuke; Wariishi, Hiroyuki; Nagai, Chifumi; Nakahara, Koichi

2013-01-01

The maturity of green coffee beans is the most influential determinant of the quality and flavor of the resultant coffee beverage. However, the chemical compounds that can be used to discriminate the maturity of the beans remain uncharacterized. We herein analyzed four distinct stages of maturity (immature, semi-mature, mature and overripe) of nine different varieties of green Coffea arabica beans hand-harvested from a single experimental field in Hawaii. After developing a high-throughput experimental system for sample preparation and liquid chromatography-mass spectrometry (LC-MS) measurement, we applied metabolic profiling, integrated with chemometric techniques, to explore the relationship between the metabolome and maturity of the sample in a non-biased way. For the multivariate statistical analyses, a partial least square (PLS) regression model was successfully created, which allowed us to accurately predict the maturity of the beans based on the metabolomic information. As a result, tryptophan was identified to be the best contributor to the regression model; the relative MS intensity of tryptophan was higher in immature beans than in those after the semi-mature stages in all arabica varieties investigated, demonstrating a universal discrimination factor for diverse arabica beans. Therefore, typtophan, either alone or together with other metabolites, may be utilized for traders as an assessment standard when purchasing qualified trading green arabica bean products. Furthermore, our results suggest that the tryptophan metabolism may be tightly linked to the development of coffee cherries and/or beans.

A liquid chromatography/electrospray ionisation tandem mass spectrometry method for the simultaneous quantification of salicylic, jasmonic and abscisic acids in Coffea arabica leaves.

Science.gov (United States)

de Sá, Marta; Ferreira, João P; Queiroz, Vagner T; Vilas-Boas, Luís; Silva, Maria C; Almeida, Maria H; Guerra-Guimarães, Leonor; Bronze, Maria R

2014-02-01

Plants have developed an efficient system of recognition that induces a complex network of signalling molecules such as salicylic acid (SA), jasmonic acid (JA) and abscisic acid (ABA) in case of a pathogenic infection. The use of specific and sensitive methods is mandatory for the analysis of compounds in these complex samples. In this study a liquid chromatography/electrospray ionisation tandem mass spectrometry method was developed and validated for the simultaneous quantification of SA, JA and ABA in Coffea arabica (L.) leaves in order to understand the role of these phytohormones in the signalling network involved in the coffee defence response against Hemileia vastatrix. The results showed that the method was specific, linear (r ≥ 0.99) in the range 0.125-1.00 µg mL⁻¹ for JA and ABA and 0.125-5.00 µg mL⁻¹ for SA, and precise (relative standard deviation ≤11%), and the limit of detection (0.010 µg g⁻¹ fresh weight) was adequate for quantifying these phytohormones in this type of matrix. In comparison with healthy leaves, those infected with H. vastatrix (resistance reaction) displayed an increase in SA level 24 h after inoculation, suggesting the involvement of an SA-dependent pathway in coffee resistance. © 2013 Society of Chemical Industry.

phiGENOME: an integrative navigation throughout bacteriophage genomes.

Science.gov (United States)

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

Genome Maps, a new generation genome browser.

Science.gov (United States)

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

Cuantificación de minerales K, Ca, Mg y P en pulpa y pergamino de café (Coffea arabica L. var. Typica

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Johanna Mendoza Abarca

2010-01-01

Full Text Available Se trabajó con muestras de café Coffea arabica L., variedad Typica de tres lugares en Ecuador: Palanda, Vilcabamba y El Pangui, seleccionados por su disponibilidad y condiciones geográficas. Se analizó potasio, calcio y magnesio por espectrofotometría de absorción atómica; y fósforo por espectrofotometría visible, utilizando en todos los casos la digestión ácida para la preparación de las muestras. Con el objetivo de mantener la trazabilidad de los residuos se realizó el beneficio húmedo del café. Los resultados obtenidos para la pulpa de café expresados en base seca fueron: K 3,1 ± 0,43 %; Ca 0,46 ± 0,06 %; Mg 0,14 ± 0,01 % y P 0,13 ± 0,01 %. Para pergamino de café: K 0,16 ± 0,02 %; Ca 0,14 ± 0,05 %; Mg 0,06 ± 0,01 % y P 0,02 ± 0,01 %. En adición, se determinaron los minerales en el grano de café. Con estos resultados podemos mencionar que la pulpa de café es una buena fuente de potasio (especialmente, magnesio y fósforo. El pergamino pudiera ser considerado como fuente de fósforo.

Purine alkaloid formation and CO2 gas exchange in dependence of development and of environmental factors in leaves of Coffea arabica L.

Science.gov (United States)

Frischknecht, P M; Eller, B M; Baumann, T W

1982-12-01

In the leaves of Coffea arabica L., purine alkaloid formation was estimated by analyzing the theobromine and caffeine content and by measuring the methylation rate of [2-(14)C]theobromine to [2-(14)C]caffeine in short-term experiments (6-24 h). At the same time, growth (in terms of dry weight and area), net photosynthesis (NPS), and dark respiration were determined. During leaf development, which was considered to be terminated when NPS was at a maximum (60-80 μmol g(-1) s(-1)) and dark respiration at a minimum (5-7.5 μmol g(-1) s(-1)), the content of theobromine and the velocity of caffeine formation were both found to decrease by a factor of more than 100. The close correlation between the theobromine content and the methylation rate is suspended when purine alkaloid formation is influenced by factors other than leaf development. Among these factors, temperature is the most effective: the velocity of caffeine biosynthesis is increased by raising the temperature and vice versa. Although the plants were well irrigated, a drastic decrease of NPS in the afternoon was observed under all environmental conditions tested. Light saturation was reached between 170-360 μmol m(-2) s(-1). The temperature optimum of NPS was shown to be very broad (24-33°C)m provided the adaptation time was sufficiently long.

Cuantificación de minerales K, Ca, Mg y P en pulpa y pergamino de café (Coffea arabica L. var. Typica

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Jorge Geovanny Figueroa Hurtado

2010-12-01

Full Text Available Se trabajó con muestras de café Coffea arabica L., variedad Typica de tres lugares en Ecuador: Palanda, Vilcabamba y El Pangui, seleccionados por su disponibilidad y condiciones geográficas. Se analizó potasio, calcio y magnesio por espectrofotometría de absorción atómica; y fósforo por espectrofotometría visible, utilizando en todos los casos la digestión ácida para la preparación de las muestras. Con el objetivo de mantener la trazabilidad de los residuos se realizó el beneficio húmedo del café. Los resultados obtenidos para la pulpa de café expresados en base seca fueron: K 3,1 ± 0,43 %; Ca 0,46 ± 0,06 %; Mg 0,14 ± 0,01 % y P 0,13 ± 0,01 %. Para pergamino de café: K 0,16 ± 0,02 %; Ca 0,14 ± 0,05 %; Mg 0,06 ± 0,01 % y P 0,02 ± 0,01 %. En adición, se determinaron los minerales en el grano de café. Con estos resultados podemos mencionar que la pulpa de café es una buena fuente de potasio (especialmente, magnesio y fósforo. El pergamino pudiera ser considerado como fuente de fósforo.

Genomics using the Assembly of the Mink Genome

DEFF Research Database (Denmark)

Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

2018-01-01

The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...

Visualization for genomics: the Microbial Genome Viewer.

NARCIS (Netherlands)

Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

2004-01-01

SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

Producción de café (Coffea arabica L. en respuesta al manejo específico de la fertilidad del suelo

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Luz Adriana Lince Salazar

2015-12-01

Full Text Available El estudio de la variabilidad espacial es el principal insumo para el manejo específico por sitio-MES, con fines de optimizar los recursos, al reducir los costos de producción de los cultivos y el impacto negativo sobre el ambiente. Con el objetivo de determinar el efecto del MES en la producción del café, durante los años 2011 y 2012 se realizó un experimento del manejo de la fertilidad del suelo en café (Coffea arabica L., Variedad Castillo® en lotes con áreas diferentes (1,0, 2,0 y 3,5 ha, ubicados en tres fincas del departamento del Quindío, Colombia. Se evaluó el efecto de tres tratamientos en la producción de café cereza: i testigo sin fertilización; ii manejo de acuerdo a los resultados de los análisis de suelo, logrados mediante un muestreo convencional en zigzag y, iii manejo por sitio específico conforme lo indicaron las áreas homogéneas, obtenidas mediante mapas de variabilidad espacial. En ninguno de los lotes hubo efecto de los tratamientos, respuesta que se relacionó con uno o más de los siguientes factores: tiempo relativamente corto de evaluación, fertilidad del suelo, reservas de los nutrientes en las plantas, y el número reducido de repeticiones (tres por tratamiento.

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

Family genome browser: visualizing genomes with pedigree information.

Science.gov (United States)

Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

2015-07-15

Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Storage of soil organic carbon in coffee (Coffea arabica L. production systems in the municipality of Líbano, Tolima, Colombia

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Hernán Jair Andrade Castañeda

2013-07-01

Full Text Available The increase in greenhouse gas emissions from anthropogenic sources has resulted in climate change, which affects all living beings. Coffee (Coffea arabica L. plantations, in monoculture or together with timber species such as salmwood (Cordia alliodora, mitigate climate change due to fixation of atmospheric CO2 that is deposited in biomass and soils. This study was carried out in the municipality of Líbano, Tolima, Colombia with the objective of defining which of the following coffee production systems store more soil organic carbon (SOC: 1 monoculture, 2 agroforestry systems (AFS with salmwood, and 3 AFS with plantain. Farms with those systems that are the most dominant in the study zone were selected. From each system, five repetitions were identified to be analyzed with a completely randomized design. In each plot or repetition, five samples for bulk density (BD using the cylinder method and a composite sample for concentration of SOC were taken and analyzed using the Walkley and Black approach. The systems of production did not significantly (p > 0.05 affect either the BD or the concentration of SOC. However, AFS with plantain tended to have less BD than monoculture and AFS with salmwood (0.83 ± 0.03 vs 0.88 ± 0.03 vs 0.92 ± 0.04 g·cm-3, respectively. These systems of production stored between 50 and 54 t·ha-1 of SOC in the top 30 cm, which indicates their capacity for climate change mitigation.

eGenomics: Cataloguing Our Complete Genome Collection III

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Dawn Field

2007-01-01

Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

Genomic Prediction from Whole Genome Sequence in Livestock: The 1000 Bull Genomes Project

DEFF Research Database (Denmark)

Hayes, Benjamin J; MacLeod, Iona M; Daetwyler, Hans D

Advantages of using whole genome sequence data to predict genomic estimated breeding values (GEBV) include better persistence of accuracy of GEBV across generations and more accurate GEBV across breeds. The 1000 Bull Genomes Project provides a database of whole genome sequenced key ancestor bulls....... In a dairy data set, predictions using BayesRC and imputed sequence data from 1000 Bull Genomes were 2% more accurate than with 800k data. We could demonstrate the method identified causal mutations in some cases. Further improvements will come from more accurate imputation of sequence variant genotypes...

ORGANIC CARBON AND TOTAL NITROGEN IN THE DENSIMETRIC FRACTIONS OF ORGANIC MATTER UNDER DIFFERENT SOIL MANAGEMEN

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MARCELO RIBEIRO VILELA PRADO

2016-01-01

Full Text Available The evaluation of land use and management by the measurement of soil organic matter and its fractions has gained attention since it helps in the understanding of the dynamics of their contribution to soil productivity, especially in tropical environments. This study was conducted in the municipality of Colorado do Oeste, state of Rondônia, Brazil and its aim was to determinethe quantity of organic carbon and total nitrogen in the light and heavy fractions of organic matter in the surface layers of a typic hapludalf under different land use systems: Native Forest: open evergreen forest, reference environment; Agroforestry System 1: teak (Tectona grandis LF and kudzu (Pueraria montana; Agroforestry System 2: coffee (Coffea canephora, marandu palisade grass (Brachiaria brizantha cv. Marandu, “pinho cuiabano” (Parkia multijuga, teak and kudzu.; Agroforestry System 3: teak and cocoa (Theobroma cacao; Silvopasture System: teak, cocoa and marandu palisade grass; and Extensive Grazing System: marandu palisade grass. The experimental design was a randomized block in split-split plots (use systems versus soil layers of 0-0.05 and 0.05-0.10 m with three replications. The results showed that relative to Native Forest, the Agroforestry System 2 had equal- and greater amounts of organic carbon and total nitrogen respectively (light and heavy fractions in the soil organic matter, with the light fraction being responsible for storage of approximately 45% and 70% of the organic carbon and total nitrogen, respectively. Therefore, the light densimetric fraction proved to be useful in the early identification of the general decline of the soil organic matter in the land use systems evaluated.

Respuesta fotosintética de Coffea arabica L. a diferentes niveles de luz y disponibilidad hídrica

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Yesid Alejandro Mariño

2014-04-01

Full Text Available El sombrío permite una mejor aclimatación del café (Coffea arabica L. en zonas donde el invierno se caracteriza por bajas temperaturas nocturnas seguido de días soleados y el verano, por altas temperaturas y lluvias ocasionales. En este estudio, realizado en Viçosa-MG, Brasil, se analizaron los efectos de dos condiciones de luminosidad (pleno sol y 15% de la radiación solar y disponibilidades de agua en el suelo sobre las relaciones hídricas y el desempeño fotosintético en C. arabica en dos épocas contrastantes. Independientemente de la época de evaluación, las plantas cultivadas en condiciones de baja disponibilidad hídrica presentaron reducciones en la fotosíntesis (A, conductancia estomática (g s y en la razón Ci/Ca en los dos tratamientos lumínicos. Estos cambios fueron acompañados con la reducción en la conductancia hidráulica y la transpiración. No se presentaron diferencias significativas en la producción cuántica efectiva, en el coeficiente de extinción no-fotoquímica y en la productividad cuántica basal de los procesos no fotoquímicos. Sobre la disponibilidad hídrica adecuada, las plantas cultivadas al sol presentaron reducciones en A, g s y Ci/Ca en la época de invierno. Adicionalmente, se encontraron limitaciones fotoquímicas con la reducción en la razón de las fluorescencias variable e inicial. Los resultados indican que cualquier recomendación de uso de sombrío como práctica de manejo debe ser tomada con precaución.

Genome U-Plot: a whole genome visualization.

Science.gov (United States)

Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

2018-05-15

The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

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Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

2016-12-01

The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Visualization for genomics: the Microbial Genome Viewer.

Science.gov (United States)

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Melhoramento do cafeeiro: XLII. Produtividade de progênies derivadas de hibridação dos cultivares Laurina e Mundo Novo Coffee breeding: XLII. Yield of progenies from crosses of Laurina and Mundo Novo cultivars of Coffea arabica L.

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Alcides Carvalho

1988-01-01

Full Text Available O cultivar Laurina de Coffea arabica L. caracteriza-se pelo pequeno porte, folhas de dimensões reduzidas, frutos afilados na base, sementes pequenas e afiladas, pequeno rendimento e reduzida produção. Apresenta, no entanto, bebida de boa qualidade e baixo teor de cafeína nas sementes. Suas principais características são controladas pela ação de um par de alelos recessivos lrlr, de acentuado efeito pleiotrópico. Devido ao atual interesse do comércio por produto de baixo teor de cafeína, iniciaram-se pesquisas tendo em vista principalmente aumentar a produtividade do 'Laurina'. Para esse fim, realizaram-se numerosas hibridações de cafeeiros do 'Laurina' com os do 'Mundo Novo' (Coffea arabica e, posteriormente, retrocruzamentos com o 'Mundo Novo'. Estudaram-se as progênies F2 e retrocruzamentos com o 'Mundo Novo' (RC em Campinas, em um experimento, anotando-se as produções por oito anos consecutivos. Separaram-se algumas progênies F2 em dois grupos, antes do plantio: normais (LrLr,Lrlr e laurina (Irlr. Como testemunhas, usaram-se progênies do 'Mundo Novo' e 'Catuaí Amarelo' de C. arabica. O conjunto de plantas F2 do grupo laurina e os retrocruzamentos tiveram produção média maior do que as plantas F2 normais, porém menor do que as testemunhas. Alguns retrocruzamentos e progênies F2 apresentaram plantas com razoável produtividade, indicando que, através de retrocruzamentos com o 'Mundo Novo', podem-se obter novos tipos comerciais com as características morfológicas do 'Laurina'. Fizeram-se considerações sobre a melhor capacidade de combinação do 'Laurina' com algumas seleções do 'Mundo Novo'.The Laurina cultivars of Coffea arabica L. has a reduced plant size, small leaves, small and pointed seeds and low yield capacity. However the seeds have a good cup quality and the desirable characteristic of low caffeine content The Laurina phenotype is supposed to be controlled by a pair of recessive alleles lrlr, with

The Sequenced Angiosperm Genomes and Genome Databases.

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Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

GenColors-based comparative genome databases for small eukaryotic genomes.

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Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

2013-01-01

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

Science.gov (United States)

Manolio, Teri A

2016-10-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. Published by Elsevier Ireland Ltd.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

Science.gov (United States)

Machado, Henrique; Gram, Lone

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

Rodent malaria parasites : genome organization & comparative genomics

NARCIS (Netherlands)

Kooij, Taco W.A.

2006-01-01

The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

Environ: E00843 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available E00843 Coffee ... Coffea ... Beverage of Rubiaceae (madder family) Coffea seed roasted,... ground, and extracted with hot water or cold water CYP1A2 inhibitor [HSA:1544] (Coffee contains Caffeine [DR:D00528] that inhibits CYP1A2.) ...

