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Sample records for aa genome oryza

  1. SSR Analysis on Diversity of AA Genome Oryza Species in the Southeast and South Asia

    Institute of Scientific and Technical Information of China (English)

    LU Jian-zhen; ZHANG Xiao-li; WANG Hai-gang; YUAN Xiao-ping; XU Qun; WANG Yi-ping; YU Han-yong; TANG Sheng-xiang; WEI Xing-hua

    2008-01-01

    To investigate genetic diversities among the AA genome Oryza species in the Southeast and South'Asia, a total of 428 accessions of the AA genome Oryza species were genotyped using 36 simple sequence repeats (SSR) markers distributed throughout the rice genome. All of the 36 SSR markers generated polymorphic bands, revealing 100% polymorphism. The number of alleles per locus ranged from 3 to 17 with the mean of 8.6. The Nei's genetic diversity index (He) ranged from 0.337 at RM455 to 0.865 at RM 169 with an average value of 0.650. The genetic diversity of the AA genome Oryza species in the Southeast Asia was obviously higher than that in the South Asia. Among the detected Oryza species in the South and Southeast Asia, O. rufipogon showed the highest genetic diversity. Meanwhile, a higher genetic differentiation (Fst) was found among the detected Oryza species in the Southeast Asia than in the South Asia. The Fst value between O. nivara and O. sativa was the highest. The results from the number of specific alleles, specific loci, and allele frequency confirmed the greater genetic variation among the detected species. In addition, the specific allele in RM161 displayed higher frequency (0.193), suggesting its important function in identifying Oryza species of AA genome.

  2. SSR Analysis on Diversity of AA Genome Oryza Species in the Southeast and South Asia

    Directory of Open Access Journals (Sweden)

    Jian-zhen LU

    2008-12-01

    Full Text Available To investigate genetic diversities among the AA genome Oryza species in the Southeast and South Asia, a total of 428 accessions of the AA genome Oryza species were genotyped using 36 simple sequence repeats (SSR markers distributed throughout the rice genome. All of the 36 SSR markers generated polymorphic bands, revealing 100% polymorphism. The number of alleles per locus ranged from 3 to 17 with the mean of 8.6. The Nei's genetic diversity index (He ranged from 0.337 at RM455 to 0.865 at RM169 with an average value of 0.650. The genetic diversity of the AA genome Oryza species in the Southeast Asia was obviously higher than that in the South Asia. Among the detected Oryza species in the South and Southeast Asia, O. rufipogon showed the highest genetic diversity. Meanwhile, a higher genetic differentiation (Fst was found among the detected Oryza species in the Southeast Asia than in the South Asia. The Fst value between O. nivara and O. sativa was the highest. The results from the number of specific alleles, specific loci, and allele frequency confirmed the greater genetic variation among the detected species. In addition, the specific allele in RM161 displayed higher frequency (0.193, suggesting its important function in identifying Oryza species of AA genome.

  3. Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus

    OpenAIRE

    Petit, J.; Bourgeois, E; Stenger, W.; Bes, M.; Droc, G.; Meynard, D.; Courtois, B.; Ghesquière, Alain; Sabot, François; Panaud, O.; Guiderdoni, E.

    2009-01-01

    Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the eleme...

  4. Seed Length Controlled by Same Locus in Four Different AA Genome Species of Genus Oryza

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yu; LI Jing; ZHOU Jia-wu; XU Peng; DENG Xian-neng; YANG Fei; DENG Wei; HU Feng-yi; TAO Da-yun

    2014-01-01

    To broaden the genetic basis and overcome the yield plateau in Asian cultivated rice, the exploitation and utilization of favorable alleles from rice species with the AA genome has become important and urgent in modern breeding programs. Four different interspecific populations were used to detect quantitative trait locus (QTL) for seed length, including a BC4F2 population derived from Oryza glumaepatula crossed with Dianjingyou 1 (a japonica cultivar), a BC4F2 population derived from O. nivara crossed with Dianjingyou 1, a BC7F1 population derived from a cross between O. longistaminata and RD23 (an indica cultivar), and a BC8F1 population derived from a cross between O. glaberrima and Dianjingyou 1. The QTLs for seed length in four different populations were termed as SL-3a, SL-3b, SL-3c and SL-3d, respectively. They had good collinearity and accounted for 49% to 60% of the phenotypic variations. Sequencing data indicated that four QTLs were different alleles of GS3 which were responsible for the seed length variation between O. sativa and its four AA genome relatives. These results will be valuable for confirming the evolution of GS3 and also be helpful for rice breeding.

  5. Progress on Transferring Elite Genes from Non-AA Genome Wild Rice into Oryza sativa through Interspecific Hybridization

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The progress of research on transferring elite genes from non-AA genome wild rice into Oryza sativa through interspecific hybridization are in three respects,that is,breeding monosomic alien addition lines (MAALs),constructing introgression lines (ILs) and analyzing the heredity of the characters and mapping the related genes.There are serious reproductive barriers,mainly incrossability and hybrid sterility,in the interspecific hybridization of O.sativa with non-AA genome wild rice.These are the 'bottleneck' for transferring elite genes from wild rice to O.sativa.Combining traditional crossing method with biotechnique is a reliable way to overcome the reproductive barriers and to improve the utilizing efficiency of non-AA genome wild rice.

  6. Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus.

    Science.gov (United States)

    Petit, Julie; Bourgeois, Emmanuelle; Stenger, Wilfried; Bès, Martine; Droc, Gaétan; Meynard, Donaldo; Courtois, Brigitte; Ghesquière, Alain; Sabot, François; Panaud, Olivier; Guiderdoni, Emmanuel

    2009-12-01

    Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element in the lineages. In that aim, we used a combination of Southern hybridization with a reverse transcriptase (RT) probe and an adapter-PCR mediated amplification, which allowed the sequencing of the genomic regions flanking Tos17 insertions. This analysis was carried out in a collection of 47 A-genome Oryza species accessions and 202 accessions of a core collection of Oryza sativa L. representative of the diversity of the species. Our Southern hybridization results show that Tos17 is present in all the accessions of the A-genome Oryza species, except for the South American species O. glumaepatula and the African species O. glaberrima and O. breviligulata. In O. sativa, the number of putative copies of Tos17 per accession ranged from 1 to 11 and multivariate analysis based on presence/absence of putative copies yielded a varietal clustering which is consistent with the isozyme classification of rice. Adapter PCR amplification and sequencing of flanking regions of Tos17 insertions in A-genome species other than O. sativa, followed by anchoring on the Nipponbare genome sequence, revealed 13 insertion sites of Tos17 in the surveyed O. rufipogon and O. longistaminata accessions, including one shared by both species. In O. sativa, the same approach revealed 25 insertions in the 6 varietal groups. Four insertion sites located on chromosomes 1, 2, 10, and 11 were found orthologous in O. rufipogon and O. sativa. The chromosome 1 insertion was also shared between O. rufipogon and O

  7. Genome evolution of Oryza

    Directory of Open Access Journals (Sweden)

    Tieyan Liu

    2014-01-01

    Full Text Available The genus Oryza is composed of approximately 24 species. Wild species of Oryza contain a largely untapped resource of agronomically important genes. As an increasing number of genomes of wild rice species have been or will be sequenced, Oryza is becoming a model system for plant comparative, functional and evolutionary genomics studies. Comparative analyses of large genomic regions and whole-genome sequences have revealed molecular mechanisms involved in genome size variation, gene movement, genome evolution of polyploids, transition of euchromatin to heterochromatin and centromere evolution in the genus Oryza. Transposon activity and removal of transposable elements by unequal recombination or illegitimate recombination are two important factors contributing to expansion or contraction of Oryza genomes. Double-strand break repair mediated gene movement, especially non-homologous end joining, is an important source of non-colinear genes. Transition of euchromatin to heterochromatin is accompanied by transposable element amplification, segmental and tandem duplication of genic segments, and acquisition of heterochromatic genes from other genomic locations. Comparative analyses of multiple genomes dramatically improve the precision and sensitivity of evolutionary inference than single-genome analyses can provide. Further investigations on the impact of structural variation, lineage-specific genes and evolution of agriculturally important genes on phenotype diversity and adaptation in the genus Oryza should facilitate molecular breeding and genetic improvement of rice.

  8. 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/.

  9. OryzaGenome: Genome Diversity Database of Wild Oryza Species.

    Science.gov (United States)

    Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi-Xuan; Han, Bin; Kurata, Nori

    2016-01-01

    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 text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited 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/.

  10. Transposable element distribution, abundance and role in genome size variation in the genus Oryza.

    Science.gov (United States)

    Zuccolo, Andrea; Sebastian, Aswathy; Talag, Jayson; Yu, Yeisoo; Kim, HyeRan; Collura, Kristi; Kudrna, Dave; Wing, Rod A

    2007-08-29

    The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop - rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation. We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus.

  11. Transposable element distribution, abundance and role in genome size variation in the genus Oryza

    Directory of Open Access Journals (Sweden)

    Collura Kristi

    2007-08-01

    Full Text Available Abstract Background The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop – rice (Oryza sativa [AA]. Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements in shaping these genomes and in their contributing to genome size variation. Results We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Conclusion Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys account for a significant portion of the genome size variations present in the Oryza genus.

  12. 基于ISSR标记的稻属AA基因组遗传多样性分析%ANALYSIS ON GENETIC DIVERSITY OF AA-GENOME ORYZA SPECIES BY ISSR MARKERS

    Institute of Scientific and Technical Information of China (English)

    段世华; 郑卓; 罗强; 龙伟雄; 廖佛才

    2013-01-01

      In order to determine genetic diversity of the AA-genome Oryza species (Poaceae), inter-simple sequence repeat (ISSR) markers from a total of 62 rice accessions collected worldwide were analyzed. These accessions encompassed six wild (O. nivara, O. rufipogon, O. barthii, O. longistaminata, O. glumaepatula, and O. meridionalis) and two cultivated (O. sativa and O. glaberrima) species. 21 selected ISSR primers that produced consistent and repeatable banding patterns revealed significant polymorphisms among the 62 rice accessions with an overall gene diversity (DG) of 0.527, indicating the power of ISSR markers in studying genetic diversity in Oryza germplasm. The consensus tree constructed on the basis of the pairwise Jaccard similarity coefficients of the ISSR banding pattern revealed an evident genetic variation relationships of the AA-genome Oryza species with high bootstrap value supports. It is concluded from this study that the Oryza species from different continents possessed close linkages and current classification of the AA-genome Oryza species suggested by Vaughan (1989) remains valid, particularly in relation to that of the Asian wild rice. The knowledge will be useful for the effective utilization of AA-genome wild Oryza species in rice breeding programs.%  为了确定稻属AA基因组物种间的遗传差异和系统进化关系,62份来自广泛地理分布的水稻品系被用于 ISSR 标记分析。这些品系包含有6个野生稻种(O. nivara, O. rufipogon、O. barthi, O. longistaminata, O. glumaepatula,和O. meridionalis)和2个栽培稻种(O. sativa 和O. glaberrima)。21条能产生良好重复性条带模式的ISSR引物被筛选出,并在62个水稻品系中揭示出非常好的多态性。全部样品的基因多样性为0.527,同时显示出ISSR标记在稻属物种遗传多样性研究中具有强大的作用。根据ISSR条带模式,利用Jaccard配对相似系数构建的一致性树状图,显示出具有良好

  13. Genomic affinity between Oryza sativa and Oryza brachyantha as ...

    African Journals Online (AJOL)

    USER

    2010-05-24

    May 24, 2010 ... brachyantha as revealed by in situ hybridization and ... Department of Genetics, Hazara University, Garden Campus Mansehra, Pakistan. Accepted 26 April ..... Oryza complex identified on the basis of molecular divergence.

  14. Comparative Analysis on Genomes from Oryza alta and Oryza latifolia by C0t-1 DNA

    Institute of Scientific and Technical Information of China (English)

    WANG De-bin; WANG Yang; WU Qi; ZHAO Hou-ming; LI Gang; QIN Rui; WANG Chun-tai; LIU Hong

    2010-01-01

    In order to reveal the origin and evolutionary relationship between two CCDD genome species, Oryza alta and Oryza latifolia, fluorescence in situ hybridization (FISH) was adopted to analyze the genomes of the two species with C0t-1 DNA from O. alta as a probe. Karyotype was also comparatively analyzed between O. alta and O. latifolia based on their similar band patterns of the hybridization signals. There were a high homology and close relationship between O. alta and O. latifolia, however, the distinction between the hybridization signals was also clear. C0t-1 DNA was proved to be species- and genome type-specific. It is suggested that C0t-1 DNA-FISH could be more efficient to analyze the genomic relationship between different species. According to the comparative analysis of highly and moderately repetitive DNA sequences between the two allotetraploidy species, O. alta and O. latifolia, the possible origin and evolutionary mechanism of allotetraploidy of Oryza were discussed.

  15. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

    Directory of Open Access Journals (Sweden)

    Szurek Boris

    2008-05-01

    Full Text Available Abstract Background Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L., a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another. Results The PXO99A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively, and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats region contains evidence of dozens of phage infections unique to the PXO99A lineage. PXO99A also contains a unique, near-perfect tandem repeat of 212 kilobases close to the replication terminus. Conclusion Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world.

  16. Construction of Oryza Sativa genome contigs by fingerprint strategy

    Institute of Scientific and Technical Information of China (English)

    TAOQUAZHOU; GUOFANHONG; 等

    1995-01-01

    We described the construction of BAC contigs of the genome of a indica variety of Oryza sativa.Guang Lu Ai 4. An entire representative(Sixfold coverage of rice chromosomes)and genetically stable BAC library of rice genome constructed in this lab has been systematically analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis.And all the images thus obtained were subject to image-processing,which consisted of preliminary location of bands,cooperative tracking of lanes by correlation of adjacent bads.a precise densitometric pass,alignment at the marker bands with the standard,optional interactive editing,and normalization of the accepted bands.The contigs were generated based on the Computer Software specially designed for genome mapping.The number of contigs with 600 kb in length on average was 464.of contigs with 1000kb in length on average was 107; of contigs with 1500 kb in length on average was Construction of Oryza Sativa genome contigs.23.Therefor,all the contigs we have obtained ampunted up to 420 megabases in length.Considering the size of rice genome(430 megabased),the contigs generated in this lab have covered nearly 98% of the rice genome.We are now in the process of mapping the contigs to chromosomes.

  17. The whole chloroplast genome of wild rice (Oryza australiensis).

    Science.gov (United States)

    Wu, Zhiqiang; Ge, Song

    2016-01-01

    The whole chloroplast genome of wild rice (Oryza australiensis) is characterized in this study. The genome size is 135,224  bp, exhibiting a typical circular structure including a pair of 25,776  bp inverted repeats (IRa,b) separated by a large single-copy region (LSC) of 82,212  bp and a small single-copy region (SSC) of 12,470  bp. The overall GC content of the genome is 38.95%. 110 unique genes were annotated, including 76 protein-coding genes, 4 ribosomal RNA genes, and 30t RNA genes. Among these, 18 are duplicated in the inverted repeat regions, 13 genes contain one intron, and 2 genes (rps12 and ycf3) have two introns.

  18. Population genomic insights into variation and evolution of Xanthomonas oryzae pv. oryzae

    Science.gov (United States)

    Midha, Samriti; Bansal, Kanika; Kumar, Sanjeet; Girija, Anil Madhusoodana; Mishra, Deo; Brahma, Kranthi; Laha, Gouri Sankar; Sundaram, Raman Meenakshi; Sonti, Ramesh V.; Patil, Prabhu B.

    2017-01-01

    Xanthomonas oryzae pv. oryzae ( Xoo) is a serious pathogen of rice causing bacterial leaf blight disease. Resistant varieties and breeding programs are being hampered by the emergence of highly virulent strains. Herein we report population based whole genome sequencing and analysis of 100 Xoo strains from India. Phylogenomic analysis revealed the clustering of Xoo strains from India along with other Asian strains, distinct from African and US Xo strains. The Indian Xoo population consists of a major clonal lineage and four minor but highly diverse lineages. Interestingly, the variant alleles, gene clusters and highly pathogenic strains are primarily restricted to minor lineages L-II to L-V and in particularly to lineage L-III. We could also find the association of an expanded CRISPR cassette and a highly variant LPS gene cluster with the dominant lineage. Molecular dating revealed that the major lineage, L-I is youngest and of recent origin compared to remaining minor lineages that seems to have originated much earlier in the past. Further, we were also able to identify core effector genes that may be helpful in efforts towards building durable resistance against this pathogen. PMID:28084432

  19. Characterization of Interspecific Hybrids Between Oryza sativa L. and Three Wild Rice Species of China by Genomic In Situ Hybridization

    Institute of Scientific and Technical Information of China (English)

    Guang-Xuan Tan; Zhi-Yong Xiong; Hua-Jun Jin; Gang Li; Li-Li Zhu; Li-Hui Shu; Guang-Cun He

    2006-01-01

    In the genus Oryza, interspecific hybrids are useful bridges for transferring the desired genes from wild species to cultivated rice (Oryza sativa L.). In the present study, hybrids between O. sativa (AA genome)and three Chinese wild rices, namely O. rufipogon (AA genome), O. officinalis (CC genome), and O. meyeriana (GG genome), were produced. Agricultural traits of the F1 hybrids surveyed were intermediate between their parents and appreciably resembled wild rice parents. Except for the O. sativa × O. rufipogon hybrid,the other F1 hybrids were completely sterile. Genomic in situ hybridization (GISH) was used for hybrid verification. Wild rice genomic DNAs were used as probes and cultivated rice DNA was used as a block. With the exception of O. rufipogon chromosomes, this method distinguished the other two wild rice and cultivated rice chromosomes at the stage of mitotic metaphase with different blocking ratios. The results suggest that a more distant phylogenetic relationship exists between O. meyeriana and O. sativa and that O. rufipogon and O. sativa share a high degree of sequence homology. The average mitotic chromosome length of O. officinalis and O. meyeriana was 1.25- and 1.51-fold that of O. sativa, respectively. 4',6'-Diamidino2-phenylindole staining showed that the chromosomes of O. officinalis and O. meyeriana harbored more heterochromatin, suggesting that the C and G genomes were amplified with repetitive sequences compared with the A genome. Although chromocenters formed by chromatln compaction were detected with wild rice-specific signals corresponding to the C and G genomes in discrete domains of the F1 hybrid interphase nuclei, the size and number of O. meyeriana chromocenters were bigger and greater than those of O. officinalis. The present results provide an important understanding of the genomic relationships and a tool for the transfer of useful genes from three native wild rice species in China to cultivars.

  20. Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication.

    Directory of Open Access Journals (Sweden)

    Li-Jun Ma

    2009-07-01

    Full Text Available Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a representative of the paraphyletic basal group of the fungal kingdom called "zygomycetes," R. oryzae is also used as a model to study fungal evolution. Here we report the genome sequence of R. oryzae strain 99-880, isolated from a fatal case of mucormycosis. The highly repetitive 45.3 Mb genome assembly contains abundant transposable elements (TEs, comprising approximately 20% of the genome. We predicted 13,895 protein-coding genes not overlapping TEs, many of which are paralogous gene pairs. The order and genomic arrangement of the duplicated gene pairs and their common phylogenetic origin provide evidence for an ancestral whole-genome duplication (WGD event. The WGD resulted in the duplication of nearly all subunits of the protein complexes associated with respiratory electron transport chains, the V-ATPase, and the ubiquitin-proteasome systems. The WGD, together with recent gene duplications, resulted in the expansion of multiple gene families related to cell growth and signal transduction, as well as secreted aspartic protease and subtilase protein families, which are known fungal virulence factors. The duplication of the ergosterol biosynthetic pathway, especially the major azole target, lanosterol 14alpha-demethylase (ERG11, could contribute to the variable responses of R. oryzae to different azole drugs, including voriconazole and posaconazole. Expanded families of cell-wall synthesis enzymes, essential for fungal cell integrity but absent in mammalian hosts, reveal potential targets for novel and R. oryzae-specific diagnostic and therapeutic treatments.

  1. Comparison of Genomes of Three Xanthomonas oryzae Bacteriophages

    Directory of Open Access Journals (Sweden)

    Chen Hui-Yi

    2007-11-01

    Full Text Available Abstract Background Xp10 and OP1 are phages of Xanthomonas oryzae pv. oryzae (Xoo, the causative agent of bacterial leaf blight in rice plants, which were isolated in 1967 in Taiwan and in 1954 in Japan, respectively. We recently isolated the Xoo phage Xop411. Results The linear Xop411 genome (44,520 bp, 58 ORFs sequenced here is 147 bp longer than that of Xp10 (60 ORFs and 735 bp longer than that of OP1 (59 ORFs. The G+C contents of OP1 (51% and Xop411 and Xp10 (52% each are less than that of the host (65%. The 9-bp 3'-overhangs (5'-GGACAGTCT-3' in Xop411 and Xp10 are absent from OP1. More of the deduced Xop411 proteins share higher degrees of identity with Xp10 than with OP1 proteins, while the right end of the genomes of Xp10 and OP1, containing all predicted promoters, share stronger homology. Xop411, Xp10, and OP1 contain 8, 7, and 6 freestanding HNH endonuclease genes, respectively. These genes can be classified into five groups depending on their possession of the HNH domain (HNN or HNH type and/or AP2 domain in intact or truncated forms. While the HNN-AP2 type endonuclease genes dispersed in the genome, the HNH type endonuclease genes, each with a unique copy, were located within the same genome context. Mass spectrometry and N-terminal sequencing showed nine Xop411 coat proteins, among which three were identified, six were assigned as coat proteins (4 and conserved phage proteins (2 in Xp10. The major coat protein, in which only the N-terminal methionine is removed, appears to exist in oligomeric forms containing 2 to 6 subunits. The three phages exhibit different patterns of domain duplication in the N-terminus of the tail fiber, which are involved in determination of the host range. Many short repeated sequences are present in and around the duplicated domains. Conclusion Geographical separation may have confined lateral gene transfer among the Xoo phages. The HNN-AP2 type endonucleases were more likely to transfer their genes

  2. Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

    DEFF Research Database (Denmark)

    Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim;

    2008-01-01

    to a genome scale metabolic model of A. oryzae. Results: Our assembled EST sequences we identified 1,046 newly predicted genes in the A. oryzae genome. Furthermore, it was possible to assign putative protein functions to 398 of the newly predicted genes. Noteworthy, our annotation strategy resulted......Background: Since ancient times the filamentous fungus Aspergillus oryzae has been used in the fermentation industry for the production of fermented sauces and the production of industrial enzymes. Recently, the genome sequence of A. oryzae with 12,074 annotated genes was released but the number...... of hypothetical proteins accounted for more than 50% of the annotated genes. Considering the industrial importance of this fungus, it is therefore valuable to improve the annotation and further integrate genomic information with biochemical and physiological information available for this microorganism and other...

  3. Comparative analysis of A, B,C and D genomes in the genus Oryza with C0t-1 DNA of C genome

    Institute of Scientific and Technical Information of China (English)

    LAN Weizhen; QIN Rui; LI Gang; HE Guangcun

    2006-01-01

    Fluorescence in situ hybridization (FISH)was applied to somatic chromosomes preparations of Oryza officinalis Wall. (CC), O. sativa L. (AA)×O. officinalis F1 hybrid (AC), backcross progenies BC1 (AAC and ACC), O. latifolia Desv. (CCDD), O. alta Swallen (CCDD) and O. punctata Kotschy (BBCC)with a labelled probe of Cot-1 DNA from O. officinalis.In O. officinalis, the homologous chromosomes showed similar signal bands probed by C0t-1 DNA and karyotype analysis was conducted based on the band patterns. Using no blocking DNA, the probe identified the chromosomes of C genome clearly, but detected few signals on chromosomes of A genome in the F1 hybrid and two backcross progenies of BC1.It is obvious that the highly and moderately repetitive DNA sequences were considerably different between C and A genomes. The chromosomes of C genome were also discriminated from the chromosomes of D-and B-genome in the tetraploid species O. latifolia, O.alta and O. punctata by C0t-1 DNA-FISH. Comparison of the fluorescence intensity on the chromosomes of B, C and D genomes in O. latifolia, O. alta,and O. punctata indicated that the differentiations between C and D genomes are less than that between C and B genomes. The relationship between C and D genomes in O. alta is closer than that of C and D genomes in O. latifolia. This would be one of the causes for the fact that both the genomes are of the same karyotype (CCDD) but belong to different species. The above results showed that the C0t-1 DNA had a high specificity of genome and species. In this paper, the origin of allotetraploid in genus Oryza is also discussed.

  4. Genomics of Aspergillus oryzae: learning from the history of Koji mold and exploration of its future.

    Science.gov (United States)

    Machida, Masayuki; Yamada, Osamu; Gomi, Katsuya

    2008-08-01

    At a time when the notion of microorganisms did not exist, our ancestors empirically established methods for the production of various fermentation foods: miso (bean curd seasoning) and shoyu (soy sauce), both of which have been widely used and are essential for Japanese cooking, and sake, a magical alcoholic drink consumed at a variety of ritual occasions, are typical examples. A filamentous fungus, Aspergillus oryzae, is the key organism in the production of all these traditional foods, and its solid-state cultivation (SSC) has been confirmed to be the secret for the high productivity of secretory hydrolases vital for the fermentation process. Indeed, our genome comparison and transcriptome analysis uncovered mechanisms for effective degradation of raw materials in SSC: the extracellular hydrolase genes that have been found only in the A. oryzae genome but not in A. fumigatus are highly induced during SSC but not in liquid cultivation. Also, the temperature reduction process empirically adopted in the traditional soy-sauce fermentation processes has been found to be important to keep strong expression of the A. oryzae-specific extracellular hydrolases. One of the prominent potentials of A. oryzae is that it has been successfully applied to effective degradation of biodegradable plastic. Both cutinase, responsible for the degradation of plastic, and hydrophobin, which recruits cutinase on the hydrophobic surface to enhance degradation, have been discovered in A. oryzae. Genomic analysis in concert with traditional knowledge and technology will continue to be powerful tools in the future exploration of A. oryzae.

  5. Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaohan [ORNL; Jawdy, Sara [ORNL; Tschaplinski, Timothy J [ORNL; Tuskan, Gerald A [ORNL

    2009-01-01

    Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine, Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression, protein motif and intron number were examined. 192, 641 and 109 SS genes were identified in Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers, roots, xylem and cambium or up-regulated by stress. Six conserved motifs in Arabidopsis and Oryza SS proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes. The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research.

  6. Random Mutagenesis of the Aspergillus oryzae Genome Results in Fungal Antibacterial Activity

    Directory of Open Access Journals (Sweden)

    Cory A. Leonard

    2013-01-01

    Full Text Available Multidrug-resistant bacteria cause severe infections in hospitals and communities. Development of new drugs to combat resistant microorganisms is needed. Natural products of microbial origin are the source of most currently available antibiotics. We hypothesized that random mutagenesis of Aspergillus oryzae would result in secretion of antibacterial compounds. To address this hypothesis, we developed a screen to identify individual A. oryzae mutants that inhibit the growth of Methicillin-resistant Staphylococcus aureus (MRSA in vitro. To randomly generate A. oryzae mutant strains, spores were treated with ethyl methanesulfonate (EMS. Over 3000 EMS-treated A. oryzae cultures were tested in the screen, and one isolate, CAL220, exhibited altered morphology and antibacterial activity. Culture supernatant from this isolate showed antibacterial activity against Methicillin-sensitive Staphylococcus aureus, MRSA, and Pseudomonas aeruginosa, but not Klebsiella pneumonia or Proteus vulgaris. The results of this study support our hypothesis and suggest that the screen used is sufficient and appropriate to detect secreted antibacterial fungal compounds resulting from mutagenesis of A. oryzae. Because the genome of A. oryzae has been sequenced and systems are available for genetic transformation of this organism, targeted as well as random mutations may be introduced to facilitate the discovery of novel antibacterial compounds using this system.

  7. Repetitive genomic sequences as a substrate for homologous integration in the Rhizopus oryzae genome.

    Science.gov (United States)

    Yuzbashev, Tigran V; Larina, Anna S; Vybornaya, Tatiana V; Yuzbasheva, Evgeniya Y; Gvilava, Ilia T; Sineoky, Sergey P

    2015-06-01

    The vast number of repetitive genomic elements was identified in the genome of Rhizopus oryzae. Such genomic repeats can be used as homologous regions for integration of plasmids. Here, we evaluated the use of two different repeats: the short (575 bp) rptZ, widely distributed (about 34 copies per genome) and the long (2053 bp) rptH, less prevalent (about 15 copies). The plasmid carrying rptZ integrated, but did so through a 2256-bp region of homology to the pyrG locus, a unique genomic sequence. Thus, the length of rptZ was below the minimal requirements for homologous strand exchange in this fungus. In contrast, rptH was used efficiently for homologous integration. The plasmid bearing this repeat integrated in multicopy fashion, with up to 25 copies arranged in tandem. The latter vector, pPyrG-H, could be a valuable tool for integration at homologous sequences, for such purposes as high-level expression of proteins. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  8. Genome analysis of rice-blast fungus Magnaporthe oryzae field isolates from southern India

    Directory of Open Access Journals (Sweden)

    Malali Gowda

    2015-09-01

    Full Text Available The Indian subcontinent is the center of origin and diversity for rice (Oryza sativa L.. The O. sativa ssp. indica is a major food crop grown in India, which occupies the first and second position in area and production, respectively. Blast disease caused by Magnaporthe oryzae is a major constraint to rice production. Here, we report the analysis of genome architecture and sequence variation of two field isolates, B157 and MG01, of the blast fungus from southern India. The 40 Mb genome of B157 and 43 Mb genome of MG01 contained 11,344 and 11,733 predicted genes, respectively. Genomic comparisons unveiled a large set of SNPs and several isolate specific genes in the Indian blast isolates. Avr genes were analyzed in several sequenced Magnaporthe strains; this analysis revealed the presence of Avr-Pizt and Avr-Ace1 genes in all the sequenced isolates. Availability of whole genomes of field isolates from India will contribute to global efforts to understand genetic diversity of M. oryzae population and to track the emergence of virulent pathotypes.

  9. Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere.

    Directory of Open Access Journals (Sweden)

    Min-Jung Kwak

    Full Text Available Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the environment, and many Methylobacterium species associated with plants produce plant growth-promoting substances. To gain insights into the life style at the phyllosphere and the genetic bases of plant growth promotion, we determined and analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in the chromosome, the bacterium has, besides most of the genes for the central metabolism, all of the essential genes for the assimilation and dissimilation of methanol that are either located in methylotrophy islands or dispersed. M. oryzae is equipped with several kinds of genes for adaptation to plant surfaces such as defense against UV radiation, oxidative stress, desiccation, or nutrient deficiency, as well as high proportion of genes related to motility and signaling. Moreover, it has an array of genes involved in metabolic pathways that may contribute to promotion of plant growth; they include auxin biosynthesis, cytokine biosynthesis, vitamin B12 biosynthesis, urea metabolism, biosorption of heavy metals or decrease of metal toxicity, pyrroloquinoline quinone biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate solubilization, and thiosulfate oxidation. Through the genome analysis of M. oryzae, we provide information on the full gene complement of M. oryzae that resides in the aerial parts of plants and enhances plant growth. The plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant growth promotion, and its potential as a candidate for a bioinoculant targeted to the phyllosphere and focused on phytostimulation are illuminated.

  10. Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza.

    Science.gov (United States)

    Kim, HyeRan; Hurwitz, Bonnie; Yu, Yeisoo; Collura, Kristi; Gill, Navdeep; SanMiguel, Phillip; Mullikin, James C; Maher, Christopher; Nelson, William; Wissotski, Marina; Braidotti, Michele; Kudrna, David; Goicoechea, José Luis; Stein, Lincoln; Ware, Doreen; Jackson, Scott A; Soderlund, Carol; Wing, Rod A

    2008-01-01

    We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.

  11. Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication

    OpenAIRE

    Zhang, Fantao; Xu, Tao; Mao, Linyong; Yan, Shuangyong; Chen, Xiwen; Wu, Zhenfeng; Chen, Rui; Luo, Xiangdong; Xie, Jiankun; Gao, Shan

    2016-01-01

    Background It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level. Results Instead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with th...

  12. Phylogeny and species delimitation of the C-genome diploid species in Oryza

    Institute of Scientific and Technical Information of China (English)

    Li-Li ZANG; Xin-Hui ZOU; Fu-Min ZHANG; Ziheng YANG; Song GE

    2011-01-01

    The diploid Oryza species with C-genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C-genome (BBCC,CCDD).Despite extensive studies,the phylogenetic relationship among the C-genome species and the taxonomic status of some taxa remain controversial.In this study,we reconstructed the phylogeny of three diploid species with C-genome (Oryza officinalis,O.rhizomatis,and O.eichingeri) based on sequences of 68 nuclear single-copy genes.We obtained a fully resolved phylogenetic tree,clearly indicating the sister relationship of O.officinalis and O.rhizomatis,with O.eichingeri being the more divergent lineage.Incongruent phylogenies of the C-genome species found in previous studies might result from lineage sorting,introgression/hybridization and limited number of genetic markers used.We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O.eichingeri.Analyses of two datasets (68 genes with a single sample,and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O.eichingeri.In addition,we evaluated the impact of the number of sampled individuals and loci on species delimitation.Our simulation suggests that sampling multiple individuals is critically important for species delimitation,particularly for closely related species.

  13. Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae.

    Directory of Open Access Journals (Sweden)

    Minfeng Xue

    Full Text Available Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide. The fungal pathogen is notorious for its ability to overcome host resistance. To better understand its genetic variation in nature, we sequenced the genomes of two field isolates, Y34 and P131. In comparison with the previously sequenced laboratory strain 70-15, both field isolates had a similar genome size but slightly more genes. Sequences from the field isolates were used to improve genome assembly and gene prediction of 70-15. Although the overall genome structure is similar, a number of gene families that are likely involved in plant-fungal interactions are expanded in the field isolates. Genome-wide analysis on asynonymous to synonymous nucleotide substitution rates revealed that many infection-related genes underwent diversifying selection. The field isolates also have hundreds of isolate-specific genes and a number of isolate-specific gene duplication events. Functional characterization of randomly selected isolate-specific genes revealed that they play diverse roles, some of which affect virulence. Furthermore, each genome contains thousands of loci of transposon-like elements, but less than 30% of them are conserved among different isolates, suggesting active transposition events in M. oryzae. A total of approximately 200 genes were disrupted in these three strains by transposable elements. Interestingly, transposon-like elements tend to be associated with isolate-specific or duplicated sequences. Overall, our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus.

  14. The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species.

    Science.gov (United States)

    Wing, Rod A; Ammiraju, Jetty S S; Luo, Meizhong; Kim, Hyeran; Yu, Yeisoo; Kudrna, Dave; Goicoechea, Jose L; Wang, Wenming; Nelson, Will; Rao, Kiran; Brar, Darshan; Mackill, Dave J; Han, Bin; Soderlund, Cari; Stein, Lincoln; SanMiguel, Phillip; Jackson, Scott

    2005-09-01

    The wild species of the genus Oryza offer enormous potential to make a significant impact on agricultural productivity of the cultivated rice species Oryza sativa and Oryza glaberrima. To unlock the genetic potential of wild rice we have initiated a project entitled the 'Oryza Map Alignment Project' (OMAP) with the ultimate goal of constructing and aligning BAC/STC based physical maps of 11 wild and one cultivated rice species to the International Rice Genome Sequencing Project's finished reference genome--O. sativa ssp. japonica c. v. Nipponbare. The 11 wild rice species comprise nine different genome types and include six diploid genomes (AA, BB, CC, EE, FF and GG) and four tetrapliod genomes (BBCC, CCDD, HHKK and HHJJ) with broad geographical distribution and ecological adaptation. In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara--thought to be the progenitor of modern cultivated rice.

  15. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences

    Directory of Open Access Journals (Sweden)

    Ganko Eric W

    2004-03-01

    Full Text Available Abstract Background LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. Results To explore the evolutionary history of long terminal repeat (LTR retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTR-retrotransposons per Mb were detected in Chromosome 10. Conclusions Gypsy-like elements were found to be >4 × more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (

  16. Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whote-Genome Duplication

    Science.gov (United States)

    Rhizopus oryzae is the primary etiologic agent of mucormycosis, an emerging lifethreatening infection. The rapid growth and angioinvasive nature of mucormycotic infections in humans result in an overall mortality rate that exceeds 50%, even with combined surgical and antifungal therapies. As part ...

  17. Genome-wide analysis of potential cross-reactive endogenous allergens in rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Fang Chao Zhu

    2015-01-01

    Full Text Available The proteins in the food are the source of common allergic components to certain patients. Current lists of plant endogenous allergens were based on the medical/clinical reports as well as laboratory results. Plant genome sequences made it possible to predict and characterize the genome-wide of putative endogenous allergens in rice (Oryza sativa L.. In this work, we identified and characterized 122 candidate rice allergens including the 22 allergens in present databases. Conserved domain analysis also revealed 37 domains among rice allergens including one novel domain (histidine kinase-, DNA gyrase B-, and HSP90-like ATPase, PF13589 adding to the allergen protein database. Phylogenetic analysis of the allergens revealed the diversity among the Prolamin superfamily and DnaK protein family, respectively. Additionally, some allergens proteins clustered on the rice chromosome might suggest the molecular function during the evolution.

  18. Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species

    Science.gov (United States)

    Asaf, Sajjad; Khan, Abdul Latif; Khan, Abdur Rahim; Waqas, Muhammad; Kang, Sang-Mo; Khan, Muhammad Aaqil; Shahzad, Raheem; Seo, Chang-Woo; Shin, Jae-Ho; Lee, In-Jung

    2016-01-01

    Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O. rufipogon. Comparison with other related species revealed that most of the genes with known function are conserved among the Poaceae members. Similarly, O. minuta mt genome shared 24 protein-coding genes, 15 tRNA genes and 1 ribosomal RNA gene with other rice species (indica and japonica). The evolutionary relationship and phylogenetic analysis revealed that O. minuta is more closely related to O. rufipogon than to any other related species. Such studies are essential to understand the evolutionary divergence among species and analyze common gene pools to combat risks in the current scenario of a changing environment. PMID:27045847

  19. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima).

    Science.gov (United States)

    Nabholz, Benoit; Sarah, Gautier; Sabot, François; Ruiz, Manuel; Adam, Hélène; Nidelet, Sabine; Ghesquière, Alain; Santoni, Sylvain; David, Jacques; Glémin, Sylvain

    2014-05-01

    The African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3000 years ago. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g. drought). Here, using RNA-seq technology, we were able to compare more than 12,000 transcripts between 9 O. glaberrima, 10 wild O. barthii and one O. meridionalis individuals. With a synonymous nucleotide diversity πs = 0.0006 per site, O. glaberrima appears as the least genetically diverse crop grass ever documented. Using approximate Bayesian computation, we estimated that O. glaberrima experienced a severe bottleneck during domestication. This demographic scenario almost fully accounts for the pattern of genetic diversity across O. glaberrima genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. Moreover, the large excess of derived nonsynonymous substitution that we detected suggests that the O. glaberrima population suffered from the 'cost of domestication'. In addition, we used this genome-scale data set to demonstrate that (i) O. barthii genetic diversity is positively correlated with recombination rate and negatively with gene density, (ii) expression level is negatively correlated with evolutionary constraint, and (iii) one region on chromosome 5 (position 4-6 Mb) exhibits a clear signature of introgression with a yet unidentified Oryza species. This work represents the first genome-wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits.

  20. Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice

    OpenAIRE

    Waters, Daniel L. E.; Nock, Catherine J; Ishikawa, Ryuji; Rice, Nicole; Henry, Robert J.

    2012-01-01

    Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively pa...

  1. Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication.

    Science.gov (United States)

    Wang, Yu; Bai, Xuefei; Yan, Chenghai; Gui, Yiejie; Wei, Xinghua; Zhu, Qian-Hao; Guo, Longbiao; Fan, Longjiang

    2012-11-01

    The lack of a MIRNA set and genome sequence of wild rice (Oryza rufipogon) has prevented us from determining the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O. rufipogon were sequenced by Illumina platform and the expression levels of microRNAs (miRNAs) were investigated by miRNA chips. A de novo O. rufipogon genome was assembled using c. 55× coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on c. 5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these, O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting a loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression differences between wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated that MIRNA genes, like protein-coding genes, might have been significantly shaped during rice domestication and could be one of the driving forces that contributed to rice domestication.

  2. A draft sequence of the rice(Oryza sativa ssp. indica) genome

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a "whole genome shotgun" approach, we have produced a draft rice genome sequence of Oryza sativa ssp. indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM- BLER, a custom-designed software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences from both indica and japanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0% of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities to facilitate genomic and genetic studies on rice biology.

  3. Genomic organization and sequence dynamics of the AvrPiz-t locus in Magnaporthe oryzae

    Institute of Scientific and Technical Information of China (English)

    Ping LI; Bin BAI; Hong-yan ZHANG; Heng ZHOU; Bo ZHOU

    2012-01-01

    Plants utilize multiple layers of defense mechanisms to fight against the invasion of diverse pathogens.The R gene mediates resistance,in most cases,dependent on the co-existence of its cognate pathogen-derived avirulence (Avr) gene.The rice blast R gene Piz-t corresponds in gene-for-gene fashion to the Magnaporthe oryzae Avrgene AvrPiz-t.In this study,we determined and compared the genomic sequences surrounding the AvrPiz-t gene in both avirulent and virulent isolates,designating as AvrPiz-t-ZB15 and avrPiz-t-70-15 regions,respectively.The sequence of the AvrPiz-t-ZB15 region is 120966 bp whereas avrPiz-t-70-15 is 146292 bp in length.The extreme sequence similarity and good synteny in gene order and content along with the absence of two predicted genes in the avrPiz-t-70-15 region were observed in the predicted protein-coding regions in the AvrPiz-t locus.Nevertheless,frequent presence/absence and highly dynamic organization of transposable elements (TEs) were identified,representing the major variation of the AvrPiz-t locus between different isolates.Moreover,TEs constitute 27.3% and 43.2%of the genomic contents of the AvrPiz-t-ZB15 and avrPiz-t-70-15 regions,respectively,indicating that TEs contribute largely to the organization and evolution of AvrPiz-t locus.The findings of this study suggest that M.oryzae could benefit in an evolutionary sense from the presence of active TEs in genes conferring avirulence and provide an ability to rapidly change and thus to overcome host R genes.

  4. Construction of a full bacterial artificial chromosome (BAC) library of Oryza sativa genome

    Institute of Scientific and Technical Information of China (English)

    TAOQUANZHOU; HAIYINGZHAO; 等

    1994-01-01

    We have constructed a full BAC library for the superior early indica variety of Oryza sativa,Guang Lu Ai 4.The MAX Efficiency DH10B with increased stability of inserts was used as BAC host cells.The potent pBelo BACII with double selection markers was used as cloning vector.The cloning efficiency we have reached was as high as 98%,and the transformation efficiency was raised up to 106 transformants/μg of large fragment DNA.The BAC recombinant transformants were picked at random and analyzed for the size of inserts,which turned out to be of 120 kb in length on average.We have obtained more than 20,000 such BAC clones.According to conventional probability equation,they covered the entire rice genome of 420,000 kb in length.The entire length of inserts of the library obtained has the 5-to 6-fold coverage of the genome.To our knowledge,this is the first reported full BAC library for a complex genome.

  5. A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes

    Directory of Open Access Journals (Sweden)

    Lin Ye

    2008-06-01

    Full Text Available Abstract Background Xanthomonas oryzae pv. oryzae (Xoo and X. oryzae pv. oryzicola (Xoc are bacterial pathogens of the worldwide staple and grass model, rice. Xoo and Xoc are closely related but Xoo invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice in many parts of the world, and Xoc colonizes the mesophyll parenchyma to cause bacterial leaf streak, a disease of emerging importance. Both pathogens depend on hrp genes for type III secretion to infect their host. We constructed a 50–70 mer oligonucleotide microarray based on available genome data for Xoo and Xoc and compared gene expression in Xoo strains PXO99A and Xoc strain BLS256 grown in the rich medium PSB vs. XOM2, a minimal medium previously reported to induce hrp genes in Xoo strain T7174. Results Three biological replicates of the microarray experiment to compare global gene expression in representative strains of Xoo and Xoc grown in PSB vs. XOM2 were carried out. The non-specific error rate and the correlation coefficients across biological replicates and among duplicate spots revealed that the microarray data were robust. 247 genes of Xoo and 39 genes of Xoc were differentially expressed in the two media with a false discovery rate of 5% and with a minimum fold-change of 1.75. Semi-quantitative-RT-PCR assays confirmed differential expression of each of 16 genes each for Xoo and Xoc selected for validation. The differentially expressed genes represent 17 functional categories. Conclusion We describe here the construction and validation of a two-genome microarray for the two pathovars of X. oryzae. Microarray analysis revealed that using representative strains, a greater number of Xoo genes than Xoc genes are differentially expressed in XOM2 relative to PSB, and that these include hrp genes and other genes important in interactions with rice. An exception was the rax genes, which are required for production of the host resistance elicitor AvrXa21

  6. Significant Comparative Characteristics between Orphan and Nonorphan Genes in the Rice (Oryza sativa L. Genome

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    Wen-Jiu Guo

    2007-01-01

    Full Text Available Microsatellites are short tandem repeats of one to six bases in genomic DNA. As microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. Orphan genes have no known homologs in existing databases. Using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (Oryza sativa ssp. Japanica cv. Nipponbare proteome. We found that a larger proportion of orphan genes are expressed after sexual maturation and under environmental pressure than nonorphan genes. Orphan genes generally have shorter protein lengths and intron size, and are faster evolving. Additionally, orphan genes have fewer PROSITE patterns with larger pattern sizes than those in nonorphan genes. The average microsatellite content and the percentage of trinucleotide repeats in orphan genes are also significantly higher than in nonorphan genes. Microsatellites are found less often in PROSITE patterns in orphan genes. Taken together, these orphan gene characteristics suggest that microsatellites play an important role in orphan gene evolution and expression.

  7. The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae.

    Science.gov (United States)

    Gibbons, John G; Salichos, Leonidas; Slot, Jason C; Rinker, David C; McGary, Kriston L; King, Jonas G; Klich, Maren A; Tabb, David L; McDonald, W Hayes; Rokas, Antonis

    2012-08-01

    The domestication of animals, plants, and microbes fundamentally transformed the lifestyle and demography of the human species [1]. Although the genetic and functional underpinnings of animal and plant domestication are well understood, little is known about microbe domestication [2-6]. Here, we systematically examined genome-wide sequence and functional variation between the domesticated fungus Aspergillus oryzae, whose saccharification abilities humans have harnessed for thousands of years to produce sake, soy sauce, and miso from starch-rich grains, and its wild relative A. flavus, a potentially toxigenic plant and animal pathogen [7]. We discovered dramatic changes in the sequence variation and abundance profiles of genes and wholesale primary and secondary metabolic pathways between domesticated and wild relative isolates during growth on rice. Our data suggest that, through selection by humans, an atoxigenic lineage of A. flavus gradually evolved into a "cell factory" for enzymes and metabolites involved in the saccharification process. These results suggest that whereas animal and plant domestication was largely driven by Neolithic "genetic tinkering" of developmental pathways, microbe domestication was driven by extensive remodeling of metabolism.

  8. Comparative Analysis of Genomes in Oryza sativa, O.officinalis, and O. meyeriana with C0t-1 DNA and Genomic DNA of Cultivated Rice

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) were applied to somatic chromosomes preparations of Oryza sativa, O. officinalis, and O. meyeriana with labeled probes of C0t-1 DNA and genomic DNA from the cultivated rice. The coverage percentage (%) and size (Mb) of C0t-1 DNA in O. sativa, O. officinalis, and O. meyeriana were 47.1 ±0.16, 38.61 ±0.13, 44.38±0.13, and 212.33± 1.21,269.42 ± 0.89, 532.56± 1.68 Mb, respectively. The coverage percentage and size of genomic DNA from O. sativa in O. officinalis and O. meyeriana were 91.0, 93.6% and 634, 1 123 Mb, respectively, in which 365 and 591 Mb in O. officinalis and O. meyeriana were from O. sativa genomic DNA, but not from repetitive sequences of O. sativa, and the uncoverage genome size in O. officinalis and O. meyeriana were 64 and 78 Mb, respectively. In addition, karyotype analysis was conducted based on the signal bands of C0t-1 DNA in O. sativa, O. officinalis, and O. meyeriana. The results showed that highly and moderately repetitive sequences in Oryza genus were conserved as the functional genes during evolution. The repetitive sequences reduplication may be one of the important causes of the genome enlargement of O. officinalis and O. meyeriana, and O. officinalis genome enlarged more slowly when compared with O. meyeriana. Based on the above results, it is concluded that O. officinalis and O. meyeriana were formed by reduplication, rearrangement, and gene selective loss during the evolution process.

  9. Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae

    DEFF Research Database (Denmark)

    Liu, Lifang; Feizi, Amir; Osterlund, Tobias

    2014-01-01

    Background: The koji mold, Aspergillus oryzae is widely used for the production of industrial enzymes due to its particularly high protein secretion capacity and ability to perform post-translational modifications. However, systemic analysis of its secretion system is lacking, generally due to th...

  10. Experimental and genomic evidence for theindica-type cytoplasmic effect inOryza sativa L. ssp.japonica

    Institute of Scientific and Technical Information of China (English)

    LIU You-hong; TANG Liang; XU Quan; MA Dian-rong; ZHAO Ming-hui; SUN Jian; CHEN Wen-fu

    2016-01-01

    Cytoplasmic effects are important agronomical phenomena that have generated widespread interest in both theory and application. In the present study, ifve high yield rice cultivars (Oryza sativa L. ssp.japonica) in large-scale cultivation in northeast China were determined to possessOryza sativa L. ssp.indica-type cytoplasmusing cytoplasmic subspecies-spe-ciifc molecular markers. This was conifrmed by cytoplasmic genome-wide single nucleotide polymorphisms (SNPs) and functional gene sequencing. Two of these ifvejaponicacultivars were core breeding parents with high yield and the other three were super-high-yield varieties registered by the Ministry of Agriculture of China. We constructed nuclear substitution lines to further demonstrate whether and how thisindica-type cytoplasm contributed to yield improvement by comparing yield components. The results showed that under the samejaponicanuclear background, the lines withindica-type cytoplasm had a signiifcant decrease in tilers in exchange for increased grain number per panicle compared with their recurrent parents. Our results implied that botanical basis of this cytoplasmic effect was to reduce the plant’s branching differentiation to pro-duce more lforal organs under the constant nutrition. Our ifndings open another door for the utilization of inter-subspeciifc hybridization for the improvement of rice cultivar.

  11. Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes.

    Science.gov (United States)

    Massa, A N; Wanjugi, H; Deal, K R; O'Brien, K; You, F M; Maiti, R; Chan, A P; Gu, Y Q; Luo, M C; Anderson, O D; Rabinowicz, P D; Dvorak, J; Devos, K M

    2011-09-01

    Nine different regions totaling 9.7 Mb of the 4.02 Gb Aegilops tauschii genome were sequenced using the Sanger sequencing technology and compared with orthologous Brachypodium distachyon, Oryza sativa (rice), and Sorghum bicolor (sorghum) genomic sequences. The ancestral gene content in these regions was inferred and used to estimate gene deletion and gene duplication rates along each branch of the phylogenetic tree relating the four species. The total gene number in the extant Ae. tauschii genome was estimated to be 36,371. The gene deletion and gene duplication rates and total gene numbers in the four genomes were used to estimate the total gene number in each node of the phylogenetic tree. The common ancestor of the Brachypodieae and Triticeae lineages was estimated to have had 28,558 genes, and the common ancestor of the Panicoideae, Ehrhartoideae, and Pooideae subfamilies was estimated to have had 27,152 or 28,350 genes, depending on the ancestral gene scenario. Relative to the Brachypodieae and Triticeae common ancestor, the gene number was reduced in B. distachyon by 3,026 genes and increased in Ae. tauschii by 7,813 genes. The sum of gene deletion and gene duplication rates, which reflects the rate of gene synteny loss, was correlated with the rate of structural chromosome rearrangements and was highest in the Ae. tauschii lineage and lowest in the rice lineage. The high rate of gene space evolution in the Ae. tauschii lineage accounts for the fact that, contrary to the expectations, the level of synteny between the phylogenetically more related Ae. tauschii and B. distachyon genomes is similar to the level of synteny between the Ae. tauschii genome and the genomes of the less related rice and sorghum. The ratio of gene duplication to gene deletion rates in these four grass species closely parallels both the total number of genes in a species and the overall genome size. Because the overall genome size is to a large extent a function of the repeated

  12. Genome-wide analysis of basic leucine zipper transcription factor families in Arabidopsis thaliana, Oryza saliva and Populus trichocarpa

    Institute of Scientific and Technical Information of China (English)

    JI Qian; ZHANG Liang-sheng; WANG Yi-fei; WANG Jian

    2009-01-01

    The basic leucine zipper (bZIP) transcription factors form a large gene family that is important in pathogen defense, light and stress signaling, etc. The Completed whole genome sequences of model plants Arabidopsis (Arabidopsis thaliana), rice (Oryza saliva) and poplar (Populus trichocarpa) constitute a valuable resource for genome-wide analysis and genomic comparative analysis, as they are representatives of the two major evolutionary lineages within the angiosperms: the monocotyledons and the dicotyledons. In this study, bioinformatics analysis identified 74, 89 and 88 bZIP genes respectively in Arabidopsis, rice and poplar. Moreover, a comprehensive overview of this gene family is presented, including the gene structure, phylogeny, chromosome distribution, conserved motifs. As a result, the plant bZIPs were organized into 10 subfamilies on basis of phylogenetic relationship. Gene duplication events during the family evolution history were also investigated. And it was further concluded that chromosomal/segmental duplication might have played a key role in gene expansion of bZIP gene family.

  13. Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level

    Directory of Open Access Journals (Sweden)

    Henrissat Bernard

    2011-01-01

    Full Text Available Abstract Background Rhizopus oryzae is a zygomycete filamentous fungus, well-known as a saprobe ubiquitous in soil and as a pathogenic/spoilage fungus, causing Rhizopus rot and mucomycoses. Results Carbohydrate Active enzyme (CAZy annotation of the R. oryzae identified, in contrast to other filamentous fungi, a low number of glycoside hydrolases (GHs and a high number of glycosyl transferases (GTs and carbohydrate esterases (CEs. A detailed analysis of CAZy families, supported by growth data, demonstrates highly specialized plant and fungal cell wall degrading abilities distinct from ascomycetes and basidiomycetes. The specific genomic and growth features for degradation of easily digestible plant cell wall mono- and polysaccharides (starch, galactomannan, unbranched pectin, hexose sugars, chitin, chitosan, β-1,3-glucan and fungal cell wall fractions suggest specific adaptations of R. oryzae to its environment. Conclusions CAZy analyses of the genome of the zygomycete fungus R. oryzae and comparison to ascomycetes and basidiomycete species revealed how evolution has shaped its genetic content with respect to carbohydrate degradation, after divergence from the Ascomycota and Basidiomycota.

  14. The Oryza map alignment project: Construction, alignment and analysis of 12 BAC fingerprint/end sequence framework physical maps that represent the 10 genome types of genus Oryza

    Science.gov (United States)

    The Oryza Map Alignment Project (OMAP) provides the first comprehensive experimental system for understanding the evolution, physiology and biochemistry of a full genus in plants or animals. We have constructed twelve deep-coverage BAC libraries that are representative of both diploid and tetraploid...

  15. Analysis of Magnaporthe oryzae genome reveals a fungal effector, which is able to induce resistance response in transgenic rice line containing resistance gene, Pi54

    Directory of Open Access Journals (Sweden)

    Soham Ray

    2016-08-01

    Full Text Available Rice blast caused by Magnaporthe oryzae is one of the most important diseases of rice. Pi54, a rice gene that imparts resistance to M. oryzae isolates prevalent in India, was already cloned but its avirulent counterpart in the pathogen was not known.. After decoding the whole genome of an avirulent isolate of M. oryzae, we predicted 11440 protein coding genes and then identified four candidate effector proteins which are exclusively expressed in the infectious structure, appresoria. In silico protein modeling followed by interaction analysis between Pi54 protein model and selected four candidate effector proteins models revealed that Mo-01947_9 protein model encoded by a gene located at chromosome 4 of M. oryzae, interacted best at the Leucine Rich Repeat domain of Pi54 protein model. Yeast-two-hybrid analysis showed that Mo-01947_9 protein physically interacts with Pi54 protein. Nicotiana benthamiana leaf infiltration assay confirmed induction of hypersensitive response in the presence of Pi54 gene in a heterologous system. Genetic complementation test also proved that Mo-01947_9 protein induces avirulence response in the pathogen in the presence of Pi54 gene. Here, we report identification and cloning of a new fungal effector gene which interacts with resistance gene Pi54 gene in rice.

  16. Complete genome sequence of Bacillus thuringiensis tenebrionis 4AA1, a typical strain with toxicity to Coleopteran insects.