ASPECTOS ESTRUTURAIS DE CAFEEIRO INFECTADO COM XYLELLA FASTIDIOSA

Directory of Open Access Journals (Sweden)

RACHEL BENETTI QUEIROZ-VOLTAN

1998-01-01

Full Text Available Estudaram-se as alterações anatômicas em folhas e caules de ramos de cafeeiros infectados com X. fastidiosa visando compreender as causas dos seus distúrbios fisiológicos. Analisaram-se amostras dos cultivares comerciais de Coffea arabica L. - Catuaí Vermelho IAC H 2077-25-81 e Mundo Novo 515-20 enxertados sobre a progênie IAC 2258 de C. canephora - e de Catuaí Vermelho IAC H 2077-25-81 sem enxertia (pé franco. As amostras foram coletadas no campo, no Núcleo Experimental de Campinas, IAC, em cafezais onde foi detectada a presença da bactéria. Analisou-se também a estrutura da folha e do caule de ramos com e sem sintomas visuais da bactéria, sendo estimada a porcentagem de obstrução dos vasos do xilema do caule. Os ramos infectados apresentaram um encurtamento dos entrenós e, com o agravamento da doença, senescência foliar precoce na sua base, resultando em pequeno número de folhas no ápice. O número e a posição dos ramos por indivíduo com tais sintomas variaram entre as plantas, sendo mais freqüentes na região basal. Esses ramos também mostraram pecíolos e área foliar reduzidos e frutos menores e agrupados, em vista de um encurtamento dos pedicelos e dos entrenós, além de uma deposição de "goma" nos vasos do xilema do caule, pecíolo e folha, assim como divisões celulares anormais no xilema, floema e córtex daquelas partes. As células do mesofilo das folhas afetadas apresentaram número reduzido de cloroplastos, associado a maior concentração de cristais de oxalato de cálcio. Sugere-se que a presença da bactéria esteja induzindo a senescência foliar que se relaciona a um ou mais fatores de estresse.Leaf and stem anatomical changes were studied in coffee plants infected with X. fastidiosa looking for the causes of the observed physiological disturbances. Samples of commercial cultivars of Coffea arabica L. were analysed - Catuaí Vermelho IAC H 2077-25-81 and Mundo Novo 515-20 grafted on the progenie IAC

Genome size analyses of Pucciniales reveal the largest fungal genomes.

Science.gov (United States)

Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

Direct somatic embryogenesis in coffea arabica L. CVS. caturra and catuaí: effect of triacontanol, light condition, and medium consistency

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Andrés M. Gatica

2008-01-01

Full Text Available Se investigó la influencia de la concentración de triacontanol (TRIA y su interacción con el ácido indolacético (AIA en la inducción de la embriogénesis somática directa en Coffea arabica L. cvs. Caturra y Catuaí. Adicionalmente, se evaluó el efecto de la condición de la luz y de la consistencia del medio de cultivo (semisólido vs. líquido. Se determinó que la mayor cantidad de embriones somáticos por explante fue de 3,9±0,5 en Caturra y 3,6±0,5 en Catuaí, en el medio de cultivo Murashige y Skoog (1962 al 50%, complementado con BAP (1,1 µM, IAA (2,85 µM y TRIA (4,55 µM. Para la consistencia del medio, la mayor cantidad de embriones somáticos en Caturra (3,2±0,2 y Catuaí (6,0±0,4 se obtuvo con el medio semisólido de Yasuda et al. (1985. En Catuaí, la mayor cantidad de embrioides se obtuvo con 16 h luz (7,6±1,0 y oscuridad (6,2±0,6 y para Caturra, con oscuridad (4,2±0,4 y 16 h luz (3,8±0,5. No se observó la formación de embriones somáticos en los explantes de Caturra y Catuaí después de 12 semanas de cultivo, en el medio líquido descrito por Yasuda et al. (1985 ni bajo ninguna de las condiciones de luz.

RPAN: rice pan-genome browser for ∼3000 rice genomes.

Science.gov (United States)

Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

2017-01-25

A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

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CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific t...

Genomics Portals: integrative web-platform for mining genomics data.

Science.gov (United States)

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

2010-01-13

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

i-Genome: A database to summarize oligonucleotide data in genomes

Directory of Open Access Journals (Sweden)

Chang Yu-Chung

2004-10-01

Full Text Available Abstract Background Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming. Results The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes. Conclusions This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes.

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics1[C][W

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F.X.; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-01-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species. PMID:23184232

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute’s genomic medicine portfolio

Science.gov (United States)

Manolio, Teri A.

2016-01-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual’s genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of “Genomic Medicine Meetings,” under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and diffficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI’s genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. PMID:27612677

Producción de café (Coffea Arabica L. en respuesta al manejo específico por sitio de la fertilidad del suelo

Directory of Open Access Journals (Sweden)

Luz Adriana Lince Salazar

2016-12-01

Full Text Available El estudio de la variabilidad espacial es el principal insumo para el manejo específico por sitio MES, con el fin de optimizar los recursos, al reducir los costos de producción de los cultivos y el impacto negativo sobre el ambiente. Con el objetivo de determinar el efecto del MES en la producción del café, durante los años 2011 y 2012 se realizó un experimento del manejo de la fertilidad del suelo en café (Coffea arabica L., Variedad Castillo® en lotes con áreas diferentes (1,0, 2,0 y 3,5 ha, ubicados en tres fincas del departamento del Quindío, Colombia. Se evaluó el efecto de tres tratamientos en la producción de café cereza: i testigo sin fertilización; ii manejo de acuerdo a los resultados de los análisis de suelo, logrados mediante un muestreo convencional en zigzag y, iii manejo por sitio específico conforme lo indicaron las áreas homogéneas, obtenidas mediante mapas de variabilidad espacial. En ninguno de los lotes hubo efecto de los tratamientos, respuesta que se relacionó con uno o más de los siguientes factores: tiempo relativamente corto de evaluación, fertilidad del suelo, reservas de los nutrientes en las plantas, y el número reducido de repeticiones (tres por tratamiento.

Comparing Mycobacterium tuberculosis genomes using genome topology networks.

Science.gov (United States)

Jiang, Jianping; Gu, Jianlei; Zhang, Liang; Zhang, Chenyi; Deng, Xiao; Dou, Tonghai; Zhao, Guoping; Zhou, Yan

2015-02-14

Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. In this work, we introduce a 'Genome Topology Network' (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of 'unfixed ortholog' has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/ , and allows re-annotating the 'lost' genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes

A universal genomic coordinate translator for comparative genomics.

Science.gov (United States)

Zamani, Neda; Sundström, Görel; Meadows, Jennifer R S; Höppner, Marc P; Dainat, Jacques; Lantz, Henrik; Haas, Brian J; Grabherr, Manfred G

2014-06-30

Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across

Genomics Portals: integrative web-platform for mining genomics data

Directory of Open Access Journals (Sweden)

Ghosh Krishnendu

2010-01-01

Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

Evaluation of biocontrol ability of native strains of Trichoderma spp on Rhizoctonia and Fusarium sp in coffee (Coffea arabica in experimental conditions

Directory of Open Access Journals (Sweden)

Nina Rudy

2016-06-01

Full Text Available Due to the indiscriminate use agrochemicals in conventional agriculture, it is causing pollution problems in the environment (soil, air and water, hence the search for alternatives that contribute to agricultural production by agro-chemical free sustainable production. This paper studies the biological control of damping off in coffee (Coffea arabica by applying antagonistic fungus Trichoderma sp. Under experimental conditions at laboratory facilities of the Academic Unit Carmen Pampa Campesina, a community of Carmen Pampa, Township Coroico. The aim of this study was to biologically control the "damping off", they found two genera that cause damping off in seedbed of coffee: Rhizoctonia sp. and Fusarium sp.To determine the percentage of growth and control in the culture medium, we used the method of counting quarters, where they gave the mycelial growth of antagonistic fungus Trichoderma sp., And the fungal pathogens Rhizoctonia sp. and Fusarium sp. Statistically there was a highly significant difference in the variable growth rate of Trichoderma sp. on pathogenic fungi Rhizoctonia sp. and Fusarium sp. at 3, 6 and 9 days that announces the time factor and treatments are interdependent. The control variable showed a highly significant difference in the time factor and treatment, but the interaction shows no significant difference this makes known factors that are independent, so the fungus Trichoderma sp. not depend on time in treatment, thus showing its inhibitory power to Rhizoctonia sp. and Fusarium sp .. This test gives references that there is antagonistic fungus control on the fungal pathogens Rhizoctonia sp. and Fusarium sp.

Genomic selection: genome-wide prediction in plant improvement.

Science.gov (United States)

Desta, Zeratsion Abera; Ortiz, Rodomiro

2014-09-01

Association analysis is used to measure relations between markers and quantitative trait loci (QTL). Their estimation ignores genes with small effects that trigger underpinning quantitative traits. By contrast, genome-wide selection estimates marker effects across the whole genome on the target population based on a prediction model developed in the training population (TP). Whole-genome prediction models estimate all marker effects in all loci and capture small QTL effects. Here, we review several genomic selection (GS) models with respect to both the prediction accuracy and genetic gain from selection. Phenotypic selection or marker-assisted breeding protocols can be replaced by selection, based on whole-genome predictions in which phenotyping updates the model to build up the prediction accuracy. Copyright © 2014 Elsevier Ltd. All rights reserved.

OryzaGenome: Genome Diversity Database of Wild Oryza Species

KAUST Repository

Ohyanagi, Hajime

2015-11-18

The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/ scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

Energy Technology Data Exchange (ETDEWEB)

McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L.; dePamphilis, Claude W.

2005-08-26

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.

Grass genomes

OpenAIRE

Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

1998-01-01

For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

Science.gov (United States)

Smith, David Roy

2017-05-01

Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise. This increase is largely because some journals have created a new category of manuscript called genome reports, which are short, fast-tracked papers describing a chromosome sequence(s), its GenBank accession number and little else. In 2015, for example, more than 2000 genome reports were published, and 2016 is poised to bring even more. Here, I highlight the growing popularity of genome reports and discuss their merits, drawbacks and impact on science and the academic publication infrastructure. Genome reports can be excellent assets for the research community, but they are also being used as quick and easy routes to a publication, and in some instances they are not peer reviewed. One of the best arguments for genome reports is that they are a citable, user-generated genomic resource providing essential methodological and biological information, which may not be present in the sequence database. But they are expensive and time-consuming avenues for achieving such a goal. © The Author 2016. Published by Oxford University Press.

Genome update: the 1000th genome - a cautionary tale

DEFF Research Database (Denmark)

Lagesen, Karin; Ussery, David; Wassenaar, Gertrude Maria

2010-01-01

conclusions for example about the largest bacterial genome sequenced. Biological diversity is far greater than many have thought. For example, analysis of multiple Escherichia coli genomes has led to an estimate of around 45 000 gene families more genes than are recognized in the human genome. Moreover......There are now more than 1000 sequenced prokaryotic genomes deposited in public databases and available for analysis. Currently, although the sequence databases GenBank, DNA Database of Japan and EMBL are synchronized continually, there are slight differences in content at the genomes level...... for a variety of logistical reasons, including differences in format and loading errors, such as those caused by file transfer protocol interruptions. This means that the 1000th genome will be different in the various databases. Some of the data on the highly accessed web pages are inaccurate, leading to false...

Diversity and communities of foliar endophytic fungi from different agroecosystems of Coffea arabica L. in two regions of Veracruz, Mexico.

Science.gov (United States)

Saucedo-García, Aurora; Anaya, Ana Luisa; Espinosa-García, Francisco J; González, María C

2014-01-01

Over the past 20 years, the biodiversity associated with shaded coffee plantations and the role of diverse agroforestry types in biodiversity conservation and environmental services have been topics of debate. Endophytic fungi, which are microorganisms that inhabit plant tissues in an asymptomatic manner, form a part of the biodiversity associated with coffee plants. Studies on the endophytic fungi communities of cultivable host plants have shown variability among farming regions; however, the variability in fungal endophytic communities of coffee plants among different coffee agroforestry systems is still poorly understood. As such, we analyzed the diversity and communities of foliar endophytic fungi inhabiting Coffea arabica plants growing in the rustic plantations and simple polycultures of two regions in the center of Veracruz, Mexico. The endophytic fungi isolates were identified by their morphological traits, and the majority of identified species correspond to species of fungi previously reported as endophytes of coffee leaves. We analyzed and compared the colonization rates, diversity, and communities of endophytes found in the different agroforestry systems and in the different regions. Although the endophytic diversity was not fully recovered, we found differences in the abundance and diversity of endophytes among the coffee regions and differences in richness between the two different agroforestry systems of each region. No consistent pattern of community similarity was found between the coffee agroforestry systems, but we found that rustic plantations shared the highest number of morphospecies. The results suggest that endophyte abundance, richness, diversity, and communities may be influenced predominantly by coffee region, and to a lesser extent, by the agroforestry system. Our results contribute to the knowledge of the relationships between agroforestry systems and biodiversity conservation and provide information regarding some endophytic fungi and

Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy.

Science.gov (United States)

Rittmann, Bruce E; Krajmalnik-Brown, Rosa; Halden, Rolf U

2008-08-01

Microorganisms can produce renewable energy in large quantities and without damaging the environment or disrupting food supply. The microbial communities must be robust and self-stabilizing, and their essential syntrophies must be managed. Pre-genomic, genomic and post-genomic tools can provide crucial information about the structure and function of these microbial communities. Applying these tools will help accelerate the rate at which microbial bioenergy processes move from intriguing science to real-world practice.

Genome Surfing As Driver of Microbial Genomic Diversity.

Science.gov (United States)

Choudoir, Mallory J; Panke-Buisse, Kevin; Andam, Cheryl P; Buckley, Daniel H

2017-08-01

Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Deep whole-genome sequencing of 90 Han Chinese genomes.

Science.gov (United States)

Lan, Tianming; Lin, Haoxiang; Zhu, Wenjuan; Laurent, Tellier Christian Asker Melchior; Yang, Mengcheng; Liu, Xin; Wang, Jun; Wang, Jian; Yang, Huanming; Xu, Xun; Guo, Xiaosen

2017-09-01

Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants. Although whole-exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole-genome sequencing data are limited for any population, and a large amount of low-frequency, population-specific variants remain uncharacterized. We have performed whole-genome sequencing at a high depth (∼×80) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genomes Project samples, including 45 Northern Han Chinese and 45 Southern Han Chinese samples. Eighty-three of these 90 have been sequenced by the 1000 Genomes Project. We have identified 12 568 804 single nucleotide polymorphisms, 2 074 210 short InDels, and 26 142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7 000 629 novel variants with low frequency (defined as minor allele frequency genome. Compared to the 1000 Genomes Project, these Han Chinese deep sequencing data enhance the characterization of a large number of low-frequency, novel variants. This will be a valuable resource for promoting Chinese genetics research and medical development. Additionally, it will provide a valuable supplement to the 1000

Fungal Genomics Program

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor

2012-03-12

The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

Comparative Genome Analysis and Genome Evolution

NARCIS (Netherlands)

Snel, Berend

2002-01-01

This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

Genome projects and the functional-genomic era.

Science.gov (United States)

Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans

2005-12-01

The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.

A Feasibility Study of Public Private Partnership in Sustainable ...

African Journals Online (AJOL)

The rainforests of the south western Ethiopian highlands are recognised as the birthplace of Coffea arabica. Ethiopia is the only country in the world where Coffea Arabica (L.) can be found in the wild. The forests that once dominated the highlands are considerably diminished during the last decades. This poses a massive ...

GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

Science.gov (United States)

Yuan, Lina; Yu, Yang; Zhu, Yanmin; Li, Yulai; Li, Changqing; Li, Rujiao; Ma, Qin; Siu, Gilman Kit-Hang; Yu, Jun; Jiang, Taijiao; Xiao, Jingfa; Kang, Yu

2017-01-25

Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa. GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.

The Perennial Ryegrass GenomeZipper – Targeted Use of Genome Resources for Comparative Grass Genomics

DEFF Research Database (Denmark)

Pfeiffer, Matthias; Martis, Mihaela; Asp, Torben

2013-01-01

(Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold......Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass...... to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous...

Population Genomics of Infectious and Integrated Wolbachia pipientis Genomes in Drosophila ananassae

Science.gov (United States)

Choi, Jae Young; Bubnell, Jaclyn E.; Aquadro, Charles F.

2015-01-01

Coevolution between Drosophila and its endosymbiont Wolbachia pipientis has many intriguing aspects. For example, Drosophila ananassae hosts two forms of W. pipientis genomes: One being the infectious bacterial genome and the other integrated into the host nuclear genome. Here, we characterize the infectious and integrated genomes of W. pipientis infecting D. ananassae (wAna), by genome sequencing 15 strains of D. ananassae that have either the infectious or integrated wAna genomes. Results indicate evolutionarily stable maternal transmission for the infectious wAna genome suggesting a relatively long-term coevolution with its host. In contrast, the integrated wAna genome showed pseudogene-like characteristics accumulating many variants that are predicted to have deleterious effects if present in an infectious bacterial genome. Phylogenomic analysis of sequence variation together with genotyping by polymerase chain reaction of large structural variations indicated several wAna variants among the eight infectious wAna genomes. In contrast, only a single wAna variant was found among the seven integrated wAna genomes examined in lines from Africa, south Asia, and south Pacific islands suggesting that the integration occurred once from a single infectious wAna genome and then spread geographically. Further analysis revealed that for all D. ananassae we examined with the integrated wAna genomes, the majority of the integrated wAna genomic regions is represented in at least two copies suggesting a double integration or single integration followed by an integrated genome duplication. The possible evolutionary mechanism underlying the widespread geographical presence of the duplicate integration of the wAna genome is an intriguing question remaining to be answered. PMID:26254486

Dramatic improvement in genome assembly achieved using doubled-haploid genomes.

Science.gov (United States)

Zhang, Hong; Tan, Engkong; Suzuki, Yutaka; Hirose, Yusuke; Kinoshita, Shigeharu; Okano, Hideyuki; Kudoh, Jun; Shimizu, Atsushi; Saito, Kazuyoshi; Watabe, Shugo; Asakawa, Shuichi

2014-10-27

Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.

Cancer genomics

DEFF Research Database (Denmark)

Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

2007-01-01

Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

Personal genomics services: whose genomes?

Science.gov (United States)

Gurwitz, David; Bregman-Eschet, Yael

2009-07-01

New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

Insights into structural variations and genome rearrangements in prokaryotic genomes.

Science.gov (United States)

Periwal, Vinita; Scaria, Vinod

2015-01-01

Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Parasite Genome Projects and the Trypanosoma cruzi Genome Initiative

Directory of Open Access Journals (Sweden)

Wim Degrave

1997-11-01

Full Text Available Since the start of the human genome project, a great number of genome projects on other "model" organism have been initiated, some of them already completed. Several initiatives have also been started on parasite genomes, mainly through support from WHO/TDR, involving North-South and South-South collaborations, and great hopes are vested in that these initiatives will lead to new tools for disease control and prevention, as well as to the establishment of genomic research technology in developing countries. The Trypanosoma cruzi genome project, using the clone CL-Brener as starting point, has made considerable progress through the concerted action of more than 20 laboratories, most of them in the South. A brief overview of the current state of the project is given

Short and long-term genome stability analysis of prokaryotic genomes.

Science.gov (United States)

Brilli, Matteo; Liò, Pietro; Lacroix, Vincent; Sagot, Marie-France

2013-05-08

Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on the other, insertions and deletions leave the backbone gene order unchanged but they alter the gene neighborhoods by breaking the syntenic regions. A complete picture about genome organization evolution therefore requires to account for both kinds of events. We developed an approach where we model chromosomes as graphs on which we compute different stability estimators; we consider genome rearrangements as well as the effect of gene insertions and deletions. In a first part of the paper, we fit a measure of backbone gene order conservation (hereinafter called backbone stability) against phylogenetic distance for over 3000 genome comparisons, improving existing models for the divergence in time of backbone stability. Intra- and inter-specific comparisons were treated separately to focus on different time-scales. The use of multiple genomes of a same species allowed to identify genomes with diverging gene order with respect to their conspecific. The inter-species analysis indicates that pathogens are more often unstable with respect to non-pathogens. In a second part of the text, we show that in pathogens, gene content dynamics (insertions and deletions) have a much more dramatic effect on genome organization stability than backbone rearrangements. In this work, we studied genome organization divergence taking into account the contribution of both genome order rearrangements and genome content dynamics. By studying species with multiple sequenced genomes available, we were

Genomic Data Commons and Genomic Cloud Pilots - Google Hangout

Science.gov (United States)

Join us for a live, moderated discussion about two NCI efforts to expand access to cancer genomics data: the Genomic Data Commons and Genomic Cloud Pilots. NCI subject matters experts will include Louis M. Staudt, M.D., Ph.D., Director Center for Cancer Genomics, Warren Kibbe, Ph.D., Director, NCI Center for Biomedical Informatics and Information Technology, and moderated by Anthony Kerlavage, Ph.D., Chief, Cancer Informatics Branch, Center for Biomedical Informatics and Information Technology. We welcome your questions before and during the Hangout on Twitter using the hashtag #AskNCI.

The genomes and comparative genomics of Lactobacillus delbrueckii phages.

Science.gov (United States)

Riipinen, Katja-Anneli; Forsman, Päivi; Alatossava, Tapani

2011-07-01

Lactobacillus delbrueckii phages are a great source of genetic diversity. Here, the genome sequences of Lb. delbrueckii phages LL-Ku, c5 and JCL1032 were analyzed in detail, and the genetic diversity of Lb. delbrueckii phages belonging to different taxonomic groups was explored. The lytic isometric group b phages LL-Ku (31,080 bp) and c5 (31,841 bp) showed a minimum nucleotide sequence identity of 90% over about three-fourths of their genomes. The genomic locations of their lysis modules were unique, and the genomes featured several putative overlapping transcription units of genes. LL-Ku and c5 virions displayed peptidoglycan hydrolytic activity associated with a ~36-kDa protein similar in size to the endolysin. Unexpectedly, the 49,433-bp genome of the prolate phage JCL1032 (temperate, group c) revealed a conserved gene order within its structural genes. Lb. delbrueckii phages representing groups a (a phage LL-H), b and c possessed only limited protein sequence homology. Genomic comparison of LL-Ku and c5 suggested that diversification of Lb. delbrueckii phages is mainly due to insertions, deletions and recombination. For the first time, the complete genome sequences of group b and c Lb. delbrueckii phages are reported.

Crecimiento de café (Coffea arabica L. durante la etapa de almácigo en respuesta a la salinidad generada por fertilizantes

Directory of Open Access Journals (Sweden)

Siavosh Sadeghian Khalajabadi

2014-12-01

Full Text Available La salinidad del suelo puede afectar negativamente el crecimiento de las plantas, e incluso causar su muerte. Esta investigación tuvo como propósito, determinar el efecto de la salinidad generada por fertilizantes en el crecimiento de café Coffea arabica L. durante la etapa de almácigo. Se recolectaron muestras de suelo en dos Estaciones Experimentales (EE de Cenicafé (Naranjal en Caldas y Timbío en Cauca y una finca cafetera (FC en Jamundí (Valle del Cauca. Bajo el diseño completamente aleatorio se evaluó para cada suelo la respuesta de café variedad Caturra a 27 tratamientos (factorial 33, resultantes de tres dosis de calcio-Ca, de magnesio-Mg y de potasio-K (0, 1 y 3 g dm-3 de suelo, empleando como fuentes sulfatos. La conductividad eléctrica (C.E., como indicador de la salinidad, se incrementó en conformidad a las dosis, con valores más altos para el Mg, seguido por K y Ca, resultado que se relacionó principalmente con el índice de salinidad de los fertilizantes y su solubilidad. Las diferencias de la C.E. entre las localidades (EE Naranjal>EE Timbío>FC Jamundí se atribuyeron a la capacidad de éstos para retener la humedad. Conforme al aumento de la salinidad disminuyó el peso de las plantas, hasta causar síntomas de toxicidad y posterior muerte. El nivel crítico de la C.E., calculado para el 90% del crecimiento relativo, correspondió en promedio a 1,1 dS m-1.

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

Science.gov (United States)

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

DEFF Research Database (Denmark)

Machado, Henrique; Gram, Lone

2017-01-01

was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.......Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...

SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

Directory of Open Access Journals (Sweden)

Kim Seungill

2008-12-01

Full Text Available Abstract Background Since the full genome sequences of Saccharomyces cerevisiae were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed. Results The Seoul National University Genome Browser (SNUGB integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets and 34 plant and animal (38 datasets species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion. Conclusion The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site http://genomebrowser.snu.ac.kr/.

Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

Energy Technology Data Exchange (ETDEWEB)

Kuo, Alan; Grigoriev, Igor

2009-04-17

Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

Arbuscular mycorrhiza alters metal uptake and the physiological response of Coffea arabica seedlings to increasing Zn and Cu concentrations in soil.

Science.gov (United States)

Andrade, S A L; Silveira, A P D; Mazzafera, P

2010-10-15

Studies on mycorrhizal symbiosis effects on metal accumulation and plant tolerance are not common in perennial crops under metal stress. The objective of this study was to evaluate the influence of mycorrhization on coffee seedlings under Cu and Zn stress. Copper (Cu) and zinc (Zn) uptake and some biochemical and physiological traits were studied in thirty-week old Coffea arabica seedlings, in response to the inoculation with arbuscular mycorrhizal fungi (AMF) and to increasing concentrations of Cu or Zn in soil. The experiments were conducted under greenhouse conditions in a 2×4 factorial design (inoculation or not with AMF and 0, 50, 150 and 450mgkg(-1) Cu or 0, 100, 300 and 900mgkg(-1) Zn). Non-mycorrhizal plants maintained a hampered and slow growth even in a soil with appropriate phosphorus (P) levels for this crop. As metal levels increased in soil, a greater proportion of the total absorbed metals were retained by roots. Foliar Cu concentrations increased only in non-mycorrhizal plants, reaching a maximum concentration of 30mgkg(-1) at the highest Cu in soil. Mycorrhization prevented the accumulation of Cu in leaves, and mycorrhizal plants showed higher Cu contents in stems, which indicated a differential Cu distribution in AMF-associated or non-associated plants. Zn distribution and concentrations in different plant organs followed a similar pattern independently of mycorrhization. In mycorrhizal plants, only the highest metal concentrations caused a reduction in biomass, leading to significant changes in some biochemical indicators, such as malondialdehyde, proline and amino acid contents in leaves and also in foliar free amino acid composition. Marked differences in these physiological traits were also found due to mycorrhization. In conclusion, AMF protected coffee seedlings against metal toxicity. Copyright © 2010 Elsevier B.V. All rights reserved.

Impacts of leaf age and heat stress duration on photosynthetic gas exchange and foliar nonstructural carbohydrates in Coffea arabica.

Science.gov (United States)

Marias, Danielle E; Meinzer, Frederick C; Still, Christopher

2017-02-01

Given future climate predictions of increased temperature, and frequency and intensity of heat waves in the tropics, suitable habitat to grow ecologically, economically, and socially valuable Coffea arabica is severely threatened. We investigated how leaf age and heat stress duration impact recovery from heat stress in C. arabica . Treated plants were heated in a growth chamber at 49°C for 45 or 90 min. Physiological recovery was monitored in situ using gas exchange, chlorophyll fluorescence (the ratio of variable to maximum fluorescence, F V / F M ), and leaf nonstructural carbohydrate (NSC) on mature and expanding leaves before and 2, 15, 25, and 50 days after treatment. Regardless of leaf age, the 90-min treatment resulted in greater F V / F M reduction 2 days after treatment and slower recovery than the 45-min treatment. In both treatments, photosynthesis of expanding leaves recovered more slowly than in mature leaves. Stomatal conductance ( g s ) decreased in expanding leaves but did not change in mature leaves. These responses led to reduced intrinsic water-use efficiency with increasing heat stress duration in both age classes. Based on a leaf energy balance model, aftereffects of heat stress would be exacerbated by increases in leaf temperature at low g s under full sunlight where C. arabica is often grown, but also under partial sunlight. Starch and total NSC content of the 45-min group significantly decreased 2 days after treatment and then accumulated 15 and 25 days after treatment coinciding with recovery of photosynthesis and F V / F M . In contrast, sucrose of the 90-min group accumulated at day 2 suggesting that phloem transport was inhibited. Both treatment group responses contrasted with control plant total NSC and starch, which declined with time associated with subsequent flower and fruit production. No treated plants produced flowers or fruits, suggesting that short duration heat stress can lead to crop failure.

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria.

Science.gov (United States)

Zhao, Meicheng; Zhi, Hui; Doust, Andrew N; Li, Wei; Wang, Yongfang; Li, Haiquan; Jia, Guanqing; Wang, Yongqiang; Zhang, Ning; Diao, Xianmin

2013-04-11

The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide. GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus. Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC'C'. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The

Genome-derived vaccines.

Science.gov (United States)

De Groot, Anne S; Rappuoli, Rino

2004-02-01

Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

JGI Fungal Genomics Program

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor V.

2011-03-14

Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

Genomic Encyclopedia of Fungi

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor

2012-08-10

Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

The Genomic Code: Genome Evolution and Potential Applications

KAUST Repository

Bernardi, Giorgio

2016-01-25

The genome of metazoans is organized according to a genomic code which comprises three laws: 1) Compositional correlations hold between contiguous coding and non-coding sequences, as well as among the three codon positions of protein-coding genes; these correlations are the consequence of the fact that the genomes under consideration consist of fairly homogeneous, long (≥200Kb) sequences, the isochores; 2) Although isochores are defined on the basis of purely compositional properties, GC levels of isochores are correlated with all tested structural and functional properties of the genome; 3) GC levels of isochores are correlated with chromosome architecture from interphase to metaphase; in the case of interphase the correlation concerns isochores and the three-dimensional “topological associated domains” (TADs); in the case of mitotic chromosomes, the correlation concerns isochores and chromosomal bands. Finally, the genomic code is the fourth and last pillar of molecular biology, the first three pillars being 1) the double helix structure of DNA; 2) the regulation of gene expression in prokaryotes; and 3) the genetic code.

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

Directory of Open Access Journals (Sweden)

Wasnick Michael

2008-03-01

Full Text Available Abstract Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any

The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.

Science.gov (United States)

Mao, Qing; Ciotlos, Serban; Zhang, Rebecca Yu; Ball, Madeleine P; Chin, Robert; Carnevali, Paolo; Barua, Nina; Nguyen, Staci; Agarwal, Misha R; Clegg, Tom; Connelly, Abram; Vandewege, Ward; Zaranek, Alexander Wait; Estep, Preston W; Church, George M; Drmanac, Radoje; Peters, Brock A

2016-10-11

Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics' standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data. These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.

Brief Guide to Genomics: DNA, Genes and Genomes

Science.gov (United States)

... clinic. Most new drugs based on genome-based research are estimated to be at least 10 to 15 years away, though recent genome-driven efforts in lipid-lowering therapy have considerably shortened that interval. According ...

MIPS plant genome information resources.

Science.gov (United States)

Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

2007-01-01

The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

Ensembl Genomes 2013: scaling up access to genome-wide data.

Science.gov (United States)

Kersey, Paul Julian; Allen, James E; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Hughes, Daniel Seth Toney; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Langridge, Nicholas; McDowall, Mark D; Maheswari, Uma; Maslen, Gareth; Nuhn, Michael; Ong, Chuang Kee; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Tuli, Mary Ann; Walts, Brandon; Williams, Gareth; Wilson, Derek; Youens-Clark, Ken; Monaco, Marcela K; Stein, Joshua; Wei, Xuehong; Ware, Doreen; Bolser, Daniel M; Howe, Kevin Lee; Kulesha, Eugene; Lawson, Daniel; Staines, Daniel Michael

2014-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

Toward genome-enabled mycology.

Science.gov (United States)

Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

2013-01-01

Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

Plantagora: modeling whole genome sequencing and assembly of plant genomes.

Directory of Open Access Journals (Sweden)

Roger Barthelson

Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

Science.gov (United States)

Puigbò, Pere; Lobkovsky, Alexander E; Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

2014-08-21

Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species. We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes. Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.

A Web-Based Comparative Genomics Tutorial for Investigating Microbial Genomes

Directory of Open Access Journals (Sweden)

Michael Strong

2009-12-01

Full Text Available As the number of completely sequenced microbial genomes continues to rise at an impressive rate, it is important to prepare students with the skills necessary to investigate microorganisms at the genomic level. As a part of the core curriculum for first-year graduate students in the biological sciences, we have implemented a web-based tutorial to introduce students to the fields of comparative and functional genomics. The tutorial focuses on recent computational methods for identifying functionally linked genes and proteins on a genome-wide scale and was used to introduce students to the Rosetta Stone, Phylogenetic Profile, conserved Gene Neighbor, and Operon computational methods. Students learned to use a number of publicly available web servers and databases to identify functionally linked genes in the Escherichia coli genome, with emphasis on genome organization and operon structure. The overall effectiveness of the tutorial was assessed based on student evaluations and homework assignments. The tutorial is available to other educators at http://www.doe-mbi.ucla.edu/~strong/m253.php.

Embryogenic potential and the expression of arabinogalactanproteins (AGPs in embryogenic cell aggregates of Coffea arabica cv. Caturra rojo under influence of CO2

Directory of Open Access Journals (Sweden)

Raúl Barbón

2002-07-01

Full Text Available The establishment and optimization of regeneration systems via somatic embryogenesis has centered traditionally on the study of the culture medium components, with little attention to other factors of the in vitro environment like the composition of the gaseous atmosphere. This work was realized with the aim to determine the embryogenic potential and the expression of arabinogalactanproteins (AGPs in embryogenic cell aggregates of Coffea arabica cv. Caturra Rojo under influence of carbon dioxide (CO2. Concentrations of 2.5% and 5.0% of CO2 stimulated a greater formation of somatic embryos (307 ES/50mgMF and 277 ES/50mgMF respectively in semisolid culture medium with better results to the controls with passive interchange and forced ventilation (195 ES/50mgMF and 107 ES/50mgMF whereas a concentration of 10.0% of CO2 inhibited the process of somatic embryogenesis (95 ES/50mgMF. In cell suspensions the formation of somatic embryos was greater with a concentration of 2.5% of CO2 (130x103 ES.l-1 in comparison with 5.0% and 10.0% of CO2 (116x103 ESl-1 and 15x103 ES.l-1 and the controls with passive interchange and forced ventilation. With a concentration of 2.5% CO2 there was a greater synthesis of Arabinogalactanproteins (AGPs at the cellular level (0.068 mg.gMF-1 and the excretion in the culture medium (2.10 mg.l-1, which coincided with the highest values of production of somatic embryos. Key Words: embryogenic cell suspensions, in vitro environment, molecular markers, somatic embryo, somatic embryogenesis

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

Science.gov (United States)

Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

2014-07-01

Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Between Two Fern Genomes

Science.gov (United States)

2014-01-01

Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

Exploring Other Genomes: Bacteria.

Science.gov (United States)

Flannery, Maura C.

2001-01-01

Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups

Directory of Open Access Journals (Sweden)

Guillermo Nourdin-Galindo

2017-10-01

Full Text Available Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these

A Genome-Wide Landscape of Retrocopies in Primate Genomes.

Science.gov (United States)

Navarro, Fábio C P; Galante, Pedro A F

2015-07-29

Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

Science.gov (United States)

Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2014-06-01

To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

Funding Opportunity: Genomic Data Centers

Science.gov (United States)

Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

MicroScope: a platform for microbial genome annotation and comparative genomics.

Science.gov (United States)

Vallenet, D; Engelen, S; Mornico, D; Cruveiller, S; Fleury, L; Lajus, A; Rouy, Z; Roche, D; Salvignol, G; Scarpelli, C; Médigue, C

2009-01-01

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of

Ebolavirus comparative genomics

DEFF Research Database (Denmark)

Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

2015-01-01

The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

SIGMA: A System for Integrative Genomic Microarray Analysis of Cancer Genomes

Directory of Open Access Journals (Sweden)

Davies Jonathan J

2006-12-01

Full Text Available Abstract Background The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes. Results We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types. Conclusion In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA of cancer genomes, can be accessed at http://sigma.bccrc.ca.