    Science.gov (United States)

    Gao, Qiuling; Zheng, Jinshui; Zhu, Lei; Ruan, Lifang; Peng, Donghai; Sun, Ming

    2015-06-20

    Bacillus thuringiensis serovar morrisoni biovar tenebrionis has been developed as an bioinsecticide to control Coleopteran insects in agriculture and forestry for a few decades. Its major crystal protein Cry3Aa was also applied to transgenic crops. Here we report the complete genome sequence of strain tenebrionis 4AA1, which has one chromosome of 5,652,292bp and six plasmids. Two crystal protein genes, cry3Aa and cry15Aa, locate on one single plasmid named pBMB51. This strain also possesses plentiful virulence factors besides crystal proteins. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Genome wide expression analysis of CBS domain containing proteins in Arabidopsis thaliana (L. Heynh and Oryza sativa L. reveals their developmental and stress regulation

    Directory of Open Access Journals (Sweden)

    Sopory Sudhir K

    2009-04-01

    Full Text Available Abstract Background In Arabidopsis thaliana (L. Heynh and Oryza sativa L., a large number of genes encode proteins of unknown functions, whose characterization still remains one of the major challenges. With an aim to characterize these unknown proteins having defined features (PDFs in plants, we have chosen to work on proteins having a cystathionine β-synthase (CBS domain. CBS domain as such has no defined function(s but plays a regulatory role for many enzymes and thus helps in maintaining the intracellular redox balance. Its function as sensor of cellular energy has also been widely suggested. Results Our analysis has identified 34 CBS domain containing proteins (CDCPs in Arabidopsis and 59 in Oryza. In most of these proteins, CBS domain coexists with other functional domain(s, which may indicate towards their probable functions. In order to investigate the role(s of these CDCPs, we have carried out their detailed analysis in whole genomes of Arabidopsis and Oryza, including their classification, nomenclature, sequence analysis, domain analysis, chromosomal locations, phylogenetic relationships and their expression patterns using public databases (MPSS database and microarray data. We have found that the transcript levels of some members of this family are altered in response to various stresses such as salinity, drought, cold, high temperature, UV, wounding and genotoxic stress, in both root and shoot tissues. This data would be helpful in exploring the so far obscure functions of CBS domain and CBS domain-containing proteins in plant stress responses. Conclusion We have identified, classified and suggested the nomenclature of CDCPs in Arabidopsis and Oryza. A comprehensive analysis of expression patterns for CDCPs using the already existing transcriptome profiles and MPSS database reveals that a few CDCPs may have an important role in stress response/tolerance and development in plants, which needs to be validated further through

  18. Genome wide expression analysis of CBS domain containing proteins in Arabidopsis thaliana (L.) Heynh and Oryza sativa L. reveals their developmental and stress regulation.

    Science.gov (United States)

    Kushwaha, Hemant R; Singh, Anil K; Sopory, Sudhir K; Singla-Pareek, Sneh L; Pareek, Ashwani

    2009-04-28

    In Arabidopsis thaliana (L.) Heynh and Oryza sativa L., a large number of genes encode proteins of unknown functions, whose characterization still remains one of the major challenges. With an aim to characterize these unknown proteins having defined features (PDFs) in plants, we have chosen to work on proteins having a cystathionine beta-synthase (CBS) domain. CBS domain as such has no defined function(s) but plays a regulatory role for many enzymes and thus helps in maintaining the intracellular redox balance. Its function as sensor of cellular energy has also been widely suggested. Our analysis has identified 34 CBS domain containing proteins (CDCPs) in Arabidopsis and 59 in Oryza. In most of these proteins, CBS domain coexists with other functional domain(s), which may indicate towards their probable functions. In order to investigate the role(s) of these CDCPs, we have carried out their detailed analysis in whole genomes of Arabidopsis and Oryza, including their classification, nomenclature, sequence analysis, domain analysis, chromosomal locations, phylogenetic relationships and their expression patterns using public databases (MPSS database and microarray data). We have found that the transcript levels of some members of this family are altered in response to various stresses such as salinity, drought, cold, high temperature, UV, wounding and genotoxic stress, in both root and shoot tissues. This data would be helpful in exploring the so far obscure functions of CBS domain and CBS domain-containing proteins in plant stress responses. We have identified, classified and suggested the nomenclature of CDCPs in Arabidopsis and Oryza. A comprehensive analysis of expression patterns for CDCPs using the already existing transcriptome profiles and MPSS database reveals that a few CDCPs may have an important role in stress response/tolerance and development in plants, which needs to be validated further through functional genomics.

  19. Biallelic and Genome Wide Association Mapping of Germanium Tolerant Loci in Rice (Oryza sativa L..

    Directory of Open Access Journals (Sweden)

    Partha Talukdar

    Full Text Available Rice plants accumulate high concentrations of silicon. Silicon has been shown to be involved in plant growth, high yield, and mitigating biotic and abiotic stresses. However, it has been demonstrated that inorganic arsenic is taken up by rice through silicon transporters under anaerobic conditions, thus the ability to efficiently take up silicon may be considered either a positive or a negative trait in rice. Germanium is an analogue of silicon that produces brown lesions in shoots and leaves, and germanium toxicity has been used to identify mutants in silicon and arsenic transport. In this study, two different genetic mapping methods were performed to determine the loci involved in germanium sensitivity in rice. Genetic mapping in the biparental cross of Bala × Azucena (an F6 population and a genome wide association (GWA study with 350 accessions from the Rice Diversity Panel 1 were conducted using 15 μM of germanic acid. This identified a number of germanium sensitive loci: some co-localised with previously identified quantitative trait loci (QTL for tissue silicon or arsenic concentration, none co-localised with Lsi1 or Lsi6, while one single nucleotide polymorphism (SNP was detected within 200 kb of Lsi2 (these are genes known to transport silicon, whose identity was discovered using germanium toxicity. However, examining candidate genes that are within the genomic region of the loci detected above reveals genes homologous to both Lsi1 and Lsi2, as well as a number of other candidate genes, which are discussed.

  20. 基因组水平预测稻瘟菌分泌蛋白组及富集分析%Prediction for Secretome from Magnaporthe oryzae at Genome Scale and Its Enrichment Analysis

    Institute of Scientific and Technical Information of China (English)

    曹继东; 刘俊; 李遂焰

    2016-01-01

    ,further the CSPs involved in the degradation of plant derived compounds were predicted. Total 789 CSPs were found in M. oryzae genome and the amino acid lengths of CSPs were mainly concentrated between 100 to 500 aa exclusively. GO function analysis of CSPs indicated that they were enriched in the secreting pathways and in the interactions with host. Interestingly,the results of KEGG metabolism and domain analysis of CSPs suggested that some of them contributed to sugar metabolism. Around 156 CSPs were recruited in the degradation of cell walls of plants. Besides,many non-classical leaderless secreted proteins were discovered in the M. oryzae secretome. In summary,by designing the informatics procedure,we predicted the secretome of M. oryzae,CSPs were able to degrade plant derived compounds such as cell walls, and some were involved in sugar metabolism. In addition,M. oryzae. harbored many non-classical leaderless secreted proteins.

  1. Whole genomic sequencing of RT98 mitochondria derived from Oryza rufipogon and northern blot analysis to uncover a cytoplasmic male sterility-associated gene.

    Science.gov (United States)

    Igarashi, Keisuke; Kazama, Tomohiko; Motomura, Keiji; Toriyama, Kinya

    2013-02-01

    Cytoplasmic male sterility (CMS) is a maternally inherited trait resulting in the failure to produce functional pollen and is often observed when an alien cytoplasm is transferred into a cultivated species. An RT98A CMS line and an RT98C fertility restorer line were obtained by successive backcrossing between Oryza rufipogon W1109 and Oryza sativa cultivar Taichung 65. To uncover the CMS-associated mitochondrial genes, we determined the complete sequence of the RT98-CMS mitochondrial genome using next-generation pyrosequencing, and searched new open reading frames (orfs) absent in a reported mitochondrial genome of O. sativa Nipponbare. Then, six candidates were selected for the CMS-associated genes based on the criteria in which they were chimeric in structure or encoded a peptide with transmembrane domains. One of the candidates, orf113, showed different transcript sizes between RT98A and RT98C on Northern blot analysis. The orf113 gene was shown to be co-transcribed with atp4 and cox3 encoding ATP synthase F0 subunit 4 and Cyt c oxidase subunit 3, respectively, and their transcripts were distinctly processed in the presence of a fertility restorer gene. Our results indicate that orf113 is a CMS-associated gene of RT98-CMS.

  2. Genetic Architecture of Cold Tolerance in Rice (Oryza sativa) Determined through High Resolution Genome-Wide Analysis

    Science.gov (United States)

    Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases se...

  3. Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa.

    Science.gov (United States)

    Xu, Ruirui; Zhang, Shizhong; Huang, Jinguang; Zheng, Chengchao

    2013-01-01

    RNA helicases are enzymes that are thought to unwind double-stranded RNA molecules in an energy-dependent fashion through the hydrolysis of NTP. RNA helicases are associated with all processes involving RNA molecules, including nuclear transcription, editing, splicing, ribosome biogenesis, RNA export, and organelle gene expression. The involvement of RNA helicase in response to stress and in plant growth and development has been reported previously. While their importance in Arabidopsis and Oryza sativa has been partially studied, the function of RNA helicase proteins is poorly understood in Zea mays and Glycine max. In this study, we identified a total of RNA helicase genes in Arabidopsis and other crop species genome by genome-wide comparative in silico analysis. We classified the RNA helicase genes into three subfamilies according to the structural features of the motif II region, such as DEAD-box, DEAH-box and DExD/H-box, and different species showed different patterns of alternative splicing. Secondly, chromosome location analysis showed that the RNA helicase protein genes were distributed across all chromosomes with different densities in the four species. Thirdly, phylogenetic tree analyses identified the relevant homologs of DEAD-box, DEAH-box and DExD/H-box RNA helicase proteins in each of the four species. Fourthly, microarray expression data showed that many of these predicted RNA helicase genes were expressed in different developmental stages and different tissues under normal growth conditions. Finally, real-time quantitative PCR analysis showed that the expression levels of 10 genes in Arabidopsis and 13 genes in Zea mays were in close agreement with the microarray expression data. To our knowledge, this is the first report of a comparative genome-wide analysis of the RNA helicase gene family in Arabidopsis, Oryza sativa, Zea mays and Glycine max. This study provides valuable information for understanding the classification and putative functions of

  4. Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40.

    Directory of Open Access Journals (Sweden)

    Myco Umemura

    Full Text Available The development of next-generation sequencing (NGS technologies has dramatically increased the throughput, speed, and efficiency of genome sequencing. The short read data generated from NGS platforms, such as SOLiD and Illumina, are quite useful for mapping analysis. However, the SOLiD read data with lengths of <60 bp have been considered to be too short for de novo genome sequencing. Here, to investigate whether de novo sequencing of fungal genomes is possible using only SOLiD short read sequence data, we performed de novo assembly of the Aspergillus oryzae RIB40 genome using only SOLiD read data of 50 bp generated from mate-paired libraries with 2.8- or 1.9-kb insert sizes. The assembled scaffolds showed an N50 value of 1.6 Mb, a 22-fold increase than those obtained using only SOLiD short read in other published reports. In addition, almost 99% of the reference genome was accurately aligned by the assembled scaffold fragments in long lengths. The sequences of secondary metabolite biosynthetic genes and clusters, whose products are of considerable interest in fungal studies due to their potential medicinal, agricultural, and cosmetic properties, were also highly reconstructed in the assembled scaffolds. Based on these findings, we concluded that de novo genome sequencing using only SOLiD short reads is feasible and practical for molecular biological study of fungi. We also investigated the effect of filtering low quality data, library insert size, and k-mer size on the assembly performance, and recommend for the assembly use of mild filtered read data where the N50 was not so degraded and the library has an insert size of ∼2.0 kb, and k-mer size 33.

  5. Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae.

    Science.gov (United States)

    Jeon, Junhyun; Choi, Jaeyoung; Lee, Gir-Won; Park, Sook-Young; Huh, Aram; Dean, Ralph A; Lee, Yong-Hwan

    2015-02-24

    DNA methylation is an important epigenetic modification that regulates development of plants and mammals. To investigate the roles of DNA methylation in fungal development, we profiled genome-wide methylation patterns at single-nucleotide resolution during vegetative growth, asexual reproduction, and infection-related morphogenesis in a model plant pathogenic fungus, Magnaporthe oryzae. We found that DNA methylation occurs in and around genes as well as transposable elements and undergoes global reprogramming during fungal development. Such reprogramming of DNA methylation suggests that it may have acquired new roles other than controlling the proliferation of TEs. Genetic analysis of DNA methyltransferase deletion mutants also indicated that proper reprogramming in methylomes is required for asexual reproduction in the fungus. Furthermore, RNA-seq analysis showed that DNA methylation is associated with transcriptional silencing of transposable elements and transcript abundance of genes in context-dependent manner, reinforcing the role of DNA methylation as a genome defense mechanism. This comprehensive approach suggests that DNA methylation in fungi can be a dynamic epigenetic entity contributing to fungal development and genome defense. Furthermore, our DNA methylomes provide a foundation for future studies exploring this key epigenetic modification in fungal development and pathogenesis.

  6. Whole mitochondrial genome sequencing and transcriptional analysis to uncover an RT102-type cytoplasmic male sterility-associated candidate Gene Derived from Oryza rufipogon.

    Science.gov (United States)

    Okazaki, Masayuki; Kazama, Tomohiko; Murata, Hayato; Motomura, Keiji; Toriyama, Kinya

    2013-09-01

    Cytoplasmic male sterility (CMS) is a maternally inherited trait in which plants fail to produce functional pollen and is associated with the expression of a novel open reading frame (orf) gene encoded by the mitochondrial genome. An RT102A CMS line and an RT102C fertility restorer line were obtained by successive backcrossing between Oryza rufipogon W1125 and O. sativa Taichung 65. Using next-generation pyrosequencing, we determined whole-genome sequences of the mitochondria in RT102-CMS cytoplasm. To identify candidates for the CMS-associated gene in RT102 mitochondria, we screened the mitochondrial genome for the presence of specific orf genes that were chimeric or whose products carried predicted transmembrane domains. One of these orf genes, orf352, which showed different transcript sizes depending on whether the restorer of fertility (Rf) gene was present or not, was identified. The orf352 gene was co-transcribed with the ribosomal protein gene rpl5, and the 2.8 kb rpl5-orf352 transcripts were processed into 2.6 kb transcripts with a cleavage at the inside of the orf352 coding region in the presence of the Rf gene. The orf352 gene is an excellent candidate for the CMS-associated gene for RT102-CMS.

  7. Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems.

    Directory of Open Access Journals (Sweden)

    Len J Wade

    Full Text Available The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7-40.7 Mb and on chromosome 8 (20.3-21.9 Mb. Across experiments, the soil type/ growth medium showed more correlations with plant growth than the container dimensions. Although the correlations among studies and genetic co-location of root traits from a range of study systems points to their potential utility to represent responses in field studies, the best correlations were observed when the two setups had some similar properties. Due to the co-location of the identified genomic regions (from introgression block analysis with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought. This study also highlights the utility of characterizing a small set of 20 genotypes for root growth, drought response, and related genomic regions.

  8. Polyploid evolution in Oryza officinalis complex of the genus Oryza

    Directory of Open Access Journals (Sweden)

    Li Changbao

    2009-10-01

    Full Text Available Abstract Background Polyploidization is a prominent process in plant evolution, whereas the mechanism and tempo-spatial process remained poorly understood. Oryza officinalis complex, a polyploid complex in the genus Oryza, could exemplify the issues not only for it covering a variety of ploidy levels, but also for the pantropical geographic pattern of its polyploids in Asia, Africa, Australia and Americas, in which a pivotal genome, the C-genome, witnessed all the polyploidization process. Results Tracing the C-genome evolutionary history in Oryza officinalis complex, this study revealed the genomic relationships, polyploid forming and diverging times, and diploidization process, based on phylogeny, molecular-clock analyses and fluorescent in situ hybridization using genome-specific probes. Results showed that C-genome split with B-genome at ca. 4.8 Mya, followed by a series of speciation of C-genome diploids (ca. 1.8-0.9 Mya, which then partook in successive polyploidization events, forming CCDD tetraploids in ca. 0.9 Mya, and stepwise forming BBCC tetraploids between ca. 0.3-0.6 Mya. Inter-genomic translocations between B- and C-genomes were identified in BBCC tetraploid, O. punctata. Distinct FISH (fluorescent in situ hybridization patterns among three CCDD species were visualized by C-genome-specific probes. B-genome was modified before forming the BBCC tetraploid, O. malampuzhaensis. Conclusion C-genome, shared by all polyploid species in the complex, had experienced different evolutionary history particularly after polyploidization, e.g., inter-genomic exchange in BBCC and genomic invasion in CCDD tetraploids. It diverged from B-genome at 4.8 Mya, then participated in the tetraploid formation spanning from 0.9 to 0.3 Mya, and spread into tropics of the disjunct continents by transcontinentally long-distance dispersal, instead of vicariance, as proposed by this study, given that the continental splitting was much earlier than the C-genome

  9. Comparative genomic analysis of the GRF genes in Chinese pear (Pyrus bretschneideri Rehd, poplar (Populous, grape (Vitis vinifera, Arabidopsis and rice (Oryza sativa

    Directory of Open Access Journals (Sweden)

    Yun Peng Cao

    2016-11-01

    Full Text Available Growth-regulating factors (GRFs are plant-specific transcription factors that have important functions in regulating plant growth and development. Previous studies on GRF family members focused either on a single or a small set of genes. Here, a comparative genomic analysis of the GRF gene family was performed in poplar (a model tree species, Arabidopsis (a model plant for annual herbaceous dicots, grape (one model plant for perennial dicots, rice (a model plant for monocots and Chinese pear (one of the economical fruit crops. In total, 58 GRF genes were identified, 12 genes in rice (Oryza sativa, 8 genes in grape (Vitis vinifera, 9 genes in Arabidopsis thaliana, 19 genes in poplar (Populus trichocarpa and 10 genes in Chinese pear (Pyrus bretschneideri. The GRF genes were divided into five subfamilies based on the phylogenetic analysis, which was supported by their structural analysis. Furthermore, microsynteny analysis indicated that highly conserved regions of microsynteny were identified in all of the five species tested. And Ka/Ks analysis revealed that purifying selection play an important role in the maintenance of GRF genes. Our results provide basic information on GRF genes in five plant species and lay the foundation for future research on the functions of these genes.

  10. Development and characterization of interspecific hybrids between Oryza sativa and O. latifolia by in situ hybridization

    Institute of Scientific and Technical Information of China (English)

    YI ChuanDeng; TANG ShuZhu; ZHOU Yong; LIANG GuoHua; GONG ZhiYun; GU MingHong

    2008-01-01

    Oryza sativa and O. latifolia belong to the AA and CCDD genomes of Oryza, respectively. In this study, interspecific hybrids of these species were obtained using the embryo rescue technique. Hybrid pani-cle traits, such as long awns, small grain, exoteric large purple stigma, grain shattering and dispersed panicles, resemble that of the paternal parent, O. latifolia, whereas there is obvious heterosis in such respects as plant height, tillering ability and vegetative vigor. Chromosome pairing and the genomic components of the hybrid were subsequently investigated using genomic in situ hybridization (GISH) and fluorescent in situ hybridization (FISH) analysis. Based on the mitotic metaphase chromosome numbers of the root tips investigated, the hybrid is a triploid with 36 chromosomes. The genomic con-stitution of the hybrid is ACD. In the meiotic metaphase I of the hybrid pollen mother cell, poor chro-mosome pairing was identified and most of the chromosomes were univalent, which resulted in com-plete male sterility in the hybrid.

  11. Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion.

    Science.gov (United States)

    Jacquemin, Julie; Ammiraju, Jetty S S; Haberer, Georg; Billheimer, Dean D; Yu, Yeisoo; Liu, Liana C; Rivera, Luis F; Mayer, Klaus; Chen, Mingsheng; Wing, Rod A

    2014-04-01

    In analyzing gene families in the whole-genome sequences available for O. sativa (AA), O. glaberrima (AA), and O. brachyantha (FF), we observed large size expansions in the AA genomes compared to FF genomes for the super-families F-box and NB-ARC, and five additional families: the Aspartic proteases, BTB/POZ proteins (BTB), Glutaredoxins, Trypsin α-amylase inhibitor proteins, and Zf-Dof proteins. Their evolutionary dynamic was investigated to understand how and why such important size variations are observed between these closely related species. We show that expansions resulted from both amplification, largely by tandem duplications, and contraction by gene losses. For the F-box and NB-ARC gene families, the genes conserved in all species were under strong purifying selection while expanded orthologous genes were under more relaxed purifying selection. In F-box, NB-ARC, and BTB, the expanded groups were enriched in genes with little evidence of expression, in comparison with conserved groups. We also detected 87 loci under positive selection in the expanded groups. These results show that most of the duplicated copies in the expanded groups evolve neutrally after duplication because of functional redundancy but a fraction of these genes were preserved following neofunctionalization. Hence, the lineage-specific expansions observed between Oryza species were partly driven by directional selection.

  12. Erratum to "Analysis of collinear regions of Oryza AA and CC genomes" [Journal of Genetics and Genomics(2009) 36, 667-677

    Institute of Scientific and Technical Information of China (English)

    Qi Feng; Tao Huang; Qiang Zhao; Jingjie Zhu; Zhixin Lin; Bin Han

    2009-01-01

    @@ In the author line on page 667, the affiliation of the author "Tao Huang" was incorrect. For the reaaer's convemence,the correct affiliation of "Tao Huang" should be "b National Center for Gene Research & Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China".

  13. Genetic relatedness of genus Oryza from Eastern Himalayan region as revealed by chloroplast matK gene

    Directory of Open Access Journals (Sweden)

    Doris Zodinpuii

    2013-12-01

    Full Text Available Phylogenetic relationship was studied in wild and cultivated rice using the chloroplast matK gene. The aligned sequence fragments were 826bp in length with 7.02% variable and 4.47% phylogenetically informative sites and the estimated Transition/Transversion bias (R was 1.97. Seven hundred and two characters were constant, 74 variable characters were parsimony-uninformative and 50 were parsimony–informative. Haplotypes of Mizoram rice and wild relatives (A genome were more similar than those of distantly related species (B, C/CD, E and G genomes. It further revealed that the EE genome species is most closely related to the CC genome and CCDD genomes. The BBCC genome species had different origins, and their maternal parents had either the BB or CC genome. An additional genome type, HHKK was recognized in O. coarctata and O. schlechteri. Within the AA genome the African, O. glaberrima and O. longistaminatea and American, O. glumipatula and O. barthii were closer to the Indian Oryza species, O. nivara and O. rufipogon. The unknown genome O. malampuzhaensis from India is closer to BB and BBCC genome containing respectively O. punctata from Cameroon and O. minuta from Philippines. CpG rich matK sequences were rich in GG and FF genotypes, whereas CpA rich sequences belonged to BB and BBCC related genomes variety.

  14. Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice.

    Science.gov (United States)

    Waters, Daniel L E; Nock, Catherine J; Ishikawa, Ryuji; Rice, Nicole; Henry, Robert J

    2012-01-01

    Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the chloroplast genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The chloroplast genomes of Australian O. rufipogon and O. meridionalis were closely related with only 32 differences. The Asian O. rufipogon chloroplast genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The Australian O. rufipogon may be a perennial form of O. meridionalis.

  15. Flux balance analysis of genome-scale metabolic model of rice (Oryza sativa): Aiming to increase biomass

    Indian Academy of Sciences (India)

    Rahul Shaw; Sudip Kundu

    2015-10-01

    Due to socio-economic reasons, it is essential to design efficient stress-tolerant, more nutritious, high yielding rice varieties. A systematic understanding of the rice cellular metabolism is essential for this purpose. Here, we analyse a genome-scale metabolic model of rice leaf using Flux Balance Analysis to investigate whether it has potential metabolic flexibility to increase the biosynthesis of any of the biomass components. We initially simulate the metabolic responses under an objective to maximize the biomass components. Using the estimated maximum value of biomass synthesis as a constraint, we further simulate the metabolic responses optimizing the cellular economy. Depending on the physiological conditions of a cell, the transport capacities of intracellular transporters (ICTs) can vary. To mimic this physiological state, we randomly vary the ICTs’ transport capacities and investigate their effects. The results show that the rice leaf has the potential to increase glycine and starch in a wide range depending on the ICTs’ transport capacities. The predicted biosynthesis pathways vary slightly at the two different optimization conditions. With the constraint of biomass composition, the cell also has the metabolic plasticity to fix a wide range of carbon-nitrogen ratio.

  16. Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae

    NARCIS (Netherlands)

    Coutinho, Pedro M; Andersen, Mikael R; Kolenova, Katarina; vanKuyk, Patricia A; Benoit, Isabelle; Gruben, Birgit S; Trejo-Aguilar, Blanca; Visser, Hans; van Solingen, Piet; Pakula, Tiina; Seiboth, Bernard; Battaglia, Evy; Aguilar-Osorio, Guillermo; de Jong, Jan F; Ohm, Robin A; Aguilar, Mariana; Henrissat, Bernard; Nielsen, Jens; Stålbrand, Henrik; de Vries, Ronald P

    The plant polysaccharide degradative potential of Aspergillus nidulans was analysed in detail and compared to that of Aspergillus niger and Aspergillus oryzae using a combination of bioinformatics, physiology and transcriptomics. Manual verification indicated that 28.4% of the A. nidulans ORFs

  17. Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae

    DEFF Research Database (Denmark)

    Coutinho, Pedro M.; Andersen, Mikael Rørdam; Kolenova, Katarina

    2009-01-01

    The plant polysaccharide degradative potential of Aspergillus nidulans was analysed in detail and compared to that of Aspergillus niger and Aspergillus oryzae using a combination of bioinformatics, physiology and transcriptomics. Manual verification indicated that 28.4% of the A. nidulans ORFs an...

  18. QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Marathi Balram

    2012-08-01

    Full Text Available Abstract Background Rice is staple food for more than half of the world’s population including two billion Asians, who obtain 60-70% of their energy intake from rice and its derivatives. To meet the growing demand from human population, rice varieties with higher yield potential and greater yield stability need to be developed. The favourable alleles for yield and yield contributing traits are distributed among two subspecies i.e., indica and japonica of cultivated rice (Oryza sativa L.. Identification of novel favourable alleles in indica/japonica will pave way to marker-assisted mobilization of these alleles in to a genetic background to break genetic barriers to yield. Results A new plant type (NPT based mapping population of 310 recombinant inbred lines (RILs was used to map novel genomic regions and QTL hotspots influencing yield and eleven yield component traits. We identified major quantitative trait loci (QTLs for days to 50% flowering (R2 = 25%, LOD = 14.3, panicles per plant (R2 = 19%, LOD = 9.74, flag leaf length (R2 = 22%, LOD = 3.05, flag leaf width (R2 = 53%, LOD = 46.5, spikelets per panicle (R2 = 16%, LOD = 13.8, filled grains per panicle (R2 = 22%, LOD = 15.3, percent spikelet sterility (R2 = 18%, LOD = 14.24, thousand grain weight (R2 = 25%, LOD = 12.9 and spikelet setting density (R2 = 23%, LOD = 15 expressing over two or more locations by using composite interval mapping. The phenotypic variation (R2 ranged from 8 to 53% for eleven QTLs expressing across all three locations. 19 novel QTLs were contributed by the NPT parent, Pusa1266. 15 QTL hotpots on eight chromosomes were identified for the correlated traits. Six epistatic QTLs effecting five traits at two locations were identified. A marker interval (RM3276-RM5709 on chromosome 4 harboring major QTLs for four traits was identified. Conclusions The present study reveals that favourable alleles for

  19. Pigment and Virulence Deficiencies Associated with Mutations in the aroE Gene of Xanthomonas oryzae pv. oryzae

    OpenAIRE

    2001-01-01

    Xanthomonadins are yellow, membrane-bound pigments produced by members of the genus Xanthomonas. We identified an ethyl methanesulfonate-induced Xanthomonas oryzae pv. oryzae mutant (BXO65) that is deficient for xanthomonadin production and virulence on rice, as well as auxotrophic for aromatic amino acids (Pig− Vir− Aro−). Reversion analysis indicated that these multiple phenotypes are due to a single mutation. A genomic library of the wild-type strain was used to isolate a 7.0-kb clone that...

  20. Genome-wide analysis and evolutionary study of sucrose non-fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza.

    Science.gov (United States)

    Saha, Jayita; Chatterjee, Chitrita; Sengupta, Atreyee; Gupta, Kamala; Gupta, Bhaskar

    2014-04-01

    The over-expression of plant specific SnRK2 gene family members by hyperosmotic stress and some by abscisic acid is well established. In this report, we have analyzed the evolution of SnRK2 gene family in different plant lineages including green algae, moss, lycophyte, dicot and monocot. Our results provide some evidences to indicate that the natural selection pressure had considerable influence on cis-regulatory promoter region and coding region of SnRK2 members in Arabidopsis and Oryza independently through time. Observed degree of sequence/motif conservation amongst SnRK2 homolog in all the analyzed plant lineages strongly supported their inclusion as members of this family. The chromosomal distributions of duplicated SnRK2 members have also been analyzed in Arabidopsis and Oryza. Massively Parallel Signature Sequencing (MPSS) database derived expression data and the presence of abiotic stress related promoter elements within the 1 kb upstream promoter region of these SnRK2 family members further strengthen the observations of previous workers. Additionally, the phylogenetic relationships of SnRK2 have been studied in all plant lineages along with their respective exon-intron structural patterns. Our results indicate that the ancestral SnRK2 gene of land plants gradually evolved by duplication and diversification and modified itself through exon-intron loss events to survive under environmental stress conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. OsSERK1 regulates rice development but not immunity to Xanthomonas oryzae pv. oryzae or Magnaporthe oryzae

    Institute of Scientific and Technical Information of China (English)

    Shimin Zuo; and Pamela C Ronald; Xiaogang Zhou; Mawsheng Chen; Shilu Zhang; Benjamin Schwessinger; Deling Ruan; Can Yuan; Jing Wang; Xuewei Chen

    2014-01-01

    Somatic embryogenesis receptor kinase (SERK) proteins play pivotal roles in regulation of plant development and immunity. The rice genome contains two SERK genes, OsSerk1 and OsSerk2. We previously demonstrated that OsSerk2 is required for rice Xa21‐mediated resistance to Xanthomonas oryzae pv. oryzae (Xoo) and for normal development. Here we report the molecular characterization of OsSerk1. Overexpres-sion of OsSerk1 results in a semi‐dwarf phenotype whereas silencing of OsSerk1 results in a reduced angle of the lamina joint. OsSerk1 is not required for rice resistance to Xoo or Magnaporthe oryzae. Overexpression of OsSerk1 in OsSerk2‐silenced lines complements phenotypes associated with brassinosteroid (BR) signaling defects, but not the disease resistance phenotype mediated by Xa21. In yeast, OsSERK1 interacts with itself forming homodimers, and also interacts with the kinase domains of OsSERK2 and BRI1, respectively. OsSERK1 is a functional protein kinase capable of auto‐phosphorylation in vitro. We conclude that, whereas OsSERK2 regulates both rice development and immunity, OsSERK1 functions in rice development but not immunity to Xoo and M. oryzae.

  2. De Novo Assembly and Characterization of Oryza officinalis Leaf Transcriptome by Using RNA-Seq

    Directory of Open Access Journals (Sweden)

    Ying Bao

    2015-01-01

    Full Text Available Although endeavors have been made to identify useful wild rice genes that can be used to improve cultivated rice, the virtual reservoir of genetic variation hidden within the wild relatives of cultivated rice is largely untapped. Here, using next-generation sequencing technology, we investigated the leaf transcriptome of a wild rice O. officinalis with CC genome. Approximately 23 million reads were produced in the species leaf transcriptome analysis and de novo assembly methods constructed 68,132 unigenes. Functional annotations for the unigenes were conducted using sequence similarity comparisons against the following databases: the nonredundant nucleotide database, the nonredundant protein database, the SWISS-PROT database, the Clusters of Orthologous Groups of proteins database, the Kyoto Encyclopedia of Genes and Genomes database, the Gene Ontology Consortium database, and the InterPro domains database. In addition, a total of 476 unigenes related to disease resistance were identified in O. officinalis, and these unigenes can serve as important genetic resources for cultivated rice breeding and quality improvement. The present study broadens our understanding of the genetic background of non-AA genomic wild rice species and it also provides a bridge to extend studies to other Oryza species with CC genomes.

  3. Identification, Biochemical Characterization, and Evolution of the Rhizopus oryzae 99-880 Polygalacturonase Gene Family

    Science.gov (United States)

    A search of the recently sequenced Rhizopus oryzae strain 99-880 genome database uncovered 18 putative polygalacturonase genes with 2 genes being identical and only 1 with similarity to a previously reported R. oryzae polygalacturonase gene. The 17 different genes share 50% to greater than 90% iden...

  4. 利用粳稻基因组DNA和Cot-1 DNA探针对普通野生稻和亚洲栽培稻的比较分析%Comparative Analysis of Oryza rufipogon Griff. and Oryza sativa with Nipponbare Genomic DNA and Cot-1 DNA Probes

    Institute of Scientific and Technical Information of China (English)

    覃瑞; 李智; 刘虹; 陈雁; 蔡朝晖; 李刚

    2012-01-01

    Using genomic DNA and Cot-1 DNA of Nipponbare as probes, GISH( genimic in situ hybridization) and Cot-1 DNA FISH (fluorescence in situ hybridization ) were adopted to analyse the genomes of japonica Nipponbare, indica Guangluai 4 and Oryza rufipogon Griff. karyotype. Homologous clustering and comparative study of the above 3 genomes were also made. The results indicated that the distribution and coverage of genomic DNA and Cot-1 DNA probes in 3 rice genomes were very similar. The coverage percentage of Cot-1 DNA in Nipponbare, Guangluai 4 and Oryza rufipogon Griff. were (47.13 ±0. 18)%, (45.89 ±0.22)% and (44.24 ±0.21 )% respectively, demonstrating the high homology and close relationship among them. The highly and moderately repetitive DNA sequences played an important role in the evolution of rice species and indica-japonica genetic differentiation, since their hybridization signal distribution had their own characteristics . The chromosomes which contain less highly and moderately repetitive DNA sequences( No. 2,5,8 ) are more active in rice genome' s evolution.%以粳稻日本晴基因组DNA和Cot-1 DNA为探针,分别对日本晴、籼稻广陆矮4号和普通野生稻的染色体组进行了基因组原位杂交(GISH)和Cot-1 DNA荧光原位杂交(FISH)分析,并对3种染色体组进行了同源聚类和比较研究.结果表明:粳稻基因组DNA和Cot-1 DNA探针信号在3种水稻染色体组中的分布状况和覆盖率相似,Cot-1 DNA的覆盖率分别为(47.13±0.18)%、(45.89±0.22)%、(44.24±0.21)%,3种水稻基因组同源性高,亲缘关系接近.Cot-1 DNA在3种水稻染色体上的杂交信号分布各有特点,中高度重复序列的变异在普通野生稻向栽培稻进化和亚洲栽培稻籼、粳分化过程中具有重要意义,中高度重复序列含量较低的2、5、8号染色体是水稻染色体组进化过程中相对活跃的成分.

  5. PENGARUH RHIZOPUS ORYZAE DAN ASPERGILLUS ORYZAE TERHADAP KUALITAS KECAP

    Directory of Open Access Journals (Sweden)

    Dewi Sabita Slamet

    2012-11-01

    Full Text Available Telah diteliti pengganti fermentasi mikroorganisme Aspergillus oryzae Rhyzopus oryzae dan campuran Aspergillus dan Rhyzopus oryzae, dengan perendaman dalam larutan garam 20% dalam waktu yang berbeda terhadap kualitas kecap.Lamanya perendaman dalam larutan garam 20% yang berbeda menghasilkan kadar protein kecap yang berbeda. Aspergillus oryzae lebih baik dalam menghasilkan enzima protease dari pada Rhyzopus oryzae.Uji organoleptik menunjukkan perbedaan tidak bermakna dalam hal rasa maupun aroma antar kecap yang dibuat dengan strain jamur yang berlainan serta waktu perendaman yang berbeda. Untuk membuat kecap, sebaiknya dilakukan perendaman dalam larutan garam 20% selama 14 hari.

  6. Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships

    OpenAIRE

    Booher, Nicholas J.; Carpenter, Sara C. D.; Sebra, Robert P.; Wang, Li; Salzberg, Steven L.; Leach, Jan E; Bogdanove, Adam J.

    2015-01-01

    Pathogen-injected, direct transcriptional activators of host genes, TAL (transcription activator-like) effectors play determinative roles in plant diseases caused by Xanthomonas spp. A large domain of nearly identical, 33–35 aa repeats in each protein mediates DNA recognition. This modularity makes TAL effectors customizable and thus important also in biotechnology. However, the repeats render TAL effector (tal) genes nearly impossible to assemble using next-generation, short reads. Here, we ...

  7. Rice (Oryza) hemoglobins

    Science.gov (United States)

    Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice (Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a sin...

  8. Genetic variation in a population of Bipolaris oryzae based on RAPD ...

    African Journals Online (AJOL)

    ONOS

    2010-09-06

    Sep 6, 2010 ... Isolates of Bipolaris oryzae were analysed by RAPD techniques to determine the ... samples for DNA extraction were grown on potato-dextrose broth ... Then for determining DNA quantity as empirical, the genomic DNA.

  9. The chemical heritage of Aspergillus flavus in A. oryzae RIB 40

    DEFF Research Database (Denmark)

    Rank, Christian; Klejnstrup, Marie Louise; Petersen, Lene Maj

    Aspergillus oryzae is a very important species in biotechnology and has been used for centuries in traditional Asian fermentation. The RIB40 strain is particularly interesting as it was one of the first genome sequenced Aspergilli together with A. flavus, a prominent food and feed contaminant...... with indications to specific genetic changes. Several new metabolites and changes in biosynthetic routes have been found in A. oryzae, indicating subtle changes in the genomic heritage from A. flavus....

  10. Photosynthetic Characteristics of Rice Transformed with Genomic DNA of Oryza minuta%转小粒野生稻基因组DNA水稻的光合性状研究

    Institute of Scientific and Technical Information of China (English)

    匡勇; 袁娇; 夏石头; 黄志远; 孙一丹; 赵炳然

    2011-01-01

    A new rice germplasm Yewei B was bred through transformed with genomic DNA of the distantly related species Oryza minuta into hybrid rice parent V20B by ear-stem injecting. Compared with V2OB, Yewei B has loose plant type, small and thin stem. The leaf area of the top 1st, top 2nd and top 3rd leaf is significantly smaller than that of V20B respectively. The content of chlorophyll of Yewei B and V20B decreased gradually from initial heading stage ( I ) to heading stage ( Ⅱ ), milk ripening stage ( Ⅲ ), wax ripening stage (Ⅳ) and yellow ripening stage ( V ), and there is no significant difference between these two varieties. However the photosynthetic rate of the top 1st, top 2nd and top 3rd leaf in Yewei B is significantly higher than that of V20B.%通过"穗茎注射法",将远缘物种小粒野生稻(Oryza minuta)的基因组DNA导入杂交水稻亲本V20B中,培育出转基因水稻新种质野威B.与亲本V20B相比,野威B的株型较松散,茎较细小,其倒1、倒2和倒3叶的叶面积均显著小于亲本的.从始穗期(Ⅰ期)、齐穗期(Ⅱ期)到乳熟期(Ⅲ期)再到黄熟期(Ⅳ期)和腊熟期(Ⅴ期),野威B和V20B的叶绿素含量逐渐降低,两者之间差异未达到显著水平,但野威B的倒1、倒2和倒3叶片的光合速率均极显著高于亲本V20B的光合速率.

  11. Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola

    Directory of Open Access Journals (Sweden)

    Fu Bin-Ying

    2010-02-01

    Full Text Available Abstract Background Non-host resistance in rice to its bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc, mediated by a maize NBS-LRR type R gene, Rxo1 shows a typical hypersensitive reaction (HR phenotype, but the molecular mechanism(s underlying this type of non-host resistance remain largely unknown. Results A microarray experiment was performed to reveal the molecular mechanisms underlying HR of rice to Xoc mediated by Rxo1 using a pair of transgenic and non-transgenic rice lines. Our results indicated that Rxo1 appeared to function in the very early step of the interaction between rice and Xoc, and could specifically activate large numbers of genes involved in signaling pathways leading to HR and some basal defensive pathways such as SA and ET pathways. In the former case, Rxo1 appeared to differ from the typical host R genes in that it could lead to HR without activating NDR1. In the latter cases, Rxo1 was able to induce a unique group of WRKY TF genes and a large set of genes encoding PPR and RRM proteins that share the same G-box in their promoter regions with possible functions in post-transcriptional regulation. Conclusions In conclusion, Rxo1, like most host R genes, was able to trigger HR against Xoc in the heterologous rice plants by activating multiple defensive pathways related to HR, providing useful information on the evolution of plant resistance genes. Maize non-host resistance gene Rxo1 could trigger the pathogen-specific HR in heterologous rice, and ultimately leading to a localized programmed cell death which exhibits the characteristics consistent with those mediated by host resistance genes, but a number of genes encoding pentatricopeptide repeat and RNA recognition motif protein were found specifically up-regulated in the Rxo1 mediated disease resistance. These results add to our understanding the evolution of plant resistance genes.

  12. Mitochondrial respiratory pathways inhibition in Rhizopus oryzae potentiates activity of posaconazole and itraconazole via apoptosis.

    Directory of Open Access Journals (Sweden)

    Fazal Shirazi

    Full Text Available The incidence of mucormycosis has increased drastically in immunocompromised patients. Also the array of targets whose inhibition results in Mucorales death is limited. Recently, researchers identified mitochondria as important regulators of detoxification and virulence mechanisms in fungi. In this context, targeting the mitochondrial respiratory chain may provide a new platform for antifungal development. We hypothesized that targeting respiratory pathways potentiates triazoles activity via apoptosis. We found that simultaneous administration of antimycin A (AA and benzohydroxamate (BHAM, inhibitors of classical and alternative mitochondrial pathways respectively, resulted in potent activity of posaconazole (PCZ and itraconazole (ICZ against Rhizopus oryzae. We observed cellular changes characteristic of apoptosis in R. oryzae cells treated with PCZ or ICZ in combination with AA and BHAM. The fungicidal activity of this combination against R. oryzae was correlated with intracellular reactive oxygen species accumulation (ROS, phosphatidylserine externalization, mitochondrial membrane depolarization, and increased caspase like activity. DNA fragmentation and condensation assays also revealed apoptosis of R. oryzae cells. These apoptotic features were prevented by the addition of the ROS scavenger N-acetyl-cysteine. Taken together, these findings suggest that the use of PCZ or ICZ in combination with AA and BHAM makes R. oryzae exquisitely sensitive to treatment with triazoles via apoptosis. This strategy may serve as a new model for the development of improved or novel antifungal agents.

  13. The Population Structure of African Cultivated Rice Oryza glaberrima (Steud.)

    DEFF Research Database (Denmark)

    Semon, Mande; Nielsen, Rasmus; Jones, Monty P.;

    2005-01-01

    Genome-wide linkage disequilibrium (LD) was investigated for 198 accessions of Oryza glaberrima using 93 nuclear microsatellite markers. Significantly elevated levels of LD were detected, even among distantly located markers. Free recombination among loci at the population genetic level was shown...

  14. Cytological mechanisms of interspecific incrossability and hybrid sterility between Oryza sativa L. and O.alta Swallen

    Institute of Scientific and Technical Information of China (English)

    FU XueLin; LU YongGen; LIU XiangDong; Li JinQuan; Feng JiuHuan

    2007-01-01

    Oryza sativa and O. alta belong to AA and CCDD genomes in Oryza, respectively. Interspecific reproductive isolation limits the transfer of favorable genes from O. alta into O. sativa. The cytological mechanisms of interspecific incrossability and hybrid sterility between O. sativa and O. alta were studied systematically in this paper. We indentified two cytological causes of interspecific incrossability. First, we observed embryo sac incompatibility that caused fertilization barriers of variable severity such as non-fertilization, fertilization stagnation and egg cell single-fertilization. Second, we observed hybrid inviability, the major cause for incrossability, apparent from hybrid embryo developmental stagnation and embryo abortion. Hybrid sterility included both embryo sac sterility and pollen sterility.The hybrid embryo sac was completely sterile and exhibited mainly embryo sac degeneration. Hybrid pollen was also sterile and mainly typical abortive. Hybrid sterility was mainly caused by severely abnormal meioses of megasporocytes and pollen mother cells; it is the most important abnormality, being chromosome sterility. Several methods are suggested to overcome the interspecific reproductive isolation between O. sativa and O. alta.

  15. 水稻白叶枯病菌GX1329基因组文库的构建及含编码TAL效应物基因的克隆的分离%Construction of a Genomic Library of Xanthomonas oryzae pv. oryzae Strain GX1329 and Isolation of Clones Containing the Genes Encoding TAL Ef- fectors

    Institute of Scientific and Technical Information of China (English)

    张子宇; 赵帅; 莫伟兰; 罗雪梅; 玉延华; 段承杰; 冯家勋

    2011-01-01

    由革兰氏阴性细菌水稻白叶枯病菌引起的水稻白叶枯病是亚洲、北美以及非洲部分地区最严重的水稻病害之一,水稻白叶枯病可使水稻减产高达50%以上。研究表明水稻白叶枯病菌的毒力主要依靠三型分泌系统所分泌的效应物。为了解水稻白叶枯病菌广西菌株GX1329中含有avrBs3/pthA家族基因的情况,本研究应用Alu I部分酶切其基因组DNA,构建了含有736个克隆的菌株GX1329的基因组文库。BamHI酶切分析随机挑取的15个文库克隆表明,克隆的外源DNA随机性良好,克隆的最小片段为27.7kb,最大为58.5kb,平均大小为39.9kb,文库克隆容量约为2.8×10^3Mb,该文库中包含基因组中任一个基因的概率为99.4%。利用来自水稻白叶枯病菌菲律宾菌株PX086的无毒基因avrXa10的第252位~第486位核苷酸序列作为探针,通过菌落原位杂交从GX1329基因组文库中筛选到37个含avrBs3/pthA家族基因的克隆。再通过Southern杂交分析,得到了17个独立克隆。这17个克隆中至少含有13个不同的avrBs3/pthA家族基因。这些基因在GX1329基因组中有的单独存在,有的两个或两个以上串联存在。本工作基本上明确了菌株GX1329基因组中avrBs3/pthA家族基因的数量,为进一步研究菌株GX1329中avrBs3/pthA家族基因的功能奠定了基础。%Bacterial leaf blight (BLB), caused by Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo), is a serious threat to yield losses in the main regions of rice growth including Asia, North America and Africa. BLB could lead to a crop loss of up to 50%. It is known that the virulence of Xoo mainly relies on type BI secre- tion system (T3SS) and its secreted effectors. To know the numbers of genes encoding avrBs3/pthA family mem- bers in Guangxi Xoo strain GX1329, a genomic DNA library containing 736 clones was successfully constructed by partially

  16. 水稻白叶枯病菌GX1329基因组文库的构建及含编码TAL效应物基因的克隆的分离%Construction of a Genomic Library of Xanthomonas oryzae pv.oryzae Strain GX1329 and Isolation of Clones Containing the Genes Encoding TAL Effectors

    Institute of Scientific and Technical Information of China (English)

    张子宇; 赵帅; 莫伟兰; 罗雪梅; 玉延华; 段承杰; 冯家勋

    2011-01-01

    Bacterial leaf blight (BLB), caused by Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo),is a serious threat to yield losses in the main regions of rice growth including Asia, North America and Africa.BLB could lead to a crop loss of up to 50%. It is known that the virulence of Xoo mainly relies on type Ⅲ secretion system (T3SS) and its secreted effectors. To know the numbers of genes encoding avrBs3/pthA family members in Guangxi Xoo strain GX1329, a genomic DNA library containing 736 clones was successfully constructed by partially digesting the genomic DNA with A lu Ⅰ . Restriction enzyme BamH Ⅰ digestion analysis of plasmids from 15 randomly chosen library clones showed that the cloned DNA in the genomic library was highly random.The size of the smallest cloned DNA in one clone was 27.7kb, the size of the biggest cloned DNA in one clone was 58.5 kb, and the average size of cloned DNA in one clone was 39.9 kb. The cloning capacity of the library is about 2.8x103 Mb with high randomness, and the probability of any one gene contained in the library was about 99.4%.Thirty-seven positive clones were screened out from the GX1329 genomic library by colony in situ hybridization using the 252th to 486th bp sequence of avrXa10 from Xoo strain PXO86 as probe. Southern hybridization analysis of the 17 clones showed that they contain at least 13 different avrBs3/pthA genes. The results also showed that the avrB.s3/pthA family genes occurred in individual or clusters in the genome of strain GX1329. This work defined the number of avrBs3/pthA family genes in the genome of GX1329, which may provide a solid basis for further studying the function of the genes.%由革兰氏阴性细菌水稻白叶枯病菌引起的水稻白叶枯病是亚洲、北美以及非洲部分地区最严重的水稻病害之一,水稻白叶枯病可使水稻减产高达50%以上.研究表明水稻白叶枯病菌的毒力主要依靠三型分泌系统所分泌的效应物.为了解

  17. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

    Science.gov (United States)

    Begum, Hasina; Spindel, Jennifer E; Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R

    2015-01-01

    Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

  18. ZINC-INDUCED FACILITATOR-LIKE family in plants: lineage-specific expansion in monocotyledons and conserved genomic and expression features among rice (Oryza sativa paralogs

    Directory of Open Access Journals (Sweden)

    Lopes Karina L

    2011-01-01

    Full Text Available Abstract Background Duplications are very common in the evolution of plant genomes, explaining the high number of members in plant gene families. New genes born after duplication can undergo pseudogenization, neofunctionalization or subfunctionalization. Rice is a model for functional genomics research, an important crop for human nutrition and a target for biofortification. Increased zinc and iron content in the rice grain could be achieved by manipulation of metal transporters. Here, we describe the ZINC-INDUCED FACILITATOR-LIKE (ZIFL gene family in plants, and characterize the genomic structure and expression of rice paralogs, which are highly affected by segmental duplication. Results Sequences of sixty-eight ZIFL genes, from nine plant species, were comparatively analyzed. Although related to MSF_1 proteins, ZIFL protein sequences consistently grouped separately. Specific ZIFL sequence signatures were identified. Monocots harbor a larger number of ZIFL genes in their genomes than dicots, probably a result of a lineage-specific expansion. The rice ZIFL paralogs were named OsZIFL1 to OsZIFL13 and characterized. The genomic organization of the rice ZIFL genes seems to be highly influenced by segmental and tandem duplications and concerted evolution, as rice genome contains five highly similar ZIFL gene pairs. Most rice ZIFL promoters are enriched for the core sequence of the Fe-deficiency-related box IDE1. Gene expression analyses of different plant organs, growth stages and treatments, both from our qPCR data and from microarray databases, revealed that the duplicated ZIFL gene pairs are mostly co-expressed. Transcripts of OsZIFL4, OsZIFL5, OsZIFL7, and OsZIFL12 accumulate in response to Zn-excess and Fe-deficiency in roots, two stresses with partially overlapping responses. Conclusions We suggest that ZIFL genes have different evolutionary histories in monocot and dicot lineages. In rice, concerted evolution affected ZIFL duplicated genes

  19. Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment

    Science.gov (United States)

    Quibod, Ian Lorenzo; Perez-Quintero, Alvaro; Booher, Nicholas J.; Dossa, Gerbert S.; Grande, Genelou; Szurek, Boris; Vera Cruz, Casiana; Bogdanove, Adam J.; Oliva, Ricardo

    2016-01-01

    Understanding the processes that shaped contemporary pathogen populations in agricultural landscapes is quite important to define appropriate management strategies and to support crop improvement efforts. Here, we took advantage of an historical record to examine the adaptation pathway of the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo) in a semi-isolated environment represented in the Philippine archipelago. By comparing genomes of key Xoo groups we showed that modern populations derived from three Asian lineages. We also showed that diversification of virulence factors occurred within each lineage, most likely driven by host adaptation, and it was essential to shape contemporary pathogen races. This finding is particularly important because it expands our understanding of pathogen adaptation to modern agriculture. PMID:27667260

  20. Cell biology of the Koji mold Aspergillus oryzae.

    Science.gov (United States)

    Kitamoto, Katsuhiko

    2015-01-01

    Koji mold, Aspergillus oryzae, has been used for the production of sake, miso, and soy sauce for more than one thousand years in Japan. Due to the importance, A. oryzae has been designated as the national micro-organism of Japan (Koku-kin). A. oryzae has been intensively studied in the past century, with most investigations focusing on breeding techniques and developing methods for Koji making for sake brewing. However, the understanding of fundamental biology of A. oryzae remains relatively limited compared with the yeast Saccharomyces cerevisiae. Therefore, we have focused on studying the cell biology including live cell imaging of organelles, protein vesicular trafficking, autophagy, and Woronin body functions using the available genomic information. In this review, I describe essential findings of cell biology of A. oryzae obtained in our study for a quarter of century. Understanding of the basic biology will be critical for not its biotechnological application, but also for an understanding of the fundamental biology of other filamentous fungi.

  1. Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L. grown at four international field sites.

    Directory of Open Access Journals (Sweden)

    Gareth J Norton

    Full Text Available The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of ∼ 300 accessions and 36.9 k single nucleotide polymorphisms (SNPs. The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel. This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel.

  2. Studies on the yield and quality characteristics of YeiweiB plants transformed with Oryza minuta genomic DNA%转小粒野生稻基因种质野威B的产量与米质性状

    Institute of Scientific and Technical Information of China (English)

    匡勇; 杨曼云; 匡逢春; 黄志远; 胡远艺; 夏石头; 赵炳然

    2011-01-01

    野威B是将小粒野生稻(Oryza minuta)的基因组DNA通过穗茎注射法导入杂交水稻亲本V20B中培育出的转基因水稻新种质.与亲本V20B相比,野威B的有效穗数和每穗总粒数小于V20B,但每穗实粒数却高于V20B,平均结实率比V20B增加11.8%,千粒重比V20B的少6 g.野威B倒1叶和倒2叶叶鞘中可溶性糖含量先降低,黄熟期略微升高,蜡熟期降低;V20B倒1叶叶鞘中可溶性糖含量变化不明显,倒2叶叶鞘中可溶性糖含量先升高,乳熟期降低,之后升高.野威B的糙米率和整精米率与V20B相近,垩白粒率比V20B降低47.5%,垩白面积下降62.1%,胶稠度比V20B的高,直链淀粉含量比V20B降低39.0%.%Yewei B, a new rice germplasm was bred through transformed with genomic DNA of Oryza minuta into V20B by earstem injecting.Compared with V20B, the effective panicles numbers and the spikelets number per panicles of Yewei B are smaller, but the filled grains per spike are higher.The average seed setting percentage of Yewei B is found to be 11.8 % higher than that of V20B, but 1 000-grain weight of Yewei B is 6 gram less than that of V20B.The content of soluble sugar in leaf sheath of the topl st and top 2nd leaf decreases first then increases slightly and then decreases again in Yewei B.In V20B, the content of soluble sugar is less distinctly changed in leaf sheath of the top 1st leaf, and it increases first then decreases and then increases again in leaf sheath of the top 2nd leaf.The brown rice percentage and head rice rate of Yewei B is similar to V20B, but the percentage of chalky grain and the area of chalkiness are 47.5% and 62.1%lower than that of V20B respectively.Gel consistency of Yewei B is higher and the content of amylose is 39.0% lower than that of V20B.

  3. Assessment of genetic diversity of Xanthomonas oryzae pv. oryzae

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@Bacterial blight of rice, caused by Xanthomonas oryzae pv. Oryzae(Xoo. ), is one of the major rice diseases in China. Making clear the shift of genetic diversity of the pathogen will provide important information for rice breeding. Strains collected from 11 provinces located in Southern region of the Changjiang River in China were assessed by using inoculation method and IS-PCR(Insertion Sequence-Based Polymerase Chain Reaction) analysis.

  4. Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Science.gov (United States)

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R

    2015-02-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  5. Genomic selection and association mapping in rice (Oryza sativa: effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Directory of Open Access Journals (Sweden)

    Jennifer Spindel

    2015-02-01

    Full Text Available Genomic Selection (GS is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  6. Analyses of Old Prokaryotic Proteins Indicate Functional Diversification in Arabidopsis and Oryza sativa

    Directory of Open Access Journals (Sweden)

    Anupama eSingh

    2016-03-01

    Full Text Available During evolution, various processes such as duplication, divergence, recombination and many other events leads to the evolution of new genes with novel functions. These evolutionary events, thus significantly impact the evolution of cellular, physiological, morphological and other phenotypic trait of organisms. While evolving, eukaryotes have acquired large number of genes from the earlier prokaryotes. This work is focused upon identification of old prokaryotic proteins in Arabidopsis and Oryza sativa genome, further highlighting their possible role(s in the two genomes. Our results suggest that with respect to their genome size, the fraction of old prokaryotic proteins is higher in Arabidopsis than in Oryza sativa. The large fractions of such proteins encoding genes were found to be localized in various endo-symbiotic organelles. The domain architecture of the old prokaryotic proteins revealed similar distribution in both Arabidopsis and Oryza sativa genomes showing their conserved evolution. In Oryza sativa, the old prokaryotic proteins were more involved in developmental processes, might be due to constant man-made selection pressure for better agronomic traits/productivity. While in Arabidopsis, these proteins were involved in metabolic functions. Overall, the analysis indicates the distinct pattern of evolution of old prokaryotic proteins in Arabidopsis and Oryza sativa.

  7. Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing

    Directory of Open Access Journals (Sweden)

    Reinhold-Hurek Barbara

    2010-12-01

    Full Text Available Abstract Background Oryza longistaminata, an AA genome type (2 n = 24, originates from Africa and is closely related to Asian cultivated rice (O. sativa L.. It contains various valuable traits with respect to tolerance to biotic and abiotic stress, QTLs with agronomically important traits and high ability to use nitrogen efficiently (NUE. However, only limited genomic or transcriptomic data of O. longistaminata are currently available. Results In this study we present the first comprehensive characterization of the O. longistaminata root transcriptome using 454 pyrosequencing. One sequencing run using a normalized cDNA library from O. longistaminata roots adapted to low N conditions generated 337,830 reads, which assembled into 41,189 contigs and 30,178 singletons. By similarity search against protein databases, putative functions were assigned to over 34,510 uni-ESTs. Comparison with ESTs derived from cultivated rice collections revealed expressed genes across different plant species, however 16.7% of the O. longistaminata ESTs had not been detected as expressed in O. sativa. Additionally, 15.7% had no significant similarity to known sequences. RT-PCR and Southern blot analyses confirmed the expression of selected novel transcripts in O. longistaminata. Conclusion Our results show that one run using a Genome Sequencer FLX from 454 Life Science/Roche generates sufficient genomic information for adequate de novo assembly of a large number of transcripts in a wild rice species, O. longistaminata. The generated sequence data are publicly available and will facilitate gene discovery in O. longistaminata and rice functional genomic studies. The large number of abundant of novel ESTs suggests different metabolic activity in O. longistaminata roots in comparison to O. sativa roots.