Genomics With Cloud Computing

OpenAIRE

Sukhamrit Kaur; Sandeep Kaur

2015-01-01

Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

Genomics technologies to study structural variations in the grapevine genome

Directory of Open Access Journals (Sweden)

Cardone Maria Francesca

2016-01-01

Full Text Available Grapevine is one of the most important crop plants in the world. Recently there was great expansion of genomics resources about grapevine genome, thus providing increasing efforts for molecular breeding. Current cultivars display a great level of inter-specific differentiation that needs to be investigated to reach a comprehensive understanding of the genetic basis of phenotypic differences, and to find responsible genes selected by cross breeding programs. While there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs on plant genomes, few data are available on copy number variation (CNV. Furthermore association between structural variations and phenotypes has been described in only a few cases. We combined high throughput biotechnologies and bioinformatics tools, to reveal the first inter-varietal atlas of structural variation (SV for the grapevine genome. We sequenced and compared four table grape cultivars with the Pinot noir inbred line PN40024 genome as the reference. We detected roughly 8% of the grapevine genome affected by genomic variations. Taken into account phenotypic differences existing among the studied varieties we performed comparison of SVs among them and the reference and next we performed an in-depth analysis of gene content of polymorphic regions. This allowed us to identify genes showing differences in copy number as putative functional candidates for important traits in grapevine cultivation.

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

Energy Technology Data Exchange (ETDEWEB)

Nordberg, Henrik [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Cantor, Michael [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dusheyko, Serge [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hua, Susan [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Poliakov, Alexander [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Shabalov, Igor [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Smirnova, Tatyana [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Grigoriev, Igor V. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dubchak, Inna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

2013-11-12

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. In this paper, we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.

Herbarium genomics

DEFF Research Database (Denmark)

Bakker, Freek T.; Lei, Di; Yu, Jiaying

2016-01-01

Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

Effects of sample treatments on genome recovery via single-cell genomics

Energy Technology Data Exchange (ETDEWEB)

Clingenpeel, Scott [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Schwientek, Patrick [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hugenholtz, Philip [Univ. of Queensland, Brisbane (Australia); Woyke, Tanja [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

2014-06-13

It is known that single-cell genomics is a powerful tool for accessing genetic information from uncultivated microorganisms. Methods of handling samples before single-cell genomic amplification may affect the quality of the genomes obtained. Using three bacterial strains we demonstrate that, compared to cryopreservation, lower-quality single-cell genomes are recovered when the sample is preserved in ethanol or if the sample undergoes fluorescence in situ hybridization, while sample preservation in paraformaldehyde renders it completely unsuitable for sequencing.

Method Development and Validation for the Determination of Caffeine: An Alkaloid from Coffea arabica by High-performance Liquid Chromatography Method.

Science.gov (United States)

Naveen, P; Lingaraju, H B; Deepak, M; Medhini, B; Prasad, K Shyam

2018-01-01

The present study was investigated to develop and validate a reversed phase high performance liquid chromatography method for the determination of caffeine from bean material of Coffee arabica. The separation was achieved on a reversed-phase C18 column using a mobile phase composed of water: methanol (50:50) at a flow rate of 1.0 mlmin-1. The detection was carried out on a UV detector at 272 nm. The developed method was validated according to the requirements for International Conference on Harmonisation (ICH) guidelines, which includes specificity, linearity, precision, accuracy, limit of detection and limit of quantitation. The developed method validates good linearity with excellent correlation coefficient (R2 > 0.999). In repeatability and intermediate precision, the percentage relative standard deviation (% RSD) of peak area was less than 1% shows high precision of the method. The recovery rate for caffeine was within 98.78% - 101.28% indicates high accuracy of the method. The low limit of detection and limit of quantitation of caffeine enable the detection and quantitation of caffeine from C. arabica at low concentrations. The developed HPLC method is a simple, rapid, precisely, accurately and widely accepted and it is recommended for efficient assays in routine work. A simple, accurate, and sensitive high-performance liquid chromatography (HPLC) method for caffeine from Coffea arabica has been developed and validated. The developed HPLC method was validated for linearity, specificity, precision, recovery, limits of detection, and limits of quantification by the International Conference on Harmonization guidelines. The results revealed that the proposed method is highly reliable. This method could be successfully applied for routine quality work analysis. Abbreviation Used: C. arabica : Coffee arabica, ICH: International Conference on Harmonisation, % RSD: Percentage Relative Standard Deviation, R2: Correlation Coefficient, ppm: Parts per million, LOD: Limits

Informational laws of genome structures

Science.gov (United States)

Bonnici, Vincenzo; Manca, Vincenzo

2016-06-01

In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

How genome complexity can explain the difficulty of aligning reads to genomes.

Science.gov (United States)

Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

2015-01-01

Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.

Phytozome Comparative Plant Genomics Portal

Energy Technology Data Exchange (ETDEWEB)

Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

2014-09-09

The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

A Taste of Algal Genomes from the Joint Genome Institute

Energy Technology Data Exchange (ETDEWEB)

Kuo, Alan; Grigoriev, Igor

2012-06-17

Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basic and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.

PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes.

Science.gov (United States)

Spannagl, Manuel; Bader, Kai; Pfeifer, Matthias; Nussbaumer, Thomas; Mayer, Klaus F X

2016-01-01

PGSB (Plant Genome and Systems Biology; formerly MIPS-Munich Institute for Protein Sequences) has been involved in developing, implementing and maintaining plant genome databases for more than a decade. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable datasets for model plant genomes as a backbone against which experimental data, e.g., from high-throughput functional genomics, can be organized and analyzed. In addition, genomes from both model and crop plants form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny) between related species on macro- and micro-levels.The genomes of many economically important Triticeae plants such as wheat, barley, and rye present a great challenge for sequence assembly and bioinformatic analysis due to their enormous complexity and large genome size. Novel concepts and strategies have been developed to deal with these difficulties and have been applied to the genomes of wheat, barley, rye, and other cereals. This includes the GenomeZipper concept, reference-guided exome assembly, and "chromosome genomics" based on flow cytometry sorted chromosomes.

Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.

Science.gov (United States)

Staats, Martijn; Erkens, Roy H J; van de Vossenberg, Bart; Wieringa, Jan J; Kraaijeveld, Ken; Stielow, Benjamin; Geml, József; Richardson, James E; Bakker, Freek T

2013-01-01

Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal

Next-Generation Genomics Facility at C-CAMP: Accelerating Genomic Research in India

Science.gov (United States)

S, Chandana; Russiachand, Heikham; H, Pradeep; S, Shilpa; M, Ashwini; S, Sahana; B, Jayanth; Atla, Goutham; Jain, Smita; Arunkumar, Nandini; Gowda, Malali

2014-01-01

Next-Generation Sequencing (NGS; http://www.genome.gov/12513162) is a recent life-sciences technological revolution that allows scientists to decode genomes or transcriptomes at a much faster rate with a lower cost. Genomic-based studies are in a relatively slow pace in India due to the non-availability of genomics experts, trained personnel and dedicated service providers. Using NGS there is a lot of potential to study India's national diversity (of all kinds). We at the Centre for Cellular and Molecular Platforms (C-CAMP) have launched the Next Generation Genomics Facility (NGGF) to provide genomics service to scientists, to train researchers and also work on national and international genomic projects. We have HiSeq1000 from Illumina and GS-FLX Plus from Roche454. The long reads from GS FLX Plus, and high sequence depth from HiSeq1000, are the best and ideal hybrid approaches for de novo and re-sequencing of genomes and transcriptomes. At our facility, we have sequenced around 70 different organisms comprising of more than 388 genomes and 615 transcriptomes – prokaryotes and eukaryotes (fungi, plants and animals). In addition we have optimized other unique applications such as small RNA (miRNA, siRNA etc), long Mate-pair sequencing (2 to 20 Kb), Coding sequences (Exome), Methylome (ChIP-Seq), Restriction Mapping (RAD-Seq), Human Leukocyte Antigen (HLA) typing, mixed genomes (metagenomes) and target amplicons, etc. Translating DNA sequence data from NGS sequencer into meaningful information is an important exercise. Under NGGF, we have bioinformatics experts and high-end computing resources to dissect NGS data such as genome assembly and annotation, gene expression, target enrichment, variant calling (SSR or SNP), comparative analysis etc. Our services (sequencing and bioinformatics) have been utilized by more than 45 organizations (academia and industry) both within India and outside, resulting several publications in peer-reviewed journals and several genomic

Extreme genomes

OpenAIRE

DeLong, Edward F

2000-01-01

The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

GenomePeek—an online tool for prokaryotic genome and metagenome analysis

Directory of Open Access Journals (Sweden)

Katelyn McNair

2015-06-01

Full Text Available As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.

GRAbB : Selective Assembly of Genomic Regions, a New Niche for Genomic Research

NARCIS (Netherlands)

Brankovics, Balázs; Zhang, Hao; van Diepeningen, Anne D; van der Lee, Theo A J; Waalwijk, Cees; de Hoog, G Sybren

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often

Comparative Genome Viewer

International Nuclear Information System (INIS)

Molineris, I.; Sales, G.

2009-01-01

The amount of information about genomes, both in the form of complete sequences and annotations, has been exponentially increasing in the last few years. As a result there is the need for tools providing a graphical representation of such information that should be comprehensive and intuitive. Visual representation is especially important in the comparative genomics field since it should provide a combined view of data belonging to different genomes. We believe that existing tools are limited in this respect as they focus on a single genome at a time (conservation histograms) or compress alignment representation to a single dimension. We have therefore developed a web-based tool called Comparative Genome Viewer (Cgv): it integrates a bidimensional representation of alignments between two regions, both at small and big scales, with the richness of annotations present in other genome browsers. We give access to our system through a web-based interface that provides the user with an interactive representation that can be updated in real time using the mouse to move from region to region and to zoom in on interesting details.

Genomics With Cloud Computing

Directory of Open Access Journals (Sweden)

Sukhamrit Kaur

2015-04-01

Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

IMA Genome-F 5G

OpenAIRE

Wingfield, Brenda D.; Barnes, Irene; Wilhelm de Beer, Z.; De Vos, Lieschen; Duong, Tuan A.; Kanzi, Aquillah M.; Naidoo, Kershney; Nguyen, Hai D.T.; Santana, Quentin C.; Sayari, Mohammad; Seifert, Keith A.; Steenkamp, Emma T.; Trollip, Conrad; van der Merwe, Nicolaas A.; van der Nest, Magriet A.

2015-01-01

The genomes of Ceratocystis eucalypticola, Chrysoporthe cubensis, Chrysoporthe deuterocubensis, Davidsoniella virescens, Fusarium temperatum, Graphilbum fragrans, Penicillium nordicum and Thielaviopsis musarum are presented in this genome announcement. These seven genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 28 Mb in the case of T. musarum to 45 Mb for Fusarium temperatum. These genomes include the first reports of genomes f...

Experimental Induction of Genome Chaos.

Science.gov (United States)

Ye, Christine J; Liu, Guo; Heng, Henry H

2018-01-01

Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations." To advance this exciting field, we need an effective experimental system to induce and characterize the karyotype reorganization process. In this chapter, an experimental protocol to induce chaotic genomes is described, following a brief discussion of the mechanism and implication of genome chaos in cancer evolution.

Genome Sequences of Oryza Species

KAUST Repository

Kumagai, Masahiko

2018-02-14

This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

Genome Sequences of Oryza Species

KAUST Repository

Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

2018-01-01

This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

Genome Variation Map: a data repository of genome variations in BIG Data Center

OpenAIRE

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2017-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research a...

Patient-controlled encrypted genomic data: an approach to advance clinical genomics

Directory of Open Access Journals (Sweden)

Trakadis Yannis J

2012-07-01

Full Text Available Abstract Background The revolution in DNA sequencing technologies over the past decade has made it feasible to sequence an individual’s whole genome at a relatively low cost. The potential value of the information generated by genomic technologies for medicine and society is enormous. However, in order for exome sequencing, and eventually whole genome sequencing, to be implemented clinically, a number of major challenges need to be overcome. For instance, obtaining meaningful informed-consent, managing incidental findings and the great volume of data generated (including multiple findings with uncertain clinical significance, re-interpreting the genomic data and providing additional counselling to patients as genetic knowledge evolves are issues that need to be addressed. It appears that medical genetics is shifting from the present “phenotype-first” medical model to a “data-first” model which leads to multiple complexities. Discussion This manuscript discusses the different challenges associated with integrating genomic technologies into clinical practice and describes a “phenotype-first” approach, namely, “Individualized Mutation-weighed Phenotype Search”, and its benefits. The proposed approach allows for a more efficient prioritization of the genes to be tested in a clinical lab based on both the patient’s phenotype and his/her entire genomic data. It simplifies “informed-consent” for clinical use of genomic technologies and helps to protect the patient’s autonomy and privacy. Overall, this approach could potentially render widespread use of genomic technologies, in the immediate future, practical, ethical and clinically useful. Summary The “Individualized Mutation-weighed Phenotype Search” approach allows for an incremental integration of genomic technologies into clinical practice. It ensures that we do not over-medicalize genomic data but, rather, continue our current medical model which is based on serving

EUPAN enables pan-genome studies of a large number of eukaryotic genomes.

Science.gov (United States)

Hu, Zhiqiang; Sun, Chen; Lu, Kuang-Chen; Chu, Xixia; Zhao, Yue; Lu, Jinyuan; Shi, Jianxin; Wei, Chaochun

2017-08-01

Pan-genome analyses are routinely carried out for bacteria to interpret the within-species gene presence/absence variations (PAVs). However, pan-genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes. Here we proposed EUPAN, a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth. In the previous studies, we demonstrated the effectiveness and high accuracy of EUPAN in the pan-genome analysis of 453 rice genomes, in which we also revealed widespread gene PAVs among individual rice genomes. Moreover, EUPAN can be directly applied to the current re-sequencing projects primarily focusing on single nucleotide polymorphisms. EUPAN is implemented in Perl, R and C ++. It is supported under Linux and preferred for a computer cluster with LSF and SLURM job scheduling system. EUPAN together with its standard operating procedure (SOP) is freely available for non-commercial use (CC BY-NC 4.0) at http://cgm.sjtu.edu.cn/eupan/index.html . ccwei@sjtu.edu.cn or jianxin.shi@sjtu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

Science.gov (United States)

Lack, Justin B; Cardeno, Charis M; Crepeau, Marc W; Taylor, William; Corbett-Detig, Russell B; Stevens, Kristian A; Langley, Charles H; Pool, John E

2015-04-01

Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets. Copyright © 2015 by the Genetics Society of America.

Recuperação do cafeeiro (Coffea arabica L. após recepa, submetido a diferentes lâminas de água e parcelamentos da adubação = Recovery of coffee tree (Coffea arabica L. after pruning under different irrigation depths

Directory of Open Access Journals (Sweden)

Kelte Resende Arantes

2009-04-01

Full Text Available Visando reduzir o período de recuperação das lavouras após a recepa, neste trabalho objetivou-se avaliar a influência de diferentes lâminas de irrigação e do parcelamento da adubação sobre o crescimento do cafeeiro. Foram utilizadas quatro diferentes lâminas de irrigação (0, 40, 80 e 120% da ECA-Precipitação e três parcelamentos da adubação com N e K (quatro, oito e 12 vezes. O experimento foi conduzido no Sul de Minas Gerais, com o cafeeiro (Coffea arabica cv. Topázio MG-1190, plantado no espaçamento de 1,8 x 0,7 m e recepado 65 meses após o plantio. O delineamentoexperimental utilizado foi em blocos casualizados com parcelas subdivididas. Os parâmetros avaliados foram altura da planta, diâmetro do ramo ortotrópico, número de internódios e diâmetro da copa. O crescimento do cafeeiro foi influenciado pela irrigação, mas não foi influenciado pelo parcelamento da adubação. A lâmina de 120% do saldo do balanço ECA - P proporcionou maior crescimento.In order to reduce the recovery period of the orchard coffeeafter pruning, this work was carried out with the objective of evaluating the influence of different irrigation depths and splitting of N and K with fertirrigation on the growth of coffee plants. The experiment was carried out in southern Minas Gerais State with coffeaarabica cv. Topázio MG-1190 implanted with 1.8 x 0.7 m spacing. Irrigations corresponded to 0, 40, 80 and 120% of the evaporation from a Class A pan – precipitation (ECA-P and N and K split in 4, 8 and 12 applications. A randomized block design with four replicationswas used. Plant height, diameter of orthotropic branches, number of internodes and crown diameter were evaluated. The fertilizer splitting was found not to provide any increase in growth of the coffee plant. The depth of 120%*ECA-P provided the greatest growth ofcoffee plants when compared to others.

GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

Science.gov (United States)

Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

2013-04-10

Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. Copyright © 2012 Elsevier B.V. All rights reserved.

The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly

Directory of Open Access Journals (Sweden)

J. W. Clouse

2016-03-01

Full Text Available Amaranth ( L. is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32, and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which -like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (, , and and their putative progenitor ( were resequenced. A single nucleotide polymorphism (SNP phylogeny supported the classification of as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for using the BioNano Genomics’ Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet ( L. and estimated, using analysis, the age of the most recent polyploidization event in amaranth.

Whole genome sequencing and bioinformatics analysis of two Egyptian genomes.

Science.gov (United States)

ElHefnawi, Mahmoud; Jeon, Sungwon; Bhak, Youngjune; ElFiky, Asmaa; Horaiz, Ahmed; Jun, JeHoon; Kim, Hyunho; Bhak, Jong

2018-05-15

We report two Egyptian male genomes (EGP1 and EGP2) sequenced at ~ 30× sequencing depths. EGP1 had 4.7 million variants, where 198,877 were novel variants while EGP2 had 209,109 novel variants out of 4.8 million variants. The mitochondrial haplogroup of the two individuals were identified to be H7b1 and L2a1c, respectively. We also identified the Y haplogroup of EGP1 (R1b) and EGP2 (J1a2a1a2 > P58 > FGC11). EGP1 had a mutation in the NADH gene of the mitochondrial genome ND4 (m.11778 G > A) that causes Leber's hereditary optic neuropathy. Some SNPs shared by the two genomes were associated with an increased level of cholesterol and triglycerides, probably related with Egyptians obesity. Comparison of these genomes with African and Western-Asian genomes can provide insights on Egyptian ancestry and genetic history. This resource can be used to further understand genomic diversity and functional classification of variants as well as human migration and evolution across Africa and Western-Asia. Copyright © 2017. Published by Elsevier B.V.

Genomic Testing

Science.gov (United States)

... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

St2-80: a new FISH marker for St genome and genome analysis in Triticeae.

Science.gov (United States)

Wang, Long; Shi, Qinghua; Su, Handong; Wang, Yi; Sha, Lina; Fan, Xing; Kang, Houyang; Zhang, Haiqin; Zhou, Yonghong

2017-07-01

The St genome is one of the most fundamental genomes in Triticeae. Repetitive sequences are widely used to distinguish different genomes or species. The primary objectives of this study were to (i) screen a new sequence that could easily distinguish the chromosome of the St genome from those of other genomes by fluorescence in situ hybridization (FISH) and (ii) investigate the genome constitution of some species that remain uncertain and controversial. We used degenerated oligonucleotide primer PCR (Dop-PCR), Dot-blot, and FISH to screen for a new marker of the St genome and to test the efficiency of this marker in the detection of the St chromosome at different ploidy levels. Signals produced by a new FISH marker (denoted St 2 -80) were present on the entire arm of chromosomes of the St genome, except in the centromeric region. On the contrary, St 2 -80 signals were present in the terminal region of chromosomes of the E, H, P, and Y genomes. No signal was detected in the A and B genomes, and only weak signals were detected in the terminal region of chromosomes of the D genome. St 2 -80 signals were obvious and stable in chromosomes of different genomes, whether diploid or polyploid. Therefore, St 2 -80 is a potential and useful FISH marker that can be used to distinguish the St genome from those of other genomes in Triticeae.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

OpenAIRE

Henrique Machado; Henrique Machado; Lone Gram

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationship...

Baculovirus Genomics

NARCIS (Netherlands)

Oers, van M.M.; Vlak, J.M.

2007-01-01

Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

Molluscan Evolutionary Genomics

Energy Technology Data Exchange (ETDEWEB)

Simison, W. Brian; Boore, Jeffrey L.

2005-12-01

In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome.

Science.gov (United States)

Zhang, Wei; Zhang, Mingyi; Zhu, Xianwen; Cao, Yaping; Sun, Qing; Ma, Guojia; Chao, Shiaoman; Yan, Changhui; Xu, Steven S; Cai, Xiwen

2018-02-01

This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.

RadGenomics project

Energy Technology Data Exchange (ETDEWEB)

Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others

2002-06-01

Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

RadGenomics project

International Nuclear Information System (INIS)

Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

2002-01-01

Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

Rumen microbial genomics

International Nuclear Information System (INIS)

Morrison, M.; Nelson, K.E.

2005-01-01

Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

Comparative genomics reveals insights into avian genome evolution and adaptation

Science.gov (United States)

Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

2015-01-01

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

Energy Technology Data Exchange (ETDEWEB)

Hu, Tina T.; Pattyn, Pedro; Bakker, Erica G.; Cao, Jun; Cheng, Jan-Fang; Clark, Richard M.; Fahlgren, Noah; Fawcett, Jeffrey A.; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hollister, Jesse D.; Ossowski, Stephan; Ottilar, Robert P.; Salamov, Asaf A.; Schneeberger, Korbinian; Spannagl, Manuel; Wang, Xi; Yang, Liang; Nasrallah, Mikhail E.; Bergelson, Joy; Carrington, James C.; Gaut, Brandon S.; Schmutz, Jeremy; Mayer, Klaus F. X.; Van de Peer, Yves; Grigoriev, Igor V.; Nordborg, Magnus; Weigel, Detlef; Guo, Ya-Long

2011-04-29

In our manuscript, we present a high-quality genome sequence of the Arabidopsis thaliana relative, Arabidopsis lyrata, produced by dideoxy sequencing. We have performed the usual types of genome analysis (gene annotation, dN/dS studies etc. etc.), but this is relegated to the Supporting Information. Instead, we focus on what was a major motivation for sequencing this genome, namely to understand how A. thaliana lost half its genome in a few million years and lived to tell the tale. The rather surprising conclusion is that there is not a single genomic feature that accounts for the reduced genome, but that every aspect centromeres, intergenic regions, transposable elements, gene family number is affected through hundreds of thousands of cuts. This strongly suggests that overall genome size in itself is what has been under selection, a suggestion that is strongly supported by our demonstration (using population genetics data from A. thaliana) that new deletions seem to be driven to fixation.

Genome Imprinting

Indian Academy of Sciences (India)

the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

Genomes to Proteomes

Energy Technology Data Exchange (ETDEWEB)

Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2009-03-01

Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

Genome Improvement at JGI-HAGSC

Energy Technology Data Exchange (ETDEWEB)

Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.

2012-03-03

Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

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Lincoln D Stein

2003-11-01

Full Text Available The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp and C. elegans (100.3 Mbp genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C

A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China.

Science.gov (United States)

Yu, Jun; Wong, Gane Ka-Shu; Liu, Siqi; Wang, Jian; Yang, Huanming

2007-06-29

In May 2000, the Beijing Institute of Genomics formally announced the launch of a comprehensive crop genome research project on rice genomics, the Chinese Superhybrid Rice Genome Project. SRGP is not simply a sequencing project targeted to a single rice (Oryza sativa L.) genome, but a full-swing research effort with an ultimate goal of providing inclusive basic genomic information and molecular tools not only to understand biology of the rice, both as an important crop species and a model organism of cereals, but also to focus on a popular superhybrid rice landrace, LYP9. We have completed the first phase of SRGP and provide the rice research community with a finished genome sequence of an indica variety, 93-11 (the paternal cultivar of LYP9), together with ample data on subspecific (between subspecies) polymorphisms, transcriptomes and proteomes, useful for within-species comparative studies. In the second phase, we have acquired the genome sequence of the maternal cultivar, PA64S, together with the detailed catalogues of genes uniquely expressed in the parental cultivars and the hybrid as well as allele-specific markers that distinguish parental alleles. Although SRGP in China is not an open-ended research programme, it has been designed to pave a way for future plant genomics research and application, such as to interrogate fundamentals of plant biology, including genome duplication, polyploidy and hybrid vigour, as well as to provide genetic tools for crop breeding and to carry along a social burden-leading a fight against the world's hunger. It began with genomics, the newly developed and industry-scale research field, and from the world's most populous country. In this review, we summarize our scientific goals and noteworthy discoveries that exploit new territories of systematic investigations on basic and applied biology of rice and other major cereal crops.

Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.

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Tamara Smokvina

Full Text Available Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis

A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes.

Science.gov (United States)

Takashima, Masako; Sriswasdi, Sira; Manabe, Ri-Ichiroh; Ohkuma, Moriya; Sugita, Takashi; Iwasaki, Wataru

2018-01-01

To construct a backbone tree consisting of basidiomycetous yeasts, draft genome sequences from 25 species of Trichosporonales (Tremellomycetes, Basidiomycota) were generated. In addition to the hybrid genomes of Trichosporon coremiiforme and Trichosporon ovoides that we described previously, we identified an interspecies hybrid genome in Cutaneotrichosporon mucoides (formerly Trichosporon mucoides). This hybrid genome had a gene retention rate of ~55%, and its closest haploid relative was Cutaneotrichosporon dermatis. After constructing the C. mucoides subgenomes, we generated a phylogenetic tree using genome data from the 27 haploid species and the subgenome data from the three hybrid genome species. It was a high-quality tree with 100% bootstrap support for all of the branches. The genome-based tree provided superior resolution compared with previous multi-gene analyses. Although our backbone tree does not include all Trichosporonales genera (e.g. Cryptotrichosporon), it will be valuable for future analyses of genome data. Interest in interspecies hybrid fungal genomes has recently increased because they may provide a basis for new technologies. The three Trichosporonales hybrid genomes described in this study are different from well-characterized hybrid genomes (e.g. those of Saccharomyces pastorianus and Saccharomyces bayanus) because these hybridization events probably occurred in the distant evolutionary past. Hence, they will be useful for studying genome stability following hybridization and speciation events. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

Science.gov (United States)

Liu, Shengyi; Liu, Yumei; Yang, Xinhua; Tong, Chaobo; Edwards, David; Parkin, Isobel A. P.; Zhao, Meixia; Ma, Jianxin; Yu, Jingyin; Huang, Shunmou; Wang, Xiyin; Wang, Junyi; Lu, Kun; Fang, Zhiyuan; Bancroft, Ian; Yang, Tae-Jin; Hu, Qiong; Wang, Xinfa; Yue, Zhen; Li, Haojie; Yang, Linfeng; Wu, Jian; Zhou, Qing; Wang, Wanxin; King, Graham J; Pires, J. Chris; Lu, Changxin; Wu, Zhangyan; Sampath, Perumal; Wang, Zhuo; Guo, Hui; Pan, Shengkai; Yang, Limei; Min, Jiumeng; Zhang, Dong; Jin, Dianchuan; Li, Wanshun; Belcram, Harry; Tu, Jinxing; Guan, Mei; Qi, Cunkou; Du, Dezhi; Li, Jiana; Jiang, Liangcai; Batley, Jacqueline; Sharpe, Andrew G; Park, Beom-Seok; Ruperao, Pradeep; Cheng, Feng; Waminal, Nomar Espinosa; Huang, Yin; Dong, Caihua; Wang, Li; Li, Jingping; Hu, Zhiyong; Zhuang, Mu; Huang, Yi; Huang, Junyan; Shi, Jiaqin; Mei, Desheng; Liu, Jing; Lee, Tae-Ho; Wang, Jinpeng; Jin, Huizhe; Li, Zaiyun; Li, Xun; Zhang, Jiefu; Xiao, Lu; Zhou, Yongming; Liu, Zhongsong; Liu, Xuequn; Qin, Rui; Tang, Xu; Liu, Wenbin; Wang, Yupeng; Zhang, Yangyong; Lee, Jonghoon; Kim, Hyun Hee; Denoeud, France; Xu, Xun; Liang, Xinming; Hua, Wei; Wang, Xiaowu; Wang, Jun; Chalhoub, Boulos; Paterson, Andrew H

2014-01-01

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. PMID:24852848

Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology

Science.gov (United States)

Ping, Zheng; Siegal, Gene P.; Almeida, Jonas S.; Schnitt, Stuart J.; Shen, Dejun

2014-01-01

Background: Genetics and genomics have radically altered our understanding of breast cancer progression. However, the genomic basis of various histopathologic features of breast cancer is not yet well-defined. Materials and Methods: The Cancer Genome Atlas (TCGA) is an international database containing a large collection of human cancer genome sequencing data. cBioPortal is a web tool developed for mining these sequencing data. We performed mining of TCGA sequencing data in an attempt to characterize the genomic features correlated with breast cancer histopathology. We first assessed the quality of the TCGA data using a group of genes with known alterations in various cancers. Both genome-wide gene mutation and copy number changes as well as a group of genes with a high frequency of genetic changes were then correlated with various histopathologic features of invasive breast cancer. Results: Validation of TCGA data using a group of genes with known alterations in breast cancer suggests that the TCGA has accurately documented the genomic abnormalities of multiple malignancies. Further analysis of TCGA breast cancer sequencing data shows that accumulation of specific genomic defects is associated with higher tumor grade, larger tumor size and receptor negativity. Distinct groups of genomic changes were found to be associated with the different grades of invasive ductal carcinoma. The mutator role of the TP53 gene was validated by genomic sequencing data of invasive breast cancer and TP53 mutation was found to play a critical role in defining high tumor grade. Conclusions: Data mining of the TCGA genome sequencing data is an innovative and reliable method to help characterize the genomic abnormalities associated with histopathologic features of invasive breast cancer. PMID:24672738

Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology

Directory of Open Access Journals (Sweden)

Zheng Ping

2014-01-01

Full Text Available Background: Genetics and genomics have radically altered our understanding of breast cancer progression. However, the genomic basis of various histopathologic features of breast cancer is not yet well-defined. Materials and Methods: The Cancer Genome Atlas (TCGA is an international database containing a large collection of human cancer genome sequencing data. cBioPortal is a web tool developed for mining these sequencing data. We performed mining of TCGA sequencing data in an attempt to characterize the genomic features correlated with breast cancer histopathology. We first assessed the quality of the TCGA data using a group of genes with known alterations in various cancers. Both genome-wide gene mutation and copy number changes as well as a group of genes with a high frequency of genetic changes were then correlated with various histopathologic features of invasive breast cancer. Results: Validation of TCGA data using a group of genes with known alterations in breast cancer suggests that the TCGA has accurately documented the genomic abnormalities of multiple malignancies. Further analysis of TCGA breast cancer sequencing data shows that accumulation of specific genomic defects is associated with higher tumor grade, larger tumor size and receptor negativity. Distinct groups of genomic changes were found to be associated with the different grades of invasive ductal carcinoma. The mutator role of the TP53 gene was validated by genomic sequencing data of invasive breast cancer and TP53 mutation was found to play a critical role in defining high tumor grade. Conclusions: Data mining of the TCGA genome sequencing data is an innovative and reliable method to help characterize the genomic abnormalities associated with histopathologic features of invasive breast cancer.

Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes.

Science.gov (United States)

Sun, Yan-Bo; Xiong, Zi-Jun; Xiang, Xue-Yan; Liu, Shi-Ping; Zhou, Wei-Wei; Tu, Xiao-Long; Zhong, Li; Wang, Lu; Wu, Dong-Dong; Zhang, Bao-Lin; Zhu, Chun-Ling; Yang, Min-Min; Chen, Hong-Man; Li, Fang; Zhou, Long; Feng, Shao-Hong; Huang, Chao; Zhang, Guo-Jie; Irwin, David; Hillis, David M; Murphy, Robert W; Yang, Huan-Ming; Che, Jing; Wang, Jun; Zhang, Ya-Ping

2015-03-17

The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

The complete mitochondrial genome of Gossypium hirsutum and evolutionary analysis of higher plant mitochondrial genomes.

Science.gov (United States)

Liu, Guozheng; Cao, Dandan; Li, Shuangshuang; Su, Aiguo; Geng, Jianing; Grover, Corrinne E; Hu, Songnian; Hua, Jinping

2013-01-01

Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes. We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes. The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.

Microbial Genomes Multiply

Science.gov (United States)

Doolittle, Russell F.

2002-01-01

The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

Genomic research perspectives in Kazakhstan

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Ainur Akilzhanova

2014-01-01

Full Text Available Introduction: Technological advancements rapidly propel the field of genome research. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics, have transformed basic and translational biomedical research. Several projects in the field of genomic and personalized medicine have been conducted at the Center for Life Sciences in Nazarbayev University. The prioritized areas of research include: genomics of multifactorial diseases, cancer genomics, bioinformatics, genetics of infectious diseases and population genomics. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine. Results: To further develop genomic and biomedical projects at Center for Life Sciences, the development of bioinformatics research and infrastructure and the establishment of new collaborations in the field are essential. Widespread use of genetic tools will allow the identification of diseases before the onset of clinical symptoms, the individualization of drug treatment, and could induce individual behavioral changes on the basis of calculated disease risk. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances, such as medicines and diagnostics. It is important to integrate research and education in the fields of genomics, personalized medicine, and bioinformatics, which will be possible with opening of the new Medical Faculty at Nazarbayev University. People in practice and training need to be educated about the key concepts of genomics and engaged so they can effectively apply their knowledge in a matter that will bring the era of genomic medicine to patient care. This requires the development of well

Efficient Breeding by Genomic Mating.

Science.gov (United States)

Akdemir, Deniz; Sánchez, Julio I

2016-01-01

Selection in breeding programs can be done by using phenotypes (phenotypic selection), pedigree relationship (breeding value selection) or molecular markers (marker assisted selection or genomic selection). All these methods are based on truncation selection, focusing on the best performance of parents before mating. In this article we proposed an approach to breeding, named genomic mating, which focuses on mating instead of truncation selection. Genomic mating uses information in a similar fashion to genomic selection but includes information on complementation of parents to be mated. Following the efficiency frontier surface, genomic mating uses concepts of estimated breeding values, risk (usefulness) and coefficient of ancestry to optimize mating between parents. We used a genetic algorithm to find solutions to this optimization problem and the results from our simulations comparing genomic selection, phenotypic selection and the mating approach indicate that current approach for breeding complex traits is more favorable than phenotypic and genomic selection. Genomic mating is similar to genomic selection in terms of estimating marker effects, but in genomic mating the genetic information and the estimated marker effects are used to decide which genotypes should be crossed to obtain the next breeding population.

The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects.

Science.gov (United States)

Papanicolaou, Alexie

2016-01-01

Many research programs on non-model species biology have been empowered by genomics. In turn, genomics is underpinned by a reference sequence and ancillary information created by so-called "genome projects". The most reliable genome projects are the ones created as part of an active research program and designed to address specific questions but their life extends past publication. In this opinion paper I outline four key insights that have facilitated maintaining genomic communities: the key role of computational capability, the iterative process of building genomic resources, the value of community participation and the importance of manual curation. Taken together, these ideas can and do ensure the longevity of genome projects and the growing non-model species community can use them to focus a discussion with regards to its future genomic infrastructure.