  8. Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution

    Directory of Open Access Journals (Sweden)

    Kishima Yuji

    2004-10-01

    Full Text Available Abstract Background Plant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. Most of them, with the exception of virus-like sequences, do not allow us to trace their origins nor to follow the process of their integration into the host genome. Recent discoveries of virus-like sequences in plant genomes led us to set the objective of elucidating the origin of the repetitive sequences. Endogenous rice tungro bacilliform virus (RTBV-like sequences (ERTBVs have been found throughout the rice genome. Here, we reconstructed putative virus structures from RTBV-like sequences in the rice genome and characterized to understand evolutionary implication, integration manner and involvements of endogenous virus segments in the corresponding disease response. Results We have collected ERTBVs from the rice genomes. They contain rearranged structures and no intact ORFs. The identified ERTBV segments were shown to be phylogenetically divided into three clusters. For each phylogenetic cluster, we were able to make a consensus alignment for a circular virus-like structure carrying two complete ORFs. Comparisons of DNA and amino acid sequences suggested the closely relationship between ERTBV and RTBV. The Oryza AA-genome species vary in the ERTBV copy number. The species carrying low-copy-number of ERTBV segments have been reported to be extremely susceptible to RTBV. The DNA methylation state of the ERTBV sequences was correlated with their copy number in the genome. Conclusions These ERTBV segments are unlikely to have functional potential as a virus. However, these sequences facilitate to establish putative virus that provided information underlying virus integration and evolutionary relationship with existing virus. Comparison of ERTBV among the Oryza AA-genome species allowed us to speculate a possible role of endogenous virus segments against its related disease.

  9. Molecular Cytogenetic Analysis of Spontaneous Interspecific Hybrid Between Oryza sativa and Oryza minuta

    Institute of Scientific and Technical Information of China (English)

    YI Chuan-deng; CHENG Xu; WANG Bei-bei; LIANG Guo-hua; GONG Zhi-yun; TANG Shu-zhu; GU Ming-hong

    2008-01-01

    Genomic in situ hybridization (GISH) is a powerful tool to characterize parental chromosomes in interspecific hybrids, including the behaviour of autosynapsis and chromosome paidng. It was used to distinguish the chromosomes of Oryza sativa from wild species in a spontaneous interspecific hybdd and to investigate the chromosome pairing at metaphase I in meiosis of the hybdd in this study. The hybrid was a triploid with 36 chromosomes according to the chromosome nurnber investigated in mitosis of root tips. During metaphase I of meiosis in the hybrid, less chromosome pairing was observed and most of the chromosomes existed as univalent. Based on GISH and FISH (Fluorescent in situ hybridization) analyses, the chromosomes of the hybrid were composed of genomes A, B and C. Thus, it was believed that the hybrid was the result of natural hybridization between cultivated rice and wild species O. minuta which was planted in experimental fields.

  10. Molecular Cytogenetic Analysis of Spontaneous Interspecific Hybrid Between Oryza sativa and Oryza minuta

    Directory of Open Access Journals (Sweden)

    Chuan-deng YI

    2008-12-01

    Full Text Available Genomic in situ hybridization (GISH is a powerful tool to characterize parental chromosomes in interspecific hybrids, including the behaviour of autosynapsis and chromosome pairing. It was used to distinguish the chromosomes of Oryza sativa from wild species in a spontaneous interspecific hybrid and to investigate the chromosome pairing at metaphase I in meiosis of the hybrid in this study. The hybrid was a triploid with 36 chromosomes according to the chromosome number investigated in mitosis of root tips. During metaphase I of meiosis in the hybrid, less chromosome pairing was observed and most of the chromosomes existed as univalent. Based on GISH and FISH (Fluorescent in situ hybridization analyses, the chromosomes of the hybrid were composed of genomes A, B and C. Thus, it was believed that the hybrid was the result of natural hybridization between cultivated rice and wild species O. minuta which was planted in experimental fields.

  11. Estimation of genome length

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The genome length is a fundamental feature of a species. This note outlined the general concept and estimation method of the physical and genetic length. Some formulae for estimating the genetic length were derived in detail. As examples, the genome genetic length of Pinus pinaster Ait. and the genetic length of chromosome Ⅵ of Oryza sativa L. were estimated from partial linkage data.

  12. Combination Patterns of Major R Genes Determine the Level of Resistance to the M. oryzae in Rice (Oryza sativa L..

    Directory of Open Access Journals (Sweden)

    Yunyu Wu

    Full Text Available Rice blast caused by Magnaporthe oryzae is the most devastating disease of rice and poses a serious threat to world food security. In this study, the distribution and effectiveness of 18 R genes in 277 accessions were investigated based on pathogenicity assays and molecular markers. The results showed that most of the accessions exhibited some degree of resistance (resistance frequency, RF >50%. Accordingly, most of the accessions were observed to harbor two or more R genes, and the number of R genes harbored in accessions was significantly positively correlated with RF. Some R genes were demonstrated to be specifically distributed in the genomes of rice sub-species, such as Pigm, Pi9, Pi5 and Pi1, which were only detected in indica-type accessions, and Pik and Piz, which were just harbored in japonica-type accessions. By analyzing the relationship between R genes and RF using a multiple stepwise regression model, the R genes Pid3, Pi5, Pi9, Pi54, Pigm and Pit were found to show the main effects against M. oryzae in indica-type accessions, while Pita, Pb1, Pik, Pizt and Pia were indicated to exhibit the main effects against M. oryzae in japonica-type accessions. Principal component analysis (PCA and cluster analysis revealed that combination patterns of major R genes were the main factors determining the resistance of rice varieties to M. oryzae, such as 'Pi9+Pi54', 'Pid3+Pigm', 'Pi5+Pid3+Pigm', 'Pi5+Pi54+Pid3+Pigm', 'Pi5+Pid3' and 'Pi5+Pit+Pid3' in indica-type accessions and 'Pik+Pib', 'Pik+Pita', 'Pik+Pb1', 'Pizt+Pia' and 'Pizt+Pita' in japonica-type accessions, which were able to confer effective resistance against M. oryzae. The above results provide good theoretical support for the rational utilization of combinations of major R genes in developing rice cultivars with broad-spectrum resistance.

  13. AA Index

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The geomagnetic aa index provides a long climatology of global geomagnetic activity using 2 antipodal observatories at Greenwich and Melbourne- IAGA Bulletin 37,...

  14. Comparative chemistry of Aspergillus oryzae (RIB40) and A. flavus (NRRL 3357)

    DEFF Research Database (Denmark)

    Rank, Christian; Klejnstrup, Marie Louise; Petersen, Lene Maj

    2012-01-01

    Aspergillus oryzae and A. flavus are important species in industrial biotechnology and food safety and have been some of the first aspergilli to be fully genome sequenced. Bioinformatic analysis has revealed 99.5% gene homology between the two species pointing towards a large coherence...... in the secondary metabolite production. In this study we report on the first comparison of secondary metabolite production between the full genome sequenced strains of A. oryzae (RIB40) and A. flavus (NRRL 3357). Surprisingly, the overall chemical profiles of the two strains were mostly very different across 15...... alkaloids related to the A. flavus metabolites ditryptophenalines and miyakamides. Generally the secondary metabolite capability of A. oryzae presents several novel end products likely to result from the domestication process from A. flavus....

  15. Role of DetR in defence is critical for virulence of Xanthomonas oryzae pv. oryzae.

    Science.gov (United States)

    Nguyen, Minh-Phuong; Park, Jongchan; Cho, Man-Ho; Lee, Sang-Won

    2016-05-01

    Like other bacteria, Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight disease in rice, possesses intracellular signalling systems, known as two-component regulatory systems (TCSs), which regulate pathogenesis and biological processes. Completion of the genome sequences of three Xoo strains has facilitated the functional study of genes, including those of TCSs, but the biological functions of most Xoo TCSs have not yet been uncovered. To identify TCSs involved in Xoo pathogenesis, we generated knockout strains lacking response regulators (RRs, a cytoplasmic signalling component of the TCS) and examined the virulence of the RR knockout strains. This study presents a knockout strain (detR(-) ) lacking the PXO_04659 gene which shows dramatically reduced virulence relative to the wild-type. Our studies to elucidate detR function in Xoo pathogenesis revealed a reduction in extracellular polysaccharide (EPS), intolerance to reactive oxygen species (ROS) and deregulation of iron homeostasis in the detR(-) strain. Moreover, gene expression of regulatory factors, including other RRs and transcription factors (TFs), was altered in the absence of DetR protein, as determined by reverse transcription-polymerase chain reaction (RT-PCR) and/or real-time quantitative RT-PCR analyses. All evidence leads to the conclusion that DetR is essential for Xoo virulence through the regulation of the Xoo defence system including EPS synthesis, ROS detoxification and iron homeostasis, solely or cooperatively with other regulatory factors.

  16. [Ferric iron absorption in deltar p f F xoo, a gene deletion mutant of Xanthomonas oryzae pv. oryzae, assayed using atomic absorption spectrophotometry].

    Science.gov (United States)

    Sun, Lei; Wu, Mao-Sen; He, Chen-Yang

    2010-04-01

    The ferric iron absorption is one of the most important limiting factors of bacterial growth of Xanthomonas oryzae pv. oryzae. It has been previously speculated that r p f F xoo might be involved in the ferric iron metabolism of the pathogen. In the present study, deltar p f F xoo, a gene deletion mutant, was generated from the wild-type strain PXO99A of Xoo through the homologous recombination, and Fe content was assayed using flame atomic absorption in PXO99A and deltar p f F xoo. The results indicated that the recovery was 99.7% and the relative standard deviation was 1.89 under optimized AAS operating conditions. The increase in Fe absorption in PXO99A and deltar p f F xoo was observed with the increasing time. However, the ferric content of deltar p f F xoo was significantly lower than that of PXO99A (P < 0.05). It is suggested that r p f F xoo is involved in iron metabolism in Xanthomonas oryzae pv. oryzae.

  17. In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1

    Directory of Open Access Journals (Sweden)

    Verdier Valérie

    2010-06-01

    Full Text Available Abstract Background Bacterial leaf blight causes significant yield losses in rice crops throughout Asia and Africa. Although both the Asian and African strains of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo, induce similar symptoms, they are nevertheless genetically different, with the African strains being more closely related to the Asian X. oryzae pv. oryzicola (Xoc. Results Changes in gene expression of the African Xoo strain MAI1 in the susceptible rice cultivar Nipponbare were profiled, using an SSH Xoo DNA microarray. Microarray hybridization was performed comparing bacteria recovered from plant tissues at 1, 3, and 6 days after inoculation (dai with bacteria grown in vitro. A total of 710 bacterial genes were found to be differentially expressed, with 407 up-regulated and 303 down-regulated. Expression profiling indicated that less than 20% of the 710 bacterial transcripts were induced in the first 24 h after inoculation, whereas 63% were differentially expressed at 6 dai. The 710 differentially expressed genes were one-end sequenced. 535 sequences were obtained from which 147 non-redundant sequences were identified. Differentially expressed genes were related to metabolism, secretion and transport, pathogen adherence to plant tissues, plant cell-wall degradation, IS elements, and virulence. In addition, various other genes encoding proteins with unknown function or showing no similarity to other proteins were also induced. The Xoo MAI1 non-redundant set of sequences was compared against several X. oryzae genomes, revealing a specific group of genes that was present only in MAI1. Numerous IS elements were also found to be differentially expressed. Quantitative real-time PCR confirmed 86% of the identified profile on a set of 14 genes selected according to the microarray analysis. Conclusions This is the first report to compare the expression of Xoo genes in planta across different time points during infection. This work shows that

  18. Identification of Chromosomes from Multiple Rice Genomes Using a Universal Molecular Cytogenetic Marker System

    Institute of Scientific and Technical Information of China (English)

    Xiaomin Tang; Weidong Bao; Wenli Zhang; Zhukuan Cheng

    2007-01-01

    To develop reliable techniques for chromosome identification is critical for cytogenetic research, especially for genomes with a large number and smaller-sized chromosomes. An efficient approach using bacterial artificial chromosome (BAG) clones as molecular cytological markers has been developed for many organisms. Herein, we present a set of chromosomal arm-specific molecular cytological markers derived from the gene-enriched regions of the sequenced rice genome. All these markers are able to generate very strong signals on the pachytene chromosomes of Oryza satlva L. (AA genome) when used as fluorescence in situ hybridization (FISH) probes. We further probed those markers to the pachytene chromosomes of O. punctata (BB genome) and O. officinalis (CC genome) and also got very strong signals on the relevant pachytene chromosomes. The signal position of each marker on the related chromosomes from the three different rice genomes was pretty much stable, which enabled us to identify different chromosomes among various rice genomes. We also constructed the karyotype for both O. punctata and O. officinalis with the BB and CC genomes, respectively, by analysis of 10 pachytene cells anchored by these chromosomal arm-specific markers.

  19. The Oryza Map Alignment Project (OMAP) introgression lines for allelic diversity and new germplasm development

    Science.gov (United States)

    The Oryza Map Alignment Project (OMAP) has developed a genus wide model system for the study of rice that will ultimately provide a complete understanding of the genus. The purpose of this project is to capitalize on the strengths of the Arizona Genomics Institute (AGI), OMAP participants and the r...

  20. Isolation and characterization of 17 different genes encoding putative endopolygalacturonase genes from Rhizopus oryzae

    Science.gov (United States)

    Polygalacturonase enzymes are a valuable aid in the retting of flax for production of linens and, more recently, production of biofuels from citrus wastes. In a search of the recently sequenced Rhizopus oryzae strain 99-880 genome database, 18 putative endopolygalacturonase genes were identified, w...

  1. Identification, Characterization, and Evolution of a Large Polygalacturonase Gene Family from Rhizopus oryzae

    Science.gov (United States)

    Polygalacturonase enzymes are a valuable aid in the retting of flax for production of linens, clarification of juices, and more recently, production of value-added products from citrus wastes. A search of the recently sequenced Rhizopus oryzae strain 99-880 genome database uncovered 18 putative pol...

  2. Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae

    Directory of Open Access Journals (Sweden)

    Zhang Jie-Qiong

    2011-01-01

    Full Text Available Abstract Background Small non-coding RNAs (sRNAs are regarded as important regulators in prokaryotes and play essential roles in diverse cellular processes. Xanthomonas oryzae pathovar oryzae (Xoo is an important plant pathogenic bacterium which causes serious bacterial blight of rice. However, little is known about the number, genomic distribution and biological functions of sRNAs in Xoo. Results Here, we performed a systematic screen to identify sRNAs in the Xoo strain PXO99. A total of 850 putative non-coding RNA sequences originated from intergenic and gene antisense regions were identified by cloning, of which 63 were also identified as sRNA candidates by computational prediction, thus were considered as Xoo sRNA candidates. Northern blot hybridization confirmed the size and expression of 6 sRNA candidates and other 2 cloned small RNA sequences, which were then added to the sRNA candidate list. We further examined the expression profiles of the eight sRNAs in an hfq deletion mutant and found that two of them showed drastically decreased expression levels, and another exhibited an Hfq-dependent transcript processing pattern. Deletion mutants were obtained for seven of the Northern confirmed sRNAs, but none of them exhibited obvious phenotypes. Comparison of the proteomic differences between three of the ΔsRNA mutants and the wild-type strain by two-dimensional gel electrophoresis (2-DE analysis showed that these sRNAs are involved in multiple physiological and biochemical processes. Conclusions We experimentally verified eight sRNAs in a genome-wide screen and uncovered three Hfq-dependent sRNAs in Xoo. Proteomics analysis revealed Xoo sRNAs may take part in various metabolic processes. Taken together, this work represents the first comprehensive screen and functional analysis of sRNAs in rice pathogenic bacteria and facilitates future studies on sRNA-mediated regulatory networks in this important phytopathogen.

  3. Rating AAs.

    Science.gov (United States)

    Carter, Susan J.

    2001-01-01

    Why alternative investments? In a word: performance. Many higher education endowment and foundation managers are making increasing commitments to alternative investments, or AAs, in order to obtain higher returns and broader diversification for their investment portfolios than public securities instruments can usually provide. Learn how to handle…

  4. 利用叶绿体基因探讨稻属BBCC基因组物种的系统起源%Phylogenetic Origin of BBCC Genome Allotetraploids in Oryza Revealed by Chloroplast Gene Sequences

    Institute of Scientific and Technical Information of China (English)

    杜家潇; 秦宗燕; 徐思; 景翔; 包颖

    2016-01-01

    基于9个叶绿体基因片段(atpA、atpB、matK、petA、psaA、psbA、psbB、psbC和rbcL),深入探讨了稻属(Oryza)3个BBCC基因组异源四倍体和5个与之相关的BB或CC基因组二倍体物种间的谱系关系.进一步的系统发育分析表明:3个具有相同BBCC基因组的四倍体物种并非同一次物种形成事件的产物,而是在不同的分布区经历了至少3次分别的物种起源.其中,四倍体Oryza punctata的母本可能来自同样分布在非洲并具有CC基因组的二倍体物种O.eichingeri;而四倍体O.malampuzhaensis和O.minuta的母本则可能来自亚洲已经灭绝的具有BB基因组的不同二倍体.研究结果不但为追溯稻属异源四倍体的复杂网状进化提供了重要的分子证据,而且拓展了我们对有花植物复杂物种形成的深入理解.

  5. Functional genomics in the rice blast fungus to unravel the fungal pathogenicity

    Institute of Scientific and Technical Information of China (English)

    Junhyun JEON; Jaehyuk CHOI; Jongsun PARK; Yong-Hwan LEE

    2008-01-01

    A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae is an economically important plant pathogenic fungus whose genome is fully sequenced. Recently we have reported the development and application of functional genomics platform technologies in M. oryzae. This model approach would have many practical ramifications in design and implementation of upcoming functional genomics studies of filamentous fungi aimed at understanding fungal pathogenicity.

  6. Detailed analysis of targeted gene mutations caused by the Platinum-Fungal TALENs in Aspergillus oryzae RIB40 strain and a ligD disruptant.

    Science.gov (United States)

    Mizutani, Osamu; Arazoe, Takayuki; Toshida, Kenji; Hayashi, Risa; Ohsato, Shuichi; Sakuma, Tetsushi; Yamamoto, Takashi; Kuwata, Shigeru; Yamada, Osamu

    2017-03-01

    Transcription activator-like effector nucleases (TALENs), which can generate DNA double-strand breaks at specific sites in the desired genome locus, have been used in many organisms as a tool for genome editing. In Aspergilli, including Aspergillus oryzae, however, the use of TALENs has not been validated. In this study, we performed genome editing of A. oryzae wild-type strain via error of nonhomologous end-joining (NHEJ) repair by transient expression of high-efficiency Platinum-Fungal TALENs (PtFg TALENs). Targeted mutations were observed as various mutation patterns. In particular, approximately half of the PtFg TALEN-mediated deletion mutants had deletions larger than 1 kb in the TALEN-targeting region. We also conducted PtFg TALEN-based genome editing in A. oryzae ligD disruptant (ΔligD) lacking the ligD gene involved in the final step of the NHEJ repair and found that mutations were still obtained as well as wild-type. In this case, the ratio of the large deletions reduced compared to PtFg TALEN-based genome editing in the wild-type. In conclusion, we demonstrate that PtFg TALENs are sufficiently functional to cause genome editing via error of NHEJ in A. oryzae. In addition, we reveal that genome editing using TALENs in A. oryzae tends to cause large deletions at the target region, which were partly suppressed by deletion of ligD.

  7. Fungal Histidine Phosphotransferase Plays a Crucial Role in Photomorphogenesis and Pathogenesis in Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Varsha C. Mohanan

    2017-05-01

    Full Text Available Two-component signal transduction (TCST pathways play crucial roles in many cellular functions such as stress responses, biofilm formation, and sporulation. The histidine phosphotransferase (HPt, which is an intermediate phosphotransfer protein in a two-component system, transfers a phosphate group to a phosphorylatable aspartate residue in the target protein(s, and up-regulates stress-activated MAP kinase cascades. Most fungal genomes carry a single copy of the gene coding for HPt, which are potential antifungal targets. However, unlike the histidine kinases (HK or the downstream response regulators (RR in two-component system, the HPts have not been well-studied in phytopathogenic fungi. In this study, we investigated the role of HPt in the model rice-blast fungal pathogen Magnaporthe oryzae. We found that in M. oryzae an additional isoform of the HPT gene YPD1 was expressed specifically in response to light. Further, the expression of light-regulated genes such as those encoding envoy and blue-light-harvesting protein, and PAS domain containing HKs was significantly reduced upon down-regulation of YPD1 in M. oryzae. Importantly, down-regulation of YPD1 led to a significant decrease in the ability to penetrate the host cuticle and in light-dependent conidiation in M. oryzae. Thus, our results indicate that Ypd1 plays an important role in asexual development and host invasion, and suggest that YPD1 isoforms likely have distinct roles to play in the rice-blast pathogen M. oryzae.

  8. Fungal histidine phosphotransferase plays a crucial role in photomorphogenesis and pathogenesis in Magnaporthe oryzae

    Science.gov (United States)

    Mohanan, Varsha C.; Chandarana, Pinal M.; Chattoo, Bharat. B.; Patkar, Rajesh N.; Manjrekar, Johannes

    2017-05-01

    Two-component signal transduction (TCST) pathways play crucial roles in many cellular functions such as stress responses, biofilm formation and sporulation. The histidine phosphotransferase (HPt), which is an intermediate phosphotransfer protein in a two-component system, transfers a phosphate group to a phosphorylatable aspartate residue in the target protein(s), and up-regulates stress-activated MAP kinase cascades. Most fungal genomes carry a single copy of the gene coding for HPt, which are potential antifungal targets. However, unlike the histidine kinases (HK) or the downstream response regulators (RR) in two-component system, the HPts have not been well studied in phytopathogenic fungi. In this study, we investigated the role of HPt in the model rice-blast fungal pathogen Magnaporthe oryzae. We found that in M. oryzae an additional isoform of the HPT gene YPD1 was expressed specifically in response to light. Further, the expression of light-regulated genes such as those encoding envoy and blue-light-harvesting protein, and PAS domain containing HKs was significantly reduced upon down-regulation of YPD1 in M. oryzae. Importantly, down-regulation of YPD1 led to a significant decrease in the ability to penetrate the host cuticle and in light-dependent conidiation in M. oryzae. Thus, our results indicate that Ypd1 plays an important role in asexual development and host invasion, and suggest that YPD1 isoforms likely have distinct roles to play in the rice-blast pathogen M. oryzae.

  9. Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae

    DEFF Research Database (Denmark)

    Udatha, D. B. R. K. Gupta; Topakas, Evangelos; Salazar, Margarita Pena;

    2015-01-01

    . oryzae genome were only partially explained by the chemical similarity of the enzyme inducers. Genes encoding enzymes that have attracted considerable interest such as cellobiose dehydrogenases and copper-dependent polysaccharide mono-oxygenases presented a substrate-specific induction. Several homology...... in 2360 reactions in the genome scale metabolic network of A. oryzae, was performed through a two-step molecular docking against the binding pockets of the transcription factors AoXlnR and AoAmyR. A total of six metabolites viz., sulfite (H2SO3), sulfate (SLF), uroporphyrinogen III (UPGIII), ethanolamine...

  10. Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome.

    Directory of Open Access Journals (Sweden)

    Gopala Krishnan S

    Full Text Available BACKGROUND: Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. RESULTS: We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts. Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58 Mbp region on chromosome 5, which suggests that some of the 'polymorphism deserts' in this and other parts of the rice genome may have originated prior to domestication due to natural selection. CONCLUSIONS: Analysis of genes in the 'polymorphism deserts' indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

  11. Characterization of interspecific hybrids and backcross progenies from a cross between Oryza minuta and Oryza sativa

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Oryza minuta, a tetraploid wild relative of cultivated rice, is an important source for the genetic improvement. Interspecific hybrids were obtained from the cross of O. sativa L. (IR24) and O. minuta (Acc. No. 101133) with 5.58% crossability, which ranged from 0.11% to 1.62% in the backcross generations. The chromosome numbers of the backcross progenies were 24 to 48. Seven yield-related traits of the parents, hybrid F1, and backcross progenies were evaluated. Simple sequence repeat markers analysis showed that the polymorphism ratio of SSR bands between IR24 and Acc. No. 101133 was 93.2%. The average donor segment number, length, donor genome size, and percentage of donor genome of 92 BC3F1 plants (2n=24) were 24.1, 17.8 cM, 438.4 cM and 26.2%, respectively. They were complex variation and uneven among the chromosomes. These introgression lines could be used to identify the favorable genes of O. minuta and provide a new platform for the genetic improvement of cultivated rice.

  12. Development and Identification of Introgression Lines from Cross of Oryza sativa and Oryza minuta

    Institute of Scientific and Technical Information of China (English)

    GUO Si-bin; WEI Yu; LI Xiao-qiong; LIU Kai-qiang; HUANG Feng-kuan; CHEN Cai-hong; GAO Guo-qing

    2013-01-01

    Introgression line population is effectively used in mapping quantitative trait loci (QTLs),identifying favorable genes,discovering hidden genetic variation,evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research.In this study,an advanced backcross and consecutive selfing strategy was used to develop introgression lines (ILs),which derived from an accession of Oryza minuta (accession No.101133) with BBCC genome,as the donor,and an elite indica cultivar IR24 (O.sativa),as the recipient.Introgression segments from O.minuta were screened using 164 polymorphic simple sequence repeat (SSR) markers in the genome of each IL.Introgressed segments carried by 131 ILs covered the whole O.sativa genome.The average number of homozygous O.minuta segments per introgression line was about 9.99.The average length of introgressed segments was approximate 14.78 cM,and about 79.64%of these segments had sizes less than 20 cM.In the genome of each introgression line,the O.minuta chromosomal segments harbored chromosomal fragments of O.sativa ranging from 1.15% to 27.6%,with an overall average of 8.57%.At each locus,the ratio of substitution of O.minuta alleles had a range of 1.5%-25.2%,with an average of 8.3% Based on the evaluation of the phenotype of these ILs,a wide range of alterations in morphological and yield-related traits were found.After inoculation,ILs 41,11 and 7 showed high resistance to bacterial blight,brown planthopper and whitebacked planthopper,respectively.These O.minuta-O.sativa ILs will serve as genetic materials for identifying and using favorable genes from O.minuta.

  13. A novel two-component system PdeK/PdeR regulates c-di-GMP turnover and virulence of Xanthomonas oryzae pv. oryzae.

    Science.gov (United States)

    Yang, Fenghuan; Tian, Fang; Sun, Lei; Chen, Huamin; Wu, Maosen; Yang, Ching-Hong; He, Chenyang

    2012-10-01

    Two-component systems (TCS) consisting of histidine kinases (HK) and response regulators (RR) play essential roles in bacteria to sense environmental signals and regulate cell functions. One type of RR is involved in metabolism of cyclic diguanylate (c-di-GMP), a ubiquitous bacterial second messenger. Although genomic studies predicted a large number of them existing in different bacteria, only a few have been studied. In this work, we characterized a novel TCS consisting of PdeK(PXO_01018)/PdeR(PXO_ 01019) from Xanthomonas oryzae pv. oryzae, which causes the bacterial leaf blight of rice. PdeR (containing GGDEF, EAL, and REC domains) was shown to have phosphodiesterase (PDE) activity in vitro by colorimetric assays and high-performance liquid chromatography analysis. The PDE activity of full-length PdeR needs to be triggered by HK PdeK. Deletion of pdeK or pdeR in X. oryzae pv. oryzae PXO99(A) had attenuated its virulence on rice. ΔpdeK and ΔpdeR secreted less exopolysaccharide than the wild type but there were no changes in terms of motility or extracellular cellulase activity, suggesting the activity of PdeK/PdeR might be specific.

  14. The rice proteogenomics database OryzaPG-DB: development, expansion and new features

    Directory of Open Access Journals (Sweden)

    Mohamed eHelmy

    2012-04-01

    Full Text Available Proteogenomics is the utilization of large-scale proteome data in genome annotation refinement. Our recently developed rice proteogenomics database (OryzaPG-DB is the first sustainable resource for rice shotgun-based proteogenomics, providing information on peptides identified in rice protein digested peptides measured by means of liquid chromatography-tandem mass spectrometry (LC-MS/MS, and mapping of the peptides to their genomic origins and the genomic novelty of each peptide. The sequences of the peptides, proteins, cDNAs and genes, and the gene annotations are available for download in FASTA and GFF3 formats, respectively. Further, an annotated visualization of the gene models, corresponding peptides and genomic novelty is available for each gene, and MS/MS spectra are available for each peptide. In this article, we discuss the utilization of OryzaPG-DB and report on its development, recent content expansions and newly added features in the current version (OryzaPG-DB v1.1.

  15. Molecular detection of Xanthomonas oryzae pv.oryzae, Xanthomonas oryzae pv. oryzicola, and Burkholderia glumae in infected rice seeds and leaves

    Institute of Scientific and Technical Information of China (English)

    Wen; Lu; Luqi; Pan; Haijun; Zhao; Yulin; Jia; Yanli; Wang; Xiaoping; Yu; Xueyan; Wang

    2014-01-01

    The polymerase chain reaction(PCR) is particularly useful for plant pathogen detection. In the present study, multiplex PCR and SYBR Green real-time PCR were developed to facilitate the simultaneous detection of three important rice pathogens, Xanthomonas oryzae pv.oryzae, X. oryzae pv. oryzicola, and Burkholderia glumae. The unique PCR primer sets were designed from portions of a putative glycosyltransferase gene of X. oryzae pv. oryzae, an Avr Rxo gene of X. oryzae pv. oryzicola, and an internal transcribed spacer(ITS) sequence of B. glumae. Using a multiplex PCR assay, X. oryzae pv. oryzae, X. oryzae pv. oryzicola, and B. glumae were detected in one PCR reaction that contained the newly developed primer set mix. Using SYBR Green real-time PCR assays, X. oryzae pv. oryzae, X. oryzae pv. oryzicola, and B. glumae were detected at 1, 1, and 10 fg μL-1, respectively. These newly designed molecular assays are sensitive and could be reliable tools for pathogen detection and disease forecasting.

  16. Diversity of Aspergillus oryzae genotypes (RFLP) isolated from traditional soy sauce production within Malaysia and Southeast Asia

    Science.gov (United States)

    DNA fingerprinting was performed on 64 strains of Aspergillus oryzae and one strain of A. sojae isolated from soysauce factories within Malaysia and Southeast Asia that use primitive traditional methods in producing 'tamari type' Cantonese soy sauce. PstI digests of total genomic DNA from each isol...

  17. The transfer RNA genes in Oryza sativa L.ssp.indica

    Institute of Scientific and Technical Information of China (English)

    WANG; Xiyin(王希胤); SHI; Xiaoli(史晓黎); HAO; Bailin(郝柏林)

    2002-01-01

    The availability of the draft genome sequence of Oryza sativa L. ssp. indica has made it possible to study the rice tRNA genes. A total of 596 tRNA genes, including 3 selenocysteine tRNA genes and one suppressor tRNA gene are identified in 127551 rice contigs. There are 45 species of tRNA genes and the revised wobble hypothesis proposed by Guthrie and Abelson is perfectly obeyed. The relationship between codon usage and the number of corresponding tRNA genes is discussed. Redundancy may exist in the present list of tRNA genes and novel ones may be found in the future. A set of 33 tRNA genes is discovered in the complete chloroplast genome of Oryza sativa L. ssp. indica. These tRNA genes are identical to those in ssp. japonica identified by us independently from the origional annotation.

  18. Genome-Wide Single-Nucleotide Polymorphisms in CMS and Restorer Lines Discovered by Genotyping Using Sequencing and Association with Marker-Combining Ability for 12 Yield-Related Traits in Oryza sativa L. subsp. Japonica

    Science.gov (United States)

    Zaid, Imdad U.; Tang, Weijie; Liu, Erbao; Khan, Sana U.; Wang, Hui; Mawuli, Edzesi W.; Hong, Delin

    2017-01-01

    Heterosis or hybrid vigor is closely related with general combing ability (GCA) of parents and special combining ability (SCA) of combinations. The evaluation of GCA and SCA facilitate selection of parents and combinations in heterosis breeding. In order to improve combining ability (CA) by molecular marker assist selection, it is necessary to identify marker loci associated with the CA. To identify the single nucleotide polymorphisms (SNP) loci associated with CA in the parental genomes of japonica rice, genome-wide discovered SNP loci were tested for association with the CA of 18 parents for 12 yield-related traits. In this study, 81 hybrids were created and evaluated to calculate the CA of 18 parents. The parents were sequenced by genotyping by sequencing (GBS) method for identification of genome-wide SNPs. The analysis of GBS indicated that the successful mapping of 9.86 × 106 short reads in the Nipponbare reference genome consists of 39,001 SNPs in parental genomes at 11,085 chromosomal positions. The discovered SNPs were non-randomly distributed within and among the 12 chromosomes of rice. Overall, 20.4% (8026) of the discovered SNPs were coding types, and 8.6% (3344) and 9.9% (3951) of the SNPs revealed synonymous and non-synonymous changes, which provide valuable knowledge about the underlying performance of the parents. Furthermore, the associations between SNPs and CA indicated that 362 SNP loci were significantly related to the CA of 12 parental traits. The identified SNP loci of CA in our study were distributed genome wide and caused a positive or negative effect on the CA of traits. For the yield-related traits, such as grain thickness, days to heading, panicle length, grain length and 1000-grain weight, a maximum number of positive SNP loci of CA were found in CMS A171 and in the restorers LC64 and LR27. On an individual basis, some of associated loci that resided on chromosomes 2, 5, 7, 9, and 11 recorded maximum positive values for the CA of traits

  19. Molecular cloning and functional characterization of a Δ6-fatty acid desaturase gene from Rhizopus oryzae.

    Science.gov (United States)

    Zhu, Yu; Zhang, Bi-Bo

    2013-09-01

    The objective was to screen for and isolate a novel enzyme with the specific activity of a Δ6-fatty acid desaturase from Rhizopus oryzae. In this study, R. oryzae was identified as a novel fungal species that produces large amounts of γ-linolenic acid. A full-length cDNA, designated here as RoD6D, with high homology to fungal Δ6-fatty acid desaturase genes was isolated from R. oryzae by using the rapid amplification of cDNA ends method. It had an open reading frame of 1176 bp encoding a deduced polypeptide of 391 amino acids. Bioinformatics analysis characterized the putative RoD6D protein as a typical membrane-bound desaturase, including three conserved histidine-rich motifs, a hydropathy profile, and a cytochrome b5 -like domain in the N terminus. When the coding sequence was expressed in the Saccharomyces cerevisiae strain INVScl, the encoded product of RoD6D exhibited Δ6-fatty acid desaturase activity that led to the accumulation of γ-linolenic acid. The corresponding genomic sequence of RoD6D was 1565 bp in length, with five introns. This is the first report on the characterization and gene cloning of a Δ6-fatty acid desaturase of R. oryzae from Douchi.

  20. Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service

    Directory of Open Access Journals (Sweden)

    Yoon Kyong-Oh

    2008-01-01

    Full Text Available Abstract Background Protein-protein interactions (PPIs play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. Phytopathogenic bacteria infect hosts through attachment to host tissue, enzyme secretion, exopolysaccharides production, toxins release, iron acquisition, and effector proteins secretion. Many such mechanisms involve some kind of protein-protein interaction in hosts. Our first aim was to predict the whole protein interaction pairs (interactome of Xanthomonas oryzae pathovar oryzae (Xoo that is an important pathogenic bacterium that causes bacterial blight (BB in rice. We developed a detection protocol to find possibly interacting proteins in its host using whole genome PPI prediction algorithms. The second aim was to build a DB server and a bioinformatic procedure for finding target proteins in Xoo for developing pesticides that block host-pathogen protein interactions within critical biochemical pathways. Description A PPI network in Xoo proteome was predicted by bioinformatics algorithms: PSIMAP, PEIMAP, and iPfam. We present the resultant species specific interaction network and host-pathogen interaction, XooNET. It is a comprehensive predicted initial PPI data for Xoo. XooNET can be used by experimentalists to pick up protein targets for blocking pathological interactions. XooNET uses most of the major types of PPI algorithms. They are: 1 Protein Structural Interactome MAP (PSIMAP, a method using structural domain of SCOP, 2 Protein Experimental Interactome MAP (PEIMAP, a common method using public resources of experimental protein interaction information such as HPRD, BIND, DIP, MINT, IntAct, and BioGrid, and 3 Domain-domain interactions, a method using Pfam domains such as iPfam. Additionally, XooNET provides information on network properties of the Xoo interactome. Conclusion XooNET is an open and free public

  1. 21 CFR 173.130 - Carbohydrase derived from Rhizopus oryzae.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Carbohydrase derived from Rhizopus oryzae. 173.130... HUMAN CONSUMPTION Enzyme Preparations and Microorganisms § 173.130 Carbohydrase derived from Rhizopus oryzae. Carbohydrase from Rhizopus oryzae may be safely used in the production of dextrose from starch...

  2. A comparison of rice chloroplast genomes

    DEFF Research Database (Denmark)

    Tang, Jiabin; Xia, Hong'ai; Cao, Mengliang

    2004-01-01

    Using high quality sequence reads extracted from our whole genome shotgun repository, we assembled two chloroplast genome sequences from two rice (Oryza sativa) varieties, one from 93-11 (a typical indica variety) and the other from PA64S (an indica-like variety with maternal origin of japonica),...

  3. [Construction of an integration vector carrying hygromycin B resistance gene and its genetic transformation in Rhizopus oryzae].

    Science.gov (United States)

    Zhang, Min; Jiang, Shaotong; Zheng, Juan; Zheng, Zhi; Li, Xingjiang; Pan, Lijun; Luo, Shuizhong

    2015-08-01

    To construct a system of genetic transformation suitable for Rhizopus oryzae, we constructed a single-exchange vector pBS-hygro carrying hygromycin B resistance gene (hph) as its selective marker using gene splicing by overlap extension PCR (SOE PCR) technique. We introduced this recombinant vector into Rhizopus oryzae AS 3.819 by PEG/CaCl2-mediated transformation of protoplast, electroporation of protoplast and germinated spores; and we studied the effects of hydrolysis time, field strength and spore germination time on transformation frequency. We conducted quantitative real-time PCR (qPCR) assay to determine the gene copy number of ldhA integrated in the genome of R. oryzae transformants and its effect on the stability of transformants. We successfully achieved R. oryzae transformants integrated with pBS-hygro-ldhA vector. The optimal hydrolysis time for protoplast production was 140 min, and the optimal field strength of electroporation pulse for protoplast was 13 kV/cm. The optimal germination time of spores for electroporation was 2.5 h, and the optimal field strength of electroporation pulse was 14 kV/cm. The transformation frequency of method based on germinated spores was generally higher than the methods based on protoplast. The qPCR test results suggested that transformants with high copy number of integration in a certain range were relatively stable. Our results provided basis and support for metabolic regulation and genetic engineering breeding of R. oryzae.

  4. Ultrastructure of Oryza glumaepatula , a wild rice species endemic of tropical America

    Directory of Open Access Journals (Sweden)

    Ethel Sánchez

    2005-06-01

    Full Text Available Oryza glumaepatula is a perennial wild rice species,endemic to tropical America, previously known as the Latin American race of Oryza rufipogon .In Costa Rica, it is found in the northern region of the country, mainly in the wetland of the Medio Queso River, Los Chiles, Alajuela. It is diploid, of AA type genome and because of its genetic relatedness to cultivated rice it is included in the O.sativa complex. We describe the ultrastructure of leaf blade, spikelet, ligule and auricles. Special emphasis is given to those traits of major taxonomic value for O.glumaepatula and to those characters that distinguish this species from O. rufipogon and O. sativa . O. glumaepatula has a leaf blade covered with tombstone-shaped, oblong and spheroid epicuticular wax papillae. It has diamond-shaped stomata surrounded by spherical papillae, rows of zipper-like silica cells, bulky prickle trichomes of ca .40 mu m in length and small hirsute trichomes of ca. 32 mu m in length.The central vein is covered with large,globular papillae of ca. 146 mu m in length,a characteristic that distinguishes this species from O.rufipogon and O.sativa. The border of the leaf blade exhibits a row of even-sized bulky prickle trichomes of ca .42.5 mu m in length.Auricles have attenuated trichomes of ca .5.5 mm in length on the edges and small bicellular trichomes of 120 mu m in length on the surface.The ligule has a large number of short attenuated trichomes on its surface of 100 mu m in length.These latter two traits have important taxonomic value since they were found in O.glumaepatula but not found in O.sativa or in O.rufipogon . The spikelet has the typical morphology of the Oryza genus. Fertile lemmas have abundant spines, a trait shared with O.rufipogon but not with O.sativa. The sterile lemmas are wing-shaped with serrated borders,a characteristic that distinguishes this species from O. rufipogon and O.sativa. All the ultrastructure characters observed in O.glumaepatula from

  5. Differentiation of Indica-Japonica rice revealed by insertion/deletion (InDel) fragments obtained from the comparative genomic study of DNA sequences between 93-11 (Indica) and Nipponbare (Japonica)

    Institute of Scientific and Technical Information of China (English)

    CAI Xingxing; LIU Jing; QIU Yinqiu; ZHAO Wei; SONG Zhiping; LU Baorong

    2007-01-01

    DNA polymorphisms from nucleotide insertion/deletions (InDels) in genomic sequences are the basis for developing InDel molecular markers.To validate the InDel primer pairs on the basis of the comparative genomic study on DNA sequences between an Indica rice 93-11 and a Japonica rice Nipponbare for identifying Indica and Japonica rice varieties and studying wild Oryza species,we studied 49 Indica,43 Japonica,and 24 wild rice accessions collected from ten Asian countries using 45 InDel primer pairs.Results indicated that of the 45 InDel primer pairs,41 can accurately identify Indica and Japonica rice varieties with a reliability of over 80%.The scatter plotting data of the principal component analysis (PCA) indicated that:(i) the InDel primer pairs can easily distinguish Indica from Japonica rice varieties,in addition to revealing their genetic differentiation;(ii) the AA-genome wild rice species showed a relatively close genetic relationship with the Indica rice varieties;and (iii)the non-AA genome wild rice species did not show evident differentiation into the Indica and Japonica types.It is concluded from the study that most of the InDel primer pairs obtained from DNA sequences of 93-11 and Nipponbare can be used for identifying lndica and Japonica rice varieties,and for studying genetic relationships of wild rice species,particularly in terms of the Indica-Japonica differentiation.

  6. Identification and analysis of in planta expressed genes of Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Mitchell Thomas K

    2010-02-01

    Full Text Available Abstract Background Infection of plants by pathogens and the subsequent disease development involves substantial changes in the biochemistry and physiology of both partners. Analysis of genes that are expressed during these interactions represents a powerful strategy to obtain insights into the molecular events underlying these changes. We have employed expressed sequence tag (EST analysis to identify rice genes involved in defense responses against infection by the blast fungus Magnaporthe oryzae and fungal genes involved in infectious growth within the host during a compatible interaction. Results A cDNA library was constructed with RNA from rice leaves (Oryza sativa cv. Hwacheong infected with M. oryzae strain KJ201. To enrich for fungal genes, subtraction library using PCR-based suppression subtractive hybridization was constructed with RNA from infected rice leaves as a tester and that from uninfected rice leaves as the driver. A total of 4,148 clones from two libraries were sequenced to generate 2,302 non-redundant ESTs. Of these, 712 and 1,562 ESTs could be identified to encode fungal and rice genes, respectively. To predict gene function, Gene Ontology (GO analysis was applied, with 31% and 32% of rice and fungal ESTs being assigned to GO terms, respectively. One hundred uniESTs were found to be specific to fungal infection EST. More than 80 full-length fungal cDNA sequences were used to validate ab initio annotated gene model of M. oryzae genome sequence. Conclusion This study shows the power of ESTs to refine genome annotation and functional characterization. Results of this work have advanced our understanding of the molecular mechanisms underpinning fungal-plant interactions and formed the basis for new hypothesis.

  7. Rice blast fungus (Magnaporthe oryzae) infects Arabidopsis via a mechanism distinct from that required for the infection of rice.

    Science.gov (United States)

    Park, Ju-Young; Jin, Jianming; Lee, Yin-Won; Kang, Seogchan; Lee, Yong-Hwan

    2009-01-01

    Magnaporthe oryzae is a hemibiotrophic fungal pathogen that causes rice (Oryza sativa) blast. Although M. oryzae as a whole infects a wide variety of monocotyledonous hosts, no dicotyledonous plant has been reported as a host. We found that two rice pathogenic strains of M. oryzae, KJ201 and 70-15, interacted differentially with 16 ecotypes of Arabidopsis (Arabidopsis thaliana). Strain KJ201 infected all ecotypes with varying degrees of virulence, whereas strain 70-15 caused no symptoms in certain ecotypes. In highly susceptible ecotypes, small chlorotic lesions appeared on infected leaves within 3 d after inoculation and subsequently expanded across the affected leaves. The fungus produced spores in susceptible ecotypes but not in resistant ecotypes. Fungal cultures recovered from necrotic lesions caused the same symptoms in healthy plants, satisfying Koch's postulates. Histochemical analyses showed that infection by the fungus caused an accumulation of reactive oxygen species and eventual cell death. Similar to the infection process in rice, the fungus differentiated to form appressorium and directly penetrated the leaf surface in Arabidopsis. However, the pathogenic mechanism in Arabidopsis appears distinct from that in rice; three fungal genes essential for pathogenicity in rice played only limited roles in causing disease symptoms in Arabidopsis, and the fungus seems to colonize Arabidopsis as a necrotroph through the secretion of phytotoxic compounds, including 9,12-octadecadienoic acid. Expression of PR-1 and PDF1.2 was induced in response to infection by the fungus, suggesting the activation of salicylic acid- and jasmonic acid/ethylene-dependent signaling pathways. However, the roles of these signaling pathways in defense against M. oryzae remain unclear. In combination with the wealth of genetic and genomic resources available for M. oryzae, this newly established pathosystem allows comparison of the molecular and cellular mechanisms underlying

  8. Antiproton Accumulator (AA)

    CERN Multimedia

    Photographic Service

    1980-01-01

    The AA in its final stage of construction, before it disappeared from view under concrete shielding. Antiprotons were first injected, stochastically cooled and accumulated in July 1980. From 1981 on, the AA provided antiprotons for collisions with protons, first in the ISR, then in the SPS Collider. From 1983 on, it also sent antiprotons, via the PS, to the Low-Energy Antiproton Ring (LEAR). The AA was dismantled in 1997 and shipped to Japan.

  9. Growth deficiency of a Xanthomonas oryzae pv. oryzae fur mutant in rice leaves is rescued by ascorbic acid supplementation.

    Science.gov (United States)

    Subramoni, Sujatha; Sonti, Ramesh V

    2005-07-01

    Xanthomonas oryzae pv. oryzae causes bacterial leaf blight, a serious disease of rice. A mutation was isolated in the ferric uptake regulator (fur) gene of X. oryzae pv. oryzae and it was shown to result in the production of siderophores in a constitutive manner. The fur mutant is hypersensitive to the metallo-antibiotic streptonigrin, a phenotype that is indicative of intracellular free-iron overload, and also exhibits a slow growth phenotype on rich medium. The fur mutant is virulence deficient, hypersensitive to hydrogen peroxide, and exhibits reduced catalase activity. Exogenous supplementation with ascorbic acid (an antioxidant) rescues the growth deficiency of the fur mutant in rice leaves. The virulence deficiency of the X. oryzae pv. oryzae fur mutant is proposed to be due, at least in part, to an impaired ability to cope with the oxidative stress conditions that are encountered during infection.

  10. Aspergillus oryzae pathways that convert phenylalanine into the flavor volatile 2-phenylethanol.

    Science.gov (United States)

    Masuo, Shunsuke; Osada, Lisa; Zhou, Shengmin; Fujita, Tomoya; Takaya, Naoki

    2015-04-01

    The filamentous fungus Aspergillus oryzae RIB40 produced 2-phenylethanol (PE) when cultured in minimum medium containing l-phenylalanine as a sole source of nitrogen. The fungus accumulated less PE in the absence of l-phenylalanine, indicating that it converted l-phenylalanine to PE. The PE production associated with fungal glucose consumption was repressed by exogenous ammonium, indicating that nitrogen-metabolite repression controls the pathway that produces PE. We identified the A. oryzae ppdA gene that is expressed at high levels in the presence of exogenous l-phenylalanine and its encoded protein was an active phenylpyruvate decarboxylase. The fungal genome encodes predicted aminotransferases of phenylalanine and PE dehydrogenases, which, together with PpdA, are likely to constitute an Erlich pathway similar to that in Saccharomyces cerevisiae that produces PE. We also identified an A. oryzae aromatic amino acid decarboxylase (AadA) that converted l-phenylalanine to phenylethylamine (PEA), and phenylalanine-inducible PEA oxidase activity in fungal cell extracts, and found that both constitute an alternative pathway through which PEA generates PE. Incubating fungal cultures with l-[(2)H8] phenylalanine to distinguish PE produced by these pathways, indicated that the fungus produced PE by both pathways, but to a greater extent by the Erlich pathway. Gene disruption of ppdA and aadA showed that both pathways participate in the fungal conversion of l-phenylalanine to PE.

  11. Biological and Genomic Differences of ERG Oncoprotein-Stratified Prostate Cancers from African and Caucasian Americans

    Science.gov (United States)

    2014-10-01

    patients. The objective of this proposal is to determine associations and racial differences of key clinico -pathologic features and SNPs for both ERG...AA men will be estimated. Regions in AA genomes that are enriched for European ancestry in cases with the fusion compared to cases without the...each point in the genome in AA men. Regions in AA genomes that are enriched for European ancestry in cases with the TMPRSS2-ERG fusion, compared to

  12. [Invasive maxilar sinusitis by Rhizopus oryzae].

    Science.gov (United States)

    Perea, S; del Palacio, A; Gil, R; de la Serna, J; Mata, R; Arribi, A

    1997-12-01

    We herein present a diabetic with non Hodgkin lymphoma patient that had been treated with steroids and developed fungal invasive sinusitis. The patient had intensive facial pain that did not respond to antibiotics and on clinical inspection had a necrotic lesion on right nasal area. A smear and biopsy tissue showed broad non septate hyphae and on cultures Rhizopus oryzae was isolated. There was an unfavorable outcome, and the patient died even though liposomal Amphotericin B was administered and surgical treatment was performed.

  13. Study on seed germination of Oryza rufipogon

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Oryza rufipogon, distributed in tropical and subtropical regions is an important germplasm for rice breeding. Dongxiang (28°14′N, 116°36′E) is the northernmost area of this species recorded in the world, and Chaling (26°50′N, 113°40′E) is near to the northern range limit. Seed dormancy commonly exists in O. rufipogon seeds.

  14. Bioconversion of Capsaicin by Aspergillus oryzae.

    Science.gov (United States)

    Lee, Minji; Cho, Jeong-Yong; Lee, Yu Geon; Lee, Hyoung Jae; Lim, Seong-Il; Park, So-Lim; Moon, Jae-Hak

    2015-07-08

    This study identified metabolites of capsaicin bioconverted by Aspergillus oryzae, which is generally used for mass production of gochujang prepared by fermenting red pepper powder in Korea. A. oryzae was incubated with capsaicin in potato dextrose broth. Capsaicin decreased depending on the incubation period, but new metabolites increased. Five capsaicin metabolites purified from the ethyl acetate fraction of the capsaicin culture were identified as N-vanillylcarbamoylbutyric acid, N-vanillyl-9-hydroxy-8-methyloctanamide, ω-hydroxycapsaicin, 8-methyl-N-vanillylcarbamoyl-6(E)-octenoic acid, and 2-methyl-N-vanillylcarbamoyl-6(Z)-octenoic acid by nuclear magnetic resonance (NMR) and mass spectrometry (MS). The capsaicin metabolites in gochujang were confirmed and quantitated by selective multiple reaction monitoring detection after liquid chromatography electrospray ionization MS using the isolated compounds as external standards. On the basis of the structures of the capsaicin metabolites, it is proposed that capsaicin metabolites were converted by A. oryzae by ω-hydroxylation, alcohol oxidation, hydrogenation, isomerization, and α- and/or β-oxidation.

  15. Rice Snl6, a cinnamoyl-CoA reductase-like gene family member, is required for NH1-mediated immunity to Xanthomonas oryzae pv. oryzae.

    Directory of Open Access Journals (Sweden)

    Rebecca S Bart

    2010-09-01

    Full Text Available Rice NH1 (NPR1 homolog 1 is a key mediator of innate immunity. In both plants and animals, the innate immune response is often accompanied by rapid cell death at the site of pathogen infection. Over-expression of NH1 in rice results in resistance to the bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo, constitutive expression of defense related genes and enhanced benzothiadiazole (BTH- mediated cell death. Here we describe a forward genetic screen that identified a suppressor of NH1-mediated lesion formation and resistance, snl6. Comparative genome hybridization and fine mapping rapidly identified the genomic location of the Snl6 gene. Snl6 is a member of the cinnamoyl-CoA reductase (CCR-like gene family. We show that Snl6 is required for NH1-mediated resistance to Xoo. Further, we show that Snl6 is required for pathogenesis-related gene expression. In contrast to previously described CCR family members, disruption of Snl6 does not result in an obvious morphologic phenotype. Snl6 mutants have reduced lignin content and increased sugar extractability, an important trait for the production of cellulosic biofuels. These results suggest the existence of a conserved group of CCR-like genes involved in the defense response, and with the potential to alter lignin content without affecting development.

  16. Mapping of a new gene for brown planthopper resistance in cultivated rice introgressed from Oryza eichingeri

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Wild rice species is an important source of useful genes for cultivated rice improvement. Some accessions of Oryza eichingeri (2n = 24, CC) from Africa confer strong resistance to brown planthopper (BPH), whitebacked planthopper (WBPH) and bacterial blight (BB). In the present study, restriction fragments length polymorphism (RFLP) and simple sequence repeats (SSR) analysis were performed on disomic backcross plants between Oryza sativa (2n = 24, AA) and O. eichingeri in order to identify the presenee of O. eichingeri segments and further to localize BPH-resistant gene. In the introgression lines, 1-6O. eichingeri segments were detected on rice chromosomes 1, 2, 6, or/and 10. The dominant BPH resistant gene, tentatively named Bph13(t), was mapped to chromosome 2, being 6.1 and 5.5 cM away from two microsatellite markers RM240 and RM250, respectively. The transfer and localization of this gene from O. eichingeri will contribute to the improvement of BPH resistance in cultivated rice.``

  17. AA magnet measurement team

    CERN Multimedia

    1978-01-01

    Quickly improvised measurement equipment for the AA (Antiproton Accumulator) was all the tight schedule permitted, but the high motivation of the team made up for the lack of convenience. From left to right: Roy Billinge (Joint AA Project Leader, the other one was Simon van der Meer); Bruno Autin, Brian Pincott, Colin Johnson.

  18. A genome browser database for rice (Oryza sativa) and Chinese ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... Northeast Asia. ... storage, integration, analysis and visualization of a wide ... integration of any biological data that can be mapped .... Screenshot of 'map view' showing the region of rice chromosomes for selection from the ...

  19. Genotype × Environment Interactions of Yield Traits in Backcross Introgression Lines Derived from Oryza sativa cv. Swarna/Oryza nivara

    Science.gov (United States)

    Balakrishnan, Divya; Subrahmanyam, Desiraju; Badri, Jyothi; Raju, Addanki Krishnam; Rao, Yadavalli Venkateswara; Beerelli, Kavitha; Mesapogu, Sukumar; Surapaneni, Malathi; Ponnuswamy, Revathi; Padmavathi, G.; Babu, V. Ravindra; Neelamraju, Sarla

    2016-01-01

    Advanced backcross introgression lines (BILs) developed from crosses of Oryza sativa var. Swarna/O. nivara accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) and modified rank-sum statistic (YSi) for yield stability. BILs viz., G3 (14S) and G6 (166S) showed yield stability across the seasons along with high mean yield performance. G3 is early in flowering with high yield and has good grain quality and medium height, hence could be recommended for most of the irrigated locations. G6 is a late duration genotype, with strong culm strength, high grain number and panicle weight. G6 has higher yield and stability than Swarna but has Swarna grain type. Among the varieties tested DRRDhan 40 and recurrent parent Swarna showed stability for yield traits across the seasons. The component traits thousand grain weight, panicle weight, panicle length, grain number and plant height explained highest genotypic percentage over environment and interaction factors and can be prioritized to dissect stable QTLs/ genes. These lines were genotyped using microsatellite markers covering the entire rice genome and also using a set of markers linked to previously reported yield QTLs. It was observed that wild derived lines with more than 70% of recurrent parent genome were stable and showed enhanced yield levels compared to genotypes with higher donor genome introgressions.

  20. Functional analysis of histone deacetylase and its role in stress response, drug resistance and solid-state cultivation in Aspergillus oryzae.

    Science.gov (United States)

    Kawauchi, Moriyuki; Iwashita, Kazuhiro

    2014-08-01

    In the eukaryotic cell, histone deacetylases (HDACs) play key roles in the regulation of fundamental cellular process such as development regulation, stress response, secondary metabolism and genome integrity. Here, we provide a comprehensive phenotypic analysis using HDAC disruptants in Aspergillus oryzae. Our study revealed that four HDACs, hdaA/Aohda1, hdaB/Aorpd3, hdaD/Aohos2 and hst4/AohstD were involved in stress response, cell wall synthesis and chromatin integrity in A. oryzae. Osmotic stress sensitivity of HDAC disruptants differed between plate cultures and liquid cultures, suggesting that HDACs adapt to the difference environmental conditions. Using a common A. oryzae fermentation medium, rice-koji, we also characterized HDACs related to growth and enzyme production to investigate which HDACs will be required for adaptation to environmental conditions and stress resistances. Because HDACs are widely conserved, our study has broad applications and may inform work with filamentous fungi and other eukaryote.

  1. The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology.

    Science.gov (United States)

    Wang, Dapeng; Xia, Yan; Li, Xinna; Hou, Lixia; Yu, Jun

    2013-01-01

    Over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice (Oryza sativa L.) subspecies, 93-11 (indica) and Nipponbare (japonica). To integrate information from genome assemblies and annotations for better analysis and application, we now introduce a comparative rice genome database, the Rice Genome Knowledgebase (RGKbase, http://rgkbase.big.ac.cn/RGKbase/). RGKbase is built to have three major components: (i) integrated data curation for rice genomics and molecular biology, which includes genome sequence assemblies, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and the relevant literature; (ii) User-friendly viewers, such as Gbrowse, GeneBrowse and Circos, for genome annotations and evolutionary dynamics and (iii) Bioinformatic tools for compositional and synteny analyses, gene family classifications, gene ontology terms and pathways and gene co-expression networks. RGKbase current includes data from five rice cultivars and species: Nipponbare (japonica), 93-11 (indica), PA64s (indica), the African rice (Oryza glaberrima) and a wild rice species (Oryza brachyantha). We are also constantly introducing new datasets from variety of public efforts, such as two recent releases-sequence data from ∼1000 rice varieties, which are mapped into the reference genome, yielding ample high-quality single-nucleotide polymorphisms and insertions-deletions.

  2. Construction of brewing-wine Aspergillus oryzae pyrG- mutant by pyrG gene deletion and its application in homology transformation.

    Science.gov (United States)

    Du, Yu; Xie, Guizhen; Yang, Chunfa; Fang, Baishan; Chen, Hongwen

    2014-06-01

    pyrG(-) host cells are indispensable for pyrG(-) based transformation system. Isolations of pyrG(-) host cells by random mutations are limited by time-consuming, unclear genetic background and potential interferences of homogenous recombination. The purpose of this study was to construct brewing-wine Aspergillus oryzae pyrG(-) mutant by site-directed mutation of pyrG gene deletion which would be used as a host for further transformation. pMD-pyrGAB, a vector carrying pyrG deletion cassette, was used to construct pyrG(-) mutant of A. oryzae. Three stable pyrG deletion mutants of A. oryzae were isolated by resistant to 5-fluoroorotic acid and confirmed by polymerase chain reaction analysis, indicating that pyrG was completely excised. The ΔpyrG mutants were applied as pyrG(-) host cells to disrupt xdh gene encoding xylitol dehydrogenase, which involves in xylitol production of A. oryzae. The xdh disruption mutants were efficiently constructed by transforming a pMD-pyrG-xdh disruption plasmid carrying pyrG, and the produced xylitol concentration of the Δxdh mutant was three times as much as that of the ΔpyrG recipient. Site-directed pyrG gene deletion is thus an effective way for the isolation of pyrG(-) host cells, and the established host-vector system could be applied in further functional genomics analysis and molecular breeding of A. oryzae.

  3. Xanthomonas oryzae pv oryzae the Causal Agent of Bacterial Leaf Blight of rice: Isolation, Characterization, and Study of Transposon Mutagenesis

    Directory of Open Access Journals (Sweden)

    Abdjad Asih Nawangsih

    2011-04-01

    Full Text Available Xanthomonas oryzae pv oryzae the Causal Agent of Bacterial Leaf Blight of rice: Isolation, Characterization, and Study of Transposon Mutagenesis. X. oryzae pv. oryzae (Xoo causes bacterial leaf blight (BLB of rice (Oryza sativa L., a major disease that constrains production of the staple crop in many countries of the world. Identification of X. oryzae pv. oryzae (Xoo was conducted based on the disease symptoms, pathogenicity, morphological, physiological, and genetic characteristics of bacterial cultures isolated from the infected plants. Fifty bacterial isolates predicted as Xoo have been successfully isolated. They are aerobic, rod shaped, and Gram negative bacteria. The isolates were evaluated for their hypersensitivity in tobacco and pathogenicity in rice plant. Fifty isolates induced hypersensitive reaction in tobacco and showed pathogenicity symptom in rice in different length. Based on physiological test, hypersensitivity and pathogenicity reactions, three bacterial isolates strongly predicted as Xoo, i.e. STG21, STG42, and STG46, were non indole formation, non pigment fluorescent, hydrolyzed casein, catalase activity positive, but negative oxidase. Partial sequencing of 16S rRNA genes of STG21 and STG42 showed 80% and 82% homology with X. oryzae, respectively, while STG46 showed 84% homology with X. campestris. Mini-Tn5 transposon mutagenesis of STG21 generated one of the mutants (M5 lossed it’s ability to induce hypersensitive reaction in tobacco plant and deficient in pathogenicity on rice. The lesion length of rice leaf caused by the mutant M5 decreased up to 80%.

  4. Monitoring homologous recombination in rice (Oryza sativa L.)

    Energy Technology Data Exchange (ETDEWEB)

    Yang Zhuanying; Tang Li [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China); Li Meiru [South China Botanic Garden, Chinese Academy of Sciences, Guangzhou 510650 (China); Chen Lei; Xu Jie [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China); Wu Goujiang [South China Botanic Garden, Chinese Academy of Sciences, Guangzhou 510650 (China); Li Hongqing, E-mail: hqli@scnu.edu.cn [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China)

    2010-09-10

    Here we describe a system to assay homologous recombination during the complete life cycle of rice (Oryza sativa L.). Rice plants were transformed with two copies of non-functional GUS reporter overlap fragments as recombination substrate. Recombination was observed in all plant organs examined, from the seed stage until the flowering stage of somatic plant development. Embryogenic cells exhibited the highest recombination ability with an average of 3 x 10{sup -5} recombination events per genome, which is about 10-fold of that observed in root cells, and two orders of that observed in leaf cells. Histological analysis revealed that recombination events occurred in diverse cell types, but preferentially in cells with small size. Examples of this included embryogenic cells in callus, phloem cells in the leaf vein, and cells located in the root apical meristem. Steady state RNA analysis revealed that the expression levels of rice Rad51 homologs are positively correlated with increased recombination rates in embryogenic calli, roots and anthers. Finally, radiation treatment of plantlets from distinct recombination lines increased the recombination frequency to different extents. These results showed that homologous recombination frequency can be effectively measured in rice using a transgene reporter assay. This system will facilitate the study of DNA damage signaling and homologous recombination in rice, a model monocot.

  5. AAS 227: Welcome!

    Science.gov (United States)

    Kohler, Susanna

    2016-01-01

    Greetings from the 227th American Astronomical Society meeting in Kissimmee, Florida! This week, along with several fellow authors from astrobites, Iwill bewritingupdates on selectedevents at themeeting and posting at the end of each day. You can follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.If youre an author or referee (or plan to be!) and youre here at the meeting, consider joining us at our Author and Referee Workshop on Wednesday in the Tallahassee room, where well be sharingsome of the exciting new features of the AAS journals. You can drop intoeither of the two-hour sessions(10 AM 12 PM or 1 PM 3 PM), and there will be afree buffet lunch at noon.Heres the agenda:Morning SessionTopic Speaker10:00 am 10:05 amIntroductionsJulie Steffen10:05 am 10:35 amChanges at AAS Journals; How to Be a Successful AAS AuthorEthan Vishniac10:35 am 11:00 amThe Peer Review ProcessButler Burton11:00 am 11:15 amAAS Nova: Sharing AAS Authors Research with the Broader CommunitySusanna Kohler11:15 am 11:30 amFixing Software and Instrumentation Publishing: New Paper Styles in AAS JournalsChris Lintott11:30 am 11:45 amMaking Article Writing Easier with the New AASTeX v6.0Greg Schwarz11:45 am 12:00 pmBringing JavaScript and Interactivity to Your AAS Journal FiguresGus MuenchLunch SessionTopic Speaker12:00 pm 12:15 pmUnified Astronomy ThesaurusKatie Frey12:15 pm 12:30 pmAAS/ADS ORCID Integration ToolAlberto Accomazzi12:30 pm 12:45 pmWorldWide Telescope and Video AbstractsJosh Peek12:45 pm 01:00 pmArizona Astronomical Data Hub (AADH)Bryan HeidornAfternoon SessionTopic Speaker01:00 pm 01:05 pmIntroductionsJulie Steffen01:05 pm 01:35 pmChanges at AAS Journals; How to Be a Successful AAS AuthorEthan Vishniac01:35 pm 02:00 pmThe Peer Review ProcessButler Burton02:00 pm 02:15 pmAAS Nova: Sharing AAS Authors Research with the Broader CommunitySusanna Kohler02:15 pm 02:30 pm

  6. Geomagnetic aa Indices

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The geomagnetic aa indices are the continuation of the series beginning in the year 1868. A full description of these indices is given in the International...

  7. AAS 228: Welcome!

    Science.gov (United States)

    Kohler, Susanna

    2016-06-01

    Greetings from the 228th American Astronomical Society meeting in San Diego, California! This week, along with a team of fellow authorsfrom astrobites, Iwill bewritingupdates on selectedevents at themeeting and posting twiceeach day. You can follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.If youre at the meeting, come stop by the AAS booth (Booth #211-213) to learn about the newly-announced partnership between AAS and astrobites and pick up some swag.And dont forget to visit the IOP booth in the Exhibit Hall (Booth #223) to learn more about the new corridors for AAS Journals and to pick up a badge pin to representyour corridor!

  8. Genomewide survey and characterization of metacaspase gene family in rice (Oryza sativa)

    Indian Academy of Sciences (India)

    Likai Wang; Hua Zhang

    2014-04-01

    Metacaspases (MCs), which are cysteine-dependent proteases found in plants, fungi, and protozoa, may be involved in programmed cell death processes, being distant relatives of metazoan caspases. In this study, we analysed the structures, phylogenetic relationship, genome localizations, expression patterns and domestic selections of eight MC genes identified in rice (OsMC). Alignment analysis of the corresponding protein sequences suggested OsMC proteins can be classified into two sub-types. The expression profiles of eight OsMC genes were analysed in 27 tissues covering the whole life cycle of rice. There are four OsMC genes uniquely expressed in mature tissues, indicating that these genes might play certain roles in senescence. Under abiotic and biotic stresses, four OsMC genes were expressed with treatments of one or more of Magnaporthe oryzae (M. oryzae) infected, pest damaged, cold stress and drought stress, indicating they might be involved in plant defense. In addition, gene trees and genetic diversity $(\\pi)$ were performed to measure whether candidate genes were selected during rice domestication. The results suggested that all the type I genes could not be domestication genes. However, two of five type II OsMC genes showed strong evidence for selective sweep, suggesting that these genes might be involved in cultivated rice domestication. These results provide a foundation for future functional genomic studies of this family in rice.

  9. Variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps) biosynthetic locus in Xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice

    Science.gov (United States)

    Patil, Prabhu B; Sonti, Ramesh V

    2004-01-01

    Background In animal pathogenic bacteria, horizontal gene transfer events (HGT) have been frequently observed in genomic regions that encode functions involved in biosynthesis of the outer membrane located lipopolysaccharide (LPS). As a result, different strains of the same pathogen can have substantially different lps biosynthetic gene clusters. Since LPS is highly antigenic, the variation at lps loci is attributed to be of advantage in evading the host immune system. Although LPS has been suggested as a potentiator of plant defense responses, interstrain variation at lps biosynthetic gene clusters has not been reported for any plant pathogenic bacterium. Results We report here the complete sequence of a 12.2 kb virulence locus of Xanthomonas oryzae pv. oryzae (Xoo) encoding six genes whose products are homologous to functions involved in LPS biosynthesis and transport. All six open reading frames (ORFs) have atypical G+C content and altered codon usage, which are the hallmarks of genomic islands that are acquired by horizontal gene transfer. The lps locus is flanked by highly conserved genes, metB and etfA, respectively encoding cystathionine gamma lyase and electron transport flavoprotein. Interestingly, two different sets of lps genes are present at this locus in the plant pathogens, Xanthomonas campestris pv. campestris (Xcc) and Xanthomonas axonopodis pv. citri (Xac). The genomic island is present in a number of Xoo strains from India and other Asian countries but is not present in two strains, one from India (BXO8) and another from Nepal (Nepal624) as well as the closely related rice pathogen, Xanthomonas oryzae pv. oryzicola (Xoor). TAIL-PCR analysis indicates that sequences related to Xac are present at the lps locus in both BXO8 and Nepal624. The Xoor strain has a hybrid lps gene cluster, with sequences at the metB and etfA ends, being most closely related to sequences from Xac and the tomato pathogen, Pseudomonas syringae pv. tomato respectively

  10. Homeobox transcription factors are required for conidiation and appressorium development in the rice blast fungus Magnaporthe oryzae.

    Directory of Open Access Journals (Sweden)

    Seryun Kim

    2009-12-01

    Full Text Available The appropriate development of conidia and appressoria is critical in the disease cycle of many fungal pathogens, including Magnaporthe oryzae. A total of eight genes (MoHOX1 to MoHOX8 encoding putative homeobox transcription factors (TFs were identified from the M. oryzae genome. Knockout mutants for each MoHOX gene were obtained via homology-dependent gene replacement. Two mutants, DeltaMohox3 and DeltaMohox5, exhibited no difference to wild-type in growth, conidiation, conidium size, conidial germination, appressorium formation, and pathogenicity. However, the DeltaMohox1 showed a dramatic reduction in hyphal growth and increase in melanin pigmentation, compared to those in wild-type. DeltaMohox4 and DeltaMohox6 showed significantly reduced conidium size and hyphal growth, respectively. DeltaMohox8 formed normal appressoria, but failed in pathogenicity, probably due to defects in the development of penetration peg and invasive growth. It is most notable that asexual reproduction was completely abolished in DeltaMohox2, in which no conidia formed. DeltaMohox2 was still pathogenic through hypha-driven appressoria in a manner similar to that of the wild-type. However, DeltaMohox7 was unable to form appressoria either on conidial germ tubes, or at hyphal tips, being non-pathogenic. These factors indicate that M. oryzae is able to cause foliar disease via hyphal appressorium-mediated penetration, and MoHOX7 is mutually required to drive appressorium formation from hyphae and germ tubes. Transcriptional analyses suggest that the functioning of M. oryzae homeobox TFs is mediated through the regulation of gene expression and is affected by cAMP and Ca(2+ signaling and/or MAPK pathways. The divergent roles of this gene set may help reveal how the genome and regulatory pathways evolved within the rice blast pathogen and close relatives.

  11. The Potential of Streptomyces as Biocontrol Agents against the Rice Blast Fungus, Magnaporthe oryzae (Pyricularia oryzae)

    Science.gov (United States)

    Law, Jodi Woan-Fei; Ser, Hooi-Leng; Khan, Tahir M.; Chuah, Lay-Hong; Pusparajah, Priyia; Chan, Kok-Gan; Goh, Bey-Hing; Lee, Learn-Han

    2017-01-01

    Rice is a staple food source for more than three billion people worldwide. However, rice is vulnerable to diseases, the most destructive among them being rice blast, which is caused by the fungus Magnaporthe oryzae (anamorph Pyricularia oryzae). This fungus attacks rice plants at all stages of development, causing annual losses of approximately 10–30% in various rice producing regions. Synthetic fungicides are often able to effectively control plant diseases, but some fungicides result in serious environmental and health problems. Therefore, there is growing interest in discovering and developing new, improved fungicides based on natural products as well as introducing alternative measures such as biocontrol agents to manage plant diseases. Streptomyces bacteria appear to be promising biocontrol agents against a wide range of phytopathogenic fungi, which is not surprising given their ability to produce various bioactive compounds. This review provides insight into the biocontrol potential of Streptomyces against the rice blast fungus, M. oryzae. The ability of various Streptomyces spp. to act as biocontrol agents of rice blast disease has been studied by researchers under both laboratory and greenhouse/growth chamber conditions. Laboratory studies have shown that Streptomyces exhibit inhibitory activity against M. oryzae. In greenhouse studies, infected rice seedlings treated with Streptomyces resulted in up to 88.3% disease reduction of rice blast. Studies clearly show that Streptomyces spp. have the potential to be used as highly effective biocontrol agents against rice blast disease; however, the efficacy of any biocontrol agent may be affected by several factors including environmental conditions and methods of application. In order to fully exploit their potential, further studies on the isolation, formulation and application methods of Streptomyces along with field experiments are required to establish them as effective biocontrol agents. PMID:28144236

  12. The Potential of Streptomyces as Biocontrol Agents against the Rice Blast Fungus, Magnaporthe oryzae (Pyricularia oryzae).

    Science.gov (United States)

    Law, Jodi Woan-Fei; Ser, Hooi-Leng; Khan, Tahir M; Chuah, Lay-Hong; Pusparajah, Priyia; Chan, Kok-Gan; Goh, Bey-Hing; Lee, Learn-Han

    2017-01-01

    Rice is a staple food source for more than three billion people worldwide. However, rice is vulnerable to diseases, the most destructive among them being rice blast, which is caused by the fungus Magnaporthe oryzae (anamorph Pyricularia oryzae). This fungus attacks rice plants at all stages of development, causing annual losses of approximately 10-30% in various rice producing regions. Synthetic fungicides are often able to effectively control plant diseases, but some fungicides result in serious environmental and health problems. Therefore, there is growing interest in discovering and developing new, improved fungicides based on natural products as well as introducing alternative measures such as biocontrol agents to manage plant diseases. Streptomyces bacteria appear to be promising biocontrol agents against a wide range of phytopathogenic fungi, which is not surprising given their ability to produce various bioactive compounds. This review provides insight into the biocontrol potential of Streptomyces against the rice blast fungus, M. oryzae. The ability of various Streptomyces spp. to act as biocontrol agents of rice blast disease has been studied by researchers under both laboratory and greenhouse/growth chamber conditions. Laboratory studies have shown that Streptomyces exhibit inhibitory activity against M. oryzae. In greenhouse studies, infected rice seedlings treated with Streptomyces resulted in up to 88.3% disease reduction of rice blast. Studies clearly show that Streptomyces spp. have the potential to be used as highly effective biocontrol agents against rice blast disease; however, the efficacy of any biocontrol agent may be affected by several factors including environmental conditions and methods of application. In order to fully exploit their potential, further studies on the isolation, formulation and application methods of Streptomyces along with field experiments are required to establish them as effective biocontrol agents.

  13. Action of Multiple Cell Wall-Degrading Enzymes Is Required for Elicitation of Innate Immune Responses During Xanthomonas oryzae pv. oryzae Infection in Rice.

    Science.gov (United States)

    Tayi, Lavanya; Maku, Roshan; Patel, Hitendra Kumar; Sonti, Ramesh V

    2016-08-01

    Xanthomonas oryzae pv. oryzae secretes a number of plant cell wall-degrading enzymes (CWDEs) whose purified preparations induce defense responses in rice. These defense responses are suppressed by X. oryzae pv. oryzae using type 3 secretion system (T3SS) effectors and a type 3 secretion system mutant (T3SS(-)) of X. oryzae pv. oryzae is an inducer of rice defense responses. We assessed the role of individual CWDEs in induction of rice defense responses during infection, by mutating them in the genetic background of a T3SS(-). We mutated the genes for five different plant CWDEs secreted by X. oryzae pv. oryzae, including two cellulases (clsA and cbsA), one xylanase (xyn), one pectinase (pglA), and an esterase (lipA), singly in a T3SS(-) background. We have demonstrated that, as compared with a T3SS(-) of X. oryzae pv. oryzae, a cbsA(-)T3SS(-), a clsA(-)T3SS(-), and a xyn(-)T3SS(-) are deficient in induction of rice immune responses such as callose deposits and programmed cell death. In comparison, a lipA(-) T3SS(-) and a pglA(-)T3SS(-) is as efficient in induction of host defense responses as a T3SS(-). Overall, these results indicate that the collective action of X. oryzae pv. oryzae-secreted ClsA, CbsA, and Xyn proteins is required for induction of rice defense responses during infection.

  14. Screening of gamma radiation-induced pathogen resistance rice lines against Xanthomonas oryzae pv. oryzae

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Chan Ju; Lee, Ha Yeon; Kim, Woong Bom; Ahmad, Raza; Moon, Jae Sun; Kwon, Suk Yoon [Korea Research Institute of Beoscience and Biotechnology, Daejeon (Korea, Republic of); Kim, Dong Sub [Korea Atomic Energy Research Institute, Jeongeup (Korea, Republic of)

    2010-09-15

    Bacterial blight is one of the most serious diseases of rice (Oryza sativa L.), and it has been known that Xanthomonas oryzae pv. oryzae (Xoo) causes this disease symptom. To develop resistance rice cultivars against Xoo, 3,000 lines of M{sub 3}, which were irradiated with gamma ray, were tested by 'scissor-dip method' primarily, and 191 putative resistant lines were selected. In M{sub 4} generation, these lines were screened again with various ways such as measuring of symptom of bacterial blight in leaf, number of tiller, fresh weight, and phenotypic segregation ratio in next generation. Finally, six resistance lines were selected. RT-PCR analysis revealed that these lines displayed high level of R-genes such as Xa21, Pi36, and Pi-ta. These results indicate that mutations by gamma ray cause disruptions of regulatory signal transduction systems of these R-genes. Furthermore, these selected mutants could be useful for the development of rice cultivar resistant to Xoo.

  15. Lethal and mutagenic effects of ion beams and γ-rays in Aspergillus oryzae

    Energy Technology Data Exchange (ETDEWEB)

    Toyoshima, Yoshiyuki, E-mail: toyoshima@yamasa.com [Soy Sauce Laboratory, Yamasa Corporation, 2-10-1 Araoicho, Choshi, Chiba 288-0056 (Japan); Takahashi, Akemi; Tanaka, Hisaki; Watanabe, Jun; Mogi, Yoshinobu; Yamazaki, Tatsuo [Soy Sauce Laboratory, Yamasa Corporation, 2-10-1 Araoicho, Choshi, Chiba 288-0056 (Japan); Hamada, Ryoko; Iwashita, Kazuhiro [Fundamental Research Division, National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashihiroshima, Hiroshima 739-0046 (Japan); Satoh, Katsuya; Narumi, Issay [Ion Beam Mutagenesis Research Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 1233 Watanuki, Takasaki, Gunma 370-1292 (Japan)

    2012-12-15

    Highlights: ► We investigated the effects of different LET radiation in A. oryzae. ► Both γ-rays and ion beams induced base substitutions, frameshifts, deletions. ► Both γ-rays and ion beams induced genome-wide large-scale mutations in A. oryzae. ► Some differences in the types and frequencies of mutations were found. ► Our results provide new basic insights into the mutation breeding of A. oryzae. - Abstract: Aspergillus oryzae is a fungus that is used widely in traditional Japanese fermentation industries. In this study, the lethal and mutagenic effects of different linear energy transfer (LET) radiation in freeze-dried conidia of A. oryzae were investigated. The lethal effect, which was evaluated by a 90% lethal dose, was dependent on the LET value of the ionizing radiation. The most lethal ionizing radiation among that tested was {sup 12}C{sup 5+} ion beams with an LET of 121 keV/μm. The {sup 12}C{sup 5+} ion beams had a 3.6-times higher lethal effect than low-LET (0.2 keV/μm) γ-rays. The mutagenic effect was evaluated by the frequency of selenate resistant mutants. {sup 12}C{sup 6+} ion beams with an LET of 86 keV/μm were the most effective in inducing selenate resistance. The mutant frequency following exposure to {sup 12}C{sup 6+} ion beams increased with an increase in dose and reached 3.47 × 10{sup −3} at 700 Gy. In the dose range from 0 to 700 Gy, {sup 12}C{sup 5+} ion beams were the second most effective in inducing selenate resistance, the mutant frequency of which reached a maximum peak (1.67 × 10{sup −3}) at 400 Gy. To elucidate the characteristics of mutation induced by ionizing radiation, mutations in the sulphate permease gene (sB) and ATP sulfurylase gene (sC) loci, the loss of function of which results in a selenate resistant phenotype, were compared between {sup 12}C{sup 5+} ion beams and γ-rays. We detected all types of transversions and transitions. For frameshifts, the frequency of a +1 frameshift was the highest in all

  16. 水稻黄单胞菌三型分泌系统效应物的研究进展%Current progresses in study on T3SS effectors of Xanthomonas oryzae

    Institute of Scientific and Technical Information of China (English)

    赵帅; 张子宇; 冯家勋

    2011-01-01

    The type Ⅲ secretion system (T3SS) effector is considered as one of the key virulence factors in Xanthomonas oryzae. X. Oryzae pv. Oryzae and X. Oryzae pv. Oryzicola cause bacterial leaf blight and bacterial leaf streak in rice, which are important bacterial diseases of rice. Based on bioinformatic analysis of the bacterial genome and other recent reports,X. Oryzae contains at least 28 classes of T3SS effectors, divided into two groups: TAL (transcription activator-like) effectors and non-TAL (non transcription activator-like) effectors. This paper reviews the number, classes, structure and host targets of T3SS effectors in X. Oryzae, which may provide a new insight into the mechanism of rice-X. Oryzae interaction, regulatory network and molecular breeding of rice.%水稻黄单胞菌(X.oryzae)三-型分泌系统(Type Ⅲ secretion system,T3SS)效应物(Effector)一直被认为是水稻黄单胞菌最重要的致病因子之一.水稻黄单胞菌水稻致病变种(Xanthomonas oryzae pv.oryzae)和水稻黄单胞菌栖稻致病变种(Xanthomonas oryzae pv.oryzicola)分别引起水稻两大细菌病害水稻白叶枯病(Bacterial leaf blight)和水稻细菌性条斑病(Bacterial leaf streak).基因组分析揭示,水稻黄单胞菌中至少存在28个类型的T3SS效应物,分为TAL(Transcription activator-like effectors)效应物和non-TAL效应物(Non transcription activator-like effectors)两大类.通过对水稻黄单胞菌中T3SS效应物的数量、种类、结构、宿主靶标等方面进行综述,为全面了解水稻-水稻黄单胞菌互作的分子机理,调控网络以及水稻分子育种提供一种新洞察力.

  17. HrcQ is necessary for Xanthomonas oryzae pv. oryzae HR-induction in non-host tobacco and pathogenicity in host rice

    Directory of Open Access Journals (Sweden)

    Xiaoping Zhang

    2013-12-01

    Full Text Available Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo, is one of the most destructive diseases of rice (Oryza sativa L. worldwide. The type III secretion system (T3SS of Xoo, encoded by the hrp (hypersensitive response and pathogenicity genes, plays critical roles in conferring pathogenicity in host rice and triggering a hypersensitive response (HR in non-host plants. To investigate the major genes conferring the pathogenicity and avirulence of Xoo, we previously constructed a random Tn5-insertion mutant library of Xoo strain PXO99A. We report here the isolation and characterization of a Tn5-insertion mutant PXM69. Tn5-insertion mutants were screened on indica rice JG30, which is highly susceptible to PXO99A, by leaf-cutting inoculation. Four mutants with reduced virulence were obtained after two rounds of screening. Among them, the mutant PXM69 had completely lost virulence to the rice host and ability to elicit HR in non-host tobacco. Southern blotting analysis showed a single copy of a Tn5-insertion in the genome of PXM69. PCR walking and sequencing analysis revealed that the Tn5 transposon was inserted at nucleotide position 70,192–70,201 in the genome of PXO99A, disrupting the type III hrc (hrp-conserved gene hrcQ, the first gene in the D operon of the hrp cluster in Xoo. To confirm the relationship between the Tn5-insertion and the avirulence phenotype of PXM69, we used the marker exchange mutagenesis to create a PXO99A mutant, ΔhrcQ::KAN, in which the hrcQ was disrupted by a kanamycin-encoding gene cassette at the same site as that of the Tn5-insertion. ΔhrcQ::KAN showed the same phenotype as mutant PXM69. Reintroduction of the wild-type hrcQ gene partially complemented the pathogenic function of PXM69. RT-PCR and cellulase secretion assays showed that the Tn5-disruption of hrcQ did not affect transcription of downstream genes in the D operon and function of the type II secretion system. Our results provide new insights into

  18. HrcQ is necessary for Xanthomonas oryzae pv. oryzae HR-induction in non-host tobacco and pathogenicity in host rice

    Institute of Scientific and Technical Information of China (English)

    Xiaoping; Zhang; Chunlian; Wang; Chongke; Zheng; Jinying; Che; Yanqiang; Li; Kaijun; Zhao

    2013-01-01

    Bacterial blight, caused by Xanthomonas oryzae pv. oryzae(Xoo), is one of the most destructive diseases of rice(Oryza sativa L.) worldwide. The type III secretion system(T3SS) of Xoo, encoded by the hrp(hypersensitive response and pathogenicity) genes, plays critical roles in conferring pathogenicity in host rice and triggering a hypersensitive response(HR) in non-host plants. To investigate the major genes conferring the pathogenicity and avirulence of Xoo, we previously constructed a random Tn5-insertion mutant library of Xoo strain PXO99A. We report here the isolation and characterization of a Tn5-insertion mutant PXM69. Tn5-insertion mutants were screened on indica rice JG30, which is highly susceptible to PXO99A, by leaf-cutting inoculation.Four mutants with reduced virulence were obtained after two rounds of screening. Among them, the mutant PXM69 had completely lost virulence to the rice host and ability to elicit HR in non-host tobacco. Southern blotting analysis showed a single copy of a Tn5-insertion in the genome of PXM69. PCR walking and sequencing analysis revealed that the Tn5 transposon was inserted at nucleotide position 70,192–70,201 in the genome of PXO99A, disrupting the type III hrc(hrp-conserved) gene hrcQ, the first gene in the D operon of the hrp cluster in Xoo. To confirm the relationship between the Tn5-insertion and the avirulence phenotype of PXM69, we used the marker exchange mutagenesis to create a PXO99Amutant, ΔhrcQ::KAN, in which the hrcQ was disrupted by a kanamycin-encoding gene cassette at the same site as that of the Tn5-insertion. ΔhrcQ::KAN showed the same phenotype as mutant PXM69. Reintroduction of the wild-type hrcQ gene partially complemented the pathogenic function of PXM69. RT-PCR and cellulase secretion assays showed that the Tn5-disruption of hrcQ did not affect transcription of downstream genes in the D operon and function of the type II secretion system. Our results provide new insights into the pathogenic

  19. Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza).

    Science.gov (United States)

    Giuliani, Rita; Koteyeva, Nuria; Voznesenskaya, Elena; Evans, Marc A; Cousins, Asaph B; Edwards, Gerald E

    2013-07-01

    The genus Oryza, which includes rice (Oryza sativa and Oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control CO(2) access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. Traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). Hypotheses of associations within, and between, structure, photosynthesis, and transpiration were tested. Two main clusters of positively interrelated leaf traits were identified: in the first cluster were structural features, leaf thickness (Thick(leaf)), mesophyll (M) cell surface area exposed to intercellular air space per unit of leaf surface area (S(mes)), and M cell size; a second group included functional traits, net photosynthetic rate, transpiration rate, M conductance to CO(2) diffusion (g(m)), stomatal conductance to gas diffusion (g(s)), and the g(m)/g(s) ratio.While net photosynthetic rate was positively correlated with gm, neither was significantly linked with any individual structural traits. The results suggest that changes in gm depend on covariations of multiple leaf (S(mes)) and M cell (including cell wall thickness) structural traits. There was an inverse relationship between Thick(leaf) and transpiration rate and a significant positive association between Thick(leaf) and leaf transpiration efficiency. Interestingly, high g(m) together with high g(m)/g(s) and a low S(mes)/g(m) ratio (M resistance to CO(2) diffusion per unit of cell surface area exposed to intercellular air space) appear to be ideal for supporting leaf photosynthesis while preserving water; in addition, thick M cell walls may be beneficial for plant drought tolerance.

  20. Analysis on Genomic Structure Changes and Diversity of Introgression Lines in Dongxiang Wild Rice (Oryza rufipogon Griff.)%东乡野生稻渐渗系基因组结构变化及多样性分析

    Institute of Scientific and Technical Information of China (English)

    邓晓娟; 罗向东; 谢建坤; 万勇; 胡标林; 曹娟芳; 戴亮芳

    2012-01-01

    [Objective] The aim of the study was to make research on genomic struc- ture variation and variety analysis of Dongxiang wild rice. [Method] Introgression groups of BC1F6 were based on donor of Oryza rufipogon Griff. and receptor of O. sativa sp. indica Kate. Strains of 239 in the group were analyzed on Polymor- phism with the help of 25 couples of SSR primers distributed in 12 pairs of chromo- somes. [Result] Gene fragments of O. rufipogon Griff. were found penetrated in the 25 microsatellite sites and most of the groups kept the parents of Xieqinzao B or DNA sequence of O. rufipogon Griff. The average rate of recurrent homozygous bands was 78.13% in the ILs, but the highest was 94.98% (amplified by primer RM131) and the lowest was 60.25% (RM171). The average rate of donor homozy- gous bands was 13.37%, but the highest was 32.64% (RM171) and the lowest was 2.93% (RM1095). There were numerous heterozygous sites in the population and the average heterozygosis rate was 5.62%, while the highest was 10.04%(RM401). Moreover, we found some parental fragments were lost and some novel fragments were not detected in either parent in BC1F6 population. The average rate of lost bands was 2.88%, while the highest was 13.39% (RM311) and the lowest was 0 (RM401). The average rate of new bands was 1%. The average of Nei's gene di- versity (He) and Shannon's Information index (I) were 0.276 and 0.457 respectively in high generation of introgression lines. [Conclusion] The study demonstrated that distant hybridization led to extensive genetic and epigenetic variations in high gener- ation of introgression lines, which expanded the base of genetic variation and laid an important foundation for rice improvement and germplasm innovation.%[目的】研究东乡野生稻渐渗系基因组结构变化及对其进行多样性分析。[方法]以东乡野生稻(O.rufipogonGriff.,供体)和栽培稻协青早B(O.sativasp.indicaKato.

  1. AAS Career Services

    Science.gov (United States)

    Marvel, Kevin B.

    2012-08-01

    The American Astronomical Society provides substantial programs in the area of Career Services.Motivated by the Society's mission to enhance and share humanity's understanding of the Universe, the AAS provides a central resource for advertising positions, interviewing opportunities at its annual winter meeting and information, workshops and networks to enable astronomers to find employment.The programs of the Society in this area are overseen by an active committee on employment and the AAS Council itself.Additional resources that help characterize the field, its growth and facts about employment such as salaries and type of jobs available are regularly summarized and reported on by the American Institute of Physics.

  2. 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.

  3. Roseomonas oryzae sp. nov., isolated from paddy rhizosphere soil.

    Science.gov (United States)

    Ramaprasad, E V V; Sasikala, Ch; Ramana, Ch V

    2015-10-01

    A non-motile, coccus-shaped, pale-pink-pigmented bacterium, designated strain JC288T, was isolated from a paddy rhizosphere soil collected from Western Ghats, Kankumbi, Karnataka, India. Cells were found to be Gram-stain-negative, and catalase- and oxidase-positive; the major fatty acids were C16 : 0, C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c/C18 : 1ω6c and C18 : 1 2-OH. The predominant respiratory quinone was Q-10 and the genomic DNA G+C content was 67.5 mol%. Strain JC288T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, four unidentified aminolipids, three unidentified phospholipids, two unidentified lipids, an aminophospholipid and a glycolipid. Hydroxyspirilloxanthin was the major carotenoid of strain JC288T. 16S rRNA gene sequence comparisons indicated that strain JC288T represents a member of the genus Roseomonas within the family Acetobacteraceae of the phylum Proteobacteria. Strain JC288T shared the highest 16S rRNA gene sequence similarity with Roseomonas rhizosphaerae YW11T (97.3 %), Roseomonas aestuarii JC17T (97.1 %), Roseomonas cervicalis CIP 104027T (95.9 %) and other members of the genus Roseomonas ( Roseomonas, for which the name Roseomonas oryzae sp. nov. is proposed. The type strain is JC288T ( = KCTC 42542T = LMG 28711T).

  4. Crystallization and preliminary crystallographic studies of LipA, a secretory lipase/esterase from Xanthomonas oryzae pv. oryzae

    Energy Technology Data Exchange (ETDEWEB)

    Aparna, Gudlur; Chatterjee, Avradip; Jha, Gopaljee; Sonti, Ramesh V.; Sankaranarayanan, Rajan, E-mail: sankar@ccmb.res.in [Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007 (India)

    2007-08-01

    The crystallization and preliminary crystallographic studies of LipA, a lipase/esterase secreted by X. oryzae pv. oryzae during its infection of rice plants, are reported. Xanthomonas oryzae pv. oryzae is the causal agent of bacterial leaf blight, a serious disease of rice. Several enzymes that are secreted through the type II secretion system of this bacterium play an important role in the plant–microbe interaction, being important for virulence and also being able to induce potent host defence responses. One of these enzymes is a secretory lipase/esterase, LipA, which shows a very weak homology to other bacterial lipases and gives a positive tributyrin plate assay. In this study, LipA was purified from the culture supernatant of an overexpressing clone of X. oryzae pv. oryzae and two types of crystals belonging to space group C2 but with two different unit-cell parameters were obtained using the hanging-drop vapour-diffusion method. Type I crystals diffract to a maximum resolution of 1.89 Å and have unit-cell parameters a = 93.1, b = 62.3, c = 66.1 Å, β = 90.8°. Type II crystals have unit-cell parameters a = 103.6, b = 54.6, c = 66.3 Å, β = 92.6° and diffract to 1.86 Å. Solvent-content analysis shows one monomer in the asymmetric unit in both the crystal forms.

  5. Identification and molecular characterization of twin-arginine translocation system (Tat) in Xanthomonas oryzae pv. oryzae strain PXO99.

    Science.gov (United States)

    Chen, Lei; Hu, Baishi; Qian, Guoliang; Wang, Chen; Yang, Wanfeng; Han, Zhicheng; Liu, Fengquan

    2009-02-01

    Xanthomonas oryzae pv. oryzae causes bacterial leaf blight, one of the most widespread and destructive bacterial diseases in rice. This study identified and characterized the contribution of the twin-arginine translocation (Tat) pathway to motility, chemotaxis, extracellular polysaccharide (EPS) production and virulence in X. oryzae pv. oryzae strain PXO99. The tatC disruption mutant (strain TCM) of strain PXO99 were generated, and confirmed both by PCR and Southern blotting. Strain PXO99 cells were highly motile in NYGB 0.3% soft agar plate. In contrast, the tatC mutation impaired motility. Furthermore, strain TCM cells lacked detectable flagella and exhibited almost no chemotaxis toward glucose under aerobic conditions, indicating that the Tat secretion pathway contributed to flagellar biogenesis and chemotactic responses. It was also observed that strain TCM exhibited a reductive production of extracellular polysaccharide (EPS) and a significant reduction of virulence on rice plants when compared with the wild type PXO99. However, the tatC mutation in strain PXO99 did not affect growth rate and the ability to induce hypersensitive response (HR) in nonhost tobacco (Nicotiana tabacum L. cv. Samsun). Our findings indicated that the Tat system of X. oryzae pv. oryzae played an important role in the pathogen's virulence.

  6. Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Ryan M. Ames

    2017-01-01

    Full Text Available Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world’s population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified. In this study, I have used network-extracted ontologies (NeXOs, hierarchical structures inferred from RNA-Seq data, to identify pathways involved in appressorium development, which in turn highlights novel genes with potential roles in this process. This study illustrates the use of NeXOs for pathway identification from large-scale genomics data and also identifies novel genes with potential roles in disease. The methods presented here will be useful to study disease processes in other pathogenic species and these data represent predictions of novel targets for intervention in M. oryzae.

  7. Roles of Forkhead-box Transcription Factors in Controlling Development, Pathogenicity, and Stress Response in Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Jaejin Park

    2014-06-01

    Full Text Available Although multiple transcription factors (TFs have been characterized via mutagenesis to understand their roles in controlling pathogenicity and infection-related development in Magnaporthe oryzae, the causal agent of rice blast, if and how forkhead-box (FOX TFs contribute to these processes remain to be characterized. Four putative FOX TF genes were identified in the genome of M. oryzae, and phylogenetic analysis suggested that two of them (MoFKH1 and MoHCM1 correspond to Ascomycota-specific members of the FOX TF family while the others (MoFOX1 and MoFOX2 are Pezizomycotina-specific members. Deletion of MoFKH1 (ΔMofkh1 resulted in reduced mycelial growth and conidial germination, abnormal septation and stress response, and reduced virulence. Similarly, ΔMohcm1 exhibited reduced mycelial growth and conidial germination. Conidia of ΔMofkh1 and ΔMohcm1 were more sensitive to one or both of the cell cycle inhibitors hydroxyurea and benomyl, suggesting their role in cell cycle control. On the other hand, loss of MoFOX1 (ΔMofox1 did not show any noticeable changes in development, pathogenicity, and stress response. Deletion of MoFOX2 was not successful even after repeated attempts. Taken together, these results suggested that MoFKH1 and Mo-HCM1 are important in fungal development and that MoFKH1 is further implicated in pathogenicity and stress response in M. oryzae.

  8. NCBI nr-aa BLAST: CBRC-GGAL-03-0025 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-GGAL-03-0025 ref|YP_450021.1| aminotransferase [Xanthomonas oryzae pv. oryzae ...MAFF 311018] ref|YP_199733.6| aspartate aminotransferase [Xanthomonas oryzae pv. oryzae KACC10331] dbj|BAE67...747.1| aminotransferase [Xanthomonas oryzae pv. oryzae MAFF 311018] YP_450021.1 5.5 30% ...

  9. AAS Oral History Project

    Science.gov (United States)

    Buxner, Sanlyn; Holbrook, Jarita; AAS Oral History Team

    2016-06-01

    Now in its fourth year, the AAS Oral History Project has interviewed over 80 astronomers from all over the world. Led by the AAS Historical Astronomy Division (HAD) and partially funded by the American Institute of Physics Niels Bohr Library and ongoing support from the AAS, volunteers have collected oral histories from astronomers at professional meetings starting in 2015, including AAS, DPS, and the IAU general assembly. Each interview lasts one and a half to two hours and focuses on interviewees’ personal and professional lives. Questions include those about one’s family, childhood, strong influences on one’s scientific career, career path, successes and challenges, perspectives on how astronomy is changing as a field, and advice to the next generation. Each interview is audio recorded and transcribed, the content of which is checked with each interviewee. Once complete, interview transcripts are posted online as part of a larger oral history library at https://www.aip.org/history-programs/niels-bohr-library/oral-histories. Future analysis will reveal a rich story of astronomers and will help the community address issues of diversity, controversies, and the changing landscape of science. We are still recruiting individuals to be interviewed from all stages of career from undergraduate students to retired and emeritus astronomers. Contact Jarita Holbrook to schedule an interview or to find out more information about the project (astroholbrook@gmail.com). Also, contact Jarita Holbrook if you would like to become an interviewer for the project.

  10. Purification and characterization of a novel hypersensitive response-inducing elicitor from Magnaporthe oryzae that triggers defense response in rice.

    Directory of Open Access Journals (Sweden)

    Mingjia Chen

    Full Text Available BACKGROUND: Magnaporthe oryzae, the rice blast fungus, might secrete certain proteins related to plant-fungal pathogen interactions. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we report the purification, characterization, and gene cloning of a novel hypersensitive response-inducing protein elicitor (MoHrip1 secreted by M. oryzae. The protein fraction was purified and identified by de novo sequencing, and the sequence matched the genomic sequence of a putative protein from M. oryzae strain 70-15 (GenBank accession No. XP_366602.1. The elicitor-encoding gene mohrip1 was isolated; it consisted of a 429 bp cDNA, which encodes a polypeptide of 142 amino acids with a molecular weight of 14.322 kDa and a pI of 4.53. The deduced protein, MoHrip1, was expressed in E. coli. And the expression protein collected from bacterium also forms necrotic lesions in tobacco. MoHrip1 could induce the early events of the defense response, including hydrogen peroxide production, callose deposition, and alkalization of the extracellular medium, in tobacco. Moreover, MoHrip1-treated rice seedlings possessed significantly enhanced systemic resistance to M. oryzae compared to the control seedlings. The real-time PCR results indicated that the expression of some pathogenesis-related genes and genes involved in signal transduction could also be induced by MoHrip1. CONCLUSION/SIGNIFICANCE: The results demonstrate that MoHrip1 triggers defense responses in rice and could be used for controlling rice blast disease.

  11. Integrated analysis of the global transcriptional response to α-amylase over-production by Aspergillus oryzae.

    Science.gov (United States)

    Vongsangnak, Wanwipa; Hansen, Kim; Nielsen, Jens

    2011-05-01

    The filamentous fungus Aspergillus oryzae is an important microbial cell factory for industrial production of many enzymes, such as α-amylase. In order to optimize the industrial enzyme production process, there is a need to understand fundamental processes underlying enzyme production, here under how enzyme production links to metabolism through global regulation. Through a genome-scale metabolic network for integrated analysis of transcriptome data and flux calculation, we identified key players (genes, enzymes, proteins, and metabolites) involved in the processes of enzyme synthesis and secretion, nucleotide metabolism, and amino acid metabolism that can be the potential targets for improving industrial enzyme production.

  12. Polygalacturonase from Sitophilus oryzae: Possible horizontal transfer of a pectinase gene from fungi to weevils

    Directory of Open Access Journals (Sweden)

    Zhicheng Shen

    2003-08-01

    Full Text Available Endo-polygalacturonase, one of the group of enzymes known collectively as pectinases, is widely distributed in bacteria, plants and fungi. The enzyme has also been found in several weevil species and a few other insects, such as aphids, but not in Drosophila melanogaster, Anopheles gambiae, or Caenorhabditis elegans or, as far as is known, in any more primitive animal species. What, then, is the genetic origin of the polygalacturonases in weevils? Since some weevil species harbor symbiotic microorganisms, it has been suggested, reasonably, that the symbionts' genomes of both aphids and weevils, rather than the insects' genomes, could encode polygalacturonase. We report here the cloning of a cDNA that encodes endo-polygalacturonase in the rice weevil, Sitophilus oryzae (L., and investigations based on the cloned cDNA. Our results, which include analysis of genes in antibiotic-treated rice weevils, indicate that the enzyme is, in fact, encoded by the insect genome. Given the apparent absence of the gene in much of the rest of the animal kingdom, it is therefore likely that the rice weevil polygalacturonase gene was incorporated into the weevil's genome by horizontal transfer, possibly from a fungus.

  13. Drought-tolerant rice germplasm developed from an Oryza officinalis transformation-competent artificial chromosome clone.

    Science.gov (United States)

    Liu, R; Zhang, H H; Chen, Z X; Shahid, M Q; Fu, X L; Liu, X D

    2015-10-29

    Oryza officinalis has proven to be a natural gene reservoir for the improvement of domesticated rice as it carries many desirable traits; however, the transfer of elite genes to cultivated rice by conventional hybridization has been a challenge for rice breeders. In this study, the conserved sequence of plant stress-related NAC transcription factors was selected as a probe to screen the O. officinalis genomic transformation-competent artificial chromosome library by Southern blot; 11 positive transformation-competent artificial chromosome clones were subsequently detected. By Agrobacterium-mediated transformation, an indica rice variety, Huajingxian 74 (HJX74), was transformed with a TAC clone harboring a NAC gene-positive genomic fragment from O. officinalis. Molecular analysis revealed that the O. officinalis genomic fragment was integrated into the genome of HJX74. The transgenic lines exhibited high tolerance to drought stress. Our results demonstrate that the introduction of stress-related transformation-competent artificial chromosome clones, coupled with a transgenic validation approach, is an effective method of transferring agronomically important genes from O. officinalis to cultivated rice.

  14. First report of wheat blast caused by magnaporthe oryzae pathotype triticum in Bangladesh

    Science.gov (United States)

    Wheat blast or ‘brusone’, caused by the ascomycetous fungus Magnaporthe oryzae B.C. Couch (synonym Pyricularia oryzae Cavara), was first identified in 1985 in Brazil. M. oryzae is composed of a range of morphologically identical but genetically different host-specific pathotypes that are specialized...

  15. Morphological and molecular characterization of fungal pathogen, Magnaphorthe oryzae

    Energy Technology Data Exchange (ETDEWEB)

    Hasan, Nor’Aishah, E-mail: aishahnh@ns.uitm.edu.my [Faculty of Applied Science, UniversitiTeknologi MARA (UiTM), Kuala Pilah, Negeri Sembilan (Malaysia); Rafii, Mohd Y., E-mail: mrafii@upm.edu.my [Institute of Tropical Agriculture, Universiti Putra Malaysia (UPM), Serdang, Selangor (Malaysia); Department of Crop Science, Universiti Putra Malaysia (UPM), Serdang, Selangor (Malaysia); Rahim, Harun A. [Agrotechnology & Bioscience Division, Malaysian Nuclear Agency, Bangi, Kajang, Selangor (Malaysia); Ali, Nusaibah Syd [Department of Plant Protection, Universiti Putra Malaysia (UPM), Serdang, Selangor (Malaysia); Mazlan, Norida [Department of Agriculture Technology, Universiti Putra Malaysia (UPM), Serdang, Selangor (Malaysia); Abdullah, Shamsiah [Faculty of Plantation and Agrotechnology, UniversitiTeknologi MARA (UiTM), Shah Alam, Selangor (Malaysia)

    2016-02-01

    Rice is arguably the most crucial food crops supplying quarter of calories intake. Fungal pathogen, Magnaphorthe oryzae promotes blast disease unconditionally to gramineous host including rice species. This disease spurred an outbreaks and constant threat to cereal production. Global rice yield declining almost 10-30% including Malaysia. As Magnaphorthe oryzae and its host is model in disease plant study, the rice blast pathosystem has been the subject of intense interest to overcome the importance of the disease to world agriculture. Therefore, in this study, our prime objective was to isolate samples of Magnaphorthe oryzae from diseased leaf obtained from MARDI Seberang Perai, Penang, Malaysia. Molecular identification was performed by sequences analysis from internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes. Phylogenetic affiliation of the isolated samples were analyzed by comparing the ITS sequences with those deposited in the GenBank database. The sequence of the isolate demonstrated at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaphorthe oryzae. Morphological observed under microscope demonstrated that the structure of conidia followed similar characteristic as M. oryzae. Finding in this study provide useful information for breeding programs, epidemiology studies and improved disease management.

  16. A reductive aminase from Aspergillus oryzae

    Science.gov (United States)

    Aleku, Godwin A.; France, Scott P.; Man, Henry; Mangas-Sanchez, Juan; Montgomery, Sarah L.; Sharma, Mahima; Leipold, Friedemann; Hussain, Shahed; Grogan, Gideon; Turner, Nicholas J.

    2017-10-01

    Reductive amination is one of the most important methods for the synthesis of chiral amines. Here we report the discovery of an NADP(H)-dependent reductive aminase from Aspergillus oryzae (AspRedAm, Uniprot code Q2TW47) that can catalyse the reductive coupling of a broad set of carbonyl compounds with a variety of primary and secondary amines with up to >98% conversion and with up to >98% enantiomeric excess. In cases where both carbonyl and amine show high reactivity, it is possible to employ a 1:1 ratio of the substrates, forming amine products with up to 94% conversion. Steady-state kinetic studies establish that the enzyme is capable of catalysing imine formation as well as reduction. Crystal structures of AspRedAm in complex with NADP(H) and also with both NADP(H) and the pharmaceutical ingredient (R)-rasagiline are reported. We also demonstrate preparative scale reductive aminations with wild-type and Q240A variant biocatalysts displaying total turnover numbers of up to 32,000 and space time yields up to 3.73 g l‑1 d‑1.

  17. A new diketopiperazine alkaloid from Aspergillus oryzae.

    Science.gov (United States)

    Shaaban, Mohamed; El-Metwally, Mohammad Magdy; Nasr, Hamdi

    2014-01-01

    Investigation of bioactive secondary metabolites from terrestrial Aspergillus oryzae sp. MMAO1 using M2 medium afforded a new diketopiperazine alkaloid, 7,9-dihydroxy-3-(1H-indol-3-ylmethyl)-8-methoxy-2,3,11,11a-tetrahydro-6H-pyrazino[1,2-b]isoquinoline-1,4-dione (1a), containing the unusual amino acid L-6,8-dihydroxy-7-methoxyphenylalanine. This was co-isolated with ditryptophenaline (2), cyclo-(Tryp,Tyr) (4), cyclo-(Pro,Val), α-cyclopiazonic acid (3), kojic acid and uridine. Re-cultivation of the fungal strain on Dox medium led to the production of bisdethio(bismethylthio)gliotoxin (5), pseurotin A (6) along with linoleic acid, α-cyclopiazonic acid (3) and kojic acid. The chemical structure of the new diketopiperazine alkaloid including the relative configuration was determined by 1D and 2D NMR spectroscopy and HR-ESI-MS spectrometry, and by comparison with the related literature. The new alkaloid (1a) showed no antimicrobial activity or cytotoxicity against brine shrimps.

  18. Cloning and expression of a IuxRhomologue from Xanthomonas oryzae pv.Oryzae

    Institute of Scientific and Technical Information of China (English)

    Liang Bin; Guo Bin; Yang Chen; Zhang Xinjun; Dai Luyuan; Yu Tengqiong; Shen Daleng

    2006-01-01

    LuxR homologues are the main components of LuxR/LuxI circuit in Quorum Sensing(QS)of Gram-negative bacteria.A luxR homologue,designated as xooR,was cloned from Ⅹ.oryzae pv.oryzae.The xooR gene is atranscription factor with 765 bp inlength,and encodes a 254-amino acid putative protein with a molecular weight and an isoelectric point of 28.3 ku and 8.72 respectively.Amino acids 15 to 171 from the N-terminus are the Autoin-bind domain of XooR whereas amino acids 191 to 245 form a helix-turn-helix(HTH)motif that serves as the DNA-binding domain.In this study,XooR was expressed as a fusion protein along with green fluorescent protein(GFP),using pET-24a-d(+),a prokaryotic expression vector.Western blot showed that the xooR gene was successfully expressed in vitro in E.coli as a XooR-GFP fusion protein with a size of 54 ku.

  19. Deciphering the Role of Tyrosine Sulfation in Xanthomonas oryzae pv. oryzae Using Shotgun Proteomic Analysis

    Directory of Open Access Journals (Sweden)

    Hye-Jee Park

    2016-06-01

    Full Text Available A bacterial tyrosine sulfotransferase, RaxST, is required for activation of rice XA21-mediated immunity, and it catalyzes sulfation of tyrosine residues of Omp1X and RaxX in Xanthomonas oryzae pv. oryzae, a causal agent of bacterial blight in rice. Although RaxST is biochemically well-characterized, biological functions of tyrosine sulfation have not been fully elucidated. We compared protein expression patterns between the wildtype and a raxST knockout mutant using shotgun proteomic analysis. Forty nine proteins displayed a more than 1.5-fold difference in their expression between the wildtype and the mutant strains. Clusters of orthologous groups analysis revealed that proteins involved in cell motility were most abundant, and phenotypic observation also showed that the twitching motility of the mutant was dramatically changed. These results indicate that tyrosine sulfation by RaxST is essential for Xoo movement, and they provide new insights into the biological roles of RaxST in cellular processes.

  20. Cloning and characterization of a new actin gene from Oryza sativa L.

    Institute of Scientific and Technical Information of China (English)

    LIANG Weihong; TANG Chaorong; WU Naihu

    2004-01-01

    Using Rho family member osRACD as bait, a new member of actin gene family -Act was isolated from Oryza sativa by yeast two-hybrid system. The full-length cDNA was cloned with 5' RACE technology, which contains an open reading frame of 1134 bp with a predicted protein of 377 amino acids. Sequence alignment revealed 96% to 81.8% identities with some known actin proteins in plants. The method of bioinformatics was used to analyze the protein modification sites, structure and evolution of the gene. Southern blot analysis showed that Act is a single-copy gene in the genome. The result of RT-PCR showed it is ubiquitously expressed in root, shoot, callus and panicle in a temporal fashion. The relationship between Rho family and actin family in evolution and function was also studied.

  1. Molecular Cloning and Characterization of Citrate Synthase Gene in Rice( Oryza sativa)

    Institute of Scientific and Technical Information of China (English)

    ZHANG Shan-shan; MING Feng; LU Qun; GUO Bin; SHEN Da-leng

    2005-01-01

    The full-length OsCS encoding citrate synthase was isolated from rice (Oryza sativa L. subsp. japonica). OsCS is 1477-bp long and encodes a 474 amino acid polypeptide. Its putative protein sequence is highly identical to Daucus carota, Nicotiana tabacum,Beta vulgaris subsp., Arabidopsis thaliana, and Citrus junos (>70%). The deduced amino-terminal sequence of OsCS showes characteristics of mitochondrial targeting signal. Southern blot analysis using ORF of the OsCS as the probe indicated that this gene exists in multiple copies in rice genome. The band with predicated size of 82 kD was detected by Western blot after being induced by 0.4 mmol/L IPTG.

  2. AvrXa3:A novel member of avrBs3 gene family from Xanthomonas oryzae pv.oryzae has a dual function

    Institute of Scientific and Technical Information of China (English)

    LI Ping; LONG Juying; HUANG Yingchun; ZHANG Yan; WANG Jinsheng

    2004-01-01

    Two positive clones pUAV45 and pUAV47 were identified from the cDNA library of JxoⅢ, a race 3 strain of Xanthomonas oryzae pv. Oryzae Dye (Xoo) in Japanese system, using Tn5 based technology. pUAV45 clone contained a 25.4 kb Xoo genomic DNA insert. Southern blot analysis with avrXa10 as the probe showed that DNA insert in pUAV45 shares homology with avrX10. Furthermore within the Xoo insert, a smaller 5.7 kb KpnI fragment (pUAVSk) was identified through hybridization with avrXa10. The transformation of pUAV45 and pUAV5k into the strain Pxo99 (race 6 in Philippine system) led to the decrease of Pxo99pathogenicity on rice cultivar Wase Aikoku 3 (Xa3) and the increase of the pathogen pathogenicity on Cas209 (Xa10). The result of sequence analysis showed that there is a 2598 bp open reading frame (ORF) within the 5.7 kb Kpn 1 fragment (pUAVSk). The ORF shared high identity (97 % ) with avrXa10. The deduced sequence of the ORF contained 8.5 tandem repeat units of 34-amino-acids, one leucine zipper (LZ), three nuclear localization signal (NLS) motifs, and an acidic activation transcriptional domain (AAD) at C-terminus.We named this ORF avrXa3 and it is classified as a new member of avrBs3 (avr/pth) family with the dual-function determined by alternations of avirulence and aggressiveness on rice cultivars carrying different ‘ R' genes.

  3. The Antiproton Accumulator (AA)

    CERN Multimedia

    1980-01-01

    Section 06 - 08*) of the AA where the dispersion (and hence the horizontal beam size) is large. One can distinguish (left to right): A vacuum-tank, two bending magnets (BST06 and BST07 in blue) with a quadrupole (QDN07, in red) in between, another vacuum-tank, a wide quadrupole (QFW08) and a further tank . The tanks are covered with heating tape for bake-out. The tank left of BST06 contained the stack core pickup for stochastic cooling (see 7906193, 7906190, 8005051), the two other tanks served mainly as vacuum chambers in the region where the beam was large. Peter Zettwoch works on BST06. *) see: H. Koziol, Antiproton Accumulator Parameter List, PS/AA/Note 84-2 (1984)

  4. Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon

    Directory of Open Access Journals (Sweden)

    N Sarla

    2005-06-01

    Full Text Available Abstract Background Cultivated rice (Oryza sativa L. is endowed with a rich genetic variability. In spite of such a great diversity, the modern rice cultivars have narrow genetic base for most of the agronomically important traits. To sustain the demand of an ever increasing population, new avenues have to be explored to increase the yield of rice. Wild progenitor species present potential donor sources for complex traits such as yield and would help to realize the dream of sustained food security. Results Advanced backcross method was used to introgress and map new quantitative trait loci (QTLs relating to yield and its components from an Indian accession of Oryza rufipogon. An interspecific BC2 testcross progeny (IR58025A/O. rufipogon//IR580325B///IR58025B////KMR3 was evaluated for 13 agronomic traits pertaining to yield and its components. Transgressive segregants were obtained for all the traits. Thirty nine QTLs were identified using interval mapping and composite interval mapping. In spite of it's inferiority for most of the traits studied, O. rufipogon alleles contributed positively to 74% of the QTLs. Thirty QTLs had corresponding occurrences with the QTLs reported earlier, indicating that these QTLs are stable across genetic backgrounds. Nine QTLs are novel and reported for the first time. Conclusion The study confirms that the progenitor species constitute a prominent source of still unfolded variability for traits of complex inheritance like yield. With the availability of the complete genome sequence of rice and the developments in the field of genomics, it is now possible to identify the genes underlying the QTLs. The identification of the genes constituting QTLs would help us to understand the molecular mechanisms behind the action of QTLs.

  5. The Antiproton Accumulator (AA)

    CERN Multimedia

    1980-01-01

    A section of the AA where the dispersion (and hence the horizontal beam size) is large. One can distinguish (left to right): A large vacuum-tank, a quadrupole (QDN09*), a bending magnet (BST08), another vacuum-tank, a wide quadrupole (QFW08) and (in the background) a further bending magnet (BST08). The tanks are covered with heating tape for bake-out. The tank left of QDN09 contained the kickers for stochastic pre-cooling (see 790621, 8002234, 8002637X), the other one served mainly as vacuum chamber in the region where the beam was large. Peter Zettwoch works on QFW08. * see: H. Koziol, Antiproton Accumulator Parameter List, PS/AA/Note 84-2 (1984) See under 7911303, 7911597X, 8004261 and 8202324. For photos of the AA in different phases of completion (between 1979 and 1982) see: 7911303, 7911597X, 8004261, 8004608X, 8005563X, 8005565X, 8006716X, 8006722X, 8010939X, 8010941X, 8202324, 8202658X, 8203628X .

  6. Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of Fungi.

    Science.gov (United States)

    Okagaki, Laura H; Nunes, Cristiano C; Sailsbery, Joshua; Clay, Brent; Brown, Doug; John, Titus; Oh, Yeonyee; Young, Nelson; Fitzgerald, Michael; Haas, Brian J; Zeng, Qiandong; Young, Sarah; Adiconis, Xian; Fan, Lin; Levin, Joshua Z; Mitchell, Thomas K; Okubara, Patricia A; Farman, Mark L; Kohn, Linda M; Birren, Bruce; Ma, Li-Jun; Dean, Ralph A

    2015-09-28

    Magnaporthaceae is a family of ascomycetes that includes three fungi of great economic importance: Magnaporthe oryzae, Gaeumannomyces graminis var. tritici, and Magnaporthe poae. These three fungi cause widespread disease and loss in cereal and grass crops, including rice blast disease (M. oryzae), take-all disease in wheat and other grasses (G. graminis), and summer patch disease in turf grasses (M. poae). Here, we present the finished genome sequence for M. oryzae and draft sequences for M. poae and G. graminis var. tritici. We used multiple technologies to sequence and annotate the genomes of M. oryzae, M. poae, and G. graminis var. tritici. The M. oryzae genome is now finished to seven chromosomes whereas M. poae and G. graminis var. tritici are sequenced to 40.0× and 25.0× coverage respectively. Gene models were developed by the use of multiple computational techniques and further supported by RNAseq data. In addition, we performed preliminary analysis of genome architecture and repetitive element DNA.

  7. Bipolaris oryzae, a novel fungal opportunist causing keratitis.

    Science.gov (United States)

    Wang, Luxia; Al-Hatmi, Abdullah M S; Lai, Xuwen; Peng, Lianghong; Yang, Chuanhong; Lai, Huangwen; Li, Jianxun; Meis, Jacques F; de Hoog, G Sybren; Zhuo, Chao; Chen, Min

    2016-05-01

    We report a case of mycotic keratitis caused by Bipolaris oryzae with predisposing trauma from a foreign body. The fungus was identified by sequencing the internal transcribed spacer region, translation elongation factor 1α (TEF1) gene, and partial glyceraldehyde-3-phosphate dehydrogenase (GPDH) gene, and the species identity was confirmed on the basis of its characteristic conidial phenotype. The patient was treated with surgical intervention and antifungal agents, including intravenous fluconazole (FLC), oral itraconazole, topical 0.15% amphotericin B eye drops, and 0.5% FLC eye drops. To our knowledge, this is the first report of mycotic keratitis caused by B. oryzae worldwide.

  8. Genetic analysis and gene mapping of a rice few-tillering mutant in early backcross populations (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    TANG; Jiabin; (

    2001-01-01

    [1]Xu, Y. B., Shen, Z. T., Diallel analysis of tiller number at different growth stages in rice (Oryza sativa L.), Theoretical and Applied Genetics, 1991, 83(2): 243-249.[2]Wu, W. R., Li, W. M., Tang, D. Z. et al., Time-related mapping of quantitative trait loci underlying tiller number in rice, Genetics, 1999, (151): 297-303.[3]Wu, P., Zhang, G ., Huang, N., Identification of QTLs controlling quantitative characters in rice using RFLP markers, Euphytica, 1996, 89(3): 349-354.[4]Khush, G . S., Breaking the yield frontier of rice, GeoJournal, 1995, 35(3): 329-332.[5]Chen, X., Themnykh, S., Xu, Y. et al., Development of microsatellite framework providing genome-wide coverage in rice (Oryzae sativa L.), Theoretical and Applied Genetics, 1997, 95(4): 553-567.[6]Panaud, O., Chen, X., McCouch, S. R. et al., Development of microsatellite markers and characterization of simple sequence length polymorphisms (SSLPs) in rice (Oryzae sativa L.), Molecular and General Genetics, 1996, (252): 597-607.[7]McCouth, S. R., Kochert, G., Yu, Z. H. et al., Molecular mapping of rice chromosomes, Theoretical and Applied Genetics, 1988, 76: 815-829.[8]Harushima, Y., Yano, M., Shomura, A. et al., A high-density rice genetic linkage map with 2275 markers using a single F2 population, Genetics, 1998, 148: 479-494.[9]Lander, E. S. et al., Mapmaker: An interactive computer for construction primary genetics linkage maps of experimental and natural populations, Genomics, 1987, (1): 174-182.[10]Kinoshita, T., Report of committee on gene symbolization, nomenclature and linkage groups, Rice Genetic Newsletter, 1995, (12): 9-153.

  9. Observations on Interspecific Hybridization Barriers Between Oryza sativa and O.brachyantha%亚洲栽培稻与短花药野生稻种间杂交障碍观察

    Institute of Scientific and Technical Information of China (English)

    傅雪琳; 刘向东; 卢永根

    2013-01-01

    亚洲栽培稻Oryza sativa与短花药野生稻O.brachyantha分别属于稻属的AA和FF染色体组,其种间杂交障碍影响了短花药野生稻有利基因向栽培稻的转移利用.本研究利用激光扫描共聚焦显微术对栽培稻与短花药野生稻杂交后杂种胚胎和胚乳发育以及杂种胚囊发育过程进行了观察.结果表明,杂交小穗双受精率高达82.93%,但是杂种胚胎发育到球形胚期停滞并开始解体,游离胚乳核未能正常细胞化而出现解体,导致杂种胚胎在发育中途夭亡,不能形成正常成熟的杂种种子.杂种胚囊发育过程中,大孢子母细胞可进行减数分裂,但形成四分体异常,导致功能大孢子异常,胚囊发育到单核或二核即出现退化现象,最终无法形成正常成熟的胚囊,表现高度的雌性不育.%Oryza sativa and O.brachyantha belong to AA and FF genomes in genus Oryza,respectively.The interspecific hybridization barrier limits the transfer of elite genes from O.brachyantha into O.sativa.By using technique of whole-mount eosin B-staining confocal laser scanning microscopy,the development of hybrid embryo and endosperm after crossing between O.sativa and O.brachyantha and embryo sac abortion process of interspecific hybrid F1 were observed.The results showed that there was a high double-fertilization ratio of 82.93% appearing in the pollinated spikelets,but hybrid embryo ceased to develop and began to degenerate at the globular-shaped stage,meanwhile,free endosperm nuclei degenerated before forming cellular endosperm.It induced hybrid embryo abortion and the matured hybrid seed failed be produced.During the process of hybrid embryo sac development,hybrid megasporocyte finished meioses,but abnormal tetrad was formed which induced abnormal functional megaspores.Embryo sac was degenerated at the stage of mono-nucleate and two-nucleate embryo sac,therefore,no normal embryo sac was formed and hybrid was highly sterile.

  10. The biosynthesis, structure and gelatinization properties of starches from wild and cultivated African rice species (Oryza barthii and Oryza glaberrima).

    Science.gov (United States)

    Wang, Kai; Wambugu, Peterson W; Zhang, Bin; Wu, Alex Chi; Henry, Robert J; Gilbert, Robert G

    2015-09-20

    The molecular structure and gelatinization properties of starches from domesticated African rice (Oryza glaberrima) and its wild progenitor (Oryza barthii) are determined and comparison made with Asian domesticated rice (Oryza sativa), the commonest commercial rice. This suggests possible enzymatic processes contributing to the unique traits of the African varieties. These have similar starch structures, including smaller amylose molecules, but larger amounts of amylose chains across the whole amylose chain-length distribution, and higher amylose contents, than O. sativa. They also show a higher proportion of two- and three-lamellae spanning amylopectin branch chains (degree of polymerization 34-100) than O. sativa, which contributes to their higher gelatinization temperatures. Fitting amylopectin chain-length distribution with a biosynthesis-based mathematical model suggests that the reason for this difference might be because O. glaberrima and O. barthii have more active SSIIIa and/or less active SBEIIb enzymes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. NCBI nr-aa BLAST: CBRC-DDIS-03-0106 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DDIS-03-0106 ref|YP_450521.1| hypothetical protein XOO_1492 [Xanthomonas oryza...e pv. oryzae MAFF 311018] ref|YP_200246.6| hypothetical protein XOO1607 [Xanthomonas oryzae pv. oryzae KACC1...0331] dbj|BAE68247.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae MAFF 311018] YP_450521.1 7e-31 28% ...

  12. Pathotype and genetic diversity amongst Indian isolates of Xanthomonas oryzae pv. oryzae.

    Directory of Open Access Journals (Sweden)

    Deo Mishra

    Full Text Available A number of rice resistance genes, called Xa genes, have been identified that confer resistance against various strains of Xanthomonas oryzae pv. oryzae (Xoo, the causal agent of bacterial blight. An understanding of pathotype diversity within the target pathogen population is required for identifying the Xa genes that are to be deployed for development of resistant rice cultivars. Among 1024 isolates of Xoo collected from 20 different states of India, 11 major pathotypes were distinguished based on their reaction towards ten Xa genes (Xa1, Xa3, Xa4, xa5, Xa7, xa8, Xa10, Xa11, xa13, Xa21. Isolates belonging to pathotype III showing incompatible interaction towards xa8, xa13 and Xa21 and compatible interaction towards the rest of Xa genes formed the most frequent (41% and widely distributed pathotype. The vast majority of the assayed Xoo isolates were incompatible with one or more Xa genes. Exceptionally, the isolates of pathotype XI were virulent on all Xa genes, but have restricted distribution. Considering the individual R-genes, Xa21 appeared as the most broadly effective, conferring resistance against 88 % of the isolates, followed in decreasing order by xa13 (84 %, xa8 (64 %, xa5 (30 %, Xa7 (17 % and Xa4 (14 %. Fifty isolates representing all the eleven pathotypes were analyzed by southern hybridization to determine their genetic relatedness using the IS1112 repeat element of Xoo. Isolates belonging to pathotype XI were the most divergent. The results suggest that one RFLP haplotype that is widely distributed all over India and is represented in strains from five different pathotypes might be an ancestral haplotype. A rice line with xa5, xa13 and Xa21 resistance genes is resistant to all strains, including those belonging to pathotype XI. This three gene combination appears to be the most suitable Xa gene combination to be deployed in Indian rice cultivars.

  13. Identification of genes required for nonhost resistance to Xanthomonas oryzae pv. oryzae reveals novel signaling components.

    Directory of Open Access Journals (Sweden)

    Wen Li

    Full Text Available BACKGROUND: Nonhost resistance is a generalized, durable, broad-spectrum resistance exhibited by plant species to a wide variety of microbial pathogens. Although nonhost resistance is an attractive breeding strategy, the molecular basis of this form of resistance remains unclear for many plant-microbe pathosystems, including interactions with the bacterial pathogen of rice, Xanthomonas oryzae pv. oryzae (Xoo. METHODS AND FINDINGS: Virus-induced gene silencing (VIGS and an assay to detect the hypersensitive response (HR were used to screen for genes required for nonhost resistance to Xoo in N. benthamiana. When infiltrated with Xoo strain YN-1, N. benthamiana plants exhibited a strong necrosis within 24 h and produced a large amount of H(2O(2 in the infiltrated area. Expression of HR- and defense-related genes was induced, whereas bacterial numbers dramatically decreased during necrosis. VIGS of 45 ACE (Avr/Cf-elicited genes revealed identified seven genes required for nonhost resistance to Xoo in N. benthamiana. The seven genes encoded a calreticulin protein (ACE35, an ERF transcriptional factor (ACE43, a novel Solanaceous protein (ACE80, a hydrolase (ACE117, a peroxidase (ACE175 and two proteins with unknown function (ACE95 and ACE112. The results indicate that oxidative burst and calcium-dependent signaling pathways play an important role in nonhost resistance to Xoo. VIGS analysis further revealed that ACE35, ACE80, ACE95 and ACE175, but not the other three ACE genes, interfered with the Cf-4/Avr4-dependent HR. CONCLUSIONS/SIGNIFICANCE: N. benthamiana plants inoculated with Xoo respond by rapidly eliciting an HR and nonhost resistance. The oxidative burst and other signaling pathways are pivotal in Xoo-N. benthamiana nonhost resistance, and genes involved in this response partially overlap with those involved in Cf/Avr4-dependent HR. The seven genes required for N. benthamiana-mediated resistance to Xoo provide a basis for further dissecting

  14. Construction of a fusion gene comprising the Taka-amylase A promoter and the Escherichia coli beta-glucuronidase gene and analysis of its expression in Aspergillus oryzae.

    Science.gov (United States)

    Tada, S; Gomi, K; Kitamoto, K; Takahashi, K; Tamura, G; Hara, S

    1991-10-01

    Northern blot analysis of glucose-grown and starch-grown mycelia of Aspergillus oryzae RIB40 was conducted using the cloned Taka-amylase A (TAA) gene as a probe. The amount of mRNA homologous to the TAA gene was increased when this fungus was grown with starch as a sole carbon source. In order to analyze the induction mechanism, we inserted the Escherichia coli uidA gene encoding beta-glucuronidase (GUS) down-stream of the TAA promoter and introduced the resultant fusion gene into the A. oryzae genome. Production of a functional GUS protein was induced by starch, but not by glucose. When the effects of various sugars on expression of the fusion gene were examined, the results suggested that the expression of the fusion gene was under control of the TAA gene promoter.

  15. Kinetics of alpha-amylase secretion in Aspergillus oryzae

    DEFF Research Database (Denmark)

    Henriksen, Anne Laurence Santerre; Carlsen, Morten; Bang de, H.

    1999-01-01

    Pulse and pulse-chase experiments have been performed to study L-[S-35] methionine incorporation and protein secretion kinetics in Aspergillus oryzae. Pulse experiments confirmed the mechanism of methionine uptake reported previously for Penicillium chrysogenum (Benko et al., 1967). Pulse...

  16. Bipolaris oryzae, a novel fungal opportunist causing keratitis

    NARCIS (Netherlands)

    Al-Hatmi, Abdullah

    2015-01-01

    We report a case of mycotic keratitis caused by Bipolaris oryzae with predisposing trauma from a foreign body. The fungus was identified by sequencing the internal transcribed spacer (ITS) region, translation elongation factor 1α (TEF1) gene and partial glyceraldehyde-3-phosphate dehydrogenase (GPDH

  17. Study on the structures of papilla of lemma in Oryza

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Structures of papilla of lemma among 23 Oryza species were investigated and classified into 6 kinds by scanning electron microscopy. The lemma surface was composed of papilla pedestals with multi-row longitudinal ordered arrangements and the papilla was inserted into pedestal. The morphology and characterization of papilla varied among species.

  18. CBS domain-containing proteins are Rhizopus oryzae ferrioxamine receptors

    Science.gov (United States)

    Background: Iron-overload patients treated with deferoxamine are uniquely susceptible to mucormycosis, because Rhizopus spp. can obtain iron from ferrioxamine (deferoxamine + Fe**3+). Previously we have identified two closely related, ferrioxamine-inducible R. oryzae genes (FOB1 and FOB2) in which ...

  19. ESTUDOS NUTRICIONAIS COM ARROZ (Oryza sativa, L.

    Directory of Open Access Journals (Sweden)

    Alfredo LAM-SÁNCHEZ

    2009-07-01

    Full Text Available

    RESUMO: Estudos com arroz (Oryza sativa, L. foram realizados a fim de determinar a variabilidade do teor de proteína em coleções de cultivares e a possibilidade de utilizar as camadas periféricas do grão na alimentação humana. Foram analisadas 626 linhagens e cultivares de arroz que mostraram uma variação quanto ao teor de proteína de 4.00 a 14.31 g/100 g de amostra. Para se extrair as camadas periféricas do grão, foi desenvolvida uma máquina experimental, que removia as camadas superficiais dos grãos de arroz integral (inteiros somente com a casca removida. Verificou-se que a quantidade de proteína do grão diminui de fora para dentro. O resíduo, que era constituído de grande parte de restos de endosperma com um teor protéico menor mas incluía o embrião, que é a primeira estrutura a se deslocar de grão no beneficiamento e contém proteínas, vitaminas, sais minerais e lípides, tinha um bom valor nutritivo. Desenvolveu-se também uma fórmula para alimentação infantil a partir da mistura de leite de vaca com arroz, com composição semelhante à do leite materno, a ser utilizada sob a forma de bebida ou mingau. Formulações com 40%-20% arroz + 60%-80% leite de vaca proporcionaram valores de Coeficiente de Eficiência Protéica (2,39 e 2,38, respectivamente que não diferiam estatisticamente do valor de 2,43 obtido na fórmula com 100% de leite de vaca. Seus preços foram 59% e 65% do obtido para o leite de vaca integral. PALAVRAS-CHAVE: Arroz; qualidade do grão; proteína; camadas periféricas; misturas arroz-leite; nutrição humana.

  20. AA quadrupole magnet

    CERN Multimedia

    1980-01-01

    Focusing magnet used for the AA (antiproton accumulator).Making an antiproton beam took a lot of time and effort. Firstly, protons were accelerated to an energy of 26 GeV in the PS and ejected onto a metal target. From the spray of emerging particles, a magnetic horn picked out 3.6 GeV antiprotons for injection into the AA through a wide-aperture focusing quadrupole magnet. For a million protons hitting the target, just one antiproton was captured, 'cooled' and accumulated. It took 3 days to make a beam of 3 x 10^11 - three hundred thousand million - antiprotons. About focusing magnets (quadrupoles): Quadrupole magnets are needed to focus the particle beams and squeeze them so that more particles collide when the beams cross. Particle beams are stored for about 10 hours in the LHC. During this time, the particles make four hundred million revolutions around the machine, travelling a distance equivalent to the diameter of the solar system.

  1. ANTAGONISTIC ACTIVITY OF SERRATIA MARCESCENS AGAINST PYRICULARIA ORYZAE

    Directory of Open Access Journals (Sweden)

    V. JAIGANESH

    2007-08-01

    Full Text Available Rice is an important crop, widely affected by quite a number of diseases that results in higher yield losses. Among the fungal diseases, blast incited by Pyricularia oryzae is a major disease. The biological method of plant disease management seems to be an alternative to chemical fungicides in managing the blast disease. A new bio control agent viz., Serratia marcescens appears to be an ideal agent for the control of P. oryzae, because it produces chitinolytic enzymes which causes degradation of the fungal cell walls, induction of plant defence reaction and certain antifungal low molecular weight molecules. A study was undertaken to investigate the effect of a new bio control agent like S. marcescens against P. oryzae. The talc based formulation of S. marcescens (@ 1.0, 1.5, 2.0 and 2.5 kg/ha was sprayed on old IR 50 rice plants in fields. Out of the six-bio protectants tested, S. marcescens was found very effective against P. oryzae under in vitro conditions. S. marcescens could be isolated from shoots as well as roots emerging from the treated seeds and the plant parts from treated seeds inhibited P. oryzae. The antagonist S. marcescens survived in the phyllosphere even 80 days after spray. The results revealed that rice blast control was achieved by spraying S. marcescens @ 1.0 kg/ha. The increasing dose of talc-based inoculum when applied on foliage increased the phyllosphere population of S. marcescens and controlled rice blast. The maximum disease control was achieved when inoculum was applied at 2.5 kg/ha.

  2. STANDARDIZING THE EXTRACTION AND EVALUATION OF ANTIMICROBIAL FRACTION FROM STREPTOMYCES SP. TC1 AGAINST XANTHOMONAS ORYZAE PV. ORYZAE

    Directory of Open Access Journals (Sweden)

    NANJUNDAN JAIVEL*, RAMASAMY RAJESH AND PONNUSAMY MARIMUTHU

    2014-08-01

    Full Text Available Streptomyces are prokaryotic microorganisms capable of producing a wide range of secondary metabolites has the capacity to fight with the competing plant pathogens and suppress the growth of them. A promising Streptomyces sp. TC1 isolate exhibited antimicrobial activity against bacterial leaf blight pathogen Xanthomonas oryzae pv. oryzae under in vitro conditions. The antimicrobial activity of TC1 culture filtrate was found to be higher at seven days of incubation. The optimized extraction of antimicrobial fractions from the culture filtrate was obtained with ethyl acetate solvent. Adjusting the pH of the culture filtrate to 3 prior to extraction process resulted in increased recovery of antimicrobial fractions. The crude antimicrobial fraction obtained from the TC1 fermentation broth exhibited a minimum inhibitory concentration value of 300 µg/ml against the test pathogen Xanthomonas oryzae pv. oryzae. The antimicrobial activity results including agar well diffusion assay and MIC experiments strongly recommend that the Streptomyces sp. TC1 can be explored for antimicrobial metabolites for bacterial blight disease control in rice.

  3. NCBI nr-aa BLAST: CBRC-ACAR-01-0713 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ACAR-01-0713 ref|YP_200709.1| glucose-galactose transporter [Xanthomonas oryza...e pv. oryzae KACC10331] gb|AAW75324.1| fucose permease [Xanthomonas oryzae pv. oryzae KACC10331] YP_200709.1 3.6 35% ...

  4. NCBI nr-aa BLAST: CBRC-LAFR-01-0180 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-LAFR-01-0180 ref|YP_453064.1| hypothetical protein XOO_4035 [Xanthomonas oryza...e pv. oryzae MAFF 311018] dbj|BAE70790.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae MAFF 311018] YP_453064.1 6.5 37% ...

  5. NCBI nr-aa BLAST: CBRC-XTRO-01-0645 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-XTRO-01-0645 ref|YP_451034.1| hypothetical protein XOO_2005 [Xanthomonas oryza...e pv. oryzae MAFF 311018] dbj|BAE68760.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae MAFF 311018] YP_451034.1 2e-41 40% ...

  6. NCBI nr-aa BLAST: CBRC-ACAR-01-0713 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ACAR-01-0713 ref|YP_450980.1| glucose-galactose transporter [Xanthomonas oryza...e pv. oryzae MAFF 311018] dbj|BAE68706.1| glucose-galactose transporter [Xanthomonas oryzae pv. oryzae MAFF 311018] YP_450980.1 4.7 35% ...

  7. Cloning and characterization of the first GH10 and GH11 xylanases from Rhizopus oryzae.

    Science.gov (United States)

    Xiao, Zhizhuang; Grosse, Stephan; Bergeron, Hélène; Lau, Peter C K

    2014-10-01

    The only available genome sequence for Rhizopus oryzae strain 99-880 was annotated to not encode any β-1,4-endoxylanase encoding genes of the glycoside hydrolase (GH) family 10 or 11. Here, we report the identification and cloning of two such members in R. oryzae strain NRRL 29086. Strain 29086 was one of several selected fungi grown on wheat or triticale bran and screened for xylanase activity among other hydrolytic actions. Its high activity (138 U/ml) in the culture supernatant led to the identification of two activity-stained proteins, designated Xyn-1 and Xyn-2 of respective molecular masses 32,000 and 22,000. These proteins were purified to electrophoretic homogeneity and characterized. The specific activities of Xyn-1 and Xyn-2 towards birchwood xylan were 605 and 7,710 U/mg, respectively. Kinetic data showed that the lower molecular weight Xyn-2 had a higher affinity (K m=3.2 ± 0.2 g/l) towards birchwood xylan than Xyn-1 by about 4-fold. The melting temperature (T m) of the two proteins, estimated to be in the range of 49.5-53.7 °C indicated that they are rather thermostable proteins. N-terminal and internal peptide sequences were obtained by chemical digestion of the purified xylanases to facilitate cloning, expression in Escherichia coli, and sequencing of the respective gene. The cloned Rhizopus xylanases were used to demonstrate release of xylose from flax shives-derived hemicellulose as model feedstock. Overall, this study expands the catalytic toolbox of GH10 and 11 family proteins that have applications in various industrial and bioproducts settings.

  8. Effect of different factors on the induced resistance of Xanthomonas oryzae pv. oryzae and relationship between the effect and active oxygen metabolism in rice seedling leaves

    Institute of Scientific and Technical Information of China (English)

    ZENGFuhua; WUYuexuan; LUOZemin

    1999-01-01

    We studied the relationship between the resistance to Xanthomonas oryzae pv, oryzae (XOO) and active oxygen species (AOS).Materials used were Yushuinuo (high resistant) and Zhefu 802 (high susceptible).Paraquat (PQ) specially generated superoxide anion (O2 ) and Tiron (4, 5-dihydroxy-1.3-benzenedisufonic acid).

  9. Reticulate evolution of the rye genome.

    Science.gov (United States)

    Martis, Mihaela M; Zhou, Ruonan; Haseneyer, Grit; Schmutzer, Thomas; Vrána, Jan; Kubaláková, Marie; König, Susanne; Kugler, Karl G; Scholz, Uwe; Hackauf, Bernd; Korzun, Viktor; Schön, Chris-Carolin; Dolezel, Jaroslav; Bauer, Eva; Mayer, Klaus F X; Stein, Nils

    2013-10-01

    Rye (Secale cereale) is closely related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to its large genome (~8 Gb) and its regional importance, genome analysis of rye has lagged behind other cereals. Here, we established a virtual linear gene order model (genome zipper) comprising 22,426 or 72% of the detected set of 31,008 rye genes. This was achieved by high-throughput transcript mapping, chromosome survey sequencing, and integration of conserved synteny information of three sequenced model grass genomes (Brachypodium distachyon, rice [Oryza sativa], and sorghum [Sorghum bicolor]). This enabled a genome-wide high-density comparative analysis of rye/barley/model grass genome synteny. Seventeen conserved syntenic linkage blocks making up the rye and barley genomes were defined in comparison to model grass genomes. Six major translocations shaped the modern rye genome in comparison to a putative Triticeae ancestral genome. Strikingly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks. This indicates that introgressive hybridizations (diploid or polyploidy hybrid speciation) and/or a series of whole-genome or chromosome duplications played a role in rye speciation and genome evolution.

  10. AAS 227: Day 1

    Science.gov (United States)

    Kohler, Susanna

    2016-01-01

    Editors Note:This week were at the 227th AAS Meeting in Kissimmee, FL. Along with several fellow authors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting at the end of each day. Follow along here or at astrobites.com, or catch ourlive-tweeted updates from the @astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Things kicked off last night at our undergraduate reception booth. Thanks to all of you who stopped by we were delightedto have so many people tell us that they already know about and useastrobites, and we were excited to introduce a new cohort of students at AAS to astrobites for the first time.Tuesday morning was the official start of the meeting. Here are just a few of the talks and workshops astrobiters attended today.Opening Address (by Becky Smethurst)The President of the AAS, aka our fearless leader Meg Urry kicked off the meeting this morning at the purely coffee powered hour of 8am this morning. She spoke about the importance of young astronomers at the meeting (heres looking at you reader!) and also the importance of the new Working Group for Accessibility and Disabilities (aka WGAD pronounced like wicked) at the AAS. The Society has made extra effort this year to make the conference accessible to all,a message which was very well received by everyone in attendance.Kavli Lecture: New Horizons Alan Stern (by Becky Smethurst)We were definitely spoilt with the first Plenary lecture at this years conference Alan Stern gave us a a review of the New Horizons mission of the Pluto Fly By (astrobites covered the mission back in July with this post). We were treated to beautiful images, wonderful results and a foray into geology.Before (Hubble) and after #NewHorizons. #thatisall #science #astro alanstern #aas227 pic.twitter.com/kkMt6RsSIR Science News (@topsciencething) January 5, 2016Some awesome facts from the lecture that blew my mind:New Horizons is now 2AU (!) beyond Pluto

  11. AAS 227: Day 2

    Science.gov (United States)

    Kohler, Susanna

    2016-01-01

    Editors Note:This week were at the 227th AAS Meeting in Kissimmee, FL. Along with several fellow authors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting at the end of each day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Welcome to Day 2 of the winter American Astronomical Society (AAS) meeting in Kissimmee! Several of us are attending the conference this year, and we will report highlights from each day here on astrobites. If youd like to see more timely updates during the day, we encourage you to follow @astrobites on twitter or search the #aas227 hashtag.Plenary Session: Black Hole Physics with the Event Horizon Telescope (by Susanna Kohler)If anyone needed motivation to wake up early this morning, they got it in the form of Feryal Ozel (University of Arizona) enthralling us all with exciting pictures, videos, and words about black holes and the Event Horizon Telescope. Ozel spoke to a packed room (at 8:30am!) about where the project currently stands, and where its heading in the future.The EHT has pretty much the coolest goal ever: actually image the event horizons of black holes in our universe. The problem is that the largest black hole we can look at (Sgr A*, in the center of our galaxy) has an event horizon size of 50 as. For this kind of resolution roughly equivalent to trying to image a DVD on the Moon! wed need an Earth-sized telescope. EHT has solved this problem by linking telescopes around the world, creating one giant, mm-wavelength effective telescope with a baseline the size of Earth.Besides producing awesome images, the EHT will be able to test properties of black-hole spacetime, the no-hair theorem, and general relativity (GR) in new regimes.Ozel walked us through some of the theory prep work we need to do now in order to get the most science out of the EHT, including devising new

  12. Identification and characterization of integron-mediated antibiotic resistance in the phytopathogen Xanthomonas oryzae pv. oryzae.

    Directory of Open Access Journals (Sweden)

    Ying Xu

    Full Text Available Four streptomycin-resistant isolates of Xanthomonas oryzae pv. oryzae (YNA7-1, YNA10-2, YNA11-2, and YNA12-2 were examined via PCR amplification for the presence of class 1, class 2, and class 3 integrons and aadA1 and aadA2 genes, which confer resistance to streptomycin and spectinomycin. The class 1 integrase gene intI1 and the aminoglycoside adenylyltransferase gene aadA1 were identified in all four resistant isolates but not in 25 sensitive isolates. PCR amplifications showed that 7790-bp, 7162-bp, 7790-bp, and 7240-bp resistance integrons with transposition gene modules (tni module in 3' conserved segments existed in YNA7-1, YNA10-2, YNA11-2, and YNA12-2, respectively. Subsequent analysis of sequences indicated that the integrons of YNA7-1 and YNA11-2 carried three gene cassettes in the order |aacA3|arr3|aadA1|. The integron of YNA10-2 carried only |arr3|aadA1| gene cassettes. The integron of YNA12-2 lacked a 550-bp sequence including part of intI1 but it still carried |aacA3|arr3|aadA1| gene cassettes. The analysis of inactive mutants and complementation tests confirmed that the aacA3 gene conferred resistance to tobramycin, kanamycin, gentamicin and netilmicin; the arr3 gene conferred resistance to rifampicin; and the aadA1 gene conferred resistance to streptomycin and spectinomycin. The resistance phenotypes of the four isolates corresponded with their resistance gene cassettes, except that YNA7-1 and YNA12-2 did not show rifampicin resistance. Sequence comparison revealed that no gene cassette array in GenBank was in the same order as in the integrons of the four resistant isolates in this study and the aadA1, which was identical in the four resistant isolates, showed 99% identity with aadA1 sequences in GenBank. The result of a stability test showed that the resistance phenotype, the aadA1 gene, and the intI1 gene were completely stable in YNA7-1 and YNA12-2 but unstable in YNA10-2 and YNA11-2. To our knowledge, this is the first

  13. Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition.

    Directory of Open Access Journals (Sweden)

    Bin He

    Full Text Available Oryza meyeriana (O. meyeriana, with a GG genome type (2n = 24, accumulated plentiful excellent characteristics with respect to resistance to many diseases such as rice shade and blast, even immunity to bacterial blight. It is very important to know if the diseases-resistant genes exist and express in this wild rice under native conditions. However, limited genomic or transcriptomic data of O. meyeriana are currently available. In this study, we present the first comprehensive characterization of the O. meyeriana transcriptome using RNA-seq and obtained 185,323 contigs with an average length of 1,692 bp and an N50 of 2,391 bp. Through differential expression analysis, it was found that there were most tissue-specifically expressed genes in roots, and next to stems and leaves. By similarity search against protein databases, 146,450 had at least a significant alignment to existed gene models. Comparison with the Oryza sativa (japonica-type Nipponbare and indica-type 93-11 genomes revealed that 13% of the O. meyeriana contigs had not been detected in O. sativa. Many diseases-resistant genes, such as bacterial blight resistant, blast resistant, rust resistant, fusarium resistant, cyst nematode resistant and downy mildew gene, were mined from the transcriptomic database. There are two kinds of rice bacterial blight-resistant genes (Xa1 and Xa26 differentially or specifically expressed in O. meyeriana. The 4 Xa1 contigs were all only expressed in root, while three of Xa26 contigs have the highest expression level in leaves, two of Xa26 contigs have the highest expression profile in stems and one of Xa26 contigs was expressed dominantly in roots. The transcriptomic database of O. meyeriana has been constructed and many diseases-resistant genes were found to express under native condition, which provides a foundation for future discovery of a number of novel genes and provides a basis for studying the molecular mechanisms associated with disease

  14. The Xanthomonas oryzae pv. oryzae PhoPQ two-component system is required for AvrXA21 activity, hrpG expression, and virulence.

    Science.gov (United States)

    Lee, Sang-Won; Jeong, Kyu-Sik; Han, Sang-Wook; Lee, Seung-Eun; Phee, Bong-Kwan; Hahn, Tae-Ryong; Ronald, Pamela

    2008-03-01

    The rice pathogen recognition receptor, XA21, confers resistance to Xanthomonas oryzae pv. oryzae strains producing the type one system-secreted molecule, AvrXA21. X. oryzae pv. oryzae requires a regulatory two-component system (TCS) called RaxRH to regulate expression of eight rax (required for AvrXA21 activity) genes and to sense population cell density. To identify other key components in this critical regulatory circuit, we assayed proteins expressed in a raxR gene knockout strain. This survey led to the identification of the phoP gene encoding a response regulator that is up-regulated in the raxR knockout strain. Next we generated a phoP knockout strain and found it to be impaired in X. oryzae pv. oryzae virulence and no longer able to activate the response regulator HrpG (hypersensitive reaction and pathogenicity G) in response to low levels of Ca2+. The impaired virulence of the phoP knockout strain can be partially complemented by constitutive expression of hrpG, indicating that PhoP controls a key aspect of X. oryzae pv. oryzae virulence through regulation of hrpG. A gene encoding the cognate putative histidine protein kinase, phoQ, was also isolated. Growth curve analysis revealed that AvrXA21 activity is impaired in a phoQ knockout strain as reflected by enhanced growth of this strain in rice lines carrying XA21. These results suggest that the X. oryzae pv. oryzae PhoPQ TCS functions in virulence and in the production of AvrXA21 in partnership with RaxRH.

  15. Prediction and Expression Analysis of miRNAs Associated with Heat Stress in Oryza sativa

    Institute of Scientific and Technical Information of China (English)

    B.SAILAJA; S.R.VOLETI; D.SUBRAHMANYAM; N.SARLA; V.VISHNU PRASANTH; V.P.BHADANA; S.K.MANGRAUTHIA

    2014-01-01

    Computational prediction of potential microRNAs (miRNAs) and their target genes was performed to identify the miRNAs and genes associated with temperature response in rice. The data of temperature-responsive miRNAs of Arabidopsis, and miRNAs and the whole genome data of rice were used to predict potential miRNAs in Oryza sativa involved in temperature response. A total of 55 miRNAs were common in both the species, and 27 miRNAs were predicted at the first time in rice. Target genes were searched for these 27 miRNAs in rice genome following stringent criteria. Real time PCR based on expression analysis of nine miRNAs showed that majority of the miRNAs were down regulated under heat stress for rice cultivar Nagina 22. Furthermore, miR169, miR1884 and miR160 showed differential expression in root and shoot tissues of rice. Identification and expression studies of miRNAs during heat stress will advance the understanding of gene regulation under stress in rice.

  16. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa.

    Science.gov (United States)

    Morin, Ryan D; Aksay, Gozde; Dolgosheina, Elena; Ebhardt, H Alexander; Magrini, Vincent; Mardis, Elaine R; Sahinalp, S Cenk; Unrau, Peter J

    2008-04-01

    The diversity of microRNAs and small-interfering RNAs has been extensively explored within angiosperms by focusing on a few key organisms such as Oryza sativa and Arabidopsis thaliana. A deeper division of the plants is defined by the radiation of the angiosperms and gymnosperms, with the latter comprising the commercially important conifers. The conifers are expected to provide important information regarding the evolution of highly conserved small regulatory RNAs. Deep sequencing provides the means to characterize and quantitatively profile small RNAs in understudied organisms such as these. Pyrosequencing of small RNAs from O. sativa revealed, as expected, approximately 21- and approximately 24-nt RNAs. The former contained known microRNAs, and the latter largely comprised intergenic-derived sequences likely representing heterochromatin siRNAs. In contrast, sequences from Pinus contorta were dominated by 21-nt small RNAs. Using a novel sequence-based clustering algorithm, we identified sequences belonging to 18 highly conserved microRNA families in P. contorta as well as numerous clusters of conserved small RNAs of unknown function. Using multiple methods, including expressed sequence folding and machine learning algorithms, we found a further 53 candidate novel microRNA families, 51 appearing specific to the P. contorta library. In addition, alignment of small RNA sequences to the O. sativa genome revealed six perfectly conserved classes of small RNA that included chloroplast transcripts and specific types of genomic repeats. The conservation of microRNAs and other small RNAs between the conifers and the angiosperms indicates that important RNA silencing processes were highly developed in the earliest spermatophytes. Genomic mapping of all sequences to the O. sativa genome can be viewed at http://microrna.bcgsc.ca/cgi-bin/gbrowse/rice_build_3/.

  17. AAS 227: Day 3

    Science.gov (United States)

    Kohler, Susanna

    2016-01-01

    Editors Note:This week were at the 227th AAS Meeting in Kissimmee, FL. Along with several fellow authors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting at the end of each day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Welcome to Day 3 of the winter American Astronomical Society (AAS) meeting in Kissimmee! Several of us are attending the conference this year, and we will report highlights from each day here on astrobites. If youd like to see more timely updates during the day, we encourage you to follow @astrobites on twitter or search the #aas227 hashtag.Henry Norris Russell Lecture: Viewing the Universe with Infrared Eyes: The Spitzer Space Telescope (by Erika Nesvold)The Henry Norris Russell Award is the highest honor given by the AAS, for a lifetime of eminence in astronomy research. This years award went to Giovanni Fazio of the Harvard-Smithsonian Center for Astrophysics. Fazio became a leader in gamma ray astronomy before switching mid-career to the study of infrared astronomy, and he gave his award lecture on the latter subject, specifically on the Spitzer Space Telescope, one of the most successful infrared telescopes of all time.Artists rendering of the Spitzer space telescope. [NASA/JPL-Caltech]Spitzer has been operating for more than twelve years, and has resulted in over six thousand papers in refereed journals in that time. The telescope sits in an Earth-trailing orbit around the Sun, and is now farther from the Earth (1.4 AU) than the Earth is from the Sun. Fazio gave the audience a fascinating overview of the science done by Spitzer over more than a decade. One of the most productive areas of research for Spitzer is the study of exoplanets, which hadnt even been discovered when the Spitzer Telescope was first conceived. Spitzers high sensitivity and ability to observe exoplanets over

  18. Effect of Preexposure to Triazoles on Susceptibility and Virulence of Rhizopus oryzae.

    Science.gov (United States)

    Bellanger, Anne-Pauline; Albert, Nathaniel D; Lewis, Russell E; Walsh, Thomas J; Kontoyiannis, Dimitrios P

    2015-12-01

    Triazole prophylaxis has become the norm in patients with hematological malignancies. Breakthrough infections caused by Mucorales during triazole prophylaxis remain a challenging problem. We found that preexposure of Rhizopus oryzae to antifungal triazoles (fluconazole, voriconazole, posaconazole, and itraconazole) did not modify the in vitro susceptibility of Rhizopus oryzae to posaconazole. In contrast, preexposure of Rhizopus to triazoles was associated with the enhanced in vitro susceptibility of R. oryzae to amphotericin B. Preexposure to posaconazole did not alter the virulence of R. oryzae in the fly model of mucormycosis.

  19. Immobilization of Isolated Lipase From Moldy Copra (Aspergillus Oryzae

    Directory of Open Access Journals (Sweden)

    Seniwati Dali

    2011-01-01

    Full Text Available Enzyme immobilization is a recovery technique that has been studied in several years, using support as a media to help enzyme dissolutions to the reaction substrate. Immobilization method used in this study was adsorption method, using specific lipase from Aspergillus oryzae. Lipase was partially purified from the culture supernatant of Aspergillus oryzae. Enzyme was immobilized by adsorbed on silica gel. Studies on free and immobilized lipase systems for determination of optimum pH, optimum temperature, thermal stability and reusability were carried out. The results showed that free lipase had optimum pH 8,2 and optimum temperature 35 °C while the immobilized lipase had optimum 8,2 and optimum temperature 45 °C. The thermal stability of the immobilized lipase, relative to that of the free lipase, was markedly increased. The immobilized lipase can be reused for at least six times.

  20. Structure, allelic diversity and selection of Asr genes, candidate for drought tolerance, in Oryza sativa L. and wild relatives.

    Science.gov (United States)

    Philippe, Romain; Courtois, Brigitte; McNally, Kenneth L; Mournet, Pierre; El-Malki, Redouane; Le Paslier, Marie Christine; Fabre, Denis; Billot, Claire; Brunel, Dominique; Glaszmann, Jean-Christophe; This, Dominique

    2010-08-01

    Asr (ABA, stress, ripening) genes represent a small gene family potentially involved in drought tolerance in several plant species. To analyze their interest for rice breeding for water-limited environments, this gene family was characterized further. Genomic organization of the gene family reveals six members located on four different chromosomes and with the same exon-intron structure. The maintenance of six members of the Asr gene family, which are the result of combination between tandem duplication and whole genome duplication, and their differential regulation under water stress, involves probably some sub-functionalization. The polymorphism of four members was studied in a worldwide collection of 204 accessions of Oryza sativa L. and 14 accessions of wild relatives (O. rufipogon and O. nivara). The nucleotide diversity of the Asr genes was globally low, but contrasted for the different genes, leading to different shapes of haplotype networks. Statistical tests for neutrality were used and compared to their distribution in a set of 111 reference genes spread across the genome, derived from another published study. Asr3 diversity exhibited a pattern concordant with a balancing selection at the species level and with a directional selection in the tropical japonica sub-group. This study provides a thorough description of the organization of the Asr family, and the nucleotide and haplotype diversity of four Asr in Oryza sativa species. Asr3 stood out as the best potential candidate. The polymorphism detected here represents a first step towards an association study between genetic polymorphisms of this gene family and variation in drought tolerance traits.

  1. Molecular progress on the mapping and cloning of functional genes for blast disease in rice (Oryza sativa L.): current status and future considerations.

    Science.gov (United States)

    Ashkani, S; Rafii, M Y; Shabanimofrad, M; Ghasemzadeh, A; Ravanfar, S A; Latif, M A

    2016-01-01

    Rice blast disease, which is caused by the fungal pathogen Magnaporthe oryzae, is a recurring problem in all rice-growing regions of the world. The use of resistance (R) genes in rice improvement breeding programmes has been considered to be one of the best options for crop protection and blast management. Alternatively, quantitative resistance conferred by quantitative trait loci (QTLs) is also a valuable resource for the improvement of rice disease resistance. In the past, intensive efforts have been made to identify major R-genes as well as QTLs for blast disease using molecular techniques. A review of bibliographic references shows over 100 blast resistance genes and a larger number of QTLs (∼500) that were mapped to the rice genome. Of the blast resistance genes, identified in different genotypes of rice, ∼22 have been cloned and characterized at the molecular level. In this review, we have summarized the reported rice blast resistance genes and QTLs for utilization in future molecular breeding programmes to introgress high-degree resistance or to pyramid R-genes in commercial cultivars that are susceptible to M. oryzae. The goal of this review is to provide an overview of the significant studies in order to update our understanding of the molecular progress on rice and M. oryzae. This information will assist rice breeders to improve the resistance to rice blast using marker-assisted selection which continues to be a priority for rice-breeding programmes.

  2. Characterization of Aspergillus oryzae aspartyl aminopeptidase expressed in Escherichia coli.

    Science.gov (United States)

    Watanabe, Jun; Tanaka, Hisaki; Akagawa, Takumi; Mogi, Yoshinobu; Yamazaki, Tatsuo

    2007-10-01

    To characterize aspartyl aminopeptidase from Aspergillus oryzae, the recombinant enzyme was expressed in Escherichia coli. The enzyme cleaves N-terminal acidic amino acids. About 30% activity was retained in 20% NaCl. Digestion of defatted soybean by the enzyme resulted in an increase in the glutamic acid content, suggesting that the enzyme is potentially responsible for the release of glutamic acid in soy sauce mash.

  3. Interspecifc hybrid plants obtained from cultivars (AA) crossed with wild Oryza species (CC)

    Institute of Scientific and Technical Information of China (English)

    TANGShengxiang; YANHuthuang; HuHulying

    1994-01-01

    Wild dee O.officinalis(CNW 258, CNW 259) and O. eichingeri (CNW 260, CNW 261) have CC genome and high resistance to brown planthopper (BPH) and whitebacked planthopper (WBPH). To transfer the resistant gene(s) of the wild rice into Asian cultivated rice, the interspecific crosses between O. sativa L. (AA) and O. officinafis and O.eiclungeri (CC) was made in present study.

  4. Cross-species bacterial artificial chromosome (BAC) library screening via overgo-based hybridization and BAC-contig mapping of a yield enhancement quantitative trait locus (QTL) yld1.1 in the Malaysian wild rice Oryza rufipogon

    OpenAIRE

    Song, Beng-Kah; Nadarajah, Kalaivani; Romanov, Michael N.; Ratnam, Wickneswari

    2005-01-01

    The construction of BAC-contig physical maps is an important step towards a partial or ultimate genome sequence analysis. Here, we describe our initial efforts to apply an overgo approach to screen a BAC library of the Malaysian wild rice species, Oryza rufipogon. Overgo design is based on repetitive element masking and sequence uniqueness, and uses short probes (approximately 40 bp), making this method highly efficient and specific. Pairs of 24-bp oligos that contain an 8-bp overlap were dev...

  5. SSR Marker Analysis on indica-japonica Differentiation of Natural Population of Oryza rufipogon in Yuanjiang, Yunnan Province

    Institute of Scientific and Technical Information of China (English)

    LI Ya-li; YANG Xiao-xi; ZHAO Feng-ping; XU Ming-hui

    2006-01-01

    By using 19 pairs of primers that could identify two subspecies (indica and japonica) of cultivated rice (Oryza sativa L.), the indica-japonica differentiation of 56 individuals from the natural population of common wild rice (Oryza rufipogon Griff.) in Yuanjiang was analyzed by SSR (microsatellite DNAs, or simple sequence repeat). Of the 19 pairs of primers, 17 pairs (89.47%) could amplify only one kind of band type among ail of the individuals, but primers RM251 and RM18 could amplify polymorphic band types. The bands amplified by 16 pairs of primers (84.21%) were identical to the indica-japonica diagnostic bands of relevant locus in cultivated rice, including 11 japonica-like loci and 4 indica-like loci. The bands amplified by the other three pairs of primers (RM18, RM202,RM205) were different from indica or japonica diagnostic bands of cultivated rice. The results showed that according to 19 loci analyzed, 84.21% of SSR loci in genomic DNA of common wild rice in Yuanjiang displayed indica-japonica differentiation and 13.79% of the loci still kept primitive, and most of the detected loci were homogenetic in the natural population.

  6. Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943.

    Science.gov (United States)

    Lu, Tingting; Yu, Shuliang; Fan, Danlin; Mu, Jie; Shangguan, Yingying; Wang, Zixuan; Minobe, Yuzo; Lin, Zhixin; Han, Bin

    2008-10-01

    A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogon Griff. W1943 for comparative analysis between wild and cultivated rice species. Two cDNA libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. Homology searching of these cDNA sequences revealed that >96.8% of the wild rice cDNAs were matched to the cultivated rice O. sativa ssp. japonica cv. Nipponbare genome sequence. However, sequence. The comparative analysis showed that O. rufipogon W1943 had greater similarity to O. sativa ssp. japonica than to ssp. indica cultivars. In addition, 17 novel rice cDNAs were identified, and 41 putative tissue-specific expression genes were defined through searching the rice massively parallel signature-sequencing database. In conclusion, these FLcDNA clones are a resource for further function verification and could be broadly utilized in rice biological studies.

  7. Transcriptome Analysis of Oryza sativa Calli Under Microgravity

    Science.gov (United States)

    Jin, Jing; Chen, Haiying; Cai, Weiming

    2015-11-01

    The transcriptome of Oryza sativacalli was analyzed on board the Chinese spaceship "Shenzhou 8" to study the effects of microgravity on plant signal transduction and secondary metabolism (as one of the experiments with SIMBOX on Shenzhou 8). Calli of Oryza sativa were pre-cultured for 4 days on ground and then loaded into the stationary platform or the rotating platform of a biological incubator, called SIMBOX, to grow in space under microgravity conditions or 1g-conditions, respectively. The calli were fixed by RNAlater after grew 324 h under microgravity. After 17 days, Shenzhou 8 returned to Earth carrying SIMBOX. Oryza sativa calli were recovered, and the RNA was extracted for transcriptome analysis. After comparing 1 gspaceflight controls-inflight controls with 1 g-ground controls, 157 probe sets with different expression levels (fold change ≥2, p<0.05) were identified. When comparing spaceflight controls to 1 g-ground controls and to 1 g-inflight controls, 678 probe sets with different expression levels (fold change ≥2, p<0.05) were identified. The fact that the same 678 probe sets were identified in these two comparisons suggests that transcription was affected under microgravity conditions. MapMan analysis was used to classify 627 microgravity responsive (MR) transcripts. The MR transcripts were mainly involved in cell wall structure, the TCA cycle, primary metabolism, transcription, protein modification and degradation, hormone metabolism, calcium regulation, receptor like kinase activity and transport.

  8. Jewelry boxes contaminated by Aspergillus oryzae: an occupational health risk?

    Science.gov (United States)

    Bellanger, Anne-Pauline; Roussel, Anaïs; Millon, Laurence; Delaforge, Marcel; Reboux, Gabriel

    2012-01-01

    In 2009, 100,000 jewelry boxes, manufactured in China, were delivered to a jewelry manufacturer in Besançon, France. All the boxes were contaminated by mold. Because the workers refused to handle these jewelry boxes, the company contacted our laboratory to determine how to deal with the problem. Three choices were available: (1) decontaminate the boxes, (2) return the boxes to the Chinese manufacturer, or (3) destroy the entire shipment. Based on microscopic identification, the culture analysis was positive for A. oryzae. This could not be confirmed by molecular techniques because of the genetic proximity of A. oryzae and A. flavus. Because A. flavus can produce aflatoxins, we tested for them using mass spectrometry. Aflatoxins B1, B2, G1, G2, and M1 were not detected; however, given the specifics of this situation, we could not discard the possibility of the presence of other aflatoxins, such as P1, B3, GM2, and ethoxyaflatoxin B2. We concluded that the contamination by A. oryzae was probably due to food products. However, because of the possible presence of aflatoxins, occupational health risks could not be entirely ruled out. The decision was therefore taken to destroy all the jewelry boxes by incineration. To avoid a similar situation we propose: (1) to maintain conditions limiting mold contamination during production (not eating on the work site, efficient ventilation systems); (2) to desiccate the products before sending them; and (3) to closely control the levels of dampness during storage and transport.

  9. Reduction of aflatoxins by Rhizopus oryzae and Trichoderma reesei.

    Science.gov (United States)

    Hackbart, H C S; Machado, A R; Christ-Ribeiro, A; Prietto, L; Badiale-Furlong, E

    2014-08-01

    This study evaluated the ability of the microorganisms Rhizopus oryzae (CCT7560) and Trichoderma reesei (QM9414), producers of generally recognized as safe (GRAS) enzymes, to reduce the level of aflatoxins B1, B2, G1, G2, and M1. The variables considered to the screening were the initial number of spores in the inoculum and the culture time. The culture was conducted in contaminated 4 % potato dextrose agar (PDA) medium, and the residual mycotoxins were determined every 24 h by HPLC-FL. The fungus R. oryzae has reduced aflatoxins B1, B2, and G1 in the 96 h and aflatoxins M1 and G2 in the range of 120 h of culture by approximately 100 %. The fungus T. reesei has reduced aflatoxins B1, B2, and M1 in the 96 h and aflatoxin G1 in the range of 120 h of culture by approximately 100 %. The highest reduction occurred in the middle of R. oryzae culture.

  10. Alternative respiration and fumaric acid production of Rhizopus oryzae.

    Science.gov (United States)

    Gu, Shuai; Xu, Qing; Huang, He; Li, Shuang

    2014-06-01

    Under the conditions of fumaric acid fermentation, Rhizopus oryzae ME-F14 possessed at least two respiratory systems. The respiration of mycelia was partially inhibited by the cytochrome respiration inhibitor antimycin A or the alternative respiration inhibitor salicylhydroxamic acid and was completely inhibited in the presence of both antimycin A and salicylhydroxamic acid. During fumaric acid fermentation process, the activity of alternative respiration had a great correlation with fumaric acid productivity; both of them reached peak at the same time. The alternative oxidase gene, which encoded the mitochondrial alternative oxidase responsible for alternative respiration in R. oryzae ME-F14, was cloned and characterized in Escherichia coli. The activity of alternative respiration, the alternative oxidase gene transcription level, as well as the fumaric acid titer were measured under different carbon sources and different carbon-nitrogen ratios. The activity of alternative respiration was found to be comparable to the transcription level of the alternative oxidase gene and the fumaric acid titer. These results indicated that the activity of the alternative oxidase was regulated at the transcription stage under the conditions tested for R. oryzae ME-F14.

  11. Iron starvation induces apoptosis in Rhizopus oryzae in vitro.

    Science.gov (United States)

    Shirazi, Fazal; Kontoyiannis, Dimitrios P; Ibrahim, Ashraf S

    2015-01-01

    Mortality associated with mucormycosis remains high despite current antifungals. Iron-starvation strategies have been shown to have promising activity against Mucorales. We hypothesized that iron starvation enhances apoptosis in Rhizopus oryzae. Apoptosis was characterized in R. oryzae transformed with RNAi plasmid targeting FTR1 expression (iron permease mutant) or empty plasmid grown in iron rich (0.125% FeCl3) and iron depleted media (YNB+1mM ferrozine and 1 mM ascorbic acid). Increased apoptosis was observed with dihydrorhodamine-123 and rhodamine-123 staining in the iron starved mutant FTR1 when compared to empty plasmid, followed by increased extracellular ATP levels. In addition, DNA fragmentation and metacaspase activity were prominent in FTR1. In contrast, Rhizopus strains grown in iron-rich medium displayed minimal apoptosis. Our results demonstrate a metacaspase dependent apoptotic process in iron deprived condition and further support the role of iron starvation strategies as an adjunct treatment for mucormycosis, a mechanism by which iron starvation affects R. oryzae.

  12. Multiple translocation of the AVR-Pita effector gene among chromosomes of the rice blast fungus Magnaporthe oryzae and related species.

    Directory of Open Access Journals (Sweden)

    Izumi Chuma

    2011-07-01

    Full Text Available Magnaporthe oryzae is the causal agent of rice blast disease, a devastating problem worldwide. This fungus has caused breakdown of resistance conferred by newly developed commercial cultivars. To address how the rice blast fungus adapts itself to new resistance genes so quickly, we examined chromosomal locations of AVR-Pita, a subtelomeric gene family corresponding to the Pita resistance gene, in various isolates of M. oryzae (including wheat and millet pathogens and its related species. We found that AVR-Pita (AVR-Pita1 and AVR-Pita2 is highly variable in its genome location, occurring in chromosomes 1, 3, 4, 5, 6, 7, and supernumerary chromosomes, particularly in rice-infecting isolates. When expressed in M. oryzae, most of the AVR-Pita homologs could elicit Pita-mediated resistance, even those from non-rice isolates. AVR-Pita was flanked by a retrotransposon, which presumably contributed to its multiple translocation across the genome. On the other hand, family member AVR-Pita3, which lacks avirulence activity, was stably located on chromosome 7 in a vast majority of isolates. These results suggest that the diversification in genome location of AVR-Pita in the rice isolates is a consequence of recognition by Pita in rice. We propose a model that the multiple translocation of AVR-Pita may be associated with its frequent loss and recovery mediated by its transfer among individuals in asexual populations. This model implies that the high mobility of AVR-Pita is a key mechanism accounting for the rapid adaptation toward Pita. Dynamic adaptation of some fungal plant pathogens may be achieved by deletion and recovery of avirulence genes using a population as a unit of adaptation.

  13. A mutation in the aroE gene affects pigment production, virulence, and chemotaxis in Xanthomonas oryzae pv. oryzae.

    Science.gov (United States)

    Kim, Hong-Il; Noh, Tae-Hwan; Lee, Chang-Soo; Park, Young-Jin

    2015-01-01

    Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight (BB) in rice. To study its function, a random insertion mutation library of Xoo was constructed using the Tn5 transposon. A mutant strain with decreased virulence against the susceptible rice cultivar IR24 was isolated from the library (aroE mutant), which also had extremely low pigment production. Thermal asymmetric interlaced-polymerase chain reaction (TAIL-PCR) and sequence analysis of the mutant revealed that the transposon was inserted into the aroE gene (encoding shikimate dehydrogenase). To investigate gene expression changes in the pigment- and virulence-deficient mutant, DNA microarray analysis was performed, which showed downregulation of 20 genes involved in the chemotaxis of Xoo. Our findings reveal that mutation of the aroE gene affects virulence and pigment production, as well as expression of genes involved in Xoo chemotaxis.

  14. Impact of Engineered Nanoparticles on Virulence of Xanthomonas oryzae pv oryzae and on Rice Sensitivity at its Infection

    Directory of Open Access Journals (Sweden)

    Giuliano Degrassi

    2014-12-01

    Full Text Available The present work of nanocotoxicity wants to propose a new plant model starting from the rice plant. The model takes into consideration the impact of engineered nanoparticles (Ag, Co, Ni, CeO2, Fe3O4, TiO2 on rice plants that were weakened by infections of Xanthomonas oryzae pv oryzae bacteria. The results indicate that some NPs increase the rice sensitivity to the pathogen while others decrease the virulence of the pathogen towards rice. No-enrichment in component metal concentration is detected in above organs of rice, with exception of Ni-NPs treatment. An imbalance of major elements in infected rice crops treated with NPs was investigated.

  15. Production of bacterial blight resistant lines from somatic hybridization between Oryza sativa L.and Oryza meyeriana L.

    Institute of Scientific and Technical Information of China (English)

    严成其; 钱凯先; 薛刚平; 吴忠长; 陈跃磊; 颜秋生; 张雪琴; 吴平

    2004-01-01

    Novel bacterial blight (BB) resistance gene(s) for rice was (were) introduced into a cultivated japonica rice variety Oryza sativa (cv. 8411), via somatic hybridization using the wild rice Oryza meyeriana as the donor of the resistance gene(s). Twenty-nine progenies of somatically hybridized plants were obtained. Seven somatically hybridized plants and their parents were used for AFLP (amplified fragment length polymorphism) analysis using 8 primer pairs. Results confirmed that these plants were somatic hybrids containing the characteristic bands of both parents. The morphology of the regenerated rice showed characters of both O. sativa and O. meyeriana. Two somatic hybrids showed highest BB resistance and the other 8 plants showed moderate resistance. The new germplasms with highest resistance have been used in the rice bfeeding program for the improvement of bacterial blight resistance.

  16. Production of bacterial blight resistant lines from somatic hybridization between Oryza sativa L. and Oryza meyeriana L.

    Institute of Scientific and Technical Information of China (English)

    严成其; 钱凯先; 薛刚平; 吴忠长; 陈跃磊; 颜秋生; 张雪琴; 吴平

    2004-01-01

    Novel bacterial blight (BB) resistance gene(s) for rice was (were) introduced into a cultivated japonica rice variety Oryza sativa (cv. 8411), via somatic hybridization using the wild rice Oryza meyeriana as the donor of the resistance gene(s). Twenty-nine progenies of somatically hybridized plants were obtained. Seven somatically hybridized plants and their parents were used for AFLP (amplified fragment length polymorphism) analysis using 8 primer pairs. Results confirmed that these plants were somatic hybrids containing the characteristic bands of both parents. The morphology of the regenerated rice showed characters of both O.sativa and O.meyeriana. Two somatic hybrids showed highest BB resistance and the other 8 plants showed moderate resistance. The new germplasms with highest resistance have been used in the rice breeding program for the improvement of bacterial blight resistance.

  17. OPTIMASI SUHU REAKSI TRANSESTERIFIKASI PADA MINYAK JERAMI PADI (ORYZA SATIVA L. MENJADI BIODIESEL DENGAN MENGGUNAKAN KATALIS CAO DARI KULIT TELUR AYAM

    Directory of Open Access Journals (Sweden)

    Tasik Sinta

    2016-11-01

    Full Text Available The research on optimization of transesterification temperature for production of biodiesel from rice straw oil (Oryza sativa L. using CaO catalyst derived from the chicken egg skin has been conducted. Production of biodiesel was conducted at varied temperatures, namely 30oC, 40oC, 50oC, 60oC and 70oC. The fatty acid compositions of the transesterification products were determined by using GC-MS and the physical and chemical characteristics were determined using SNI Methods 04-7182-2006. The AAS result suggested that the chicken egg skin contained 91.41% CaO. The optimum transesterification temperature was 60oC producing 90,8405% methyl ester. The results of GC-MS showed that the highest percentage of fatty acid was methyl oleic (44.56%.

  18. AAS 228: Day 4

    Science.gov (United States)

    Kohler, Susanna

    2016-06-01

    Editors Note: Lastweek we were at the 228th AAS Meeting in San Diego, CA. Here is a final post aboutselectedevents on the last day of the meeting, written by authors fromastrobites.com, a grad-student collaborative project with which we recently announced a new partnership! Starting in July,keep an eye out for astrobites postsat AAS Nova in between Highlights(i.e., on Tuesdays and Thursdays).Were excited to be working together to bring you more recent astronomy research from AAS journals!Extrasolar Planets: Detection (by Leonardo dos Santos)Thursdays first session on exoplanets was about detecting these distant worlds, and the opening talk was given by Robert Siverd (Las Cumbres Observatory). He describes the NRES, a network of spectrographs that will look for exoplanets using the radial velocity method. One of the coolest aspects of this instrument is that it will feature an on the fly scheduling system that will perform observations as efficiently as possible. The spectrograph is still being tested, but a unit will be deployed at CTIO later this year.@lcogt contracted by @NASA_TESS for follow up of their candidates. #aas228 Jessie Christiansen (@aussiastronomer) June 16, 2016Measuring the depths of transits and eclipses in Spitzer has been problematic in the past, since the Spitzer instrument IRAC (InfraRed Array Camera) has a non-uniform response in its detectors pixels. But, as reported by James Ingalls (Spitzer Science Center, Caltech), observers are circumventing this issue by using what they call the staring mode (avoiding large pointing jumps) and an algorithm to pick sweet spot pixels. Moreover, the results from the IRAC Data Challenge are helping to better understand its behavior. Giuseppe Morello (University College London), on the other hand, explained how his research group gets rid of instrumental effects from IRAC using machine learning. This method removes systematics from exoplanet transit data no matter if the noise source is from an instrument or

  19. Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina.

    Directory of Open Access Journals (Sweden)

    Volker U Schwartze

    2014-08-01

    Full Text Available Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD, (ii despite the relatively high incidence of introns, alternative splicing (AS is not frequently observed for the generation of paralogs and in response to stress, (iii the content of repetitive elements is strikingly low (<5%, (iv L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1-4 copies usually found in other fungi. More findings are: (i lower content of tRNAs, but unique codons in L. corymbifera, (ii Over 25% of the proteins are apparently specific for L. corymbifera. (iii L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors in comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.

  20. Draft Genome Sequence of the Rice Kernel Smut Tilletia horrida Strain QB-1.

    Science.gov (United States)

    Wang, Na; Ai, Peng; Tang, Yangfan; Zhang, Jing; Dai, Xiaojuan; Li, Ping; Zheng, Aiping

    2015-06-25

    Tilletia horrida is the most destructive fungal pathogen of rice (Oryza sativa L.). The 20,105,270-bp draft genome sequence of T. horrida strain QB-1 is reported here. Genes encoding proteins associated with key virulence factors were predicted, and this can provide information for understanding the pathogenic mechanisms in T. horrida.

  1. Draft Genome Sequence of the Rice Kernel Smut Tilletia horrida Strain QB-1

    Science.gov (United States)

    Wang, Na; Ai, Peng; Tang, Yangfan; Zhang, Jing; Dai, Xiaojuan; Li, Ping

    2015-01-01

    Tilletia horrida is the most destructive fungal pathogen of rice (Oryza sativa L.). The 20,105,270-bp draft genome sequence of T. horrida strain QB-1 is reported here. Genes encoding proteins associated with key virulence factors were predicted, and this can provide information for understanding the pathogenic mechanisms in T. horrida. PMID:26112782

  2. High Rate of Chimeric Gene Origination by Retroposition in Plant Genomes

    DEFF Research Database (Denmark)

    Wang, Wen; Zheng, Hongkung; Fan, Chuanzhu

    2006-01-01

    and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons...

  3. A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.

    Science.gov (United States)

    Zuccolo, Andrea; Bowers, John E; Estill, James C; Xiong, Zhiyong; Luo, Meizhong; Sebastian, Aswathy; Goicoechea, José Luis; Collura, Kristi; Yu, Yeisoo; Jiao, Yuannian; Duarte, Jill; Tang, Haibao; Ayyampalayam, Saravanaraj; Rounsley, Steve; Kudrna, Dave; Paterson, Andrew H; Pires, J Chris; Chanderbali, Andre; Soltis, Douglas E; Chamala, Srikar; Barbazuk, Brad; Soltis, Pamela S; Albert, Victor A; Ma, Hong; Mandoli, Dina; Banks, Jody; Carlson, John E; Tomkins, Jeffrey; dePamphilis, Claude W; Wing, Rod A; Leebens-Mack, Jim

    2011-01-01

    Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome. Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella. When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.

  4. AAS 227: Day 4

    Science.gov (United States)

    Kohler, Susanna

    2016-01-01

    Editors Note:This week were at the 227th AAS Meeting in Kissimmee, FL. Along with several fellow authors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting at the end of each day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Welcome to Day 4 of the winter American Astronomical Society (AAS) meeting in Kissimmee! Several of us are attending the conference this year, and we will report highlights from each day here on astrobites. If youd like to see more timely updates during the day, we encourage you to follow @astrobites on twitter or search the #aas227 hashtag.Helen B. Warner Prize: Origins of Structure in Planetary Systems (by Erika Nesvold)Another excellent prize lecture started off todays sessions. The Helen B. Warner Prize is awarded for achievement in observational or theoretical astrophysics by a young researcher (no more than eight years after their Ph.D.). This years Warner Prize was presented to Ruth Murray-Clay of UC Santa Barbara. For her award lecture, Murray-Clay told us all about planetary system architecture: the number, masses, and orbits of planets in a given system.Ruth Murray-Clay [photo from http://web.physics.ucsb.edu/ ~murray/biocv.html]The underlying question motivating this type of research is: How rare is the Solar System? In other words, how likely is it that a given planetary system will have rocky planets close to their star, gas giants farther out, and ice giants at the outer reaches of the system? Answering this question will help us solve the physics problem of how and where planets form, and will also help us on our search for other planets like Earth.The data on exoplanet population from transit and radial velocity observations and from direct imaging tell us that our Solar System is not common (many systems we observe have much more eccentric gas giants), but that doesnt

  5. Identification of secreted proteins of Aspergillus oryzae associated with growth on solid cereal substrates

    NARCIS (Netherlands)

    Biesebeke, R. te; Boussier, A.; Biezen, N. van; Hondel, C.A.M.J.J. van den; Punt, P.J.

    2006-01-01

    Filamentous growth of Aspergillus oryzae on solid cereal substrates involves secretion of substrate converting enzymes and a solid substrate specific polarised hyphal growth phenotype. To identify proteins produced under these specific conditions, the extracts of A. oryzae grown on wheat-based media

  6. Identification of secreted proteins of Aspergillus oryzae associated with growth on solid cereal substrates

    NARCIS (Netherlands)

    Biesebeke, R. te; Boussier, A.; Biezen, N. van; Hondel, C.A.M.J.J. van den; Punt, P.J.

    2006-01-01

    Filamentous growth of Aspergillus oryzae on solid cereal substrates involves secretion of substrate converting enzymes and a solid substrate specific polarised hyphal growth phenotype. To identify proteins produced under these specific conditions, the extracts of A. oryzae grown on wheat-based media

  7. High Affinity Iron Permease is Required for Virulence of Rhizopus oryzae

    Science.gov (United States)

    Rhizopus oryzae is the most common cause of mucormycosis. Clinical and animal model data clearly demonstrate that the presence of elevated available serum iron predisposes the host to develop mucormycosis. The high affinity iron permease gene (rFTR1) is required for R. oryzae iron transport in iro...

  8. First Report of Rhizopus oryzae as a Postharvest Pathogen of Apple in Korea

    OpenAIRE

    Kwon, Jin-Hyeuk; Kim, Jinwoo; Kim, Won-Il

    2011-01-01

    Soft rot in apple caused by Rhizopus oryzae was found for the first time in Korea. A detailed description of the specimen is given along with its internal transcribed spacer rDNA sequence. The fungus was identified as Rhizopus oryzae based on the mycological characteristics, molecular data, and pathogenicity testing.

  9. Comparison of expression of secondary metabolite biosynthesis cluster genes in Aspergillus flavus, A. parasiticus, and A. oryzae.

    Science.gov (United States)

    Ehrlich, Kenneth C; Mack, Brian M

    2014-06-23

    Fifty six secondary metabolite biosynthesis gene clusters are predicted to be in the Aspergillus flavus genome. In spite of this, the biosyntheses of only seven metabolites, including the aflatoxins, kojic acid, cyclopiazonic acid and aflatrem, have been assigned to a particular gene cluster. We used RNA-seq to compare expression of secondary metabolite genes in gene clusters for the closely related fungi A. parasiticus, A. oryzae, and A. flavus S and L sclerotial morphotypes. The data help to refine the identification of probable functional gene clusters within these species. Our results suggest that A. flavus, a prevalent contaminant of maize, cottonseed, peanuts and tree nuts, is capable of producing metabolites which, besides aflatoxin, could be an underappreciated contributor to its toxicity.

  10. Comparison of Expression of Secondary Metabolite Biosynthesis Cluster Genes in Aspergillus flavus, A. parasiticus, and A. oryzae

    Directory of Open Access Journals (Sweden)

    Kenneth C. Ehrlich

    2014-06-01

    Full Text Available Fifty six secondary metabolite biosynthesis gene clusters are predicted to be in the Aspergillus flavus genome. In spite of this, the biosyntheses of only seven metabolites, including the aflatoxins, kojic acid, cyclopiazonic acid and aflatrem, have been assigned to a particular gene cluster. We used RNA-seq to compare expression of secondary metabolite genes in gene clusters for the closely related fungi A. parasiticus, A. oryzae, and A. flavus S and L sclerotial morphotypes. The data help to refine the identification of probable functional gene clusters within these species. Our results suggest that A. flavus, a prevalent contaminant of maize, cottonseed, peanuts and tree nuts, is capable of producing metabolites which, besides aflatoxin, could be an underappreciated contributor to its toxicity.

  11. In vitro antibacterial activity of sphaeropsidins and chemical derivatives toward Xanthomonas oryzae pv. oryzae, the causal agent of rice bacterial blight.

    Science.gov (United States)

    Evidente, Antonio; Venturi, Vittorio; Masi, Marco; Degrassi, Giuliano; Cimmino, Alessio; Maddau, Lucia; Andolfi, Anna

    2011-12-27

    Sphaeropsidin A, the main phytotoxin produced by Diplodia cupressi, as well as the two natural analogues sphaeropsidins B and C and 14 derivatives obtained by chemical modifications were assayed for antibacterial activity against Xanthomonas oryzae pv. oryzae, Pseudomonas fuscovaginae, and Burkholderia glumae, the causal agents of severe bacterial rice diseases. The results showed a strong and specific activity of sphaeropsidin A against X. oryzae pv. oryzae, while no activity was observed against the other two pathogens. The results of structure-activity relationship studies showed that structural features important to impart this antibacterial activity are the presence of the C-7 carbonyl group and the hemiketalic lactone functionality. The C-13 vinyl group, the double bond of ring C, and/or the tertiary C-9 hydroxy group, as well as the pimarane arrangement of the tricylic carbon skeleton, were also important for the antibacterial activity. These findings may be useful in designing novel compounds for practical applications in agriculture.

  12. Suppression of Rice Blast by Preinoculation with Avirulent Pyricularia oryzae and the Nonrice Pathogen Bipolaris sorokiniana.

    Science.gov (United States)

    Manandhar, H K; Lyngs Jørgensen, H J; Mathur, S B; Smedegaard-Petersen, V

    1998-07-01

    ABSTRACT Avirulent isolates of Pyricularia oryzae and isolates of Bipolaris sorokiniana, a nonrice pathogen, were used to suppress rice blast caused by P. oryzae. In greenhouse experiments, both fungi substantially reduced leaf blast when applied 24 h or more before the pathogen. B. sorokiniana, but not avirulent isolates of P. oryzae, systemically reduced disease in leaf 5 when applied to whole plants at the four-leaf stage. In field experiments, both fungi were able to reduce neck blast significantly. No increase in grain yield was obtained by using avirulent isolates of P. oryzae, whereas five sprays with B. sorokiniana from seedling to heading stages increased the grain yield in two of three experiments conducted at two locations in Nepal. The significant increase in yield was observed under high inoculum pressure of P. oryzae. Induced resistance is suggested to be involved in the suppression of disease.

  13. Secreted fungal sulfhydryl oxidases: sequence analysis and characterisation of a representative flavin-dependent enzyme from Aspergillus oryzae

    Directory of Open Access Journals (Sweden)

    Faccio Greta

    2010-08-01

    Full Text Available Abstract Background Sulfhydryl oxidases are flavin-dependent enzymes that catalyse the formation of de novo disulfide bonds from free thiol groups, with the reduction of molecular oxygen to hydrogen peroxide. Sulfhydryl oxidases have been investigated in the food industry to remove the burnt flavour of ultraheat-treated milk and are currently studied as potential crosslinking enzymes, aiming at strengthening wheat dough and improving the overall bread quality. Results In the present study, potential sulfhydryl oxidases were identified in the publicly available fungal genome sequences and their sequence characteristics were studied. A representative sulfhydryl oxidase from Aspergillus oryzae, AoSOX1, was expressed in the fungus Trichoderma reesei. AoSOX1 was produced in relatively good yields and was purified and biochemically characterised. The enzyme catalysed the oxidation of thiol-containing compounds like glutathione, D/L-cysteine, beta-mercaptoethanol and DTT. The enzyme had a melting temperature of 57°C, a pH optimum of 7.5 and its enzymatic activity was completely inhibited in the presence of 1 mM ZnSO4. Conclusions Eighteen potentially secreted sulfhydryl oxidases were detected in the publicly available fungal genomes analysed and a novel proline-tryptophan dipeptide in the characteristic motif CXXC, where X is any amino acid, was found. A representative protein, AoSOX1 from A. oryzae, was produced in T. reesei in an active form and had the characteristics of sulfhydryl oxidases. Further testing of the activity on thiol groups within larger peptides and on protein level will be needed to assess the application potential of this enzyme.

  14. The ColRS system of Xanthomonas oryzae pv. oryzae is required for virulence and growth in iron-limiting conditions.

    Science.gov (United States)

    Subramoni, Sujatha; Pandey, Alok; Vishnu Priya, M R; Patel, Hitendra Kumar; Sonti, Ramesh V

    2012-09-01

    Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight of rice, produces siderophores only under iron-limiting conditions. We screened 15 400 mTn5-induced mutants of X. oryzae pv. oryzae and isolated 27 mutants that produced siderophores even under iron-replete conditions. We found that the mTn5 insertions in 25 of these mutants were in or close to six genes. Mutants with insertions in five of these genes [colS, XOO1806 (a conserved hypothetical protein), acnB, prpR and prpB] exhibited a deficiency for growth on iron-limiting medium and a decrease in virulence. Insertions in a sixth gene, XOO0007 (a conserved hypothetical protein), were found to affect the ability to grow on iron-limiting medium, but did not affect the virulence. Targeted gene disruptants for colR (encoding the predicted cognate regulatory protein for ColS) also exhibited a deficiency for growth on iron-limiting medium and a decrease in virulence. colR and colS mutants were defective in the elicitation of hypersensitive response symptoms on the nonhost tomato. In addition, colR and colS mutants induced a rice basal defence response, suggesting that they are compromised in the suppression of host innate immunity. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) analysis demonstrated that a functional ColRS system is required for the optimal expression of several genes encoding components of the type 3 secretion system (T3SS) of X. oryzae pv. oryzae. Our results demonstrate the role of several novel genes, including colR/colS, in the promotion of growth on iron-limiting medium and the virulence of X. oryzae pv. oryzae.

  15. The RpfB-Dependent Quorum Sensing Signal Turnover System Is Required for Adaptation and Virulence in Rice Bacterial Blight Pathogen Xanthomonas oryzae pv. oryzae.

    Science.gov (United States)

    Wang, Xing-Yu; Zhou, Lian; Yang, Jun; Ji, Guang-Hai; He, Ya-Wen

    2016-03-01

    Xanthomonas oryzae pv. oryzae, the bacterial blight pathogen of rice, produces diffusible signal factor (DSF) family quorum sensing signals to regulate virulence. The biosynthesis and perception of DSF family signals require components of the rpf (regulation of pathogenicity factors) cluster. In this study, we report that RpfB plays an essential role in DSF family signal turnover in X. oryzae pv. oryzae PXO99A. The production of DSF family signals was boosted by deletion of the rpfB gene and was abolished by its overexpression. The RpfC/RpfG-mediated DSF signaling system negatively regulates rpfB expression via the global transcription regulator Clp, whose activity is reversible in the presence of cyclic diguanylate monophosphate. These findings indicate that the DSF family signal turnover system in PXO99A is generally consistent with that in Xanthomonas campestris pv. campestris. Moreover, this study has revealed several specific roles of RpfB in PXO99A. First, the rpfB deletion mutant produced high levels of DSF family signals but reduced extracellular polysaccharide production, extracellular amylase activity, and attenuated pathogenicity. Second, the rpfB/rpfC double-deletion mutant was partially deficient in xanthomonadin production. Taken together, the RpfB-dependent DSF family signal turnover system is a conserved and naturally presenting signal turnover system in Xanthomonas spp., which plays unique roles in X. oryzae pv. oryzae adaptation and pathogenesis.

  16. A collection of glycosyltransferases from rice (Oryza sativa) exposed to atrazine.

    Science.gov (United States)

    Lu, Yi Chen; Yang, Sheng Ning; Zhang, Jing Jing; Zhang, Jia Jun; Tan, Li Rong; Yang, Hong

    2013-12-01

    The rice (Oryza sativa) GTs belong to a super family possibly with hundreds of members. However, which GTs are involved in plant response to toxic chemicals is unknown. Here, we demonstrated 59 novel GT genes screened from our recent genome-wide sequencing datasets of rice crops exposed to atrazine (a herbicide persistent in ecosystems). Analysis of GT genes showed that most of the GTs contain functional domains typically found in proteins transferring glycosyl moieties to their target compounds. A phylogenetic analysis revealed that many GT genes from different families have diverse cis-elements necessary for response to biotic and environmental stresses. Experimental validation for the GTs was undertaken through a microarray, and 36 GT genes were significantly detected with an expression pattern similar to that from deep-sequencing datasets. Furthermore, 12 GT genes were randomly selected and confirmed by quantitative real-time RT-PCR. Finally, the special activity of total GTs was determined in rice roots and shoots, with an increased activity under the atrazine exposure. This response was closely associated with atrazine absorption in the rice tissues. These results indicate that exposure to atrazine can trigger specific GT genes and enzyme activities in rice.

  17. Sequence analysis of ORF IV RTBV isolated from tungro infected Oryza sativa L. cv Ciherang

    Science.gov (United States)

    Hastilestari, Bernadetta Rina; Astuti, Dwi; Estiati, Amy; Nugroho, Satya

    2015-09-01

    The Effort to increase rice production is often constrained by pest and disease such as Tungro. The Tungro disease is caused by the joint infection with two dissimilar viruses; a bacil-form-DNA virus, the Rice tungro bacilliform virus(RTBV) and the spherical RNA virus, Rice tungro spherical virus (RTSV) and transmitted by Green leafhopper (Nephotettix virescens). The symptom of disease is caused by the presence of RTBV. The genome of RTBV consists of four Open reading frames (ORFs) which encode functional proteins. Of the four, ORF IV is unique because it exists only in RTBV. The most efficient method of generating disease resistance plants is to look for natural sources of resistance genes in wild or germplasm and then transfer the gene and the accompanying resistance in cultivated crop varieties. The aim of this study is, therefore, to isolate and analyze of 1170 bp gene of ORF 4 of Tungro virus isolated from an Indonesian rice cultivar, Ciherang (Oryza sativa L. cv Indica). DNA sequencing analysis using BLAST showed 94% similarity with the reference sequence gen bank Acc.M65026.1. The comparisons and mutation analysis of DNA sequences were discussed in this research.

  18. Systematic characterization of the peroxidase gene family provides new insights into fungal pathogenicity in Magnaporthe oryzae.

    Science.gov (United States)

    Mir, Albely Afifa; Park, Sook-Young; Abu Sadat, Md; Kim, Seongbeom; Choi, Jaeyoung; Jeon, Junhyun; Lee, Yong-Hwan

    2015-07-02

    Fungal pathogens have evolved antioxidant defense against reactive oxygen species produced as a part of host innate immunity. Recent studies proposed peroxidases as components of antioxidant defense system. However, the role of fungal peroxidases during interaction with host plants has not been explored at the genomic level. Here, we systematically identified peroxidase genes and analyzed their impact on fungal pathogenesis in a model plant pathogenic fungus, Magnaporthe oryzae. Phylogeny reconstruction placed 27 putative peroxidase genes into 15 clades. Expression profiles showed that majority of them are responsive to in planta condition and in vitro H2O2. Our analysis of individual deletion mutants for seven selected genes including MoPRX1 revealed that these genes contribute to fungal development and/or pathogenesis. We identified significant and positive correlations among sensitivity to H2O2, peroxidase activity and fungal pathogenicity. In-depth analysis of MoPRX1 demonstrated that it is a functional ortholog of thioredoxin peroxidase in Saccharomyces cerevisiae and is required for detoxification of the oxidative burst within host cells. Transcriptional profiling of other peroxidases in ΔMoprx1 suggested interwoven nature of the peroxidase-mediated antioxidant defense system. The results from this study provide insight into the infection strategy built on evolutionarily conserved peroxidases in the rice blast fungus.

  19. QTL detection and elite alleles mining for stigma traits in Oryza sativa by association mapping

    Directory of Open Access Journals (Sweden)

    Xiaojing Dang

    2016-08-01

    Full Text Available Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across two years and assessed their genotypic variation with 249 simple sequence repeat (SSR markers. By combining phenotypic and genotypic data, a genome-wide association (GWA map was generated. Large phenotypic variations in stigma length (STL, stigma brush-shaped part length (SBPL and stigma non-brush-shaped part length (SNBPL were found. Significant positive correlations were identified among stigma traits. In total, 2,072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future.

  20. Genes for iron-sulphur cluster assembly are targets of abiotic stress in rice, Oryza sativa.

    Science.gov (United States)

    Liang, Xuejiao; Qin, Lu; Liu, Peiwei; Wang, Meihuan; Ye, Hong

    2014-03-01

    Iron-sulphur (Fe-S) cluster assembly occurs in chloroplasts, mitochondria and cytosol, involving dozens of genes in higher plants. In this study, we have identified 41 putative Fe-S cluster assembly genes in rice (Oryza sativa) genome, and the expression of all genes was verified. To investigate the role of Fe-S cluster assembly as a metabolic pathway, we applied abiotic stresses to rice seedlings and analysed Fe-S cluster assembly gene expression by qRT-PCR. Our data showed that genes for Fe-S cluster assembly in chloroplasts of leaves are particularly sensitive to heavy metal treatments, and that Fe-S cluster assembly genes in roots were up-regulated in response to iron toxicity, oxidative stress and some heavy metal assault. The effect of each stress treatment on the Fe-S cluster assembly machinery demonstrated an unexpected tissue or organelle specificity, suggesting that the physiological relevance of the Fe-S cluster assembly is more complex than thought. Furthermore, our results may reveal potential candidate genes for molecular breeding of rice.

  1. Tourist C transposable elements are closely associated with genes expressed in flowers of rice (Oryza sativa).

    Science.gov (United States)

    Iwamoto, M; Higo, K

    2003-03-01

    Tourist elements comprise a group of transposable elements in plants. One of these elements, Tourist-OsaCatA(a Tourist C element), has been found in the 5; flanking region of a catalase gene, CatA, in rice (Oryza sativa). Using reverse transcriptase-PCR (RT-PCR) analyses of leaves, roots, flowers and developing seeds of rice, we assessed the transcription levels of ten known genes containing Tourist C elements, and of three additional putative genes for which expressed sequence tags (ESTs) including Tourist C elements have been isolated. We found that nine of the ten known genes and two of the three represented by ESTs were expressed in at least one of the organs we analyzed, and all of the genes detected were expressed in flowers, usually in stamens or pistils. We also assessed the expression of the 29 Tourist C-containing hypothetical coding sequences (CDSs) obtained so far by high-throughput genomic sequencing. We found that CDSs of all 11 genes whose transcripts were detectable by RT-PCR were expressed in flowers, especially in stamens or pistils. In contrast, RT-PCR analyses of genes or CDSs associated with other miniature inverted-repeat transposable elements (MITEs), such as Tourist D, Gaijin, Explorer, and Castaway, showed that some of them were expressed only minimally or not at all in flowers. Therefore, compared with other MITEs, Tourist C elements seem to show a strong association with genes that are expressed in the flowers of rice.

  2. An improved Agrobacterium-mediated transformation of recalcitrant indica rice (Oryza sativa L.) cultivars.

    Science.gov (United States)

    Shri, Manju; Rai, Arti; Verma, Pankaj Kumar; Misra, Prashant; Dubey, Sonali; Kumar, Smita; Verma, Sikha; Gautam, Neelam; Tripathi, Rudra Deo; Trivedi, Prabodh Kumar; Chakrabarty, Debasis

    2013-04-01

    Agrobacterium-mediated transformation of indica rice varieties has been quite difficult as these are recalcitrant to in vitro responses. In the present study, we established a high-efficiency Agrobacterium tumefaciens-mediated transformation system of rice (Oryza sativa L. ssp. indica) cv. IR-64, Lalat, and IET-4786. Agrobacterium strain EHA-101 harboring binary vector pIG121-Hm, containing a gene encoding for β-glucuronidase (GUS) and hygromycin resistance, was used in the transformation experiments. Manipulation of different concentrations of acetosyringone, days of co-culture period, bacterial suspension of different optical densities (ODs), and the concentrations of L-cysteine in liquid followed by solid co-culture medium was done for establishing the protocol. Among the different co-culture periods, 5 days of co-culture with bacterial cells (OD600 nm = 0.5-0.8) promoted the highest frequency of transformation (83.04 %) in medium containing L-cysteine (400 mg l(-1)). Putative transformed plants were analyzed for the presence of a transgene through genomic PCR and GUS histochemical analyses. Our results also suggest that different cultural conditions and the addition of L-cysteine in the co-culture medium improve the Agrobacterium-mediated transformation frequencies from an average of 12.82 % to 33.33 % in different indica rice cultivars.

  3. Ripening for improving the quality of inoculated cheese Rhizopus oryzae

    Directory of Open Access Journals (Sweden)

    ARTINI PANGASTUTI

    2010-01-01

    Full Text Available Estikomah SA, Sutarno, Pangastuti A 2010. Ripening for improving the quality of inoculated cheese Rhizopus oryzae. Nusantara Bioscience 2: 1-6. Cheese is dairy product resulted from fermented milk in which the fermentation process can be done by lactic acid bacteria or fungus. Rhizopus oryzae is able to produce lactic acid, protease and lipase. The ripening process changes the taste and texture. The purpose of this study is ripening to improve the quality of inoculated cheese R. oryzae. In this research the ripening was conducted the concentration variation of temperature (5oC, 10oC, 15oC, and time (7 days, 14 days. The procedure of research consisted of two steps, namely un-ripened cheese preparation followed by ripening cheese preparation. Cheese produced in this study analyzed the value of pH, fat content, protein content, amino acid levels and identification of microbe with ANOVA then followed by DMRT at 5% level of significance. Data results were analyzed with the like’s nonparametric statistical test, followed by Fridman Wilcoxon Signed Rank Test (WSRT at 5% level significance. The results showed that the preferred ripened cheese panelist was at a temperature of 15oC for 14 days. Ripening conditions affect pH, fat content, protein content and do not affect the levels of amino acids that formed ripened cheese. The best quality ripened cheese i.e. at a temperature of 15°C for 14 days, had a pH value of 4.40, the highest protein content of 9.78%, and fat content of 35.02%. The results of identified microbe in un-ripened cheese and ripened cheese include Enterococcus hirae (Enterococcus faecalis, Bacillus subtilis, and Aspergillus sp.

  4. Pemeraman untuk meningkatkan kualitas keju yang diinnokulasi Rhizopus oryzae

    Directory of Open Access Journals (Sweden)

    SOLIKAH ANA ESTIKOMAH

    2010-11-01

    Full Text Available Estikomah SA, Sutarno, Pangastuti A. 2010. Pemeraman untuk meningkatkaan kualitas keju yang diinokulasi Rhizopus oryzae. Bioteknologi 7: 55-62. Keju merupakan makanan hasil fermentasi dari susu yang proses fermentasinya dilakukan oleh bakteri asam laktat maupun jamur. Rhizopus oryzae diketahui mampu menghasilkan asam laktat, protease, dan lipase. Perubahan cita rasa dan tekstur keju terjadi selama pemeraman keju. Tujuan penelitian ini adalah untuk meningkatkan kualitas keju yang diinokulasi R. oryzae melalui pemeraman. Pemeraman dilakukan dengan variasi waktu (7, 14 hari dan suhu (5ºC, 10ºC, 15ºC. Penelitian ini terdiri dua tahap, yaitu pembuataan keju mentah diikuti pemeraman keju mentah tersebut. Keju penelitian dianalisis nilai pH, kadar lemak, kadar protein, kadar asam amino dan diidentifikasi mikrobanya. Data hasil penellitian dianalisis dengan uji siidik ragam (ANAVA, kemudian dilanjutkan dengan uji berjarak ganda Duncan (DMRT pada taraf signifikansi 5%. Data hasil tingkat kesukaan dianalisis dengan statistik nonparametrik uji Fridman yang dilanjutkaan dengan Wilcoxon Signed Rank Test (WSRT pada taraf sigifikansi 5%. Hasil penelitian menunjukkan bahwa keju peram yang disukai panelis adalah keju peram pada suhu 15ºC selama 14 hari. Kondisi pemeraman berpengaruh terhadap nilai pH, kadar lemak,, kadar proteinn dan tidak berpengaruh pada kadar asam amino. Kualitas keju peram terbaik terdapat pada kondisi suhu 15°C selama 14 hari, memiliki nilai pH 4,40, kadar protein tertinggi yaitu sebesar 99,78%, dan kadar lemak sebesar 35,02%. Hasil identifikasi mikroba pada keju mentah dan keju peram meliputi Enterococcus hirae (Enterococcus faecalis, Bacillus subtilis, dan Aspergillus sp.

  5. Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

    OpenAIRE

    Ziwen He; Weiwei Zhai; Haijun Wen; Tian Tang; Yu Wang; Xuemei Lu; Greenberg, Anthony J.; Hudson, Richard R; Chung-I Wu; Suhua Shi

    2011-01-01

    Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) ...

  6. Subcutaneous mucormycosis caused by Rhizopus oryzae: probable nosocomial acquired infection

    Directory of Open Access Journals (Sweden)

    Flávio de Queiroz Telles Filho

    1985-08-01

    Full Text Available The Authors present a case of subcutaneous mucormycosis occurring in a patient with clinical and biochemical evidence of diabetic ketoacidosis. The clinical, mycological and histopathological features are described, emphasizing the relevance of a rapid diagnosis in order to stablish early treatment. The clinical forms of mucormycosis and the main associated conditions are briefly reviewed as well as the most probable conditions which may lead to the enhanced susceptibility to infection in the diabetic patient in ketoacidosis. The recovery of Rhizopus oryzae from the air of the room of the patient suggests a nosocomial infection acquired through contamination of venous puncture site by air borne spores.

  7. Evidence for biotrophic lifestyle and biocontrol potential of dark septate endophyte Harpophora oryzae to rice blast disease.

    Directory of Open Access Journals (Sweden)

    Zhen-Zhu Su

    Full Text Available The mutualism pattern of the dark septate endophyte (DSE Harpophora oryzae in rice roots and its biocontrol potential in rice blast disease caused by Magnaporthe oryzae were investigated. Fluorescent protein-expressing H. oryzae was used to monitor the colonization pattern. Hyphae invaded from the epidermis to the inner cortex, but not into the root stele. Fungal colonization increased with root tissue maturation, showing no colonization in the meristematic zone, slight colonization in the elongation zone, and heavy colonization in the differentiation zone. H. oryzae adopted a biotrophic lifestyle in roots accompanied by programmed cell death. Real-time PCR facilitated the accurate quantification of fungal growth and the respective plant response. The biocontrol potential of H. oryzae was visualized by inoculation with eGFP-tagged M. oryzae in rice. H. oryzae protected rice from M. oryzae root invasion by the accumulation of H2O2 and elevated antioxidative capacity. H. oryzae also induced systemic resistance against rice blast. This systemic resistance was mediated by the OsWRKY45-dependent salicylic acid (SA signaling pathway, as indicated by the strongly upregulated expression of OsWRKY45. The colonization pattern of H. oryzae was consistent with the typical characteristics of DSEs. H. oryzae enhanced local resistance by reactive oxygen species (ROS and high antioxidative level and induced OsWRKY45-dependent SA-mediated systemic resistance against rice blast.

  8. Evidence for biotrophic lifestyle and biocontrol potential of dark septate endophyte Harpophora oryzae to rice blast disease.

    Science.gov (United States)

    Su, Zhen-Zhu; Mao, Li-Juan; Li, Na; Feng, Xiao-Xiao; Yuan, Zhi-Lin; Wang, Li-Wei; Lin, Fu-Cheng; Zhang, Chu-Long

    2013-01-01

    The mutualism pattern of the dark septate endophyte (DSE) Harpophora oryzae in rice roots and its biocontrol potential in rice blast disease caused by Magnaporthe oryzae were investigated. Fluorescent protein-expressing H. oryzae was used to monitor the colonization pattern. Hyphae invaded from the epidermis to the inner cortex, but not into the root stele. Fungal colonization increased with root tissue maturation, showing no colonization in the meristematic zone, slight colonization in the elongation zone, and heavy colonization in the differentiation zone. H. oryzae adopted a biotrophic lifestyle in roots accompanied by programmed cell death. Real-time PCR facilitated the accurate quantification of fungal growth and the respective plant response. The biocontrol potential of H. oryzae was visualized by inoculation with eGFP-tagged M. oryzae in rice. H. oryzae protected rice from M. oryzae root invasion by the accumulation of H2O2 and elevated antioxidative capacity. H. oryzae also induced systemic resistance against rice blast. This systemic resistance was mediated by the OsWRKY45-dependent salicylic acid (SA) signaling pathway, as indicated by the strongly upregulated expression of OsWRKY45. The colonization pattern of H. oryzae was consistent with the typical characteristics of DSEs. H. oryzae enhanced local resistance by reactive oxygen species (ROS) and high antioxidative level and induced OsWRKY45-dependent SA-mediated systemic resistance against rice blast.

  9. NCBI nr-aa BLAST: CBRC-LAFR-01-0180 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-LAFR-01-0180 ref|YP_202918.1| hypothetical protein XOO4279 [Xanthomonas oryzae... pv. oryzae KACC10331] gb|AAW77533.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae KACC10331] YP_202918.1 5.0 37% ...

  10. NCBI nr-aa BLAST: CBRC-DYAK-04-0090 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DYAK-04-0090 ref|YP_451289.1| YapH protein [Xanthomonas oryzae pv. oryzae MAFF... 311018] dbj|BAE69015.1| YapH protein [Xanthomonas oryzae pv. oryzae MAFF 311018] YP_451289.1 0.044 24% ...

  11. NCBI nr-aa BLAST: CBRC-LAFR-01-0066 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-LAFR-01-0066 ref|YP_201438.1| drug resistance translocase [Xanthomonas oryzae ...pv. oryzae KACC10331] gb|AAW76053.1| drug resistance translocase [Xanthomonas oryzae pv. oryzae KACC10331] YP_201438.1 2.2 31% ...

  12. NCBI nr-aa BLAST: CBRC-BTAU-01-2358 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-BTAU-01-2358 ref|YP_200700.1| hypothetical protein XOO2061 [Xanthomonas oryzae... pv. oryzae KACC10331] gb|AAW75315.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae KACC10331] YP_200700.1 2.4 31% ...

  13. NCBI nr-aa BLAST: CBRC-ACAR-01-0222 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ACAR-01-0222 ref|YP_201677.1| hypothetical protein XOO3038 [Xanthomonas oryzae... pv. oryzae KACC10331] gb|AAW76292.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae KACC10331] YP_201677.1 0.004 27% ...

  14. NCBI nr-aa BLAST: CBRC-TBEL-01-1996 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TBEL-01-1996 ref|YP_202056.1| hypothetical protein XOO3417 [Xanthomonas oryzae... pv. oryzae KACC10331] gb|AAW76671.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae KACC10331] YP_202056.1 2.5 23% ...

  15. NCBI nr-aa BLAST: CBRC-MEUG-01-2504 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MEUG-01-2504 ref|YP_001915750.1| hypothetical protein PXO_02997 [Xanthomonas o...ryzae pv. oryzae PXO99A] gb|ACD61218.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae PXO99A] YP_001915750.1 0.33 35% ...

  16. NCBI nr-aa BLAST: CBRC-XTRO-01-0645 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-XTRO-01-0645 ref|YP_200775.1| hypothetical protein XOO2136 [Xanthomonas oryzae... pv. oryzae KACC10331] gb|AAW75390.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae KACC10331] YP_200775.1 3e-41 40% ...

  17. NCBI nr-aa BLAST: CBRC-TNIG-22-0185 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TNIG-22-0185 ref|YP_451103.1| manganese transport protein [Xanthomonas oryzae ...pv. oryzae MAFF 311018] dbj|BAE68829.1| manganese transport protein [Xanthomonas oryzae pv. oryzae MAFF 311018] YP_451103.1 0.030 28% ...

  18. NCBI nr-aa BLAST: CBRC-TNIG-22-0185 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TNIG-22-0185 ref|YP_200844.1| putative manganese transport protein MntH [Xanth...omonas oryzae pv. oryzae KACC10331] gb|AAW75459.1| manganese transport protein [Xanthomonas oryzae pv. oryzae KACC10331] YP_200844.1 0.030 28% ...

  19. NCBI nr-aa BLAST: CBRC-PMAR-01-0384 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PMAR-01-0384 ref|YP_200844.1| putative manganese transport protein MntH [Xanth...omonas oryzae pv. oryzae KACC10331] gb|AAW75459.1| manganese transport protein [Xanthomonas oryzae pv. oryzae KACC10331] YP_200844.1 1.7 33% ...

  20. De Novo Transcriptome Sequencing of Oryza officinalis Wall ex Watt to Identify Disease-Resistance Genes

    Directory of Open Access Journals (Sweden)

    Bin He

    2015-12-01

    Full Text Available Oryza officinalis Wall ex Watt is one of the most important wild relatives of cultivated rice and exhibits high resistance to many diseases. It has been used as a source of genes for introgression into cultivated rice. However, there are limited genomic resources and little genetic information publicly reported for this species. To better understand the pathways and factors involved in disease resistance and accelerating the process of rice breeding, we carried out a de novo transcriptome sequencing of O. officinalis. In this research, 137,229 contigs were obtained ranging from 200 to 19,214 bp with an N50 of 2331 bp through de novo assembly of leaves, stems and roots in O. officinalis using an Illumina HiSeq 2000 platform. Based on sequence similarity searches against a non-redundant protein database, a total of 88,249 contigs were annotated with gene descriptions and 75,589 transcripts were further assigned to GO terms. Candidate genes for plant–pathogen interaction and plant hormones regulation pathways involved in disease-resistance were identified. Further analyses of gene expression profiles showed that the majority of genes related to disease resistance were all expressed in the three tissues. In addition, there are two kinds of rice bacterial blight-resistant genes in O. officinalis, including two Xa1 genes and three Xa26 genes. All 2 Xa1 genes showed the highest expression level in stem, whereas one of Xa26 was expressed dominantly in leaf and other 2 Xa26 genes displayed low expression level in all three tissues. This transcriptomic database provides an opportunity for identifying the genes involved in disease-resistance and will provide a basis for studying functional genomics of O. officinalis and genetic improvement of cultivated rice in the future.

  1. Identification and gene prediction of a 24 kb region containing xa5, a recessive bacterial blight resistance gene in rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    ZHONG Yiming; JIANG Guanghuai; CHEN Xuewei; XIA Zhihui; LI Xiaobing; ZHU Lihuang; ZHAI Wenxue

    2003-01-01

    Rice xa5 gene provides recessive, race-specific resistance to bacterial blight disease caused by the pathogen Xanthomonas oryzae pv. oryzae and has great value for research and breeding. In an effort to clone xa5, an F2 population of 4892 individuals was developed from the xa5 near isogenic lines, IR24 and IRBB5. A fine mapping procedure was conducted and tightly linked RFLP markers were used to screen a BAC library of IRBB56, a resistant rice line containing the xa5 gene. A 213 kb contig covering the xa5 locus was constructed. According to the sequences from the International Rice Genome Sequening Project (IRGSP), the Chinese Superhybrid Rice Genome Project (SRGP) and some sub-clones of the contig, twelve SSLP and CAPS markers were developed for fine mapping. The xa5 gene was mapped to a 0.3 cM interval between markers K5 and T4, which spanned an interval of approximately 24 kb, co-segregating with marker T2. Sequence analysis of the 24 kb region revealed that an ABC transporter and a basal transcription factor (TFIIa) were potential candidates for the xa5 resistance gene product. The molecular mechanism by which the xa5 gene provides recessive, race-specific resistance to bacterial blight will be elucidated by the functional tests of the 24 kb DNA and the candidate genes.

  2. Cladal relatedness among Aspergillus oryzae isolates and Aspergillus flavus S and L morphotype isolates.

    Science.gov (United States)

    Chang, Perng-Kuang; Ehrlich, Kenneth C; Hua, Sui-Sheng T

    2006-04-25

    Aspergillus flavus is the main etiological agent for aflatoxin contamination of crops. Its close relative, A. oryzae, does not produce aflatoxins and has been widely used to produce fermented foods. We compared the phylogeny of A. oryzae isolates and L- and S-type sclerotial isolates of A. flavus using single nucleotide polymorphisms in the omtA gene in the aflatoxin biosynthesis gene cluster and deletions in and distal to the norB-cypA intergenic region as phylogenetic signals. Aflatoxin-producing ability and sclerotial size also were weighted in the analysis. Like A. flavus, the A. oryzae isolates form a polyphyletic assemblage. A. oryzae isolates in one clade strikingly resemble an A. flavus subgroup of atoxigenic L-type isolates. All toxigenic S-type isolates closely resemble another subgroup of atoxigenic L-type isolates. Because atoxigenic S-type isolates are extremely rare, we hypothesize that loss of aflatoxin production in S-type isolates may occur concomitantly with a change to L-type sclerotia. All toxigenic L-type isolates, unlike A. oryzae, have a 1.0 kb deletion in the norB-cypA region. Although A. oryzae isolates, like S-type, have a 1.5 kb deletion in the norB-cypA region, none were cladally related to S-type A. flavus isolates. Our results show that A. flavus populations are genetically diverse. A. oryzae isolates may descend from certain atoxigenic L-type A. flavus isolates.

  3. WRKY transcription factor genes in wild rice Oryza nivara.

    Science.gov (United States)

    Xu, Hengjian; Watanabe, Kenneth A; Zhang, Liyuan; Shen, Qingxi J

    2016-08-01

    The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants. Bioinformatic analyses suggest that most of OnWRKY genes could be induced by salicylic acid, abscisic acid, and drought. Abundant potential MAPK phosphorylation sites in OnWRKYs suggest that activities of most OnWRKYs can be regulated by phosphorylation. Phylogenetic analyses of OnWRKYs support a novel hypothesis that ancient group IIc OnWRKYs were the original ancestors of only some group IIc and group III WRKYs. The analyses also offer strong support that group IIc OnWRKYs containing the HVE sequence in their zinc finger motifs were derived from group Ia WRKYs. This study provides a solid foundation for the study of the evolution and functions of WRKY genes in O. nivara.

  4. Produksi Gula Reduksi oleh Rhizopus oryzae dari Substrat Bekatul

    Directory of Open Access Journals (Sweden)

    ARTINI PANGASTUTI

    2005-05-01

    Full Text Available Rice bran was produced from rice-hulling process. Rice bran was contain high starch, therefore it was used to saccharification process. The aim of this research was to study the optimum concentration of rice bran to produce reducing sugar on saccharification process by Rhizopus oryzae. The 100 mL-rice bran medium (5, 10, 15, 20, 25, and 30% were sterilized at 1210C, for 15 minutes and inoculated with R. oryzae (± 2x106 cfu and incubated for3 days. The concentration of reducing sugar, starch, pH value, and biomass were analyzed everyday. Concentration of starch was decreasing during saccharification process. However, the concentration of reducing sugar was maximum at first day saccharification. The optimum concentration of rice bran for saccharification process was showed by maximum production of reducing sugar (15,347 mg/mL; it was in 20% concentration of medium. The pH value was decreasing during saccharification process, and the biomass was reversed.

  5. Toward understanding of rice innate immunity against Magnaporthe oryzae.

    Science.gov (United States)

    Azizi, P; Rafii, M Y; Abdullah, S N A; Nejat, N; Maziah, M; Hanafi, M M; Latif, M A; Sahebi, M

    2016-01-01

    The blast fungus, Magnaporthe oryzae, causes serious disease on a wide variety of grasses including rice, wheat and barley. The recognition of pathogens is an amazing ability of plants including strategies for displacing virulence effectors through the adaption of both conserved and variable pathogen elicitors. The pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) were reported as two main innate immune responses in plants, where PTI gives basal resistance and ETI confers durable resistance. The PTI consists of extracellular surface receptors that are able to recognize PAMPs. PAMPs detect microbial features such as fungal chitin that complete a vital function during the organism's life. In contrast, ETI is mediated by intracellular receptor molecules containing nucleotide-binding (NB) and leucine rich repeat (LRR) domains that specifically recognize effector proteins produced by the pathogen. To enhance crop resistance, understanding the host resistance mechanisms against pathogen infection strategies and having a deeper knowledge of innate immunity system are essential. This review summarizes the recent advances on the molecular mechanism of innate immunity systems of rice against M. oryzae. The discussion will be centered on the latest success reported in plant-pathogen interactions and integrated defense responses in rice.

  6. Safety evaluation of a lipase expressed in Aspergillus oryzae.

    Science.gov (United States)

    Greenough, R J; Perry, C J; Stavnsbjerg, M

    1996-02-01

    A programme of studies was conducted to establish the safety of a lipase artificially expressed in Aspergillus oryzae to be used in the detergent industry and as a processing aid in the baking industry. Laboratory animal studies were used to assess general and inhalation toxicity, skin sensitization, and skin and eye irritation. Its potential to cause mutagenicity and chromosomal aberrations was assessed in microbial and tissue culture in vitro studies. The pathogenicity of A. oryzae, the organism used to produce the lipase, was also assessed in laboratory animals. Basic ecotoxicity in a variety of test species was studied. General and inhalation toxicity was low. There was evidence of mild skin irritation. There was no evidence of eye irritation, skin sensitization, mutagenic potential, chromosomal aberrations, exotoxicity or notable pathogenicity. Comparison of these results with human exposure levels and previously published data indicates that the lipase appears safe for consumers in the given applications, requires no special occupational health precautions in manufacture and is of low environmental impact. Furthermore, the organism used in production of the lipase hs no notable pathogenicity.

  7. Enhanced acid tolerance of Rhizopus oryzae during fumaric acid production.

    Science.gov (United States)

    Liu, Ying; Lv, Chunwei; Xu, Qing; Li, Shuang; Huang, He; Ouyang, Pingkai

    2015-02-01

    Ensuring a suitable pH in the culture broth is a major problem in microorganism-assisted industrial fermentation of organic acids. To address this issue, we investigated the physiological changes in Rhizopus oryzae at different extracellular pH levels and attempted to solve the issue of cell shortage under low pH conditions. We compared various parameters, such as membrane fatty acids' composition, intracellular pH, and adenosine triphosphate (ATP) concentration. It was found that the shortage of intracellular ATP might be the main reason for the low rate of fumaric acid production by R. oryzae under low pH conditions. When 1 g/l citrate was added to the culture medium at pH 3.0, the intracellular ATP concentration increased from 0.4 to 0.7 µmol/mg, and the fumaric acid titer was enhanced by 63% compared with the control (pH 3.0 without citrate addition). The final fumaric acid concentration at pH 3.0 reached 21.9 g/l after 96 h of fermentation. This strategy is simple and feasible for industrial fumaric acid production under low pH conditions.

  8. A.A., constructivism, and reflecting teams.

    Science.gov (United States)

    Nevels, B

    1997-12-01

    Numerous studies and clinical anecdotes reveal a relationship between attendance at A.A. meetings and/or degree of involvement in A.A. and maintenance of sobriety. Hypotheses as to how A.A. and/or the A.A. meeting is helpful to its members have ranged from a focus on factors common to all therapy groups, to aspects of A.A. "treatment" which are behavioral in nature. Presented here is another way of understanding A.A.'s effectiveness within the frame of more recent, constructivistic approaches to family therapy. In particular, the A.A. topic meeting is compared to the reflecting team concept of Tom Anderson.

  9. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees, and whole-genome-based data

    Science.gov (United States)

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining data sets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data, and mol...

  10. Cell wall degrading enzyme induced rice innate immune responses are suppressed by the type 3 secretion system effectors XopN, XopQ, XopX and XopZ of Xanthomonas oryzae pv. oryzae.

    Science.gov (United States)

    Sinha, Dipanwita; Gupta, Mahesh Kumar; Patel, Hitendra Kumar; Ranjan, Ashish; Sonti, Ramesh V

    2013-01-01

    Innate immune responses are induced in plants and animals through perception of Damage Associated Molecular Patterns. These immune responses are suppressed by pathogens during infection. A number of studies have focussed on identifying functions of plant pathogenic bacteria that are involved in suppression of Pathogen Associated Molecular Pattern induced immune responses. In comparison, there is very little information on functions used by plant pathogens to suppress Damage Associated Molecular Pattern induced immune responses. Xanthomonasoryzae pv. oryzae, a gram negative bacterial pathogen of rice, secretes hydrolytic enzymes such as LipA (Lipase/Esterase) that damage rice cell walls and induce innate immune responses. Here, we show that Agrobacterium mediated transient transfer of the gene for XopN, a X. oryzae pv. oryzae type 3 secretion (T3S) system effector, results in suppression of rice innate immune responses induced by LipA. A xopN (-) mutant of X. oryzae pv. oryzae retains the ability to suppress these innate immune responses indicating the presence of other functionally redundant proteins. In transient transfer assays, we have assessed the ability of 15 other X. oryzae pv. oryzae T3S secreted effectors to suppress rice innate immune responses. Amongst these proteins, XopQ, XopX and XopZ are suppressors of LipA induced innate immune responses. A mutation in any one of the xopN, xopQ, xopX or xopZ genes causes partial virulence deficiency while a xopN (-) xopX (-) double mutant exhibits a greater virulence deficiency. A xopN (-) xopQ (-) xopX (-) xopZ (-) quadruple mutant of X. oryzae pv. oryzae induces callose deposition, an innate immune response, similar to a X. oryzae pv. oryzae T3S(-) mutant in rice leaves. Overall, these results indicate that multiple T3S secreted proteins of X. oryzae pv. oryzae can suppress cell wall damage induced rice innate immune responses.

  11. Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides.

    Science.gov (United States)

    Doan, Thanh Thi Ngoc; Kim, Jin-Kwang; Ngo, Ho-Phuong-Thuy; Tran, Huyen-Thi; Cha, Sun-Shin; Min Chung, Kyung; Huynh, Kim-Hung; Ahn, Yeh-Jin; Kang, Lin-Woo

    2014-03-01

    D-Alanine-D-alanine ligase (DDL) catalyzes the biosynthesis of d-alanyl-d-alanine, an essential bacterial peptidoglycan precursor, and is an important drug target for the development of antibacterials. We determined four different crystal structures of DDL from Xanthomonas oryzae pv. oryzae (Xoo) causing Bacteria Blight (BB), which include apo, ADP-bound, ATP-bound, and AMPPNP-bound structures at the resolution between 2.3 and 2.0 Å. Similarly with other DDLs, the active site of XoDDL is formed by three loops from three domains at the center of enzyme. Compared with d-alanyl-d-alanine and ATP-bound TtDDL structure, the γ-phosphate of ATP in XoDDL structure was shifted outside toward solution. We swapped the ω-loop (loop3) of XoDDL with those of Escherichia coli and Helicobacter pylori DDLs, and measured the enzymatic kinetics of wild-type XoDDL and two mutant XoDDLs with the swapped ω-loops. Results showed that the direct interactions between ω-loop and other two loops are essential for the active ATP conformation for D-ala-phosphate formation.

  12. Molecular and pathogenic characterization of new Xanthomonas oryzae pv. oryzae strains from the coastline region of Fangchenggang city in China.

    Science.gov (United States)

    Yang, Shu-Qing; Liu, Shu-Yan; Zhao, Shuai; Yu, Yan-Hua; Li, Rong-Bai; Duan, Cheng-Jie; Tang, Ji-Liang; Feng, Jia-Xun

    2013-04-01

    Virulence assays and DNA polymorphism analyses were used to characterize 33 Xanthomonas oryzae pv. oryzae (Xoo) strains collected from the coastline region of Fangchenggang city in China. Two new pathogenic races (FXP1 and FXP2), were determined by leaf-clipping inoculation of 12 near-isogenic International Rice-Bacterial Blight (IRBB) rice lines, each containing a single resistance gene. Race FXP1 consisted of twenty-eight strains that were incompatible on IRBB5 and IRBB7, while race FXP2 included five strains that were incompatible on IRBB5 and IRBB7 and moderately virulent on IRBB8 containing the xa8 gene. Restriction fragment length polymorphism (RFLP) analysis revealed that each probe of avrXa10 and IS1112 resolved two haplotypes. In a dendrogram generated from the combined RFLP data, the 33 Xoo strains were resolved into two clusters. There was a weak correlation (r = 0.53) between race and haplotype. All of the rice cultivars planted in the coastline region of Fangchenggang city were susceptible to the representative Xoo strains tested above. However, we found that four rice cultivars used as breeding materials in the laboratory could fully resist infection by the Xoo strains, suggesting that the isolated Xoo strains could be used to detect resistant rice cultivars suitable for planting in the local rice field.

  13. Identification of Intergeneric Hybrid Plants Between Oryza sativa and O. minuta via GISH and RAPD

    Institute of Scientific and Technical Information of China (English)

    YU Shun-wu; CHEN Bao-tang; TAO Ai-lin; ZHANG Duan-pin

    2003-01-01

    To transfer desirable resistance traits from O. minuta to O. sativa, intergeneric hybrid plants between O. sativa (AA, 2n=2X=24) and O. minuta (BBCC, 2n=4X=48) were produced by embryo rescue after sexual cross. Morphological observation and chromosome counts indicated their hybrid status (ABC, 2n =3X=36). Genomic in situ hybridization (GISH) was further applied to confirm the parentage of the chromosomes of F1 hybrids. Chromosomes of O. minuta and O. sativa were distinguishable in the hybrids in different fluorescence colors. GISH indicated that A and BC chromosomes were not randomly assembled in a cell.RAPD profiles unequivocally revealed their hybrids with double parent patterns. The results of blast tests showed that the hybrids had obtained disease resistance from O. minuta, and had a level of susceptibility between the parents.

  14. Genome-wide transcription analyses in rice using tiling microarrays

    DEFF Research Database (Denmark)

    Li, Lei; Wang, Xiangfeng; Stolc, Viktor;

    2006-01-01

    Sequencing and computational annotation revealed several features, including high gene numbers, unusual composition of the predicted genes and a large number of genes lacking homology to known genes, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species....... We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions...... activity between duplicated segments of the genome. Collectively, our results provide the first whole-genome transcription map useful for further understanding the rice genome. Udgivelsesdato: 2006-Jan...

  15. Laboratory Astrophysics Division of the AAS (LAD)

    Science.gov (United States)

    Salama, Farid; Drake, R. P.; Federman, S. R.; Haxton, W. C.; Savin, D. W.

    2012-01-01

    The purpose of the Laboratory Astrophysics Division (LAD) is to advance our understanding of the Universe through the promotion of fundamental theoretical and experimental research into the underlying processes that drive the Cosmos. LAD represents all areas of astrophysics and planetary sciences. The first new AAS Division in more than 30 years, the LAD traces its history back to the recommendation from the scientific community via the White Paper from the 2006 NASA-sponsored Laboratory Astrophysics Workshop. This recommendation was endorsed by the Astronomy and Astrophysics Advisory Committee (AAAC), which advises the National Science Foundation (NSF), the National Aeronautics and Space Administration (NASA), and the U.S. Department of Energy (DOE) on selected issues within the fields of astronomy and astrophysics that are of mutual interest and concern to the agencies. In January 2007, at the 209th AAS meeting, the AAS Council set up a Steering Committee to formulate Bylaws for a Working Group on Laboratory Astrophysics (WGLA). The AAS Council formally established the WGLA with a five-year mandate in May 2007, at the 210th AAS meeting. From 2008 through 2012, the WGLA annually sponsored Meetings in-a-Meeting at the AAS Summer Meetings. In May 2011, at the 218th AAS meeting, the AAS Council voted to convert the WGLA, at the end of its mandate, into a Division of the AAS and requested draft Bylaws from the Steering Committee. In January 2012, at the 219th AAS Meeting, the AAS Council formally approved the Bylaws and the creation of the LAD. The inaugural gathering and the first business meeting of the LAD were held at the 220th AAS meeting in Anchorage in June 2012. You can learn more about LAD by visiting its website at http://lad.aas.org/ and by subscribing to its mailing list.

  16. Kinetic studies of acid inactivation of alpha-amylase from Aspergillus oryzae

    DEFF Research Database (Denmark)

    Carlsen, Morten; Nielsen, Jens Bredal; Villadsen, John

    1996-01-01

    The stability of alpha-amylase from Aspergillus oryzae has been studied at different pH. The enzyme is extremely stable at neutral pH (pH 5-8), whereas outside this pH-range a substantial loss of activity is observed. The acid-inactivation of alpha-amylase from A. oryzae was monitored on-line by ......The stability of alpha-amylase from Aspergillus oryzae has been studied at different pH. The enzyme is extremely stable at neutral pH (pH 5-8), whereas outside this pH-range a substantial loss of activity is observed. The acid-inactivation of alpha-amylase from A. oryzae was monitored on...

  17. High-level expression and characterization of a chimeric lipase from Rhizopus oryzae for biodiesel production

    OpenAIRE

    Yu, Xiao-Wei; Sha, Chong; Guo, Yong-Liang; Xiao, Rong; Xu, Yan

    2013-01-01

    Background Production of biodiesel from non-edible oils is receiving increasing attention. Tung oil, called “China wood oil” is one kind of promising non-edible biodiesel oil in China. To our knowledge, tung oil has not been used to produce biodiesel by enzymatic method. The enzymatic production of biodiesel has been investigated extensively by using Rhizopus oryzae lipase as catalyst. However, the high cost of R. oryzae lipase remains a barrier for its industrial applications. Through differ...

  18. Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.)

    OpenAIRE

    Yi Zhou; Ping Yang; Fenglei Cui; Fantao Zhang; Xiangdong Luo; Jiankun Xie

    2016-01-01

    Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.), and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling...

  19. A successful treatment of rhinocerebral mucormycosis due to Rhizopus oryzae

    Directory of Open Access Journals (Sweden)

    Rasoul Mohammadi

    2014-01-01

    Full Text Available Mucormycosis is an invasive fungal infection caused by filamentous fungi of the Mucoraceae family. The genera most commonly responsible are Mucor or Rhizopus. The disease occurs mostly in association with diabetic ketoacidosis. Mucormycosis has an extremely high death rate even when aggressive surgery is done. Death rates range from 25-85% depending on the body area involved. A case of rhinocerebral mucormycosis in a 65-year-old diabetic male patient typically presenting as headache, especially in parietal and frontal lobes, with nose and left eye discharge. After clinical and laboratory examination, mucormycosis was diagnosed, and Rhizopus oryzae was isolated. Systemic therapy with amphotericin B administered intravenously then replaced by posaconazole by a combination of aggressive surgery. The patient was treated and followed up for one year. We emphasize the importance of early detection and aggressive treatment in the management of this fatal disease.

  20. Oxygen dynamics in submerged rice (Oryza sativa L.)

    DEFF Research Database (Denmark)

    Colmer, Timothy D.; Pedersen, Ole

    2008-01-01

    Complete submergence of plants prevents direct O2 and CO2 exchange with air. Underwater photosynthesis can result in marked diurnal changes in O2 supply to submerged plants. Dynamics in pO2 had not been measured directly for submerged rice (Oryza sativa), but in an earlier study, radial O2 loss...... from roots showed an initial peak following shoot illumination.  O2 dynamics in shoots and roots of submerged rice were monitored during light and dark periods, using O2 microelectrodes. Tissue sugar concentrations were also measured.  On illumination of shoots of submerged rice, pO2 increased rapidly...... of magnitude higher than in darkness, enhancing also pO2 in roots.The initial peak in pO2 following illumination of submerged rice was likely to result from high initial rates of net photosynthesis, fuelled by CO2 accumulated during the dark period. Nevertheless, since sugars decline with time in submerged...

  1. Monoolein production by triglycerides hydrolysis using immobilized Rhizopus oryzae lipase.

    Science.gov (United States)

    Ghattas, Nesrine; Abidi, Ferid; Galai, Said; Marzouki, M Nejib; Salah, Abderraouf Ben

    2014-07-01

    Lipase extracted from Rhizopus oryzae was immobilized in alginate gel beads. The effects of the immobilization conditions, such as, alginate concentration, CaCl2 concentration and amount of initial enzyme on retained activity (specific activity ratio of entrapped active lipase to free lipase) were investigated. The optimal conditions for lipase entrapment were determined: 2% (w/v) alginate concentration, 100mM CaCl2 and enzyme ratio of 2000IU/mL.In such conditions, immobilized lipase by inclusion in alginate showed a highest stability and activity, on olive oil hydrolysis reaction where it could be reused for 10 cycles. After 15min of hydrolysis reaction, the mass composition of monoolein, diolein and triolein were about 78%, 10% and 12%. Hydrolysis' products purification by column chromatography lead to a successful separation of reaction compounds and provide a pure fraction of monoolein which is considered as the widest used emulsifier in food and pharmaceutical industries.

  2. Interaction of malathion, an organophosphorus pesticide with Rhizopus oryzae biomass

    Energy Technology Data Exchange (ETDEWEB)

    Chatterjee, Subhankar; Das, Sujoy K.; Chakravarty, Rajdeep; Chakrabarti, Adrita [Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India); Ghosh, Subrata [West Bengal Pollution Control Board, Paribesh Bhawan, Kakinara, 24 Parganas (N), PIN - 743126 (India); Guha, Arun K., E-mail: bcakg@mahendra.iacs.res.in [Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India)

    2010-02-15

    Adsorption of malathion on Rhizopus oryzae biomass (ROB) with special reference to binding mechanism has been described. ROB has been found to adsorb {approx}85% of malathion from its aqueous solution as against 47-68% by other fungal biomasses. Hydrogen ion concentration does not influence the adsorption of malathion by ROB which follows Langmuir-Freundlich dual equilibrium isotherm model (r{sup 2} = 0.998). Both physical and chemical interactions are responsible for binding of malathion on ROB. Scanning electron micrographs and EDXA spectra exhibit adsorption of the pesticide on cell surface of ROB. Studies with cell surface polysaccharides show that chitosan through its amine groups contributes largely in the adsorption of malathion. Extraction of lipids from ROB decreases its adsorption capacity to the extent of 36.37-94.02%, depending on the polarity of the solvent.

  3. Impressions of Alcoholics Anonymous (AA) Group Cohesion: A Case for a Nonspecific Factor Predicting Later AA Attendance.

    Science.gov (United States)

    Rice, Samara Lloyd; Tonigan, J Scott

    2012-01-04

    Social support for abstinence in Alcoholics Anonymous (AA) has been reported to be a consistent factor accounting for AA benefit. However, the nonspecific or unintended effects of such support remain poorly understood and rarely investigated. This prospective study investigated how one nonspecific factor-perceived AA group cohesiveness-predicted increased practice of AA-related behaviors. Findings indicated that impressions of AA group cohesion predicted increased AA attendance, the practice of prescribed AA activities, and self-reported AA usefulness. It appears that a sense of belongingness predicts subsequent engagement in the AA social network that, in turn, is predictive of increased abstinence.

  4. EFICIÊNCIA DE FUNGICIDAS NO CONTROLE DE MANCHA PARDA (Bipolaris oryzae EM ARROZ (Oryza sativa EFFICIENCY OF FUNGICIDES IN THE CONTROL OF RICE (Oryza sativa BROWN SPOT (Bipolaris oryzae

    Directory of Open Access Journals (Sweden)

    Eric Guicherit

    2007-09-01

    Full Text Available

    Em situações nas quais a brusone tem pouca importância na sanidade da lavoura de arroz, o controle da mancha parda (Bipolaris Oryzõe pode mostrar-se altamente eficiente com pulverizações de fungicidas no campo. Assim, realizou-se um experimento em Indiara (GO com o objetivo de comparar a eficácia de diferentes produtos fungicidas no controle da mancha parda em condições pouco favoráveis à brusone. Foram comparados difenoconazole, propiconazole e tryfloxystrobin em diferentes combinações e dosagens, e os resultados mostraram que, em situações nas quais a brusone tem pouca importância na sanidade da lavoura do arroz, o controle da mancha parda pode mostrar-se altamente eficiente com pulverizações de fungicidas no campo.

    PALAVRAS-CHAVE: Helminthosporium oryzae; controle químico; patógeno; doença.

    In situations where the blight (Pyricularia grisea is not limiting the rice crop, the brown spot (Bipolaris oryzae control can be extremely efficient with field sprayings. This experiment was conduced in Indiara (GO aiming to compare the efficiency of different fungicides in one or two dosages in the control of brown spot under low blight conditions. All treatments showed efficiency in the control of brown spot, with no signifficant difference among them.

    KEY-WORDS: Chemical control; pathogens; disease.

  5. CHROMIUM BIOREMOVAL FROM TANNERY INDUSTRIES EFFLUENT BY ASPERGILLUS ORYZAE

    Directory of Open Access Journals (Sweden)

    M. Nouri Sepehr, S. Nasseri, M. Mazaheri Assadi and K. Yaghmaian

    2005-10-01

    Full Text Available Recently laboratory studies had recognized the capability of alge, fungi, and bacteria in the removal of heavy metals from industrial effluent. In this research, growth of Aspergillus oryzae in the tanning house effluent, and its capability in chromium bioremoval were assessed. Aspergillus oryzae can grow in different concentration of Cr+, 120-1080 mg/l. Maximum biomass growth and chromium removal rate at pH, 3.3, Cr+3 concentration equal to 240 mg/l and inoculum size equal to 0.12% (dry weight were 0.25% (dry weight and 94.2%, respectively. Effects of various factors such as pH, temperature, shaking velocity and nutrients were also investigated. At optimum conditions (ie: pH=5; temperature=30ºC, shaking velocity = 150 rpm, and nitrogen source of dihydrogen ammonium phosphate concentration=0.3%, biomass growth and chromium removal rate were found as 0.45% of dry weight and 99.8%, respectively. Effect of detention time showed that after 30h, biomass growth and chromium removal rate were 0.28% and 97.6%, respectively. Statistical studies on factors such as pH, temperature, shaking velocity, type and concentration of nutrients on the “biomass growth” and “residual chromium”, showed that all of the factors had significant effects ( α = 0.05, P < 0.001 . Therefore A.niger capable grow in the tannery industries effluent with 240 mg/l chromium and 97.6% chromium removal rate .

  6. Production of flavor compounds from olive mill waste by Rhizopus oryzae and Candida tropicalis.

    Science.gov (United States)

    Guneser, Onur; Demirkol, Asli; Yuceer, Yonca Karagul; Togay, Sine Ozmen; Hosoglu, Muge Isleten; Elibol, Murat

    The purpose of this study was to investigate the production of flavor compounds from olive mill waste by microbial fermentation of Rhizopus oryzae and Candida tropicalis. Olive mill waste fermentations were performed in shake and bioreactor cultures. Production of flavor compounds from olive mill waste was followed by Gas Chromatography-Mass spectrometry, Gas chromatography- olfactometry and Spectrum Sensory Analysis(®). As a result, 1.73-log and 3.23-log cfu/mL increases were observed in the microbial populations of R. oryzae and C. tropicalis during shake cultures, respectively. C. tropicalis can produce a higher concentration of d-limonene from olive mill waste than R. oryzae in shake cultures. The concentration of d-limonene was determined as 185.56 and 249.54μg/kg in the fermented olive mill waste by R. oryzae and C. tropicalis in shake cultures respectively. In contrast, R. oryzae can produce a higher concentration of d-limonene (87.73μg/kg) d-limonene than C. tropicalis (11.95μg/kg) in bioreactor cultures. Based on sensory analysis, unripe olive, wet towel, sweet aromatic, fermented aromas were determined at high intensity in olive mill waste fermented with R. oryzae meanwhile olive mill waste fermented with C. tropicalis had only a high intensity of unripe olive and oily aroma. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  7. Linoleic and linolenic acids analysis of soybean tofu with Rhizopus oryzae and Rhizopus oligosporus as coagulant

    Directory of Open Access Journals (Sweden)

    SUPYANI

    2009-07-01

    Full Text Available Sudaryatiningsih C, Supyani. 2009. Linoleic and linolenic acids analysis of soybean tofu with Rhizopus oryzae and Rhizopus oligosporus as coagulant. Nusantara Bioscience 1: 110-116. The aims of this research are to know the potency of Rhizopus oligosporus and Rhizopus oryzae as a coagulant in tofu processing for increasing the amount of linoleic and linolenic acids, and to know the time that needed by R. oligosporus and R. oryzae for increasing the amount of linoleic and linolenic acids. It uses PDA for inoculating fungi, and it is done at Sub-Lab Chemistry, Central Laboratory for Mathematics and Natural Sciences, Sebelas Maret University, Surakarta. The tofu making was done in “Dele Emas” Tofu Factory, Surakarta. Analysis of linoleic and linolenic acids were done by Gas Chromatography, in LPPT-UGM Yogyakarta. The conclusion of this research are R. oligosporus dan R. oryzae having a potency as a coagulant in tofu processing for increasing the amount of linoleic and linolenic acids. R. oryzae needs 18 hours to coagulate the tofu, and R. oligosporus needs 12 hours for the same process. The highest amount of linoleic and linolenic acids were obtained by R. oryzae at 6 hours of fermentation (0.26% and 0.14%, and 24 hours of fermentation by R. oligosporus (0.06% and 0.04%.

  8. Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice.

    Science.gov (United States)

    Brozynska, Marta; Copetti, Dario; Furtado, Agnelo; Wing, Rod A; Crayn, Darren; Fox, Glen; Ishikawa, Ryuji; Henry, Robert J

    2016-11-27

    The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

  9. The Xanthomonas oryzae pv. oryzae PilZ Domain Proteins Function Differentially in Cyclic di-GMP Binding and Regulation of Virulence and Motility.

    Science.gov (United States)

    Yang, Fenghuan; Tian, Fang; Chen, Huamin; Hutchins, William; Yang, Ching-Hong; He, Chenyang

    2015-07-01

    The PilZ domain proteins have been demonstrated to be one of the major types of receptors mediating cyclic di-GMP (c-di-GMP) signaling pathways in several pathogenic bacteria. However, little is known about the function of PilZ domain proteins in c-di-GMP regulation of virulence in the bacterial blight pathogen of rice Xanthomonas oryzae pv. oryzae. Here, the roles of PilZ domain proteins PXO_00049 and PXO_02374 in c-di-GMP binding, regulation of virulence and motility, and subcellular localization were characterized in comparison with PXO_02715, identified previously as an interactor with the c-di-GMP receptor Filp to regulate virulence. The c-di-GMP binding motifs in the PilZ domains were conserved in PXO_00049 and PXO_02374 but were less well conserved in PXO_02715. PXO_00049 and PXO_02374 but not PXO_02715 proteins bound to c-di-GMP with high affinity in vitro, and the R(141) and R(10) residues in the PilZ domains of PXO_00049 and PXO_02374, respectively, were crucial for c-di-GMP binding. Gene deletion of PXO_00049 and PXO_02374 resulted in significant increases in virulence and hrp gene transcription, indicating their negative regulation of virulence via type III secretion system expression. All mutants showed significant changes in sliding motility but not exopolysaccharide production and biofilm formation. In trans expression of the full-length open reading frame (ORF) of each gene in the relevant mutants led to restoration of the phenotype to wild-type levels. Moreover, PXO_00049 and PXO_02374 displayed mainly multisite subcellular localizations, whereas PXO_02715 showed nonpolar distributions in the X. oryzae pv. oryzae cells. Therefore, this study demonstrated the different functions of the PilZ domain proteins in mediation of c-di-GMP regulation of virulence and motility in X. oryzae pv. oryzae.

  10. Ketoglutarate transport protein KgtP is secreted through the type III secretion system and contributes to virulence in Xanthomonas oryzae pv. oryzae.

    Science.gov (United States)

    Guo, Wei; Cai, Lu-Lu; Zou, Hua-Song; Ma, Wen-Xiu; Liu, Xi-Ling; Zou, Li-Fang; Li, Yu-Rong; Chen, Xiao-Bin; Chen, Gong-You

    2012-08-01

    The phytopathogenic prokaryote Xanthomonas oryzae pv. oryzae is the causal agent of bacterial leaf blight (BB) of rice and utilizes a type III secretion system (T3SS) to deliver T3SS effectors into rice cells. In this report, we show that the ketoglutarate transport protein (KgtP) is secreted in an HpaB-independent manner through the T3SS of X. oryzae pv. oryzae PXO99(A) and localizes to the host cell membrane for α-ketoglutaric acid export. kgtP contained an imperfect PIP box (plant-inducible promoter) in the promoter region and was positively regulated by HrpX and HrpG. A kgtP deletion mutant was impaired in bacterial virulence and growth in planta; furthermore, the mutant showed reduced growth in minimal media containing α-ketoglutaric acid or sodium succinate as the sole carbon source. The reduced virulence and the deficiency in α-ketoglutaric acid utilization by the kgtP mutant were restored to wild-type levels by the presence of kgtP in trans. The expression of OsIDH, which is responsible for the synthesis of α-ketoglutaric acid in rice, was enhanced when KgtP was present in the pathogen. To our knowledge, this is the first report demonstrating that KgtP, which is regulated by HrpG and HrpX and secreted by the T3SS in Xanthomonas oryzae pv. oryzae, transports α-ketoglutaric acid when the pathogen infects rice.

  11. Association mapping and genetic dissection of nitrogen use efficiency-related traits in rice (Oryza sativa L.).

    Science.gov (United States)

    Liu, Zhiyi; Zhu, Chengsong; Jiang, Yue; Tian, Yunlu; Yu, Jun; An, Hongzhou; Tang, Weijie; Sun, Juan; Tang, Jianpeng; Chen, Gaoming; Zhai, Huqu; Wang, Chunming; Wan, Jianmin

    2016-05-01

    The increases in the usage of nitrogen fertilizer result in deleterious impacts on the environment; thus, there is an urgent need to improve nitrogen use efficiency (NUE) in crops including rice (Oryza sativa L.). Attentions have focused on quantitative trait loci (QTL) mapping of NUE-related traits using single experimental population, but to date, very few studies have taken advantage of association mapping to examine hundreds of lines for identifying potentially novel QTLs in rice. Here, we conducted association analysis on NUE-related traits using a population containing 184 varieties, which were genotyped with 157 genome-wide simple sequence repeat (SSR) markers. We detected eight statistically significant marker loci associating with NUE-related traits, of which two QTLs at RM5639 and RM3628 harbored known NUE-related genes GS1;2 and AspAt3, respectively. At a novel NUE-related locus RM5748, we developed Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers and searched for putative NUE-related genes which are close to the associated SNP marker. Based on a transcriptional map of N stress responses constructed by our lab, we evaluated expressions of the NUE-related genes in this region and validated their effect on NUE. Meanwhile, we analyzed NUE-related alleles of the eight loci that could be utilized in marker-assisted selection. Moreover, we estimated breeding values of all the varieties through genomic prediction approach that could be beneficial for rice NUE enhancement.

  12. Evidence for Biotrophic Lifestyle and Biocontrol Potential of Dark Septate Endophyte Harpophora oryzae to Rice Blast Disease

    OpenAIRE

    Zhen-Zhu Su; Li-Juan Mao; Na Li; Xiao-Xiao Feng; Zhi-Lin Yuan; Li-Wei Wang; Fu-Cheng Lin; Chu-Long Zhang

    2013-01-01

    The mutualism pattern of the dark septate endophyte (DSE) Harpophora oryzae in rice roots and its biocontrol potential in rice blast disease caused by Magnaporthe oryzae were investigated. Fluorescent protein-expressing H. oryzae was used to monitor the colonization pattern. Hyphae invaded from the epidermis to the inner cortex, but not into the root stele. Fungal colonization increased with root tissue maturation, showing no colonization in the meristematic zone, slight colonization in the e...

  13. Molecular Evolution of the TAC1 Gene from Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    Jiahuan Jiang; Lubin Tan; Zuofeng Zhu; Yongcai Fu; Fengxia Liu; Hongwei Cai; Chuanqing Sun

    2012-01-01

    Tiller angle is a key feature of the architecture of cultivated rice (Oryza sativa),since it determines planting density and influences rice yield.Our previous work identified Tiller Angle Control 1 (TAC1) as a major quantitative trait locus that controls rice tiller angle.To further clarify the evolutionary characterization of the TAC1 gene,we compared a TAC1-containing 3164-bp genomic region among 113 cultivated varieties and 48 accessions of wild rice,including 43 accessions of O.rufipogon and five accessions of O.nivara.Only one single nucleotide polymorphism (SNP),a synonymous substitution,was detected in TAC1 coding regions of the cultivated rice varieties,whereas one synonymous and one nonsynonymous SNP were detected among the TAC1 coding regions of wild rice accessions.These data indicate that little natural mutation and modification in the TAC1 coding region occurred within the cultivated rice and its progenitor during evolution.Nucleotide diversities in the TAC1 gene regions of O.sativa and O.rufipogon of 0.00116 and 0.00112,respectively,further indicate that TAC1 has been highly conserved during the course of rice domestication.A functional nucleotide polymorphism (FNP) of TAC1 was only found in the japonica rice group.A neutrality test revealed strong selection,especially in the 3'-flanking region of the TAC1 coding region containing the FNP in the japonica rice group.However,no selection occurred in the indica and wild-rice groups.A phylogenetic tree derived from TAC1 sequence analysis suggests that the indica and japonica subspecies arose independently during the domestication of wild rice.

  14. A Novel Manganese Efflux System, YebN, Is Required for Virulence by Xanthomonas oryzae pv. oryzae

    Science.gov (United States)

    Li, Chunxia; Tao, Jun; Mao, Daqing; He, Chaozu

    2011-01-01

    Manganese ions (Mn2+) play a crucial role in virulence and protection against oxidative stress in bacterial pathogens. Such pathogens appear to have evolved complex mechanisms for regulating Mn2+ uptake and efflux. Despite numerous studies on Mn2+ uptake, however, only one efflux system has been identified to date. Here, we report on a novel Mn2+ export system, YebN, in Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial leaf blight. Compared with wild-type PXO99, the yebN mutant was highly sensitive to Mn2+ and accumulated high concentrations of intracellular manganese. In addition, we found that expression of yebN was positively regulated by Mn2+ and the Mn2+-dependent transcription regulator, MntR. Interestingly, the yebN mutant was more tolerant to methyl viologen and H2O2 in low Mn2+ medium than PXO99, but more sensitive in high Mn2+ medium, implying that YebN plays an important role in Mn2+ homoeostasis and detoxification of reactive oxygen species (ROS). Notably, deletion of yebN rendered Xoo sensitive to hypo-osmotic shock, suggesting that YebN may protect against such stress. That mutation of yebN substantially reduced the Xoo growth rate and lesion formation in rice implies that YebN could be involved in Xoo fitness in host. Although YebN has two DUF204 domains, it lacks homology to any known metal transporter. Hence, this is the first report of a novel metal export system that plays essential roles in hypo-osmotic and oxidative stress, and virulence. Our results lay the foundations for elucidating the complex and fascinating relationship between metal homeostasis and host-pathogen interactions. PMID:21789199

  15. Identification of an avirulence gene,avrxa5,from the rice pathogen Xanthomonas oryzae pv.oryzae

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Xanthomonas oryzae pv.oryzae,the causal agent of bacterial blight in rice,interacts with rice plants in a gene-for-gene manner.The specificity of the interaction is dictated by avirulence(avr) genes in the pathogen and resistance(R) genes in the host.To date,no avr genes that correspond to recessive R genes have been isolated.We isolated an avrBs3/pthA family gene,avrxa5,from our previously isolated clone p58,which was originally from strain JXOIII.The avrxa5 gene converted the PXO99A strain from compatible to incompatible in rice cultivars containing the recessive xa5 gene,but not in those containing the dominant Xa5 gene.Sequencing indicated that avrxa5,which is highly similar to members of the avrBs3/pthA family,encodes a protein of 1238 amino acid residues with a conserved carboxy-terminal region containing three nuclear localization signals and a transcription activation domain.It has 19.5 34-amino-acid direct repeats,but the 13th amino acid is missing in the fifth and ninth repetitive units.Domain swapping of the repetitive regions between avrxa5 and avrXa7 changed the avirulence specificity of the genes in xa5 and Xa7 rice lines,respectively.This indicates that avrxa5 is distinct from previously characterized avrBs3/pthA members.The specificity of avrxa5 toward recessive xa5 in rice could help us better understand the molecular mechanisms of plant-pathogen specific interactions.

  16. A novel manganese efflux system, YebN, is required for virulence by Xanthomonas oryzae pv. oryzae.

    Science.gov (United States)

    Li, Chunxia; Tao, Jun; Mao, Daqing; He, Chaozu

    2011-01-01

    Manganese ions (Mn(2+)) play a crucial role in virulence and protection against oxidative stress in bacterial pathogens. Such pathogens appear to have evolved complex mechanisms for regulating Mn(2+) uptake and efflux. Despite numerous studies on Mn(2+) uptake, however, only one efflux system has been identified to date. Here, we report on a novel Mn(2+) export system, YebN, in Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial leaf blight. Compared with wild-type PXO99, the yebN mutant was highly sensitive to Mn(2+) and accumulated high concentrations of intracellular manganese. In addition, we found that expression of yebN was positively regulated by Mn(2+) and the Mn(2+)-dependent transcription regulator, MntR. Interestingly, the yebN mutant was more tolerant to methyl viologen and H(2)O(2) in low Mn(2+) medium than PXO99, but more sensitive in high Mn(2+) medium, implying that YebN plays an important role in Mn(2+) homoeostasis and detoxification of reactive oxygen species (ROS). Notably, deletion of yebN rendered Xoo sensitive to hypo-osmotic shock, suggesting that YebN may protect against such stress. That mutation of yebN substantially reduced the Xoo growth rate and lesion formation in rice implies that YebN could be involved in Xoo fitness in host. Although YebN has two DUF204 domains, it lacks homology to any known metal transporter. Hence, this is the first report of a novel metal export system that plays essential roles in hypo-osmotic and oxidative stress, and virulence. Our results lay the foundations for elucidating the complex and fascinating relationship between metal homeostasis and host-pathogen interactions.

  17. Mapping of quantitative trait loci for fiber and lignin contents from an interspecific cross Oryza sativa×Oryza rufipogon

    Institute of Scientific and Technical Information of China (English)

    Jian-kun XIE; Xiang-li KONG; Jie CHEN; Biao-lin HU; Piao WEN; Jie-yun ZHUANG; Jin-song BAO

    2011-01-01

    Rice straw is always regarded as a by-product of rice production,but it could be a significant energy source for ruminant animals.Knowledge of the genetic variation and genetic architecture of cell wall traits will facilitate rice breeders by improving relevant traits through selective breeding and genetic engineering.The common wild rice,Oryza rufipogon Griff.,which is considered to be the progenitor of Oryza sativa,has been widely utilized for the identification of genes of agronomic importance for rice genetic improvement.In the present study,the mapping of quantitative trait loci (QTLs) for acid detergent fiber (ADF),neutral detergent fiber (NDF),acid detergent lignin (ADL),and ADL/NDF ratio was carried out in two environments using a backcrossed inbred line (BIL) population derived from a cross between the recurrent parent Xieqingzao B (XB) and an accession of Dongxiang wild rice (DWR).The results indicated that all four traits tested were continuously distributed among the BILs,but many BILs showed transgressive segregation.A total of 16 QTLs were identified for the four traits,but no QTLs were in common in two environments,suggesting that environment has dramatic effects on fiber and lignin syntheses.Compared to the QTL positions for grain yield-related traits,there were no unfavorable correlations between grain yield components and cell wall traits in this population.The QTLs identified in this study are useful for the development of dual-purpose rice varieties that are high in grain yield and are also high in straw quality.

  18. Microstructural and Mechanical Characterization of a Dissimilar Friction Stir-Welded AA5083-AA7B04 Butt Joint

    Science.gov (United States)

    Chen, Yu; Ding, Hua; Cai, Zhihui; Zhao, Jingwei; Li, Jizhong

    2016-12-01

    Friction stir welding (FSW) has been used for joining AA5083 and AA7B04 alloy sheets with the aim of studying the microstructure and the mechanical properties of dissimilar FSW joints obtained by varying the initial base metal state of AA7B04 alloy. The results show that the initial base metal state has a significant impact on the material flow during dissimilar FSW. As compared with the joints placing hard alloy (artificially aged AA7B04-AA or naturally aged AA7B04-NA) on the retreating side, it becomes easier transporting AA5083 from advancing side to retreating side when soft alloy (annealed AA7B04-O) is placed on the retreating side. The atomic diffusion does not occur at the interface between AA5083 and AA7B04, indicating that the mixing of the two materials is merely mechanical. Grain refinement is observed in the stir zone. The failure location during tensile tests is different depending on the initial base metal state. The joints (AA5083/AA7B04-AA and AA5083/AA7B04-O) fail in the base metal on the soft material side which corresponds to the minimum values in hardness profiles. Differently, the joints (AA5083/AA5083 and AA5083/AA7B04-O) fail in the stir zone due to the presence of defects including "zigzag line," kissing bond and discontinuous voids.

  19. Microstructural and Mechanical Characterization of a Dissimilar Friction Stir-Welded AA5083-AA7B04 Butt Joint

    Science.gov (United States)

    Chen, Yu; Ding, Hua; Cai, Zhihui; Zhao, Jingwei; Li, Jizhong

    2017-02-01

    Friction stir welding (FSW) has been used for joining AA5083 and AA7B04 alloy sheets with the aim of studying the microstructure and the mechanical properties of dissimilar FSW joints obtained by varying the initial base metal state of AA7B04 alloy. The results show that the initial base metal state has a significant impact on the material flow during dissimilar FSW. As compared with the joints placing hard alloy (artificially aged AA7B04-AA or naturally aged AA7B04-NA) on the retreating side, it becomes easier transporting AA5083 from advancing side to retreating side when soft alloy (annealed AA7B04-O) is placed on the retreating side. The atomic diffusion does not occur at the interface between AA5083 and AA7B04, indicating that the mixing of the two materials is merely mechanical. Grain refinement is observed in the stir zone. The failure location during tensile tests is different depending on the initial base metal state. The joints (AA5083/AA7B04-AA and AA5083/AA7B04-O) fail in the base metal on the soft material side which corresponds to the minimum values in hardness profiles. Differently, the joints (AA5083/AA5083 and AA5083/AA7B04-O) fail in the stir zone due to the presence of defects including "zigzag line," kissing bond and discontinuous voids.

  20. Ultrastructural morphologic description of the wild rice species Oryza latifolia (Poaceae in Costa Rica

    Directory of Open Access Journals (Sweden)

    Ethel Sánchez

    2003-06-01

    Full Text Available The wild rice species Oryza latifolia is endemic to Tropical America, allotetraploid and has a CCDD genome type. It belongs to the officinalis group of the genus Oryza. This species is widely distributed through-out the lowlands of Costa Rica and it is found on different life zones, having great morphologic diversity. The purpose of this research is to perform a morphologic description of O. latifolia samples of three Costa Rican localities (Carara, Liberia and Cañas and to see if the phenotypic diversity of the species is reflected at the ultra-structure level. Structures such as the leaf blade, ligule, auricles and spikelet were analyzed. Leaf blade morphology of the specimens from the three localities is characterized by the presence of diamond-shaped stomata with papillae, zipper-like rows of silica cells; a variety of evenly distributed epicuticular wax papillae and bulky prickle trichomes. The central vein of the leaf blade from the Cañas populations is glabrous, while those from Carara and Liberia have abundant papillae. There are also differences among the borders of the leaf blade between these locations. Cañas and Liberia present alternating large and small prickle trichomes ca. 81 and 150 µm, while Carara exhibits even sized prickle trichomes of ca. 93 µm. Auricles from Cañas are rectangular and present long trichomes along the surface ca. 1.5 mm, while those of Liberia and Carara wrap the culm and exhibit trichomes only in the borders. The ligule from the plants of Carara has an acute distal tip, while that of Cañas and Liberia is blunt. The Liberia spikelet has large lignified spines while Cañas and Carara show flexible trichomes.La especie silvestre Oryza latifolia es endémica de América, tetraploide y de genoma CCDD. Pertenece a las especies del género Oryza del grupo officinalis. Presenta una amplia distribución en las tierras bajas de Costa Rica y se le encuentra en varias zonas de vida, mostrando una gran diversidad

  1. Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park.

    Science.gov (United States)

    Romano, Christine; D'Imperio, Seth; Woyke, Tanja; Mavromatis, Konstantinos; Lasken, Roger; Shock, Everett L; McDermott, Timothy R

    2013-05-01

    We describe the complete genome sequences of four closely related Hydrogenobaculum sp. isolates (≥ 99.7% 16S rRNA gene identity) that were isolated from the outflow channel of Dragon Spring (DS), Norris Geyser Basin, in Yellowstone National Park (YNP), WY. The genomes range in size from 1,552,607 to 1,552,931 bp, contain 1,667 to 1,676 predicted genes, and are highly syntenic. There are subtle differences among the DS isolates, which as a group are different from Hydrogenobaculum sp. strain Y04AAS1 that was previously isolated from a geographically distinct YNP geothermal feature. Genes unique to the DS genomes encode arsenite [As(III)] oxidation, NADH-ubiquinone-plastoquinone (complex I), NADH-ubiquinone oxidoreductase chain, a DNA photolyase, and elements of a type II secretion system. Functions unique to strain Y04AAS1 include thiosulfate metabolism, nitrate respiration, and mercury resistance determinants. DS genomes contain seven CRISPR loci that are almost identical but are different from the single CRISPR locus in strain Y04AAS1. Other differences between the DS and Y04AAS1 genomes include average nucleotide identity (94.764%) and percentage conserved DNA (80.552%). Approximately half of the genes unique to Y04AAS1 are predicted to have been acquired via horizontal gene transfer. Fragment recruitment analysis and marker gene searches demonstrated that the DS metagenome was more similar to the DS genomes than to the Y04AAS1 genome, but that the DS community is likely comprised of a continuum of Hydrogenobaculum genotypes that span from the DS genomes described here to an Y04AAS1-like organism, which appears to represent a distinct ecotype relative to the DS genomes characterized.

  2. PKA activity is essential for relieving the suppression of hyphal growth and appressorium formation by MoSfl1 in Magnaporthe oryzae.

    Directory of Open Access Journals (Sweden)

    Yang Li

    2017-08-01

    Full Text Available In the rice blast fungus Magnaporthe oryzae, the cAMP-PKA pathway regulates surface recognition, appressorium turgor generation, and invasive growth. However, deletion of CPKA failed to block appressorium formation and responses to exogenous cAMP. In this study, we generated and characterized the cpk2 and cpkA cpk2 mutants and spontaneous suppressors of cpkA cpk2 in M. oryzae. Our results demonstrate that CPKA and CPK2 have specific and overlapping functions, and PKA activity is essential for appressorium formation and plant infection. Unlike the single mutants, the cpkA cpk2 mutant was significantly reduced in growth and rarely produced conidia. It failed to form appressoria although the intracellular cAMP level and phosphorylation of Pmk1 MAP kinase were increased. The double mutant also was defective in plant penetration and Mps1 activation. Interestingly, it often produced fast-growing spontaneous suppressors that formed appressoria but were still non-pathogenic. Two suppressor strains of cpkA cpk2 had deletion and insertion mutations in the MoSFL1 transcription factor gene. Deletion of MoSFL1 or its C-terminal 93-aa (MoSFL1ΔCT was confirmed to suppress the defects of cpkA cpk2 in hyphal growth but not appressorium formation or pathogenesis. We also isolated 30 spontaneous suppressors of the cpkA cpk2 mutant in Fusarium graminearum and identified mutations in 29 of them in FgSFL1. Affinity purification and co-IP assays showed that this C-terminal region of MoSfl1 was essential for its interaction with the conserved Cyc8-Tup1 transcriptional co-repressor, which was reduced by cAMP treatment. Furthermore, the S211D mutation at the conserved PKA-phosphorylation site in MoSFL1 partially suppressed the defects of cpkA cpk2. Overall, our results indicate that PKA activity is essential for appressorium formation and proper activation of Pmk1 or Mps1 in M. oryzae, and phosphorylation of MoSfl1 by PKA relieves its interaction with the Cyc8-Tup1 co

  3. The dawn of fungal pathogen genomics.

    Science.gov (United States)

    Xu, Jin-Rong; Peng, You-Liang; Dickman, Martin B; Sharon, Amir

    2006-01-01

    Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced fungal genomes. Several important plant pathogenic fungi are among those that have been sequenced or are being sequenced. Additional fungal pathogens are likely to be sequenced in the near future. Analysis of the available genomes has provided useful information about genes that may be important for plant infection and colonization. Genome features, such as repetitive sequences, telomeres, conserved syntenic blocks, and expansion of pathogenicity-related genes, are discussed in detail with Magnaporthe oryzae (M. grisea) and Fusarium graminearum as examples. Functional and comparative genomic studies in plant pathogenic fungi, although still in the early stages and limited to a few pathogens, have enormous potential to improve our understanding of the molecular mechanisms involved in host-pathogen interactions. Development of advanced genomics tools and infrastructure is critical for efficient utilization of the vast wealth of available genome sequence information and will form a solid foundation for systems biology studies of plant pathogenic fungi.

  4. Use of the Aspergillus oryzae actin gene promoter in a novel reporter system for exploring antifungal compounds and their target genes.

    Science.gov (United States)

    Marui, Junichiro; Yoshimi, Akira; Hagiwara, Daisuke; Fujii-Watanabe, Yoshimi; Oda, Ken; Koike, Hideaki; Tamano, Koichi; Ishii, Tomoko; Sano, Motoaki; Machida, Masayuki; Abe, Keietsu

    2010-08-01

    Demand for novel antifungal drugs for medical and agricultural uses has been increasing because of the diversity of pathogenic fungi and the emergence of drug-resistant strains. Genomic resources for various living species, including pathogenic fungi, can be utilized to develop novel and effective antifungal compounds. We used Aspergillus oryzae as a model to construct a reporter system for exploring novel antifungal compounds and their target genes. The comprehensive gene expression analysis showed that the actin-encoding actB gene was transcriptionally highly induced by benomyl treatment. We therefore used the actB gene to construct a novel reporter system for monitoring responses to cytoskeletal stress in A. oryzae by introducing the actB promoter::EGFP fusion gene. Distinct fluorescence was observed in the reporter strain with minimum background noise in response to not only benomyl but also compounds inhibiting lipid metabolism that is closely related to cell membrane integrity. The fluorescent responses indicated that the reporter strain can be used to screen for lead compounds affecting fungal microtubule and cell membrane integrity, both of which are attractive antifungal targets. Furthermore, the reporter strain was shown to be technically applicable for identifying novel target genes of antifungal drugs triggering perturbation of fungal microtubules or membrane integrity.

  5. Further increased production of free fatty acids by overexpressing a predicted transketolase gene of the pentose phosphate pathway in Aspergillus oryzae faaA disruptant.

    Science.gov (United States)

    Tamano, Koichi; Miura, Ai

    2016-09-01

    Free fatty acids are useful as source materials for the production of biodiesel fuel and various chemicals such as pharmaceuticals and dietary supplements. Previously, we attained a 9.2-fold increase in free fatty acid productivity by disrupting a predicted acyl-CoA synthetase gene (faaA, AO090011000642) in Aspergillus oryzae. In this study, we achieved further increase in the productivity by overexpressing a predicted transketolase gene of the pentose phosphate pathway in the faaA disruptant. The A. oryzae genome is predicted to have three transketolase genes and overexpression of AO090023000345, one of the three genes, resulted in phenotypic change and further increase (corresponding to an increased production of 0.38 mmol/g dry cell weight) in free fatty acids at 1.4-fold compared to the faaA disruptant. Additionally, the biomass of hyphae increased at 1.2-fold by the overexpression. As a result, free fatty acid production yield per liter of liquid culture increased at 1.7-fold by the overexpression.

  6. Comparison and Validation of Putative Pathogenicity-Related Genes Identified by T-DNA Insertional Mutagenesis and Microarray Expression Profiling in Magnaporthe oryzae

    Science.gov (United States)

    Wáng, Ying; Tan, Qi; Gao, Ying Nv; Li, Yan

    2017-01-01

    High-throughput technologies of functional genomics such as T-DNA insertional mutagenesis and microarray expression profiling have been employed to identify genes related to pathogenicity in Magnaporthe oryzae. However, validation of the functions of individual genes identified by these high-throughput approaches is laborious. In this study, we compared two published lists of genes putatively related to pathogenicity in M. oryzae identified by T-DNA insertional mutagenesis (comprising 1024 genes) and microarray expression profiling (comprising 236 genes), respectively, and then validated the functions of some overlapped genes between the two lists by knocking them out using the method of target gene replacement. Surprisingly, only 13 genes were overlapped between the two lists, and none of the four genes selected from the overlapped genes exhibited visible phenotypic changes on vegetative growth, asexual reproduction, and infection ability in their knockout mutants. Our results suggest that both of the lists might contain large proportions of unrelated genes to pathogenicity and therefore comparing the two gene lists is hardly helpful for the identification of genes that are more likely to be involved in pathogenicity as we initially expected.

  7. [The application of genome editing in identification of plant gene function and crop breeding].

    Science.gov (United States)

    Xiangchun, Zhou; Yongzhong, Xing

    2016-03-01

    Plant genome can be modified via current biotechnology with high specificity and excellent efficiency. Zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system are the key engineered nucleases used in the genome editing. Genome editing techniques enable gene targeted mutagenesis, gene knock-out, gene insertion or replacement at the target sites during the endogenous DNA repair process, including non-homologous end joining (NHEJ) and homologous recombination (HR), triggered by the induction of DNA double-strand break (DSB). Genome editing has been successfully applied in the genome modification of diverse plant species, such as Arabidopsis thaliana, Oryza sativa, and Nicotiana tabacum. In this review, we summarize the application of genome editing in identification of plant gene function and crop breeding. Moreover, we also discuss the improving points of genome editing in crop precision genetic improvement for further study.

  8. AA, closed orbit observation pickup

    CERN Multimedia

    CERN PhotoLab

    1980-01-01

    Electrostatic pickups around the circumference of the AA served for the measurement of the closed orbits across the wide momentum range of +- 3% to either side of central orbit. The pickups were of the "shoebox" type, with diagonal cuts, a horizontal and a vertical one mechanically coupled together. They were located where they would not require extra space. The wide ones (very wide indeed: 70 cm), like the one we see here, were placed inside the vacuum chamber of the wide quadrupoles QFW, at maximum dispersion. See also 8001372, 8001383, 8010045

  9. AA, closed orbit observation pickup

    CERN Multimedia

    CERN PhotoLab

    1980-01-01

    Electrostatic pickups around the circumference of the AA served for the measurement of the closed orbits across the wide momentum range of +- 3% to either side of central orbit. The pickups were of the "shoebox" type, with diagonal cuts, a horizontal and a vertical one mechanically coupled together. They were located where they would not require extra space. The wide ones (very wide indeed: 70 cm), like the one we see here, were placed inside the vacuum chamber of the wide quadrupoles, QFW, at maximum dispersion. See also 8001372,8001383, 8010042

  10. AA, closed orbit observation pickup

    CERN Multimedia

    1980-01-01

    Electrostatic pickups around the circumference of the AA served for the measurement of the closed orbits across the wide momentum range of +- 3% to either side of central orbit. The pickups were of the "shoebox" type, with diagonal cuts, a horizontal and a vertical one mechanically coupled together. They were located where they would not require extra space. The small ones, like the one we see here, were inserted into the vacuum chamber of the BLG (long and narrow) bending magnets. See also 8001372, 8010042, 8010045

  11. AA, closed orbit observation pickup

    CERN Multimedia

    CERN PhotoLab

    1980-01-01

    Electrostatic pickups around the circumference of the AA served for the measurement of the closed orbits across the wide momentum range of +- 3% to either side of central orbit. The pickups were of the "shoebox" type, with diagonal cuts, a horizontal and a vertical one mechanically coupled together. They were located where they would not require extra space. The small ones, like the one we see here, were inserted into the vacuum chamber of the BLG (long and narrow) bending magnets. Werner Sax contemplates his achievement. See also 8001383, 8010042, 8010045.

  12. What can comparative genomics tell us about species concepts in the genus Aspergillus?

    Energy Technology Data Exchange (ETDEWEB)

    Rokas, Antonis; payne, gary; Federova, Natalie D.; Baker, Scott E.; Machida, Masa; yu, Jiujiang; georgianna, D. R.; Dean, Ralph A.; Bhatnagar, Deepak; Cleveland, T. E.; Wortman, Jennifer R.; Maiti, R.; Joardar, V.; Amedeo, Paolo; Denning, David W.; Nierman, William C.

    2007-12-15

    Understanding the nature of species" boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus - N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species.

  13. Loss of a 1.6 Mb chromosome in Pyricularia oryzae harboring two alleles of AvrPik leads to acquisition of virulence to rice cultivars containing resistance alleles at the Pik locus.

    Science.gov (United States)

    Kusaba, Motoaki; Mochida, Taiga; Naridomi, Takeshi; Fujita, Yoshikatsu; Chuma, Izumi; Tosa, Yukio

    2014-11-01

    A small and extra chromosome of 1.6 Mb was previously identified in a Pyricularia oryzae strain, 84R-62B. To understand a role of the 1.6 Mb chromosome in the pathogenic changeability of P. oryzae, we performed experiments designed to characterize the 1.6 Mb chromosome in the present study. A gene family encoding secreted protein Pex31s in P. oryzae consists of five homologs, Pex31-A to -E. Among them, Pex31-A and -D are known to be recognized by Pik-m and Pik/Pik-m/Pik-p, respectively. In the present study, we identified Pex31-A and -D in the genome of 84R-62B. Segregation analyses using an F1 population between 84R-62B and another rice blast strain, Y93-245c-2, revealed a strong linkage between the two homologs and the 1.6 Mb chromosome of 84R-62B. A CHEF-Southern analysis revealed an association between the 1.6 Mb chromosome and the homologs, indicating that both homologs are located on the 1.6 Mb chromosome of 84R-62B. The loss of the 1.6 Mb chromosome was observed in subcultures of a F1 progeny, F1-327. These subcultures concomitantly acquired virulence on Pik, Pik-m, and Pik-p. The present study is the first report showing that loss of a small and extra chromosome leads to pathogenic mutation of P. oryzae and may provide a new insight into the mechanisms generating pathogenic variation of this fungus.

  14. AAS 228: Day 3 afternoon

    Science.gov (United States)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Wikipedia Year of Science Editathon (by Meredith Rawls)Whats your first go-to source for an unfamiliar topic on the internet? If you said Wikipedia, youre not alone. For many people, Wikipedia is the primary source of information about astronomy and science. However, many Wikipedia articles about science topics are incomplete or missing, and women are underrepresented among scientists with biographies.To address this, the AAS Astronomy Education Board teamed up with the Wiki Education Foundation to host an edit-a-thon as part of the Wikipedia Year of Science. More than forty attendees spent the better part of three hours working through tutorials, creating new articles, and editing existing ones. The session was generously sponsored by the Simons Foundation.The Year of Science initiative seeks to bring Wikipedia editing skills to the classroom and help new editors find sustainable ways to contribute to Wikipedia in the long term. Anybody can create a free account and start editing!As a first-time Wikipedia contributor, I took the time to go through nearly all the tutorial exercises and familiarize myself with the process of editing a page. I decided to flesh out one section in an existing page about asteroseismology. Others created biography pages from scratch or selected various astronomical topics to write about. To me, the editing process felt like a cross between writing a blog post and a journal article, in a hack day type environment. Working through the tutorial and some examples renewed my empathy for learners who are tackling a new skill set for the first time. A full summary of our

  15. Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics.

    Science.gov (United States)

    Biswas, Prasun; Chakraborty, Sukanya; Dutta, Smritikana; Pal, Amita; Das, Malay

    2016-01-01

    Bamboos are an important member of the subfamily Bambusoideae, family Poaceae. The plant group exhibits wide variation with respect to the timing (1-120 years) and nature (sporadic vs. gregarious) of flowering among species. Usually flowering in woody bamboos is synchronous across culms growing over a large area, known as gregarious flowering. In many monocarpic bamboos this is followed by mass death and seed setting. While in sporadic flowering an isolated wild clump may flower, set little or no seed and remain alive. Such wide variation in flowering time and extent means that the plant group serves as repositories for genes and expression patterns that are unique to bamboo. Due to the dearth of available genomic and transcriptomic resources, limited studies have been undertaken to identify the potential molecular players in bamboo flowering. The public release of the first bamboo genome sequence Phyllostachys heterocycla, availability of related genomes Brachypodium distachyon and Oryza sativa provide us the opportunity to study this long-standing biological problem in a comparative and functional genomics framework. We identified bamboo genes homologous to those of Oryza and Brachypodium that are involved in established pathways such as vernalization, photoperiod, autonomous, and hormonal regulation of flowering. Additionally, we investigated triggers like stress (drought), physiological maturity and micro RNAs that may play crucial roles in flowering. We also analyzed available transcriptome datasets of different bamboo species to identify genes and their involvement in bamboo flowering. Finally, we summarize potential research hurdles that need to be addressed in future research.

  16. Rice-Map: a new-generation rice genome browser

    Directory of Open Access Journals (Sweden)

    Luo Jingchu

    2011-03-01

    Full Text Available Abstract Background The concurrent release of rice genome sequences for two subspecies (Oryza sativa L. ssp. japonica and Oryza sativa L. ssp. indica facilitates rice studies at the whole genome level. Since the advent of high-throughput analysis, huge amounts of functional genomics data have been delivered rapidly, making an integrated online genome browser indispensable for scientists to visualize and analyze these data. Based on next-generation web technologies and high-throughput experimental data, we have developed Rice-Map, a novel genome browser for researchers to navigate, analyze and annotate rice genome interactively. Description More than one hundred annotation tracks (81 for japonica and 82 for indica have been compiled and loaded into Rice-Map. These pre-computed annotations cover gene models, transcript evidences, expression profiling, epigenetic modifications, inter-species and intra-species homologies, genetic markers and other genomic features. In addition to these pre-computed tracks, registered users can interactively add comments and research notes to Rice-Map as User-Defined Annotation entries. By smoothly scrolling, dragging and zooming, users can browse various genomic features simultaneously at multiple scales. On-the-fly analysis for selected entries could be performed through dedicated bioinformatic analysis platforms such as WebLab and Galaxy. Furthermore, a BioMart-powered data warehouse "Rice Mart" is offered for advanced users to fetch bulk datasets based on complex criteria. Conclusions Rice-Map delivers abundant up-to-date japonica and indica annotations, providing a valuable resource for both computational and bench biologists. Rice-Map is publicly accessible at http://www.ricemap.org/, with all data available for free downloading.

  17. Development of Oryza rufipogon and O. sativa Introgression Lines and Assessment for Yield-related Quantitative Trait Loci

    Institute of Scientific and Technical Information of China (English)

    Lubin Tan; Fengxia Liu; Wei Xue; Guijuan Wang; Sheng Ye; Zuofeng Zhu; Yongcai Fu; Xiangkun Wang; Chuanqing Sun

    2007-01-01

    Introgression lines population was effectively used in mapping quantitative trait loci (QTLs), identifying favorable genes, discovering hidden genetic variation, evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research. In this study, an advanced backcross and consecutive selfing strategy was used to develop introgression lines (ILs), which derived from an accession of Oryza rufipogon Griff, collected from Yuanjiang County, Yunnan Province of China, as the donor, and an elite indica cultivar Teqing (O. sativa L.), as the recipient. Introgression segments from O. rufipogon were screened using 179 polymorphic simple sequence repeats (SSR) markers in the genome of each IL. Introgressed segments carried by the introgression lines population contained 120 ILs covering the whole O. rufipogon genome. The mean number of homozygous O. rufipogon segments per introgression line was about 3.88. The average length of introgressed segments was approximate 25.5 cM, and about 20.8% of these segments had sizes less than 10 cM. The genome of each IL harbored the chromosomal fragments of O. rufipogon ranging from 0.54% to 23.7%, with an overall average of 5.79%. At each locus, the ratio of substitution of O. rufipogon alleles had a range of 1.67-9.33, with an average of 5.50. A wide range of alterations in morphological and yield-related traits were also found in the introgression lines population. Using single-point analysis, a total of 37 putative QTLs for yield and yield components were detected at two sites with 7%-20% explaining the phenotypic variance. Nineteen QTLs (51.4%) were detected at both sites, and the alleles from O. rufipogon at fifteen loci (40.5%) improved the yield and yield components in the Teqing background. These O. rufipogon-O. sativa introgression lines will serve as genetic materials for identifying and using favorable genes from common wild rice.

  18. Expression, crystallization and preliminary X-ray crystallographic analysis of XometC, a cystathionine γ-lyase-like protein from Xanthomonas oryzae pv. oryzae

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, Phuong-Thuy Ho; Kim, Jin-Kwang [Department of Advanced Technology Fusion, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701 (Korea, Republic of); Kim, Hyesoon [Major in Life Science, College of Natural Sciences, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743 (Korea, Republic of); Jung, Junho [Department of Advanced Technology Fusion, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701 (Korea, Republic of); Ahn, Yeh-Jin [Major in Life Science, College of Natural Sciences, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743 (Korea, Republic of); Kim, Jeong-Gu; Lee, Byoung-Moo [Microbial Genetics Division, National Institute of Agricultural Biotechnology (NIAB), Rural Development Administration (RDA), Suwon 441-707 (Korea, Republic of); Kang, Hee-Wan, E-mail: kanghw2@hknu.ac.kr [Graduate School of Biotechnology and Information, Hankyong National University, Ansung 456-749 (Korea, Republic of); Kang, Lin-Woo, E-mail: kanghw2@hknu.ac.kr [Department of Advanced Technology Fusion, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701 (Korea, Republic of)

    2008-08-01

    XometC, a cystathionine γ-lyase-like protein from X. oryzae pv. oryzae and an antibacterial drug-target protein against bacterial blight, was cloned, purified and crystallized. Preliminary X-ray crystallographic analysis of XometC crystals was carried out. Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight of rice (Oryza sativa L.), one of the most devastating diseases of rice in most rice-growing countries. XometC, a cystathionine γ-lyase (CGL) like protein that is an antibacterial drug-target protein against Xoo, was cloned, expressed, purified and crystallized. CGL catalyzes the second step in the reverse-transsulfuration pathway, which is essential for the metabolic interconversion of the sulfur-containing amino acids cysteine and methionine. Crystals of two different shapes, plate-shaped and pyramid-shaped, diffracted to 2.9 and 3.2 Å resolution and belonged to the primitive orthogonal space group P2{sub 1}2{sub 1}2{sub 1} and the tetragonal space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = 73.0, b = 144.9, c = 152.3 Å and a = b = 78.2, c = 300.7 Å, respectively. For the P2{sub 1}2{sub 1}2{sub 1} crystals, three or four monomers exist in the asymmetric unit with a corresponding V{sub M} of 3.02 or 2.26 Å{sup 3} Da{sup −1} and a solvent content of 59.3 or 45.7%. For the P4{sub 1} (or P4{sub 3}) crystals, four or five monomers exist in the asymmetric unit with a corresponding V{sub M} of 2.59 or 2.09 Å{sup 3} Da{sup −1} and a solvent content of 52.5 or 40.6%.

  19. Resistência de cultivares de arroz a Rhizoctonia solani e Rhizoctonia oryzae Resistance of rice cultivars to Rhizoctonia solani and Rhizoctonia oryzae

    Directory of Open Access Journals (Sweden)

    Anne Sitarama Prabhu

    2002-05-01

    Full Text Available Isolados de Rhizoctonia solani e Rhizoctonia oryzae, agentes causais da queima-da-bainha e mancha-da-bainha, respectivamente, foram coletados em lavouras de arroz irrigado no Estado do Tocantins. O objetivo deste trabalho foi avaliar a resistência de 12 cultivares de arroz a essas doenças, sob condições artificiais de inoculação, em casa de vegetação. Não houve correlação entre resistência das cultivares a R. oryzae e R. solani quanto ao comprimento da lesão na bainha infectada pelo método de palito de dentes. A relação entre tamanho da lesão na bainha e folha foi linear e significativamente negativa (r = -0,66, PIsolates of Rhizoctonia solani and Rhizoctonia oryzae, the causal agents of sheath blight and sheath rot diseases, respectively, were collected from irrigated rice fields in the State of Tocantins, Brazil. The main objective of the investigation was to assess the resistance of 12 genotypes to these diseases, under artificial inoculation tests in greenhouse condition. There was no correlation between the resistance of cultivars to R. oryzae and R. solani for lesion extension on sheath infection obtained by the toothpick method. The relationship between lesion size on sheath and leaf was linear and significantly negative (r = -0.66, P<=0.05, thereby indicating that there is no relationship between resistance of sheath and leaf to infection by R. solani in rice cultivars. Among the early maturing genotypes Labelle was highly susceptible in all methods of inoculation. The area under disease progress curve based on lesion height on the culm and the inoculation method with rice husk and grain were found more adequate for determining the differences in the degree of resistance among cultivars. Leaves exhibited resistance to infection by R. oryzae in inoculation tests with mycelial discs.

  20. [A novel method of the genome-wide prediction for the target genes and its application].

    Science.gov (United States)

    Zhang, Jing-Jing; Feng, Jing; Zhu, Ying-Guo; Li, Yang-Sheng

    2006-10-01

    Based on the protein databases of several model species, this study developed a new method of the Genome-wide prediction for the target genes, using Hidden Markov model by Perl programming. The advantages of this method are high throughput, high quality and easy prediction, especially in the case of multi-domains proteins families. By this method, we predicted the PPR and TPR proteins families in whole genome of several model species. There were 536 PPR proteins and 199 TPR proteins in Oryza sativa ssp. japonica, 519 PPR proteins and 177 TPR proteins in Oryza sativa L. ssp. indica, 735 PPR proteins and 292 TPR proteins in Arabidopsis thaliana, 6 PPR proteins and 32 TPR proteins in Cyanidioschyzon merolae. Synechococcus and Thermophilic archaebacterium did not have PPR proteins. By contrast, 10 TPR proteins were found in Synechococcus and 4 TPR proteins were found in Thermophilic archaebacterium. Moreover, of these results, some further bioinformatics analyses were conducted.

  1. Autolysis of Aspergillus oryzae Mycelium and Effect on Volatile Flavor Compounds of Soy Sauce.

    Science.gov (United States)

    Xu, Ning; Liu, Yaqi; Hu, Yong; Zhou, Mengzhou; Wang, Chao; Li, Dongsheng

    2016-08-01

    The autolyzed mycelia of Aspergillus oryzae are rich in proteins, nucleic acids, sugar, and other biomacromolecules, and are one of the main contributors to the flavor profile of commercially important fermented goods, including soy sauce and miso. We induced autolysis of the mycelia of A. oryzae over 1 to 10 d, and found that the maximum dissolved amounts of total protein and nucleic acid ratio accounted for 28.63% and 88.93%, respectively. The organic acid content, such as citric acid, tartaric acid, succinic acid, lactic acid, and acetic acid, initially increased and then decreased as autolysis progressed, corresponding to changes in pH levels. The main characteristic flavor compounds in soy sauce, namely, ethanol, 2-phenylethanol, and 2-methoxy-4-vinylphenol, were all detected in the autolysate. Subsequently, we tested the effect of adding mycelia of A. oryzae during the fermentation process of soy sauce for 60 d, and found that addition of 1.2‰ A. oryzae mycelia provided the richest flavor. Overall, our findings suggest that compounds found in the autolysate of A. oryzae may promote the flavor compounds of soy sauce, such as alcohols, aldehydes, phenols, and esters. © 2016 Institute of Food Technologists®

  2. Pentachlorophenol sorption in nylon fiber and removal by immobilized Rhizopus oryzae ENHE.

    Science.gov (United States)

    León-Santiestebán, Hugo; Meraz, Mónica; Wrobel, Kazimierz; Tomasini, Araceli

    2011-06-15

    This study describes pentachlophenol (PCP) sorption in nylon fiber in which Rhizopus oryzae ENHE was immobilized to remove the chemical compound. The experimental sorption data were analyzed using the Langmuir, Freundlich, and Redlich-Peterson isotherm models using non-linear error functions to fit the experimental data to the three models. Results showed that the isotherm obtained from the data fitted the three models used. However, the g parameter from Redlich-Peterson model showed that the isotherm obtained approaches the Freundlich model. This support reached the sorption equilibrium concentration at 3mg PCPg(-1)nylon. To study PCP removal capability by R. oryzae ENHE and to eliminate the error caused by PCP sorbed by the nylon fiber during its quantification, nylon fiber at PCP equilibrium sorption concentration was used to immobilize R. oryzae ENHE. It was found that this fungus grew within nylon fiber cubes in presence or not of PCP, even when PCP caused growth inhibition. Maximum biomass accumulated into nylon cubes without PCP was of 32 mg biomass g(-1)nylon and into nylon cubes at PCP equilibrium concentration was of 18 mg g(-1)nylon. The results showed that R. oryzae ENHE immobilized into nylon fiber removed 88.6% and 92% of PCP in cultures with 12.5 and 25 mg PCPL(-1), as initial concentration, respectively. This is the first work to report that a zygomycete, such as R. oryzae ENHE, immobilized into nylon fiber kept its potential to remove PCP.

  3. Transcriptome analysis of Rhizopus oryzae in response to xylose during fumaric acid production.

    Science.gov (United States)

    Xu, Qing; Liu, Ying; Li, Shuang; Jiang, Ling; Huang, He; Wen, Jianping

    2016-08-01

    Xylose is one of the most abundant lignocellulosic components, but it cannot be used by R. oryzae for fumaric acid production. Here, we applied high-throughput RNA sequencing to generate two transcriptional maps of R. oryzae following fermentation in glucose or xylose. The differential expression analysis showed that, genes involved in amino acid metabolism, fatty acid metabolism, and gluconeogenesis, were up-regulated in response to xylose. Moreover, we discovered the potential presence of oxidative stress in R. oryzae during xylose fermentation. To adapt to this unfavorable condition, R. oryzae displayed reduced growth and induce of a number of antioxidant enzymes, including genes involved in glutathione, trehalose synthesis, and the proteasomal pathway. These responses might divert the flow of carbon required for the accumulation of fumaric acid. Furthermore, using high-throughput RNA sequencing, we identified a large number of novel transcripts and a substantial number of genes that underwent alternative splicing. Our analysis provides remarkable insight into the mechanisms underlying xylose fermentation by R. oryzae. These results may reveal potential target genes or strategies to improve xylose fermentation.

  4. Systematic analysis of rice (Oryza sativa) metabolic responses to herbivory.

    Science.gov (United States)

    Alamgir, Kabir Md; Hojo, Yuko; Christeller, John T; Fukumoto, Kaori; Isshiki, Ryutaro; Shinya, Tomonori; Baldwin, Ian T; Galis, Ivan

    2016-02-01

    Plants defend against attack from herbivores by direct and indirect defence mechanisms mediated by the accumulation of phytoalexins and release of volatile signals, respectively. While the defensive arsenals of some plants, such as tobacco and Arabidopsis are well known, most of rice's (Oryza sativa) defence metabolites and their effectiveness against herbivores remain uncharacterized. Here, we used a non-biassed metabolomics approach to identify many novel herbivory-regulated metabolic signatures in rice. Most were up-regulated by herbivore attack while only a few were suppressed. Two of the most prominent up-regulated signatures were characterized as phenolamides (PAs), p-coumaroylputrescine and feruloylputrescine. PAs accumulated in response to attack by both chewing insects, i.e. feeding of the lawn armyworm (Spodoptera mauritia) and the rice skipper (Parnara guttata) larvae, and the attack of the sucking insect, the brown planthopper (Nilaparvata lugens, BPH). In bioassays, BPH insects feeding on 15% sugar solution containing p-coumaroylputrescine or feruloylputrescine, at concentrations similar to those elicited by heavy BPH attack in rice, had a higher mortality compared to those feeding on sugar diet alone. Our results highlight PAs as a rapidly expanding new group of plant defence metabolites that are elicited by herbivore attack, and deter herbivores in rice and other plants.

  5. Fe deficiency induced changes in rice (Oryza sativa L.) thylakoids.

    Science.gov (United States)

    Wang, Yuwen; Xu, Chao; Li, Kang; Cai, Xiaojie; Wu, Min; Chen, Guoxiang

    2017-01-01

    Iron deficiency is an important abiotic stress that limits productivity of crops all over the world. We selected a hybrid rice (Oryza sativa L.), LYPJ, which is super high-yield and widely cultured in China, to investigate changes in the components and structure of thylakoid membranes and photosynthetic performance in response to iron deficiency. Our results demonstrated that photosystem I (PSI) is the primary target for iron deficiency, while the changes in photosystem II (PSII) are important for rebuilding a balance in disrupted energy utilization and dissipation caused by differential degradation of photosynthetic components. The result of immunoblot analysis suggested that the core subunit PsaA declined drastically, while PsbA remained relatively stable. Furthermore, several organizational changes of the photosynthetic apparatus were found by BN-PAGE, including a marked decrease in the PSI core complexes, the Cytb 6 /f complex, and the trimeric form of the LHCII antenna, consistent with the observed unstacking grana. The fluorescence induction analysis indicated a descending PSII activity with energy dissipation enhanced markedly. In addition, we proposed that the crippled CO2 assimilation could be compensated by the enhanced of phosphoenolpyruvate carboxylase (PEPC), which is suggested by the decreased ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and photosynthetic efficiency.

  6. The WRKY Gene Family in Rice (Oryza sativa)

    Institute of Scientific and Technical Information of China (English)

    Christian A. Ross; Yue Liu; Qingxi J. Shen

    2007-01-01

    WRKYgenes encode transcription factors that are involved in the regulation of various biological processes. These zinc-finger proteins, especially those members mediating stress responses, are uniquely expanded in plants. To facilitate the study of the evolutionary history and functions of this supergene family, we performed an exhaustive search for WRKY genes using HMMER and a Hidden Markov Model that was specifically trained for rice. This work resulted in a comprehensive list of WRKY gene models in Oryza sativa L. ssp. indica and L. ssp. japonica. Mapping of these genes to individual chromosomes facilitated elimination of the redundant, leading to the identification of 98 WRKY genes in japonica and 102 in indica rice. These genes were further categorized according to the number and structure of their zinc-finger domains. Based on a phylogenetic tree of the conserved WRKY domains and the graphic display of WRKY loci on corresponding indica and japonica chromosomes, we identified possible WRKY gene duplications within, and losses between the two closely related rice subspecies. Also reviewed are the roles of WRKY genes in disease resistance and responses to salicylic acid and jasmonic acid, seed development and germination mediated by gibberellins, other developmental processes including senescence, and responses to abiotic stresses and abscisic acid in rice and other plants. The signaling pathways mediating WRKY gene expression are also discussed.

  7. Phylogeny of Plant CAMTAs and Role of AtCAMTAs in Nonhost Resistance to Xanthomonas oryzae pv. oryzae.

    Science.gov (United States)

    Rahman, Hafizur; Yang, Juan; Xu, You-Ping; Munyampundu, Jean-Pierre; Cai, Xin-Zhong

    2016-01-01

    regulated the immunity triggered by flg22 and nonhost resistance to Xanthomonas oryzae pv. oryzae via repressing accumulation of reactive oxygen species probably by targeting CBP60G, EDS1, and NDR1 and involving SA pathway.

  8. Phylogeny of plant CAMTAs and role of AtCAMTAs in nonhost resistance to Xanthomonas oryzae pv. oryzae

    Directory of Open Access Journals (Sweden)

    Hafizur eRahman

    2016-02-01

    negatively regulated the immunity triggered by flg22 and nonhost resistance to Xanthomonas oryzae pv. oryzae via repressing accumulation of reactive oxygen species probably by targeting CBP60G, EDS1 and NDR1 and involving SA pathway.

  9. Identification of growth phenotype-related genes in Aspergillus oryzae by heterologous macroarray and suppression subtractive hybridization

    NARCIS (Netherlands)

    Biesebeke, R. te; Levin, A.; Sagt, C.; Bartels, J.; Goosen, T.; Ram, A.; Hondel, C. van den; Punt, P.

    2005-01-01

    Aspergillus oryzae requires polarized growth for colonization of solid substrates, and this growth phenotype differs from that seen in liquid medium. Various experimental approaches were used to identify genes that are differentially expressed when A. oryzae is grown on wheat kernels and in a wheat-

  10. Identification of growth phenotype-related genes in Aspergillus oryzae by heterologous macroarray and suppression subtractive hybridization

    NARCIS (Netherlands)

    Biesebeke, R. te; Levin, A.; Sagt, C.; Bartels, J.; Goosen, T.; Ram, A.; Hondel, C. van den; Punt, P.

    2005-01-01

    Aspergillus oryzae requires polarized growth for colonization of solid substrates, and this growth phenotype differs from that seen in liquid medium. Various experimental approaches were used to identify genes that are differentially expressed when A. oryzae is grown on wheat kernels and in a wheat-

  11. Evaluation of commercial soy sauce koji strains of Aspergillus oryzae for γ-aminobutyric acid (GABA) production.

    Science.gov (United States)

    Ab Kadir, Safuan; Wan-Mohtar, Wan Abd Al Qadr Imad; Mohammad, Rosfarizan; Abdul Halim Lim, Sarina; Sabo Mohammed, Abdulkarim; Saari, Nazamid

    2016-10-01

    In this study, four selected commercial strains of Aspergillus oryzae were collected from soy sauce koji. These A. oryzae strains designated as NSK, NSZ, NSJ and NST shared similar morphological characteristics with the reference strain (A. oryzae FRR 1675) which confirmed them as A. oryzae species. They were further evaluated for their ability to produce γ-aminobutyric acid (GABA) by cultivating the spore suspension in a broth medium containing 0.4 % (w/v) of glutamic acid as a substrate for GABA production. The results showed that these strains were capable of producing GABA; however, the concentrations differed significantly (P GABA concentration was obtained from NSK (194 mg/L) followed by NSZ (63 mg/L), NSJ (51.53 mg/L) and NST (31.66 mg/L). Therefore, A. oryzae NSK was characterized and the sequence was found to be similar to A. oryzae and A. flavus with 99 % similarity. The evolutionary distance (K nuc) between sequences of identical fungal species was calculated and a phylogenetic tree prepared from the K nuc data showed that the isolate belonged to the A. oryzae species. This finding may allow the development of GABA-rich ingredients using A. oryzae NSK as a starter culture for soy sauce production.

  12. rFTR1 is Required for Pathogenesis, and appears to be an Essential Gene, of Rhizopus oryzae

    Science.gov (United States)

    BACKGROUND: Rhizopus oryzae is a multinucleated fungus responsible for the majority of cases of mucormycosis. The high affinity iron permease gene (rFTR1) is required for R. oryzae iron transport in iron-limited environments. We sought to disrupt the gene to define its role in virulence. METHODS: ...

  13. Identification of growth phenotype-related genes in Aspergillus oryzae by heterologous macroarray and suppression subtractive hybridization

    NARCIS (Netherlands)

    Biesebeke, R. te; Levin, A.; Sagt, C.; Bartels, J.; Goosen, T.; Ram, A.; Hondel, C. van den; Punt, P.

    2005-01-01

    Aspergillus oryzae requires polarized growth for colonization of solid substrates, and this growth phenotype differs from that seen in liquid medium. Various experimental approaches were used to identify genes that are differentially expressed when A. oryzae is grown on wheat kernels and in a

  14. AAS 228: Day 1 morning

    Science.gov (United States)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Come visit astrobites at the AAS booth we have swag!Things kicked off last night at our undergraduate reception booth. Thanks to all of you who stopped by we were delightedto hear from undergrads who already know and love the site, educators who want to use it in their classrooms, and students who had not yet been introduced to astrobites and were excited about a new resource!For the rest of the meeting we will be stationed at theAAS booth in the exhibit hall (booth #211-213), so drop by if you want to learn more (or pick up swag: weve got lots of stickers and sunglasses)!Mondaymorning was the official start of the meeting. Here are just a few of the talks and workshops astrobiters attended this morning.Opening Address(by Susanna Kohler)AAS President Meg Urry kicked off the meeting this morning at 8am with an overview of some of the great endeavors AAS is supporting. We astrobiters had personal motivation to drag ourselves out of bed that early: during this session, Urryannounced the new partnership between AAS and astrobites!Urry touched on some difficult topics in her welcome, including yesterdays tragedy in Orlando. Shereiteratedthe AASs support fortheCommittee for Sexual-Orientation and Gender Minorities in Astronomy (SGMA). She also reminded meeting attendees about the importance ofkeeping conference interactions professional, and pointed to the meetings anti-harassment policy.Partnership Announcement (by Michael Zevin)This morning, the American Astronomical Society announced the new partnership that it will have with Astrobites! We are beyond excited to embark on this new partnership with the

  15. A BAC end view of the Musa acuminata genome

    Directory of Open Access Journals (Sweden)

    Town Christopher D

    2007-06-01

    Full Text Available Abstract Background Musa species contain the fourth most important crop in developing countries. Here, we report the analysis of 6,252 BAC end-sequences, in order to view the sequence composition of the Musa acuminata genome in a cost effective and efficient manner. Results BAC end sequencing generated 6,252 reads representing 4,420,944 bp, including 2,979 clone pairs with an average read length after cleaning and filtering of 707 bp. All sequences have been submitted to GenBank, with the accession numbers DX451975 – DX458350. The BAC end-sequences, were searched against several databases and significant homology was found to mitochondria and chloroplast (2.6%, transposons and repetitive sequences (36% and proteins (11%. Functional interpretation of the protein matches was carried out by Gene Ontology assignments from matches to Arabidopsis and was shown to cover a broad range of categories. From protein matching regions of Musa BAC end-sequences, it was determined that the GC content of coding regions was 47%. Where protein matches encompassed a start codon, GC content as a function of position (5' to 3' across 129 bp sliding windows generates a "rice-like" gradient. A total of 352 potential SSR markers were discovered. The most abundant simple sequence repeats in four size categories were AT-rich. After filtering mitochondria and chloroplast matches, thousands of BAC end-sequences had a significant BLASTN match to the Oryza sativa and Arabidopsis genome sequence. Of these, a small number of BAC end-sequence pairs were shown to map to neighboring regions of the Oryza sativa genome representing regions of potential microsynteny. Conclusion Database searches with the BAC end-sequences and ab initio analysis identified those reads likely to contain transposons, repeat sequences, proteins and simple sequence repeats. Approximately 600 BAC end-sequences contained protein sequences that were not found in the existing available Musa expressed

  16. The rice bacterial pathogen Xanthomonas oryzae pv. oryzae produces 3-hydroxybenzoic acid and 4-hydroxybenzoic acid via XanB2 for use in xanthomonadin, ubiquinone, and exopolysaccharide biosynthesis.

    Science.gov (United States)

    Zhou, Lian; Huang, Tin-Wei; Wang, Jia-Yuan; Sun, Shuang; Chen, Gongyou; Poplawsky, Alan; He, Ya-Wen

    2013-10-01

    Xanthomonas oryzae pv. oryzae, the causal agent of rice bacterial blight, produces membrane-bound yellow pigments, referred to as xanthomonadins. Xanthomonadins protect the pathogen from photodamage and host-induced perioxidation damage. They are also required for epiphytic survival and successful host plant infection. Here, we show that XanB2 encoded by PXO_3739 plays a key role in xanthomonadin and coenzyme Q8 biosynthesis in X. oryzae pv. oryzae PXO99A. A xanB2 deletion mutant exhibits a pleiotropic phenotype, including xanthomonadin deficiency, producing less exopolysaccharide (EPS), lower viability and H2O2 resistance, and lower virulence. We further demonstrate that X. oryzae pv. oryzae produces 3-hydroxybenzoic acid (3-HBA) and 4-hydroxybenzoic acid (4-HBA) via XanB2. 3-HBA is associated with xanthomonadin biosynthesis while 4-HBA is mainly used as a precursor for coenzyme Q (CoQ)8 biosynthesis. XanB2 is the alternative source of 4-HBA for CoQ8 biosynthesis in PXO99A. These findings suggest that the roles of XanB2 in PXO99A are generally consistent with those in X. campestris pv. campestris. The present study also demonstrated that X. oryzae pv. oryzae PXO99A has evolved several specific features in 3-HBA and 4-HBA signaling. First, our results showed that PXO99A produces less 3-HBA and 4-HBA than X. campestris pv. campestris and this is partially due to a degenerated 4-HBA efflux pump. Second, PXO99A has evolved unique xanthomonadin induction patterns via 3-HBA and 4-HBA. Third, our results showed that 3-HBA or 4-HBA positively regulates the expression of gum cluster to promote EPS production in PXO99A. Taken together, the results of this study indicate that XanB2 is a key metabolic enzyme linking xanthomonadin, CoQ, and EPS biosynthesis, which are collectively essential for X. oryzae pv. oryzae pathogenesis.

  17. NCBI nr-aa BLAST: CBRC-OSAT-07-0071 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-OSAT-07-0071 ref|NP_001060484.1| Os07g0650600 [Oryza sativa (japonica cultivar...-group)] dbj|BAC20065.2| BLE2 protein [Oryza sativa (japonica cultivar-group)] dbj|BAD32037.1| BLE2 protein [Oryza sativa (japon...ica cultivar-group)] dbj|BAF22398.1| Os07g0650600 [Oryza sativa (japonica cultivar-group)] NP_001060484.1 0.0 59% ...

  18. NCBI nr-aa BLAST: CBRC-OSAT-07-0069 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-OSAT-07-0069 ref|NP_001060484.1| Os07g0650600 [Oryza sativa (japonica cultivar...-group)] dbj|BAC20065.2| BLE2 protein [Oryza sativa (japonica cultivar-group)] dbj|BAD32037.1| BLE2 protein [Oryza sativa (japon...ica cultivar-group)] dbj|BAF22398.1| Os07g0650600 [Oryza sativa (japonica cultivar-group)] NP_001060484.1 1e-165 52% ...

  19. NCBI nr-aa BLAST: CBRC-OSAT-07-0070 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-OSAT-07-0070 ref|NP_001060484.1| Os07g0650600 [Oryza sativa (japonica cultivar...-group)] dbj|BAC20065.2| BLE2 protein [Oryza sativa (japonica cultivar-group)] dbj|BAD32037.1| BLE2 protein [Oryza sativa (japon...ica cultivar-group)] dbj|BAF22398.1| Os07g0650600 [Oryza sativa (japonica cultivar-group)] NP_001060484.1 1e-124 52% ...

  20. NCBI nr-aa BLAST: CBRC-OSAT-07-0038 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-OSAT-07-0038 ref|NP_001060484.1| Os07g0650600 [Oryza sativa (japonica cultivar...-group)] dbj|BAC20065.2| BLE2 protein [Oryza sativa (japonica cultivar-group)] dbj|BAD32037.1| BLE2 protein [Oryza sativa (japon...ica cultivar-group)] dbj|BAF22398.1| Os07g0650600 [Oryza sativa (japonica cultivar-group)] NP_001060484.1 0.0 55% ...

  1. Data set from the phosphoproteomic analysis of Magnaporthe oryzae-responsive proteins in susceptible and resistant rice cultivars

    Directory of Open Access Journals (Sweden)

    Yunfeng Li

    2015-06-01

    Full Text Available Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is the most destructive disease of rice and causes tremendous losses of rice yield worldwide. To explore the molecular mechanisms involved in the rice–M. oryzae interaction, we conducted a time-course phosphoproteomic analysis of leaf samples from resistant and susceptible rice cultivars infected with M. oryzae. This data article contains additional results and analysis of M. oryzae-regulated phosphoproteins in rice leaves [1]. We report the analysis of M. oryzae-regulated phosphoproteins at all time points, including Venn diagram analysis, close-up views, relative intensities, and functional category, and the MS spectra of representative phosphoprotein and representative phosphorylated peptides.

  2. Fermentation Kinetics of Media Optimization for the Production of Alpha Amylase by a New Isolate of Aspergillus Oryzae

    Institute of Scientific and Technical Information of China (English)

    Ikram-ul-Haq; Roheena Abdullah; Hamid Mukhtar; Muhammad Nauman Aftab

    2007-01-01

    The present study is concerned with the isolation and screening of different strains of Aspergillus oryzae for the production of alpha amylase. Ninety strains were isolated from soil and tested for the production of alpha amylase in shake flasks. Of all the strains tested,Aspergillus oryzae GCB-32 and Aspergillus oryzae GCB-35 gave maximum production of alpha amylase. Different culture media were screened for maximum production of alpha amylase by both the strains Aspergillus oryzae GCB-32 and Aspergillus oryzae GCB-35. Kinetic analysis revealed that the values of product yield coefficient (Yp/x) and specific product yield coefficient( qp ) were found highly significant (p ≤ 0.05 ) when medium M1 was used for the enzyme production.

  3. First circulating beam in the AA

    CERN Multimedia

    1980-01-01

    On 3 July 1980, two years after project authorization, beam circulated for the first time in the AA. It was a 3.56 GeV/c proton test beam. We see an expecting crowd, minutes before the happy event. The persons are too numerous to name them all, but the 3 most prominent ones are at the centre (left to right): Roy Billinge (Joint AA Project Leader, with his hand on the control box), Eifionydd Jones (white shirt), Simon van der Meer (spiritus rector and Joint AA Project Leader). The first antiprotons were injected, made to circulate and cooled soon after, on 14 July 1980.

  4. Tithonia diversifolia, Moringa oleifera and Piper auritum: Alternatives for the control of Sitophilus oryzae

    Directory of Open Access Journals (Sweden)

    Leticia Jiménez Álvarez

    2016-07-01

    Full Text Available With the objective to determine the effect exerted by vegetable powders of Tithonia diversifolia (Hemsl A. Gray, Moringa oleifera (Lam y Piper auritum Kunth on Sitophilus oryzae L., this experiment was performed. In the execution, adult insects were taken to evaluate the increase of them. Petri dishes of 9 cm with 10 insects were used inside additionally 5 g of rice (Oryza sativa L. and 0.4 g of powder was added botanical species (T. diversifolia, M. oleifera, P. auritum previously dried at 40 0C for 72 hours and finely ground. At 40 days the test mounted, the number of insects present per plate was counted, and after testing, Z Multiple Comparison was performed using the software Stadistix. The results allowed us to conclude that these plant species are a viable alternative for the control of S. oryzae.

  5. Influence of carbon source on alpha-amylase production by Aspergillus oryzae

    DEFF Research Database (Denmark)

    Carlsen, Morten; Nielsen, Jens

    2001-01-01

    The influence of the carbon source on a-amylase production by Aspergillus oryzae was quantified in carbon-limited chemostat cultures. The following carbon sources were investigated: maltose, maltodextrin (different chain lengths), glucose, fructose, galactose, sucrose, glycerol, mannitol and acet......The influence of the carbon source on a-amylase production by Aspergillus oryzae was quantified in carbon-limited chemostat cultures. The following carbon sources were investigated: maltose, maltodextrin (different chain lengths), glucose, fructose, galactose, sucrose, glycerol, mannitol...... and acetate. A. oryzae did not grow on galactose as the sole carbon source, but galactose was co-metabolized together with glucose. Relative to that on low glucose concentration (below 10 mg/l), productivity was found to be higher during growth on maltose and maltodextrins, whereas it was lower during growth...

  6. Morphological and molecular characterization of Magnaporthe oryzae (fungus) from infected rice leaf samples

    Science.gov (United States)

    Muni, Nurulhidayah Mat; Nadarajah, Kalaivani

    2014-09-01

    Magnaporthe oryzae is a plant-pathogenic fungus that causes a serious disease affecting rice called rice blast. Outbreaks of rice blast have been a threat to the global production of rice. This fungal disease is estimated to cause production losses of US55 million each year in South and Southeast Asia. It has been used as a primary model for elucidating various aspects of the host-pathogen interaction with its host. We have isolated five isolates of Magnaporthe oryzae from diseased leaf samples obtained from the field at Kompleks Latihan MADA, Kedah, Malaysia. We have identified the isolates using morphological and microscopic studies on the fungal spores and the lesions on the diseased leaves. Amplification of the internal transcribed spacer (ITS) was carried out with universal primers ITS1 and ITS4. The sequence of each isolates showed at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaporthe oryzae.

  7. Enhanced L-(+)-lactic acid production by an adapted strain of Rhizopus oryzae using corncob hydrolysate

    DEFF Research Database (Denmark)

    Bai, Dongmei; Li, S.Z.; Liu, Z.L.

    2008-01-01

    -isomer and a simple nutrition requirement by the fungus. Production of-L-(+)-lactic acid by R. oryzae using xylose has been reported; however, its yield and conversion rate are poor compared with that of using glucose. In this study, we report an adapted R. oryzae strain HZS6 that significantly improved efficiency......Corncob is an economic feedstock and more than 20 million tons of corncobs are produced annually in China. Abundant xylose can be potentially converted from the large amount of hemicellulosic materials in corncobs, which makes the crop residue an attractive alternative substrate for a value......-added production of a variety of bioproducts. Lactic acid can be used as a precursor for poly-lactic acid production. Although current industrial lactic acid is produced by lactic acid bacteria using enriched medium, production by Rhizopus oryzae is preferred due to its exclusive formation of the...

  8. Comparative Analysis of the Korean Population of Magnaporthe oryzae by Multilocus Microsatellite Typing

    Directory of Open Access Journals (Sweden)

    Jaehyuk Choi

    2013-12-01

    Full Text Available Rice blast fungus, Magnaporthe oryzae, inflicts serious damage to global rice production. Due to high variability of this fungal pathogen, resistance of newly-released rice cultivars is easily broken down. To understand the population structure of M. oryzae, we analyzed the genetic diversity of the Korean population using multilocus microsatellite typing. Eleven microsatellite markers were applied to the population of 190 rice isolates which had been collected in Korea for two decades since the 1980’s. Average values of gene diversity and allele frequency were 0.412 and 6.5, respectively. Comparative analysis of the digitized allele information revealed that the Korean population exhibited a similar level of allele diversity to the integrated diversity of the world populations, suggesting a particularly high diversity of the Korean population. Therefore, these microsatellite markers and the comprehensive collection of field isolates will be useful genetic resources to identify the genetic diversity of M. oryzae population.

  9. Triterpenoid glycosides from Medicago sativa as antifungal agents against Pyricularia oryzae.

    Science.gov (United States)

    Abbruscato, Pamela; Tosi, Solveig; Crispino, Laura; Biazzi, Elisa; Menin, Barbara; Picco, Anna M; Pecetti, Luciano; Avato, Pinarosa; Tava, Aldo

    2014-11-19

    The antifungal properties of saponin mixtures from alfalfa (Medicago sativa L.) tops and roots, the corresponding mixtures of prosapogenins from tops, and purified saponins and sapogenins against the causal agent of rice blast Pyricularia oryzae isolates are presented. In vitro experiments highlighted a range of activities, depending upon the assayed metabolite. The antifungal effects of the most promising prosapogenin mixture from alfalfa tops were confirmed by means of in planta tests using three different Italian cultivars of rice (Oryza sativa L. ssp. japonica), known to possess high, medium, and low blast resistance. The evidenced antifungal properties of the tested metabolites allowed some considerations on their structure-activity relationship. Results indicate that prosapogenins are active compounds to prevent the fungal attack of P. oryzae on different rice cultivars. Therefore, if properly formulated, these substances could represent a promising and environmentally friendly treatment to control rice blast.

  10. Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae

    Science.gov (United States)

    Ho, Yuen Ting

    2016-01-01

    Background The rice receptor kinase XA21 confers robust resistance to the bacterial pathogen Xanthomonas oryzaepv. oryzae(Xoo). We previously reported that XA21 is cleaved in transgenic plants overexpressing XA21 with a GFP tag (Ubi-XA21-GFP) and that the released C-terminal domain is localized to the nucleus. XA21 carries a predicted nuclear localization sequence (NLS) that directs the C-terminal domain to the nucleus in transient assays, whereas alanine substitutions in the NLS disrupt the nuclear localization. Methods To determine if the predicted NLS is required for XA21-mediated immunity in planta, we generated transgenic plants overexpressing an XA21 variant carrying the NLS with the same alanine substitutions (Ubi-XA21nls-GFP). Results Ubi-XA21nls-GFP plants displayed slightly longer lesion lengths, higher Xoobacterial populations after inoculation and lower levels of reactive oxygen species production compared with the Ubi-XA21-GFP control plants. However, the Ubi-XA21nls-GFP plants express lower levels of protein than that observed in Ubi-XA21-GFP. Discussion These results demonstrate that the predicted NLS is not required for XA21-mediated immunity.

  11. Crucial roles of abscisic acid biogenesis in virulence of rice blast fungus Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Carla eSpence

    2015-12-01

    Full Text Available Rice suffers dramatic yield losses due to blast pathogen Magnaporthe oryzae. Pseudomonas chlororaphis EA105, a bacterium that was isolated from the rice rhizosphere, inhibits M. oryzae. It was shown previously that pre-treatment of rice with EA105 reduced the size of blast lesions through JA- and ETH-mediated ISR. ABA acts antagonistically towards SA, JA, and ETH signaling, to impede plant defense responses. EA105 may be reducing the virulence of M. oryzae by preventing the pathogen from up-regulating the key ABA biosynthetic gene NCED3 in rice roots, as well as a β-glucosidase likely involved in activating conjugated inactive forms of ABA. However, changes in total ABA concentrations were not apparent, provoking the question of whether ABA concentration is an indicator of ABA signaling and response. In the rice-M. oryzae interaction, ABA plays a dual role in disease severity by increasing plant susceptibility and accelerating pathogenesis in the fungus itself. ABA is biosynthesized by M. oryzae. Further, exogenous ABA increased spore germination and appressoria formation, distinct from other plant growth regulators. EA105, which inhibits appressoria formation, counteracted the virulence-promoting effects of ABA on M. oryzae. The role of endogenous fungal ABA in blast disease was confirmed through the inability of a knockout mutant impaired in ABA biosynthesis to form lesions on rice. Therefore, it appears that EA105 is invoking multiple strategies in its protection of rice from blast including direct mechanisms as well as those mediated through plant signaling. ABA is a molecule that is likely implicated in both tactics.

  12. Osa-miR169 Negatively Regulates Rice Immunity against the Blast Fungus Magnaporthe oryzae

    Science.gov (United States)

    Li, Yan; Zhao, Sheng-Li; Li, Jin-Lu; Hu, Xiao-Hong; Wang, He; Cao, Xiao-Long; Xu, Yong-Ju; Zhao, Zhi-Xue; Xiao, Zhi-Yuan; Yang, Nan; Fan, Jing; Huang, Fu; Wang, Wen-Ming

    2017-01-01

    miR169 is a conserved microRNA (miRNA) family involved in plant development and stress-induced responses. However, how miR169 functions in rice immunity remains unclear. Here, we show that miR169 acts as a negative regulator in rice immunity against the blast fungus Magnaporthe oryzae by repressing the expression of nuclear factor Y-A (NF-YA) genes. The accumulation of miR169 was significantly increased in a susceptible accession but slightly fluctuated in a resistant accession upon M. oryzae infection. Consistently, the transgenic lines overexpressing miR169a became hyper-susceptible to different M. oryzae strains associated with reduced expression of defense-related genes and lack of hydrogen peroxide accumulation at the infection site. Consequently, the expression of its target genes, the NF-YA family members, was down-regulated by the overexpression of miR169a at either transcriptional or translational level. On the contrary, overexpression of a target mimicry that acts as a sponge to trap miR169a led to enhanced resistance to M. oryzae. In addition, three of miR169’s target genes were also differentially up-regulated in the resistant accession upon M. oryzae infection. Taken together, our data indicate that miR169 negatively regulates rice immunity against M. oryzae by differentially repressing its target genes and provide the potential to engineer rice blast resistance via a miRNA. PMID:28144248

  13. Effect of supplementation of arachidonic acid (AA) or a combination of AA plus docosahexaenoic acid on breastmilk fatty acid composition

    NARCIS (Netherlands)

    Smit, EN; Koopmann, M; Boersma, ER; Muskiet, FAJ

    2000-01-01

    We investigated whether supplementation with arachidonic acid (20:4 omega 6; AA), ora combination of AA and docosahexaenoic acid (22:6 omega 3; DHA) would affect human milk polyunsaturated fatty acid (PUFA) composition. Ten women were daily supplemented with 300 mg AA, eight with 300 mg AA, 110 mg e

  14. Effect of supplementation of arachidonic acid (AA) or a combination of AA plus docosahexaenoic acid on breastmilk fatty acid composition

    NARCIS (Netherlands)

    Smit, EN; Koopmann, M; Boersma, ER; Muskiet, FAJ

    We investigated whether supplementation with arachidonic acid (20:4 omega 6; AA), ora combination of AA and docosahexaenoic acid (22:6 omega 3; DHA) would affect human milk polyunsaturated fatty acid (PUFA) composition. Ten women were daily supplemented with 300 mg AA, eight with 300 mg AA, 110 mg

  15. Friction Stir Weldabilities of AA1050-H24 and AA6061-T6 Aluminum Alloys

    Institute of Scientific and Technical Information of China (English)

    Huijie LIU; Hidetoshi FUJIN; Masakatsu MAEDA; Kiyoshi NOGI

    2005-01-01

    The friction stir weldabilities of the strain-hardened AA1050-H24 and precipitate-hardened AA6061-T6 aluminum alloys were examined to reveal the effects of material properties on the friction stir welding behavior. The experimental results are obtlained. (1) For AA1050-H24, the weld can possess smoother surface ripples; there is no elliptical weld nugget in the weld; there is no discernible interface between the stir zone and the thermomechanically affected zone;and the internal defect of the weld looks like a long crack and is located in the lower part of the weld. (2) For AA6061-T6, the weld usually possesses slightly rougher surface ripples; an elliptical weld nugget clearly exists in the weld; there are discernible interfaces among the weld nugget, thermomechanically affected zone and heat affected zone; and the internal defect of the weld is similar to that of the AA1050-H24 weld. (3) The effective range of welding parameters for AA1050-H24 is narrow, while the one for AA6061-T6 is very wide. (4) The maximum tensile strength efficiency of the AA1050-H24 joints is similar to that of the AA6061-T6 joints, i.e. 79% and 77%, respectively.

  16. Identification and toxigenic potential of the industrially important fungi, Aspergillus oryzae and Aspergillus sojae

    DEFF Research Database (Denmark)

    Jørgensen, Thomas R

    2007-01-01

    Mold strains belonging to the species Aspergillus oryzae and Aspergillus sojae are highly valued as koji molds in the traditional preparation of fermented foods, such as miso, sake, and shoyu, and as protein production hosts in modern industrial processes. A. oryzae and A. sojae are relatives...... of the wild molds Aspergillus flavus and Aspergillus parasiticus. All four species are classified to the A. flavus group. Strains of the A. flavus group are characterized by a high degree of morphological similarity. Koji mold species are generally perceived of as being nontoxigenic, whereas wild molds...

  17. Investigation of the biological roles of autophagy in appressorium morphogenesis in Magnaporthe oryzae

    Institute of Scientific and Technical Information of China (English)

    Xiao-hong LIU; Fu-cheng LIN

    2008-01-01

    Magnaporthe oryzae has been used as a primary model organism for investigating fungus-plant interaction. Many researches focused on molecular mechanisms of appressorium formation to restrain this fungal pathogen. Autophagy is a very high conserved process in eukaryotic cells. Recently, autophagy has been considered as a key process in development and differentiation in M. oryzae. In this report, we present and discuss the current state of our knowledge on gene expression in appressorium formation and the progress in autophagy of rice blast fungi.

  18. Cytological analysis for meiotic patterns in wild rice (Oryza rufipogon Griff.

    Directory of Open Access Journals (Sweden)

    Sutanu Sarkar

    2017-03-01

    Full Text Available The present report explores the chromosomal patterns during meiosis as a fundamental cell division study in wild rice (Oryza rufipogon Griff.. Cytological assays revealed normal meiosis in most cases but in some instances meiotic abnormalities such as weak desynapsis, univalent and quadrivalent formation, translocation, spindle abnormalities and precocious movement of chromosomes were noticed. Interestingly, this wild species also has the bi-nucleoli in first meiotic stages alike the cultivated species of Oryza (O. sativa. The present investigation emphatically addresses the questions of high adaptability of wild rice supported by high pollen fertility for their potential to strong fitness in nature.

  19. The power of alternative assessments (AAs)

    Institute of Scientific and Technical Information of China (English)

    张千茜

    2013-01-01

    This article starts by discussing the potential disadvantages of traditional assessment towards young English as a Second Language (ESL) learners within the American public school education system. In response to such disadvantages, researchers ’call for the implementation of alternative assessments (AAs) is therefore introduced along with the various benefits of AAs. However, the current mainstream education policy in the US, namely No Child Left Behind (NCLB) Policy, is still largely based on the tra-ditional ways of testing, making policy-oriented implementation of AAs on large scales remarkably difficult. After careful analysis, the author points out several implications concerning how, under such an existing policy of NCLB, can practitioners effectively accommodate young ESL learners by applying the power of AAs.

  20. 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...

  1. Magnetic horn of the Antiproton Accumulator (AA)

    CERN Multimedia

    Photographic Service

    1988-01-01

    In the 1960s, the invention of this "current sheet lens" has helped to greatly improve the flux of neutrino beams. It was used again at the AA, collecting antiprotons from the production target at angles too large to fit into the acceptance of the AA. It was machined from aluminium to a thickness of 1.4 mm and pulsed at 400 kA for 15 microseconds (half-sine).

  2. Crystal Structures of Peptide Deformylase from Rice Pathogen Xanthomonas oryzae pv. oryzae in Complex with Substrate Peptides, Actinonin, and Fragment Chemical Compounds.

    Science.gov (United States)

    Ngo, Ho-Phuong-Thuy; Ho, Thien-Hoang; Lee, Inho; Tran, Huyen-Thi; Sur, Bookyo; Kim, Seunghwan; Kim, Jeong-Gu; Ahn, Yeh-Jin; Cha, Sun-Shin; Kang, Lin-Woo

    2016-10-05

    Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight on rice; this species is one of the most destructive pathogenic bacteria in rice cultivation worldwide. Peptide deformylase (PDF) catalyzes the removal of the N-formyl group from the N-terminus of newly synthesized polypeptides in bacterial cells and is an important target to develop antibacterial agents. We determined crystal structures of Xoo PDF (XoPDF) at up to 1.9 Å resolution, which include apo, two substrate-bound (methionine-alanine or methionine-alanine-serine), an inhibitor-bound (actinonin), and six fragment chemical-bound structures. Six fragment chemical compounds were bound in the substrate-binding pocket. The fragment chemical-bound structures were compared to the natural PDF inhibitor actinonin-bound structure. The fragment chemical molecules will be useful to design an inhibitor specific to XoPDF and a potential pesticide against Xoo.

  3. Practical Utilization of OryzaExpress and Plant Omics Data Center Databases to Explore Gene Expression Networks in Oryza Sativa and Other Plant Species.

    Science.gov (United States)

    Kudo, Toru; Terashima, Shin; Takaki, Yuno; Nakamura, Yukino; Kobayashi, Masaaki; Yano, Kentaro

    2017-01-01

    Analysis of a gene expression network (GEN), which is constructed based on similarity of gene expression profiles, is a widely used approach to gain clues for new biological insights. The recent abundant availability of transcriptome data in public databases is enabling GEN analysis under various experimental conditions, and even comparative GEN analysis across species. To provide a platform to gain biological insights from public transcriptome data, valuable databases have been created and maintained. This chapter introduces the web database OryzaExpress, providing omics information on Oryza sativa (rice). The integrated database Plant Omics Data Center, supporting a wide variety of plant species, is also described to compare omics information among multiple plant species.

  4. Patogenicidade de Helminthosporium oryzae a algumas espécies de gramíneas Pathogenicity of Helminthosporium oryzae against some grass species

    Directory of Open Access Journals (Sweden)

    V.H. Artigiani Filho

    1995-04-01

    Full Text Available O fungo Helminthosporium oryzae é um patógeno do arroz. Devido a sua variabilidade patogênica, foi investigada a possibilidade deste fungo infectar outras gramíneas. Através de inoculação artificial, ficou demonstrada a capacidade deste patógeno provocar infecção em aveia, cana, centeio, sorgo, trigo, Brachiaria decumbens e Panicum maximum. Assim, estas espécies vegetais podem ser consideradas potenciais hospedeiros do fungo na natureza.Helminthosporium oryzae is a rice pathogen. Due to its variability in pathogenicity, the possibility of this fungus Infecting other grasses was investigated. The capacity of this pathogen was demonstrated to be able to infect oat, sugar-cane, rye, sorghum, wheat, Brachiaria decumbens and Panicum maximum through artificial inoculations. Therefore, those plant species can be considered potencial hosts for the fungus in nature.

  5. Identiifcation of differentially-expressed genes of rice in overlapping responses to bacterial infection by Xanthomonas oryzae pv. oryzae and nitrogen deifciency

    Institute of Scientific and Technical Information of China (English)

    YU Chao; CHEN Hua-min; TIAN Fang; BI Yong-mei; Rothstein J Steven; Leach E Jan; HE Chen-yang

    2015-01-01

    Bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of high nitrogen (N) responsive diseases. Rice plants became more disease resistant with decreasing N suggesting that the crosstalk between disease resistance and N utilization pathways might exist. However, the co-regulatory components in such crosstalk have not been elucidated. Here, we comparatively analyzed the gene expression proifling of rice under Xoo inoculation, low N treatment, or a combi-nation of both stresses, and identiifed the differential y-expressed genes (DEGs) in overlapping responses. These DEGs were involved in different biological processes, including innate immunity and nitrogen metabolism. The randomly-selected DEGs expression was validated by quantitative real-time PCR assays. Temporal expression of six genes from different functional categories suggested that N condition was the dominant factor when both stresses were present. These DEGs identiifed provide novel insights into the coordinated regulatory mechanism in biotic and abiotic stress responses in rice.

  6. Domestication and geographic origin of Oryza sativa in China: insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon.

    Science.gov (United States)

    Wei, Xin; Qiao, Wei-Hua; Chen, You-Tao; Wang, Rong-Sheng; Cao, Li-Rong; Zhang, Wan-Xia; Yuan, Nan-Nan; Li, Zi-Chao; Zeng, Han-Lai; Yang, Qing-Wen

    2012-10-01

    Previous studies have indicated that China is one of the domestication centres of Asian cultivated rice (Oryza sativa), and common wild rice (O. rufipogon) is the progenitor of O. sativa. However, the number of domestication times and the geographic origin of Asian cultivated rice in China are still under debate. In this study, 100 accessions of Asian cultivated rice and 111 accessions of common wild rice in China were selected to examine the relationship between O. sativa and O. rufipogon and thereby infer the domestication and evolution of O. sativa in China through sequence analyses of six gene regions, trnC-ycf6 in chloroplast genomes, cox3 in mitochondrial genomes and ITS, Ehd1, Waxy, Hd1 in nuclear genomes. The results indicated that the two subspecies of O. sativa (indica and japonica) were domesticated independently from different populations of O. rufipogon with gene flow occurring later from japonica to indica; Southern China was the genetic diversity centre of O. rufipogon, and the Pearl River basin near the Tropic of Cancer was the domestication centre of O. sativa in China.

  7. Complete genome sequence of Bacillus thuringiensis YC-10, a novel active strain against plant-parasitic nematodes.

    Science.gov (United States)

    Cheng, Feixue; Wang, Jian; Song, Zhiqiang; Cheng, Ju'e; Zhang, Deyong; Liu, Yong

    2015-09-20

    Bacillus thuringiensis is an important microbial biopesticide for controlling agricultural pests by the production of toxic parasporal crystals proteins.Here,we report the finished annotated genome sequence of B. thuringiensis YC-10,which is highly toxic to nematodes.The complete genome sequence consists of a circular chromosome and nine circular plasmids,which the biggest plasmid harbors six parasporal crystals proteins genes consisting of cry1Aa, cry1Ac, cry1Ia, cry2Aa, cry2Ab and cryB1. The crystals proteins of Cry1Ia and Cry1Aa have high nematicidal activity against Meloidogyne incognita.

  8. Exploration of plant genomes in the FLAGdb++ environment

    Directory of Open Access Journals (Sweden)

    Leplé Jean-Charles

    2011-03-01

    Full Text Available Abstract Background In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. Results The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. Conclusion Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features.

  9. Impact of genomics approaches on plant genetics and physiology.

    Science.gov (United States)

    Tabata, Satoshi

    2002-08-01

    Comprehensive analysis of genetic information in higher plants is under way for several plants of biological and agronomical importance. Among them, Arabidopsis thaliana, a member of Brassica family, and Oryza sativa(rice) have been chosen as model plants most suitable for genome analysis. Sequencing of the genome of A. thaliana was completed in December 2000, and rice genome sequencing is in progress. The accumulated genome sequences, together with the hundreds of thousands of ESTs from several tens of plant species, have drastically changed the strategy of plant genetics. By utilizing the information on the genome and gene structures, comprehensive approaches for genome-wide functional analysis of the genes, including transcriptome analysis using microarray systems and a comprehensive analysis of a large number of insertion mutant lines, have been widely adopted. As a consequence, a large quantity of information on both the structure and function of genes in these model plants has been accumulated. However, other plant species may have their own characteristics and advantages to study individual phenomena. Application of knowledge from the model plants to other plant species and vice versa through the common language, namely the genome information, should facilitate understanding of the genetic systems underlying a variety of biological phenomena. Introduction of this common language may not be very simple, especially in the case of complex pathways such as a process of cell-covering formation. Nevertheless, it should be emphasized that genomics approaches are the most promising way to understand these processes.

  10. Efectividad biológica delazoxystrobin para el control de pyricularia oryzae cav. y cercospora oryzae miyake. en arroz de temporal en Veracruz, México

    Directory of Open Access Journals (Sweden)

    Enrique Becerra

    2001-01-01

    Full Text Available El estado de Veracruz, México, siembra anualmente 22000 ha de arroz de temporal con un rendimiento medio de 3,5 t/ha, debido principalmente a problemas de sequía lo cual favorece la presencia de hongos como Pyricularia oryzae Cav. (quema del arroz y Cercospora oryzae Miyake. (Mancha angosta. Con el objeto de conocer el comportamiento de nuevos fungicidas se evaluó la eficacia del Azoxystrobin en el control de estos hongos. El experimento se estableció en el municipio de Tres Valles, Veracruz, durante el temporal de 1999, con semilla de Milagro Filipino Depurado. El diseño estadístico utilizado fue bloques al azar con cuatro repeticiones. Los tratamientos evaluados fueron: Azoxystrobin a 0,2, 0,4 y 0,6 l/ha vs Tecto60 a 0,5 kg/ha y un testigo sin aplicación. Estos fueron aplicados al presentarse los primeros síntomas de las enfermedades. Se evaluó la incidencia, número de lesiones en 20 plantas, índice de intensidad, el rendimiento de grano y fitotoxicidad. Se encontró que el Azoxystrobin obtuvo mejores resultados que el Tecto 60 y éste a su vez que el testigo no tratado. El mejor control para P. oryzae y C. oryzae y el mayor rendimiento de grano (4432 kg/ha se logró cuando se aplicó Azoxystrobin en dosis de 0,6 l/ha, aunque con 0,2 y 0,4 l/ha de este fungicida tuvo un buen control de estas enfermedades. Ninguno de los fungicidas causó toxicidad al arroz

  11. AVALIAÇÃO DE RESISTÊNCIA EM VARIEDADES DE ARROZ (Oryza sativa L. AO ATAQUE DO Sitophilus oryzae LINNAEUS, 1763 (COLEOPTERA: CURCULIONIDAE

    Directory of Open Access Journals (Sweden)

    SOUSA, Joseane Rodrigues

    2010-04-01

    Full Text Available The resistance of rice varieties to the attack of Sitophilus oryzae Linnaeus, 1763 (Coleoptera: Curculionidae was evaluated in an experiment conducted in the laboratory of the Universidade Estadual do Maranhão, in a randomized completely design with 19 treatments in six replications. The varieties used in this study were from field experiment conducted in Miranda do Norte, MA between the months of january to may 2006. We evaluated the emerged insects total at 35 and 60 days after harvest and at 35 days was determined thepercentage of grains with defects in the skin. The results showed that the varieties Nenenzinho and Branco Tardão were, respectively, in the two storage periods (35 and 60 days after harvest the most resistant to attack by S. oryzae as the variety Branco Tardão was the most susceptible in both storage of periods.A resistência de variedades de arroz ao ataque do Sitophilus oryzae, Linnaeus, 1763 (Coleoptera: Curculionidae foi avaliada em experimento conduzido em laboratório na Universidade Estadual do Maranhão, em delineamento experimental inteiramente casualizado com 19 tratamentos em seis repetições. As variedades utilizadas nesta pesquisa foram provenientes de experimento conduzido em campo no município de Miranda do Norte, MA entre os meses de janeiro a maio de 2006. Foram avaliados o total de insetos emergidos aos 35 e 60dias após a colheita e aos 35 dias foi determinado o percentual de grãos com defeitos na casca. Os resultados evidenciaram que as variedades Agulha e Nenenzinho foram, respectivamente, nos dois períodos de armazenamento (35 e 60 dias após a colheita as mais resistentes ao ataque de S