In vitro AND in vivo ANTHELMINTIC EFFECT OF Coffea arabica RESIDUES AGAINTS AN Haemonchus contortus ISOLATE WITH LOW SUSCEPTIBILITY TO TANNINS

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G.I. Ortiz-Ocampo

2016-05-01

Full Text Available The present study evaluated in vitro and in vivo anthelmintic (AH effect of the percolated by-product of Coffea arabica against a Haemonchus contortus isolate with low susceptibility to tannins. Firstly, the susceptibility to tannins of Paraíso H. contortus isolate was evaluated with the in vitro larval exsheathment inhibition assay (LEIA using an acetone:water (70:30 extract of Acacia pennatula. Afterwards, the in vitro AH effect of acetone:water extracts of percolated C. arabica by-products (Clean and Smooth (CS and Shade Grown (SG Starbucks® were evaluated. Then, the in vivo AH effect was determined in growing sheep (4 months old and 15.2 kg bodyweight, infected with H. contortus (Paraiso isolate and fed with a diet containing the percolated by-product of C. arabica. Three experimental groups were formed (n = 6 lambs: GC Group (control diet without C. arabica, GCA Group (feed containing 10% C. arabica and, GCA+PEG (polyethilenglycol Group (feed with 10% C. arabica + PEG as a tannin inhibitor. Fecal samples were obtained daily from the rectum of lambs (days 1 to 20 of the study. The H. contortus isolate tolerated the A. pennatula extract at concentrations of 150 and 300 μg extract/ml PBS (P > 0.05, which confirmed its low susceptibility to tannins. The C. arabica CS extract reduced the exsheatment from 150 μg of extract/ml PBS and the SG variety from 1200 μg of extract/ml PBS (P0.05. In conclusion, the C. arabica percolated by-product extracts showed in vitro AH effect against exsheathment. However, the consumption of feed containing 10% of the percolated by-product did not show an in vivo AH effect in sheep infected with the Paraiso H. contortus isolate. The latter could be due to the low susceptibility towards the secondary compounds of tannin rich plants of the H. contortus isolate used in this study.

Genomic prediction using subsampling

OpenAIRE

Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

2017-01-01

Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng.

Science.gov (United States)

Jayakodi, Murukarthick; Choi, Beom-Soon; Lee, Sang-Choon; Kim, Nam-Hoon; Park, Jee Young; Jang, Woojong; Lakshmanan, Meiyappan; Mohan, Shobhana V G; Lee, Dong-Yup; Yang, Tae-Jin

2018-04-12

The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page. This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.

Genome Modeling System: A Knowledge Management Platform for Genomics.

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Malachi Griffith

2015-07-01

Full Text Available In this work, we present the Genome Modeling System (GMS, an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395 and matched lymphoblastoid line (HCC1395BL. These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

Ancient genomes

OpenAIRE

Hoelzel, A Rus

2005-01-01

Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

Governance in genomics: a conceptual challenge for public health genomics law

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Tobias Schulte in den Bäumen

2006-12-01

Full Text Available Increasing levels of genomic knowledge has led to awareness that new governance issues need to be taken into consideration. While some countries have created new statutory laws in the last 10 years, science supports the idea that genomic data should be treated like other medical data. In this article we discuss the three core models of governance in medical law on a conceptual level. The three models, the Medical, Public Health and Fundamental Rights Model stress different values, or in legal terms serve different principles. The Medical Model stands for expert knowledge and the standardisation of quality in healthcare. The Public Health Model fosters a social point of view as it advocates distribution justice in healthcare and an awareness of healthcare as a broader concept. The Fundamental Rights Model focuses on individual rights such as the right to privacy and autonomy. We argue that none of the models can be used in a purist fashion as governance in genomics should enable society and individuals to protect individual rights, to strive for a distribution justice and to ensure the quality of genomic services in one coherent process. Thus, genomic governance in genomics requires procedural law and a set of applicable principles. The principle which underlies all three models is the principle of medical beneficence. Therefore genomic governance should refer to it as a key principle when conflicting rights of individuals or communities need to be balanced.

Genetical Genomics for Evolutionary Studies

NARCIS (Netherlands)

Prins, J.C.P.; Smant, G.; Jansen, R.C.

2012-01-01

Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

Human social genomics.

Directory of Open Access Journals (Sweden)

Steven W Cole

2014-08-01

Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

Reference-quality genome sequence of Aegilops tauschii, the source of wheat D genome, shows that recombination shapes genome structure and evolution

Science.gov (United States)

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat and an important genetic resource for wheat. A reference-quality sequence for the Ae. tauschii genome was produced with a combination of ordered-clone sequencing, whole-genome shotgun sequencing, and BioNano optical geno...

Genomic taxonomy of vibrios

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Iida Tetsuya

2009-10-01

Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

Comparative genome analysis of Bacillus cereus group genomes withBacillus subtilis

Energy Technology Data Exchange (ETDEWEB)

Anderson, Iain; Sorokin, Alexei; Kapatral, Vinayak; Reznik, Gary; Bhattacharya, Anamitra; Mikhailova, Natalia; Burd, Henry; Joukov, Victor; Kaznadzey, Denis; Walunas, Theresa; D' Souza, Mark; Larsen, Niels; Pusch,Gordon; Liolios, Konstantinos; Grechkin, Yuri; Lapidus, Alla; Goltsman,Eugene; Chu, Lien; Fonstein, Michael; Ehrlich, S. Dusko; Overbeek, Ross; Kyrpides, Nikos; Ivanova, Natalia

2005-09-14

Genome features of the Bacillus cereus group genomes (representative strains of Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis sub spp israelensis) were analyzed and compared with the Bacillus subtilis genome. A core set of 1,381 protein families among the four Bacillus genomes, with an additional set of 933 families common to the B. cereus group, was identified. Differences in signal transduction pathways, membrane transporters, cell surface structures, cell wall, and S-layer proteins suggesting differences in their phenotype were identified. The B. cereus group has signal transduction systems including a tyrosine kinase related to two-component system histidine kinases from B. subtilis. A model for regulation of the stress responsive sigma factor sigmaB in the B. cereus group different from the well studied regulation in B. subtilis has been proposed. Despite a high degree of chromosomal synteny among these genomes, significant differences in cell wall and spore coat proteins that contribute to the survival and adaptation in specific hosts has been identified.

What does it mean to be genomically literate?: National Human Genome Research Institute Meeting Report.

Science.gov (United States)

Hurle, Belen; Citrin, Toby; Jenkins, Jean F; Kaphingst, Kimberly A; Lamb, Neil; Roseman, Jo Ellen; Bonham, Vence L

2013-08-01

Genomic discoveries will increasingly advance the science of medicine. Limited genomic literacy may adversely impact the public's understanding and use of the power of genetics and genomics in health care and public health. In November 2011, a meeting was held by the National Human Genome Research Institute to examine the challenge of achieving genomic literacy for the general public, from kindergarten to grade 12 to adult education. The role of the media in disseminating scientific messages and in perpetuating or reducing misconceptions was also discussed. Workshop participants agreed that genomic literacy will be achieved only through active engagement between genomics experts and the varied constituencies that comprise the public. This report summarizes the background, content, and outcomes from this meeting, including recommendations for a research agenda to inform decisions about how to advance genomic literacy in our society.

Ultrafast comparison of personal genomes

OpenAIRE

Mauldin, Denise; Hood, Leroy; Robinson, Max; Glusman, Gustavo

2017-01-01

We present an ultra-fast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into 'genome fingerprints' that can be readily compared across sequencing technologies and reference versions. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. This enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative s...

Bioinformatics decoding the genome

CERN Multimedia

CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

2006-01-01

Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

DEFF Research Database (Denmark)

Gopalakrishnan, Shyam; Samaniego Castruita, Jose Alfredo; Sinding, Mikkel Holger Strander

2017-01-01

Background An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a......Background An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data...... that regardless of the reference genome choice, most evolutionary genomic analyses yield qualitatively similar results, including those exploring the structure between the wolves and dogs using admixture and principal component analysis. However, we do observe differences in the genomic coverage of re-mapped...

The Small Nuclear Genomes of Selaginella Are Associated with a Low Rate of Genome Size Evolution.

Science.gov (United States)

Baniaga, Anthony E; Arrigo, Nils; Barker, Michael S

2016-06-03

The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

1000 Bull Genomes - Toward genomic Selectionf from whole genome sequence Data in Dairy and Beef Cattle

NARCIS (Netherlands)

Hayes, B.; Daetwyler, H.D.; Fries, R.; Guldbrandtsen, B.; Mogens Sando Lund, M.; Didier A. Boichard, D.A.; Stothard, P.; Veerkamp, R.F.; Hulsegge, B.; Rocha, D.; Tassell, C.; Mullaart, E.; Gredler, B.; Druet, T.; Bagnato, A.; Goddard, M.E.; Chamberlain, H.L.

2013-01-01

Genomic prediction of breeding values is now used as the basis for selection of dairy cattle, and in some cases beef cattle, in a number of countries. When genomic prediction was introduced most of the information was to thought to be derived from linkage disequilibrium between markers and causative

Musa sebagai Model Genom

Directory of Open Access Journals (Sweden)

RITA MEGIA

2005-12-01

Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

Human-specific HERV-K insertion causes genomic variations in the human genome.

Directory of Open Access Journals (Sweden)

Wonseok Shin

Full Text Available Human endogenous retroviruses (HERV sequences account for about 8% of the human genome. Through comparative genomics and literature mining, we identified a total of 29 human-specific HERV-K insertions. We characterized them focusing on their structure and flanking sequence. The results showed that four of the human-specific HERV-K insertions deleted human genomic sequences via non-classical insertion mechanisms. Interestingly, two of the human-specific HERV-K insertion loci contained two HERV-K internals and three LTR elements, a pattern which could be explained by LTR-LTR ectopic recombination or template switching. In addition, we conducted a polymorphic test and observed that twelve out of the 29 elements are polymorphic in the human population. In conclusion, human-specific HERV-K elements have inserted into human genome since the divergence of human and chimpanzee, causing human genomic changes. Thus, we believe that human-specific HERV-K activity has contributed to the genomic divergence between humans and chimpanzees, as well as within the human population.

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

Science.gov (United States)

Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

2017-06-01

Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Genomic Resource and Genome Guided Comparison of Twenty Type Strains of the Genus Methylobacterium

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Vasvi Chaudhry

2017-12-01

Full Text Available Bacteria of the genus Methylobacterium are widespread in diverse habitats ranging from soil, water and plant (phyllosphere, rhizosphere and endosphere. In the present study, we in house generated genomic data resource of six type strains along with fourteen database genomes of the Methylobacterium genus to carry out phylogenomic, taxonomic, comparative and ecological studies of this genus. Overall, the genus shows high diversity and genetic variation primarily due to its ability to acquire genetic material from diverse sources through horizontal gene transfer. As majority of species identified in this study are plant associated with their genomes equipped with methylotrophy and photosynthesis related gene along with genes for plant probiotic traits. Most of the species genomes are equipped with genes for adaptation and defense for UV radiation, oxidative stress and desiccation. The genus has an open pan-genome and we predicted the role of gain/loss of prophages and CRISPR elements in diversity and evolution. Our genomic resource with annotation and analysis provides a platform for interspecies genomic comparisons in the genus Methylobacterium, and to unravel their natural genome diversity and to study how natural selection shapes their genome with the adaptive mechanisms which allow them to acquire diverse habitat lifestyles. This type strains genomic data display power of Next Generation Sequencing in rapidly creating resource paving the way for studies on phylogeny and taxonomy as well as for basic and applied research for this important genus.

Genomic instability following irradiation

International Nuclear Information System (INIS)

Hacker-Klom, U.B.; Goehde, W.

2001-01-01

Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

Evolution of small prokaryotic genomes

Directory of Open Access Journals (Sweden)

David José Martínez-Cano

2015-01-01

Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

Insights into Conifer Giga-Genomes1

Science.gov (United States)

De La Torre, Amanda R.; Birol, Inanc; Bousquet, Jean; Ingvarsson, Pär K.; Jansson, Stefan; Jones, Steven J.M.; Keeling, Christopher I.; MacKay, John; Nilsson, Ove; Ritland, Kermit; Street, Nathaniel; Yanchuk, Alvin; Zerbe, Philipp; Bohlmann, Jörg

2014-01-01

Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world’s forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20–30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes. PMID:25349325

Genome chaos: survival strategy during crisis.

Science.gov (United States)

Liu, Guo; Stevens, Joshua B; Horne, Steven D; Abdallah, Batoul Y; Ye, Karen J; Bremer, Steven W; Ye, Christine J; Chen, David J; Heng, Henry H

2014-01-01

Genome chaos, a process of complex, rapid genome re-organization, results in the formation of chaotic genomes, which is followed by the potential to establish stable genomes. It was initially detected through cytogenetic analyses, and recently confirmed by whole-genome sequencing efforts which identified multiple subtypes including "chromothripsis", "chromoplexy", "chromoanasynthesis", and "chromoanagenesis". Although genome chaos occurs commonly in tumors, both the mechanism and detailed aspects of the process are unknown due to the inability of observing its evolution over time in clinical samples. Here, an experimental system to monitor the evolutionary process of genome chaos was developed to elucidate its mechanisms. Genome chaos occurs following exposure to chemotherapeutics with different mechanisms, which act collectively as stressors. Characterization of the karyotype and its dynamic changes prior to, during, and after induction of genome chaos demonstrates that chromosome fragmentation (C-Frag) occurs just prior to chaotic genome formation. Chaotic genomes seem to form by random rejoining of chromosomal fragments, in part through non-homologous end joining (NHEJ). Stress induced genome chaos results in increased karyotypic heterogeneity. Such increased evolutionary potential is demonstrated by the identification of increased transcriptome dynamics associated with high levels of karyotypic variance. In contrast to impacting on a limited number of cancer genes, re-organized genomes lead to new system dynamics essential for cancer evolution. Genome chaos acts as a mechanism of rapid, adaptive, genome-based evolution that plays an essential role in promoting rapid macroevolution of new genome-defined systems during crisis, which may explain some unwanted consequences of cancer treatment.

Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria

Directory of Open Access Journals (Sweden)

Keeling Patrick J

2007-09-01

Full Text Available Abstract Background Dinoflagellates comprise an ecologically significant and diverse eukaryotic phylum that is sister to the phylum containing apicomplexan endoparasites. The mitochondrial genome of apicomplexans is uniquely reduced in gene content and size, encoding only three proteins and two ribosomal RNAs (rRNAs within a highly compacted 6 kb DNA. Dinoflagellate mitochondrial genomes have been comparatively poorly studied: limited available data suggest some similarities with apicomplexan mitochondrial genomes but an even more radical type of genomic organization. Here, we investigate structure, content and expression of dinoflagellate mitochondrial genomes. Results From two dinoflagellates, Crypthecodinium cohnii and Karlodinium micrum, we generated over 42 kb of mitochondrial genomic data that indicate a reduced gene content paralleling that of mitochondrial genomes in apicomplexans, i.e., only three protein-encoding genes and at least eight conserved components of the highly fragmented large and small subunit rRNAs. Unlike in apicomplexans, dinoflagellate mitochondrial genes occur in multiple copies, often as gene fragments, and in numerous genomic contexts. Analysis of cDNAs suggests several novel aspects of dinoflagellate mitochondrial gene expression. Polycistronic transcripts were found, standard start codons are absent, and oligoadenylation occurs upstream of stop codons, resulting in the absence of termination codons. Transcripts of at least one gene, cox3, are apparently trans-spliced to generate full-length mRNAs. RNA substitutional editing, a process previously identified for mRNAs in dinoflagellate mitochondria, is also implicated in rRNA expression. Conclusion The dinoflagellate mitochondrial genome shares the same gene complement and fragmentation of rRNA genes with its apicomplexan counterpart. However, it also exhibits several unique characteristics. Most notable are the expansion of gene copy numbers and their arrangements

Correction for Measurement Error from Genotyping-by-Sequencing in Genomic Variance and Genomic Prediction Models

DEFF Research Database (Denmark)

Ashraf, Bilal; Janss, Luc; Jensen, Just

sample). The GBSeq data can be used directly in genomic models in the form of individual SNP allele-frequency estimates (e.g., reference reads/total reads per polymorphic site per individual), but is subject to measurement error due to the low sequencing depth per individual. Due to technical reasons....... In the current work we show how the correction for measurement error in GBSeq can also be applied in whole genome genomic variance and genomic prediction models. Bayesian whole-genome random regression models are proposed to allow implementation of large-scale SNP-based models with a per-SNP correction...... for measurement error. We show correct retrieval of genomic explained variance, and improved genomic prediction when accounting for the measurement error in GBSeq data...

Genomic research in Eucalyptus.

Science.gov (United States)

Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

2005-09-01

Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

Genome Sequences of Marine Shrimp Exopalaemon carinicauda Holthuis Provide Insights into Genome Size Evolution of Caridea.

Science.gov (United States)

Yuan, Jianbo; Gao, Yi; Zhang, Xiaojun; Wei, Jiankai; Liu, Chengzhang; Li, Fuhua; Xiang, Jianhai

2017-07-05

Crustacea, particularly Decapoda, contains many economically important species, such as shrimps and crabs. Crustaceans exhibit enormous (nearly 500-fold) variability in genome size. However, limited genome resources are available for investigating these species. Exopalaemon carinicauda Holthuis, an economical caridean shrimp, is a potential ideal experimental animal for research on crustaceans. In this study, we performed low-coverage sequencing and de novo assembly of the E. carinicauda genome. The assembly covers more than 95% of coding regions. E. carinicauda possesses a large complex genome (5.73 Gb), with size twice higher than those of many decapod shrimps. As such, comparative genomic analyses were implied to investigate factors affecting genome size evolution of decapods. However, clues associated with genome duplication were not identified, and few horizontally transferred sequences were detected. Ultimately, the burst of transposable elements, especially retrotransposons, was determined as the major factor influencing genome expansion. A total of 2 Gb repeats were identified, and RTE-BovB, Jockey, Gypsy, and DIRS were the four major retrotransposons that significantly expanded. Both recent (Jockey and Gypsy) and ancestral (DIRS) originated retrotransposons responsible for the genome evolution. The E. carinicauda genome also exhibited potential for the genomic and experimental research of shrimps.

Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution

DEFF Research Database (Denmark)

Dewhurst, Sally M.; McGranahan, Nicholas; Burrell, Rebecca A.

2014-01-01

The contribution of whole-genome doubling to chromosomal instability (CIN) and tumor evolution is unclear. We use long-term culture of isogenic tetraploid cells from a stable diploid colon cancer progenitor to investigate how a genome-doubling event affects genome stability over time. Rare cells...

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.

Science.gov (United States)

Holt, Carson; Yandell, Mark

2011-12-22

Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of today's projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing 'gold-standard' gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies. We present MAKER2, a genome annotation and data management tool designed for second-generation genome projects. MAKER2 is a multi-threaded, parallelized application that can process second-generation datasets of virtually any size. We show that MAKER2 can produce accurate annotations for novel genomes where training-data are limited, of low quality or even non-existent. MAKER2 also provides an easy means to use mRNA-seq data to improve annotation quality; and it can use these data to update legacy annotations, significantly improving their quality. We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations for manual review. MAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets.

Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

Science.gov (United States)

Abe, Takashi; Hamano, Yuta; Ikemura, Toshimichi

2014-01-01

A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method "BLSOM" for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12 Drosophila species, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.

Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology

DEFF Research Database (Denmark)

Cao, Hongzhi; Hastie, Alex R.; Cao, Dandan

2014-01-01

mutations; however, none of the current detection methods are comprehensive, and currently available methodologies are incapable of providing sufficient resolution and unambiguous information across complex regions in the human genome. To address these challenges, we applied a high-throughput, cost......-effective genome mapping technology to comprehensively discover genome-wide SVs and characterize complex regions of the YH genome using long single molecules (>150 kb) in a global fashion. RESULTS: Utilizing nanochannel-based genome mapping technology, we obtained 708 insertions/deletions and 17 inversions larger...... fosmid data. Of the remaining 270 SVs, 260 are insertions and 213 overlap known SVs in the Database of Genomic Variants. Overall, 609 out of 666 (90%) variants were supported by experimental orthogonal methods or historical evidence in public databases. At the same time, genome mapping also provides...

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

Science.gov (United States)

Swain, Martin T; Tsai, Isheng J; Assefa, Samual A; Newbold, Chris; Berriman, Matthew; Otto, Thomas D

2012-06-07

Genome projects now produce draft assemblies within weeks owing to advanced high-throughput sequencing technologies. For milestone projects such as Escherichia coli or Homo sapiens, teams of scientists were employed to manually curate and finish these genomes to a high standard. Nowadays, this is not feasible for most projects, and the quality of genomes is generally of a much lower standard. This protocol describes software (PAGIT) that is used to improve the quality of draft genomes. It offers flexible functionality to close gaps in scaffolds, correct base errors in the consensus sequence and exploit reference genomes (if available) in order to improve scaffolding and generating annotations. The protocol is most accessible for bacterial and small eukaryotic genomes (up to 300 Mb), such as pathogenic bacteria, malaria and parasitic worms. Applying PAGIT to an E. coli assembly takes ∼24 h: it doubles the average contig size and annotates over 4,300 gene models.

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.

Science.gov (United States)

Kersey, Paul J; Staines, Daniel M; Lawson, Daniel; Kulesha, Eugene; Derwent, Paul; Humphrey, Jay C; Hughes, Daniel S T; Keenan, Stephan; Kerhornou, Arnaud; Koscielny, Gautier; Langridge, Nicholas; McDowall, Mark D; Megy, Karine; Maheswari, Uma; Nuhn, Michael; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Wilson, Derek; Yates, Andrew; Birney, Ewan

2012-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.

Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.

Science.gov (United States)

Jeong, Young-Min; Kim, Namshin; Ahn, Byung Ohg; Oh, Mijin; Chung, Won-Hyong; Chung, Hee; Jeong, Seongmun; Lim, Ki-Byung; Hwang, Yoon-Jung; Kim, Goon-Bo; Baek, Seunghoon; Choi, Sang-Bong; Hyung, Dae-Jin; Lee, Seung-Won; Sohn, Seong-Han; Kwon, Soo-Jin; Jin, Mina; Seol, Young-Joo; Chae, Won Byoung; Choi, Keun Jin; Park, Beom-Seok; Yu, Hee-Ju; Mun, Jeong-Hwan

2016-07-01

This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome. Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.

Lophotrochozoan mitochondrial genomes

Energy Technology Data Exchange (ETDEWEB)

Valles, Yvonne; Boore, Jeffrey L.

2005-10-01

Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

Science.gov (United States)

Thorvaldsdóttir, Helga; Robinson, James T; Mesirov, Jill P

2013-03-01

Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license.

Causes of genome instability

DEFF Research Database (Denmark)

Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

2015-01-01

function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

The Banana Genome Hub

Science.gov (United States)

Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

2013-01-01

Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

Atrativo para as abelhas Apis mellifera e polinização em café (Coffea arabica L.

Directory of Open Access Journals (Sweden)

Darclet Teresinha Malerbo-Souza

2003-01-01

Full Text Available O presente experimento foi conduzido em Jaboticabal, SP, e teve como objetivos estudar uma cultura de café (Coffea arabica L., var. Mundo Novo, quanto à biologia floral, a freqüência e comportamento dos insetos na flor, testar o produto Bee-HereR (Hoescht Shering Agrevo do Brasil Ltda quanto a sua atratividade para as abelhas Apis mellifera e verificar a produção de frutos com e sem a visita dos insetos. Para isso, foram verificados o tempo do desenvolvimento e quantidade de açúcar solúvel do néctar das flores; freqüência das visitações dos insetos, no decorrer do dia, por meio de contagem do número de insetos visitando as flores, a cada 60 minutos, das 8 às 17 horas, 10 minutos em cada horário; tempo (em segundos e tipo de coleta (néctar e/ou pólen dos insetos mais freqüentes; perda de botões florais; porcentagem de flores que se transformaram em frutos; tempo de formação e contagem dos grãos de café, observando-se a porcentagem de frutificação em flores visitadas ou não pelos insetos. Também foram realizados testes por pulverização utilizando-se o produto Bee-HereR , diluído em xarope e em água, em diferentes horários. A flor durou, em média, cerca de 3 dias desde sua abertura até o murchamento. A quantidade de açúcares do néctar apresentou diferença significativa entre os horários, sendo maior às 8 horas (em média, 102,18 ± 8,75 mg de carboidratos totais por flor. A abelha A. mellifera foi o inseto mais freqüente nas flores de café, coletando, principalmente, néctar no decorrer do dia. A perda de botões florais causada pelas chuvas foi, em média, 26,50 ± 11,70%. O tempo para a formação do fruto foi 6 meses e o número de frutos decorrentes do tratamento descoberto foi maior (38,79% e 168,38%, em 1993 e 1994, respectivamente que do tratamento coberto. Apesar da eficiência do produto Bee-HereR ser afetada pelas condições climáticas, ele pode ser usado para atrair as abelhas A. mellifera na

Comparative genomics reveals insights into avian genome evolution and adaptation

DEFF Research Database (Denmark)

Zhang, Guojie; Li, Cai; Li, Qiye

2014-01-01

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, ...

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

Science.gov (United States)

Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

2016-01-04

The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Human genetics and genomics a decade after the release of the draft sequence of the human genome

Science.gov (United States)

2011-01-01

Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with respect to advances in genotyping technologies. These developments are vital for the emergence of genome-wide association studies in the investigation of complex diseases and traits. In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing studies such as the 1000 Genomes Project and the International Cancer Genome Consortium. The high-throughput sequencing and sequence-capture technologies are also providing new opportunities to study Mendelian disorders through exome sequencing and whole-genome sequencing. This paper reviews these major developments in human genetics and genomics over the past decade. PMID:22155605

The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

DEFF Research Database (Denmark)

Gopalakrishnan, Shyam; Samaniego Castruita, Jose Alfredo; Sinding, Mikkel Holger Strander

2017-01-01

Background An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a......Background An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data...

Cephalopod genomics

DEFF Research Database (Denmark)

Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

2012-01-01

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

Organizational heterogeneity of vertebrate genomes.

Science.gov (United States)

Frenkel, Svetlana; Kirzhner, Valery; Korol, Abraham

2012-01-01

Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

Organizational heterogeneity of vertebrate genomes.

Directory of Open Access Journals (Sweden)

Svetlana Frenkel

Full Text Available Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

Genomic signal processing

CERN Document Server

Shmulevich, Ilya

2007-01-01

Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score.

Science.gov (United States)

Lee, Hayan; Schatz, Michael C

2012-08-15

Genome resequencing and short read mapping are two of the primary tools of genomics and are used for many important applications. The current state-of-the-art in mapping uses the quality values and mapping quality scores to evaluate the reliability of the mapping. These attributes, however, are assigned to individual reads and do not directly measure the problematic repeats across the genome. Here, we present the Genome Mappability Score (GMS) as a novel measure of the complexity of resequencing a genome. The GMS is a weighted probability that any read could be unambiguously mapped to a given position and thus measures the overall composition of the genome itself. We have developed the Genome Mappability Analyzer to compute the GMS of every position in a genome. It leverages the parallelism of cloud computing to analyze large genomes, and enabled us to identify the 5-14% of the human, mouse, fly and yeast genomes that are difficult to analyze with short reads. We examined the accuracy of the widely used BWA/SAMtools polymorphism discovery pipeline in the context of the GMS, and found discovery errors are dominated by false negatives, especially in regions with poor GMS. These errors are fundamental to the mapping process and cannot be overcome by increasing coverage. As such, the GMS should be considered in every resequencing project to pinpoint the 'dark matter' of the genome, including of known clinically relevant variations in these regions. The source code and profiles of several model organisms are available at http://gma-bio.sourceforge.net

The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies.

Science.gov (United States)

Argout, X; Martin, G; Droc, G; Fouet, O; Labadie, K; Rivals, E; Aury, J M; Lanaud, C

2017-09-15

Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes. We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome. We combined four Illumina large insert size mate paired libraries with 52x of Pacific Biosciences long reads to correct misassembled regions and reduced the number of scaffolds. We then used genotyping by sequencing (GBS) methods to increase the proportion of the assembly anchored to chromosomes. The scaffold number decreased from 4,792 in assembly V1 to 554 in V2 while the scaffold N50 size has increased from 0.47 Mb in V1 to 6.5 Mb in V2. A total of 96.7% of the assembly was anchored to the 10 chromosomes compared to 66.8% in the previous version. Unknown sites (Ns) were reduced from 10.8% to 5.7%. In addition, we updated the functional annotations and performed a new RefSeq structural annotation based on RNAseq evidence. Theobroma cacao Criollo genome version 2 will be a valuable resource for the investigation of complex traits at the genomic level and for future comparative genomics and genetics studies in cacao tree. New functional tools and annotations are available on the Cocoa Genome Hub ( http://cocoa-genome-hub.southgreen.fr ).

Conversion of nicotinic acid to trigonelline is catalyzed by N-methyltransferase belonged to motif B′ methyltransferase family in Coffea arabica

International Nuclear Information System (INIS)

Mizuno, Kouichi; Matsuzaki, Masahiro; Kanazawa, Shiho; Tokiwano, Tetsuo; Yoshizawa, Yuko; Kato, Misako

2014-01-01

Graphical abstract: Trigonelline synthase catalyzes the conversion of nicotinic acid to trigonelline. We isolated and characterized trigonelline synthase gene(s) from Coffea arabica. - Highlights: • Trigonelline is a major compound in coffee been same as caffeine is. • We isolated and characterized trigonelline synthase gene. • Coffee trigonelline synthases are highly homologous with coffee caffeine synthases. • This study contributes the fully understanding of pyridine alkaloid metabolism. - Abstract: Trigonelline (N-methylnicotinate), a member of the pyridine alkaloids, accumulates in coffee beans along with caffeine. The biosynthetic pathway of trigonelline is not fully elucidated. While it is quite likely that the production of trigonelline from nicotinate is catalyzed by N-methyltransferase, as is caffeine synthase (CS), the enzyme(s) and gene(s) involved in N-methylation have not yet been characterized. It should be noted that, similar to caffeine, trigonelline accumulation is initiated during the development of coffee fruits. Interestingly, the expression profiles for two genes homologous to caffeine synthases were similar to the accumulation profile of trigonelline. We presumed that these two CS-homologous genes encoded trigonelline synthases. These genes were then expressed in Escherichiacoli, and the resulting recombinant enzymes that were obtained were characterized. Consequently, using the N-methyltransferase assay with S-adenosyl[methyl- 14 C]methionine, it was confirmed that these recombinant enzymes catalyzed the conversion of nicotinate to trigonelline, coffee trigonelline synthases (termed CTgS1 and CTgS2) were highly identical (over 95% identity) to each other. The sequence homology between the CTgSs and coffee CCS1 was 82%. The pH-dependent activity curve of CTgS1 and CTgS2 revealed optimum activity at pH 7.5. Nicotinate was the specific methyl acceptor for CTgSs, and no activity was detected with any other nicotinate derivatives, or with

Conversion of nicotinic acid to trigonelline is catalyzed by N-methyltransferase belonged to motif B′ methyltransferase family in Coffea arabica

Energy Technology Data Exchange (ETDEWEB)

Mizuno, Kouichi, E-mail: koumno@akita-pu.ac.jp [Faculty of Bioresource Sciences, Akita Prefectural University, Akita City, Akita 010-0195 (Japan); Matsuzaki, Masahiro [Faculty of Bioresource Sciences, Akita Prefectural University, Akita City, Akita 010-0195 (Japan); Kanazawa, Shiho [Graduate School of Humanities and Sciences, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo 112-8610 (Japan); Tokiwano, Tetsuo; Yoshizawa, Yuko [Faculty of Bioresource Sciences, Akita Prefectural University, Akita City, Akita 010-0195 (Japan); Kato, Misako [Graduate School of Humanities and Sciences, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo 112-8610 (Japan)

2014-10-03

Graphical abstract: Trigonelline synthase catalyzes the conversion of nicotinic acid to trigonelline. We isolated and characterized trigonelline synthase gene(s) from Coffea arabica. - Highlights: • Trigonelline is a major compound in coffee been same as caffeine is. • We isolated and characterized trigonelline synthase gene. • Coffee trigonelline synthases are highly homologous with coffee caffeine synthases. • This study contributes the fully understanding of pyridine alkaloid metabolism. - Abstract: Trigonelline (N-methylnicotinate), a member of the pyridine alkaloids, accumulates in coffee beans along with caffeine. The biosynthetic pathway of trigonelline is not fully elucidated. While it is quite likely that the production of trigonelline from nicotinate is catalyzed by N-methyltransferase, as is caffeine synthase (CS), the enzyme(s) and gene(s) involved in N-methylation have not yet been characterized. It should be noted that, similar to caffeine, trigonelline accumulation is initiated during the development of coffee fruits. Interestingly, the expression profiles for two genes homologous to caffeine synthases were similar to the accumulation profile of trigonelline. We presumed that these two CS-homologous genes encoded trigonelline synthases. These genes were then expressed in Escherichiacoli, and the resulting recombinant enzymes that were obtained were characterized. Consequently, using the N-methyltransferase assay with S-adenosyl[methyl-{sup 14}C]methionine, it was confirmed that these recombinant enzymes catalyzed the conversion of nicotinate to trigonelline, coffee trigonelline synthases (termed CTgS1 and CTgS2) were highly identical (over 95% identity) to each other. The sequence homology between the CTgSs and coffee CCS1 was 82%. The pH-dependent activity curve of CTgS1 and CTgS2 revealed optimum activity at pH 7.5. Nicotinate was the specific methyl acceptor for CTgSs, and no activity was detected with any other nicotinate derivatives, or

Sequencing of a new target genome: the Pediculus humanus humanus (Phthiraptera: Pediculidae) genome project.

Science.gov (United States)

Pittendrigh, B R; Clark, J M; Johnston, J S; Lee, S H; Romero-Severson, J; Dasch, G A

2006-11-01

The human body louse, Pediculus humanus humanus (L.), and the human head louse, Pediculus humanus capitis, belong to the hemimetabolous order Phthiraptera. The body louse is the primary vector that transmits the bacterial agents of louse-borne relapsing fever, trench fever, and epidemic typhus. The genomes of the bacterial causative agents of several of these aforementioned diseases have been sequenced. Thus, determining the body louse genome will enhance studies of host-vector-pathogen interactions. Although not important as a major disease vector, head lice are of major social concern. Resistance to traditional pesticides used to control head and body lice have developed. It is imperative that new molecular targets be discovered for the development of novel compounds to control these insects. No complete genome sequence exists for a hemimetabolous insect species primarily because hemimetabolous insects often have large (2000 Mb) to very large (up to 16,300 Mb) genomes. Fortuitously, we determined that the human body louse has one of the smallest genome sizes known in insects, suggesting it may be a suitable choice as a minimal hemimetabolous genome in which many genes have been eliminated during its adaptation to human parasitism. Because many louse species infest birds and mammals, the body louse genome-sequencing project will facilitate studies of their comparative genomics. A 6-8X coverage of the body louse genome, plus sequenced expressed sequence tags, should provide the entomological, evolutionary biology, medical, and public health communities with useful genetic information.

Theory of microbial genome evolution

Science.gov (United States)

Koonin, Eugene

Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

Applied Genomics of Foodborne Pathogens

DEFF Research Database (Denmark)

and customized source of information designed for and accessible to microbiologists interested in applying cutting-edge genomics in food safety and public health research. This book fills this void with a well-selected collection of topics, case studies, and bioinformatics tools contributed by experts......This book provides a timely and thorough snapshot into the emerging and fast evolving area of applied genomics of foodborne pathogens. Driven by the drastic advance of whole genome shot gun sequencing (WGS) technologies, genomics applications are becoming increasingly valuable and even essential...... at the forefront of foodborne pathogen genomics research....

Genome Variation Map: a data repository of genome variations in BIG Data Center.

Science.gov (United States)

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2018-01-04

The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genome Variation Map: a data repository of genome variations in BIG Data Center

Science.gov (United States)

Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang

2018-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473

The bonobo genome compared with the chimpanzee and human genomes

Science.gov (United States)

Prüfer, Kay; Munch, Kasper; Hellmann, Ines; Akagi, Keiko; Miller, Jason R.; Walenz, Brian; Koren, Sergey; Sutton, Granger; Kodira, Chinnappa; Winer, Roger; Knight, James R.; Mullikin, James C.; Meader, Stephen J.; Ponting, Chris P.; Lunter, Gerton; Higashino, Saneyuki; Hobolth, Asger; Dutheil, Julien; Karakoç, Emre; Alkan, Can; Sajjadian, Saba; Catacchio, Claudia Rita; Ventura, Mario; Marques-Bonet, Tomas; Eichler, Evan E.; André, Claudine; Atencia, Rebeca; Mugisha, Lawrence; Junhold, Jörg; Patterson, Nick; Siebauer, Michael; Good, Jeffrey M.; Fischer, Anne; Ptak, Susan E.; Lachmann, Michael; Symer, David E.; Mailund, Thomas; Schierup, Mikkel H.; Andrés, Aida M.; Kelso, Janet; Pääbo, Svante

2012-01-01

Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours1–4, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other. PMID:22722832

Fungal Genomics for Energy and Environment

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor V.

2013-03-11

Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome

NARCIS (Netherlands)

Sharp, Andrew J.; Hansen, Sierra; Selzer, Rebecca R.; Cheng, Ze; Regan, Regina; Hurst, Jane A.; Stewart, Helen; Price, Sue M.; Blair, Edward; Hennekam, Raoul C.; Fitzpatrick, Carrie A.; Segraves, Rick; Richmond, Todd A.; Guiver, Cheryl; Albertson, Donna G.; Pinkel, Daniel; Eis, Peggy S.; Schwartz, Stuart; Knight, Samantha J. L.; Eichler, Evan E.

2006-01-01

Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome, we investigated 130 regions that we hypothesized as candidates for previously undescribed genomic

The fishes of Genome 10K

KAUST Repository

Bernardi, Giacomo

2012-09-01

The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

The fishes of Genome 10K

KAUST Repository

Bernardi, Giacomo; Wiley, Edward O.; Mansour, Hicham; Miller, Michael R.; Ortí , Guillermo; Haussler, David H.; O'Brien, Stephen J O; Ryder, Oliver A.; Venkatesh, Byrappa

2012-01-01

The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease

NARCIS (Netherlands)

Versteeg, Bart; Bruisten, Sylvia M.; Pannekoek, Yvonne; Jolley, Keith A.; Maiden, Martin C. J.; van der Ende, Arie; Harrison, Odile B.

2018-01-01

Background: Chlamydia trachomatis (Ct) plasmid has been shown to encode genes essential for infection. We evaluated the population structure of Ct using whole-genome sequence data (WGS). In particular, the relationship between the Ct genome, plasmid and disease was investigated. Results: WGS data

Yeast genome sequencing:

DEFF Research Database (Denmark)

Piskur, Jure; Langkjær, Rikke Breinhold

2004-01-01

For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

Genome size variation affects song attractiveness in grasshoppers: evidence for sexual selection against large genomes.

Science.gov (United States)

Schielzeth, Holger; Streitner, Corinna; Lampe, Ulrike; Franzke, Alexandra; Reinhold, Klaus

2014-12-01

Genome size is largely uncorrelated to organismal complexity and adaptive scenarios. Genetic drift as well as intragenomic conflict have been put forward to explain this observation. We here study the impact of genome size on sexual attractiveness in the bow-winged grasshopper Chorthippus biguttulus. Grasshoppers show particularly large variation in genome size due to the high prevalence of supernumerary chromosomes that are considered (mildly) selfish, as evidenced by non-Mendelian inheritance and fitness costs if present in high numbers. We ranked male grasshoppers by song characteristics that are known to affect female preferences in this species and scored genome sizes of attractive and unattractive individuals from the extremes of this distribution. We find that attractive singers have significantly smaller genomes, demonstrating that genome size is reflected in male courtship songs and that females prefer songs of males with small genomes. Such a genome size dependent mate preference effectively selects against selfish genetic elements that tend to increase genome size. The data therefore provide a novel example of how sexual selection can reinforce natural selection and can act as an agent in an intragenomic arms race. Furthermore, our findings indicate an underappreciated route of how choosy females could gain indirect benefits. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

The tiger genome and comparative analysis with lion and snow leopard genomes.

Science.gov (United States)

Cho, Yun Sung; Hu, Li; Hou, Haolong; Lee, Hang; Xu, Jiaohui; Kwon, Soowhan; Oh, Sukhun; Kim, Hak-Min; Jho, Sungwoong; Kim, Sangsoo; Shin, Young-Ah; Kim, Byung Chul; Kim, Hyunmin; Kim, Chang-Uk; Luo, Shu-Jin; Johnson, Warren E; Koepfli, Klaus-Peter; Schmidt-Küntzel, Anne; Turner, Jason A; Marker, Laurie; Harper, Cindy; Miller, Susan M; Jacobs, Wilhelm; Bertola, Laura D; Kim, Tae Hyung; Lee, Sunghoon; Zhou, Qian; Jung, Hyun-Ju; Xu, Xiao; Gadhvi, Priyvrat; Xu, Pengwei; Xiong, Yingqi; Luo, Yadan; Pan, Shengkai; Gou, Caiyun; Chu, Xiuhui; Zhang, Jilin; Liu, Sanyang; He, Jing; Chen, Ying; Yang, Linfeng; Yang, Yulan; He, Jiaju; Liu, Sha; Wang, Junyi; Kim, Chul Hong; Kwak, Hwanjong; Kim, Jong-Soo; Hwang, Seungwoo; Ko, Junsu; Kim, Chang-Bae; Kim, Sangtae; Bayarlkhagva, Damdin; Paek, Woon Kee; Kim, Seong-Jin; O'Brien, Stephen J; Wang, Jun; Bhak, Jong

2013-01-01

Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species.

From Genomics to Gene Therapy: Induced Pluripotent Stem Cells Meet Genome Editing.

Science.gov (United States)

Hotta, Akitsu; Yamanaka, Shinya

2015-01-01

The advent of induced pluripotent stem (iPS) cells has opened up numerous avenues of opportunity for cell therapy, including the initiation in September 2014 of the first human clinical trial to treat dry age-related macular degeneration. In parallel, advances in genome-editing technologies by site-specific nucleases have dramatically improved our ability to edit endogenous genomic sequences at targeted sites of interest. In fact, clinical trials have already begun to implement this technology to control HIV infection. Genome editing in iPS cells is a powerful tool and enables researchers to investigate the intricacies of the human genome in a dish. In the near future, the groundwork laid by such an approach may expand the possibilities of gene therapy for treating congenital disorders. In this review, we summarize the exciting progress being made in the utilization of genomic editing technologies in pluripotent stem cells and discuss remaining challenges toward gene therapy applications.

The tiger genome and comparative analysis with lion and snow leopard genomes

Science.gov (United States)

Cho, Yun Sung; Hu, Li; Hou, Haolong; Lee, Hang; Xu, Jiaohui; Kwon, Soowhan; Oh, Sukhun; Kim, Hak-Min; Jho, Sungwoong; Kim, Sangsoo; Shin, Young-Ah; Kim, Byung Chul; Kim, Hyunmin; Kim, Chang-uk; Luo, Shu-Jin; Johnson, Warren E.; Koepfli, Klaus-Peter; Schmidt-Küntzel, Anne; Turner, Jason A.; Marker, Laurie; Harper, Cindy; Miller, Susan M.; Jacobs, Wilhelm; Bertola, Laura D.; Kim, Tae Hyung; Lee, Sunghoon; Zhou, Qian; Jung, Hyun-Ju; Xu, Xiao; Gadhvi, Priyvrat; Xu, Pengwei; Xiong, Yingqi; Luo, Yadan; Pan, Shengkai; Gou, Caiyun; Chu, Xiuhui; Zhang, Jilin; Liu, Sanyang; He, Jing; Chen, Ying; Yang, Linfeng; Yang, Yulan; He, Jiaju; Liu, Sha; Wang, Junyi; Kim, Chul Hong; Kwak, Hwanjong; Kim, Jong-Soo; Hwang, Seungwoo; Ko, Junsu; Kim, Chang-Bae; Kim, Sangtae; Bayarlkhagva, Damdin; Paek, Woon Kee; Kim, Seong-Jin; O’Brien, Stephen J.; Wang, Jun; Bhak, Jong

2013-01-01

Tigers and their close relatives (Panthera) are some of the world’s most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats’ hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species. PMID:24045858

Human Genome Project

Energy Technology Data Exchange (ETDEWEB)

Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

1998-01-04

The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

Human Genome Program

Energy Technology Data Exchange (ETDEWEB)

1993-01-01

The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

Genomic insight into the common carp (Cyprinus carpio genome by sequencing analysis of BAC-end sequences

Directory of Open Access Journals (Sweden)

Wang Jintu

2011-04-01

Full Text Available Abstract Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio, a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3

Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences

Science.gov (United States)

2011-01-01

Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of

A decade of human genome project conclusion: Scientific diffusion about our genome knowledge.

Science.gov (United States)

Moraes, Fernanda; Góes, Andréa

2016-05-06

The Human Genome Project (HGP) was initiated in 1990 and completed in 2003. It aimed to sequence the whole human genome. Although it represented an advance in understanding the human genome and its complexity, many questions remained unanswered. Other projects were launched in order to unravel the mysteries of our genome, including the ENCyclopedia of DNA Elements (ENCODE). This review aims to analyze the evolution of scientific knowledge related to both the HGP and ENCODE projects. Data were retrieved from scientific articles published in 1990-2014, a period comprising the development and the 10 years following the HGP completion. The fact that only 20,000 genes are protein and RNA-coding is one of the most striking HGP results. A new concept about the organization of genome arose. The ENCODE project was initiated in 2003 and targeted to map the functional elements of the human genome. This project revealed that the human genome is pervasively transcribed. Therefore, it was determined that a large part of the non-protein coding regions are functional. Finally, a more sophisticated view of chromatin structure emerged. The mechanistic functioning of the genome has been redrafted, revealing a much more complex picture. Besides, a gene-centric conception of the organism has to be reviewed. A number of criticisms have emerged against the ENCODE project approaches, raising the question of whether non-conserved but biochemically active regions are truly functional. Thus, HGP and ENCODE projects accomplished a great map of the human genome, but the data generated still requires further in depth analysis. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:215-223, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

[Genome editing of industrial microorganism].

Science.gov (United States)

Zhu, Linjiang; Li, Qi

2015-03-01

Genome editing is defined as highly-effective and precise modification of cellular genome in a large scale. In recent years, such genome-editing methods have been rapidly developed in the field of industrial strain improvement. The quickly-updating methods thoroughly change the old mode of inefficient genetic modification, which is "one modification, one selection marker, and one target site". Highly-effective modification mode in genome editing have been developed including simultaneous modification of multiplex genes, highly-effective insertion, replacement, and deletion of target genes in the genome scale, cut-paste of a large DNA fragment. These new tools for microbial genome editing will certainly be applied widely, and increase the efficiency of industrial strain improvement, and promote the revolution of traditional fermentation industry and rapid development of novel industrial biotechnology like production of biofuel and biomaterial. The technological principle of these genome-editing methods and their applications were summarized in this review, which can benefit engineering and construction of industrial microorganism.

Genome Update: alignment of bacterial chromosomes

DEFF Research Database (Denmark)

Ussery, David; Jensen, Mette; Poulsen, Tine Rugh

2004-01-01

There are four new microbial genomes listed in this month's Genome Update, three belonging to Gram-positive bacteria and one belonging to an archaeon that lives at pH 0; all of these genomes are listed in Table 1⇓. The method of genome comparison this month is that of genome alignment and, as an ...

Genome-wide analysis of wild-type Epstein-Barr virus genomes derived from healthy individuals of the 1,000 Genomes Project.

Science.gov (United States)

Santpere, Gabriel; Darre, Fleur; Blanco, Soledad; Alcami, Antonio; Villoslada, Pablo; Mar Albà, M; Navarro, Arcadi

2014-04-01

Most people in the world (∼90%) are infected by the Epstein-Barr virus (EBV), which establishes itself permanently in B cells. Infection by EBV is related to a number of diseases including infectious mononucleosis, multiple sclerosis, and different types of cancer. So far, only seven complete EBV strains have been described, all of them coming from donors presenting EBV-related diseases. To perform a detailed comparative genomic analysis of EBV including, for the first time, EBV strains derived from healthy individuals, we reconstructed EBV sequences infecting lymphoblastoid cell lines (LCLs) from the 1000 Genomes Project. As strain B95-8 was used to transform B cells to obtain LCLs, it is always present, but a specific deletion in its genome sets it apart from natural EBV strains. After studying hundreds of individuals, we determined the presence of natural EBV in at least 10 of them and obtained a set of variants specific to wild-type EBV. By mapping the natural EBV reads into the EBV reference genome (NC007605), we constructed nearly complete wild-type viral genomes from three individuals. Adding them to the five disease-derived EBV genomic sequences available in the literature, we performed an in-depth comparative genomic analysis. We found that latency genes harbor more nucleotide diversity than lytic genes and that six out of nine latency-related genes, as well as other genes involved in viral attachment and entry into host cells, packaging, and the capsid, present the molecular signature of accelerated protein evolution rates, suggesting rapid host-parasite coevolution.

Fueling the Future with Fungal Genomes

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor V.

2014-10-27

Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics will lead to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such ‘parts’ suggested by comparative genomics and functional analysis in these areas are presented here.

Genomic individuality and its biological implications.

Science.gov (United States)

Zhao, J

1996-06-01

It is a widely accepted fundamental concept that all somatic genomes of a human individual are identical to each other. The theoretical basis of this concept is that all of these somatic genomes are the descendants of the genome of a single fertilized cell as well as the simple replicated products of asexual reproduction, thus not forming any new recombined genomes. The question here is whether such a concept might only represent one side of somatic genome biology and, even worse, whether it has perhaps already led to a very prevalent misconception that within the organism body, there exists no variability among individual somatic genomes. A hypothesis, called genomic individuality, is proposed, simply saying that every individual somatic genome, perhaps with rare exceptions, has its own unique or individual 'genetic identity' or 'fingerprint', which is characterized by its distinctive sequences or patterns of deoxyribonucleic acid molecules, or both. Thus, no two somatic genomes can be identical to each other in every or all aspects, and consequently, there must be a great deal of genomic variation present within the body of any multicellular organism. The concept or hypothesis of genomic individuality would not only provide a more complete understanding of genome biology, but also suggest a new insight into the studies of the biology of cells and organisms.

Comparative genomics of Lactobacillus and other LAB

DEFF Research Database (Denmark)

Wassenaar, Trudy M.; Lukjancenko, Oksana

2014-01-01

that of the others, with the two Streptococcus species having the shortest genomes. The widest distribution in genome content was observed for Lactobacillus. The number of tRNA and rRNA gene copies varied considerably, with exceptional high numbers observed for Lb. delbrueckii, while these numbers were relatively......The genomes of 66 LABs, belonging to five different genera, were compared for genome size and gene content. The analyzed genomes included 37 Lactobacillus genomes of 17 species, six Lactococcus lactis genomes, four Leuconostoc genomes of three species, six Streptococcus genomes of two species...

One bacterial cell, one complete genome.

Directory of Open Access Journals (Sweden)

Tanja Woyke

2010-04-01

Full Text Available While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200-900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA. Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs, indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

One Bacterial Cell, One Complete Genome

Energy Technology Data Exchange (ETDEWEB)

Woyke, Tanja; Tighe, Damon; Mavrommatis, Konstantinos; Clum, Alicia; Copeland, Alex; Schackwitz, Wendy; Lapidus, Alla; Wu, Dongying; McCutcheon, John P.; McDonald, Bradon R.; Moran, Nancy A.; Bristow, James; Cheng, Jan-Fang

2010-04-26

While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200?900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

Mitochondrial genome sequences and comparative genomics ofPhytophthora ramorum and P. sojae

Energy Technology Data Exchange (ETDEWEB)

Martin, Frank N.; Douda, Bensasson; Tyler, Brett M.; Boore,Jeffrey L.

2007-01-01

The complete sequences of the mitochondrial genomes of theoomycetes of Phytophthora ramorum and P. sojae were determined during thecourse of their complete nuclear genome sequencing (Tyler, et al. 2006).Both are circular, with sizes of 39,314 bp for P. ramorum and 42,975 bpfor P. sojae. Each contains a total of 37 identifiable protein-encodinggenes, 25 or 26 tRNAs (P. sojae and P. ramorum, respectively)specifying19 amino acids, and a variable number of ORFs (7 for P. ramorum and 12for P. sojae) which are potentially additional functional genes.Non-coding regions comprise approximately 11.5 percent and 18.4 percentof the genomes of P. ramorum and P. sojae, respectively. Relative to P.sojae, there is an inverted repeat of 1,150 bp in P. ramorum thatincludes an unassigned unique ORF, a tRNA gene, and adjacent non-codingsequences, but otherwise the gene order in both species is identical.Comparisons of these genomes with published sequences of the P. infestansmitochondrial genome reveals a number of similarities, but the gene orderin P. infestans differs in two adjacent locations due to inversions.Sequence alignments of the three genomes indicated sequence conservationranging from 75 to 85 percent and that specific regions were morevariable than others.

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.

Science.gov (United States)

Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

2017-01-04

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists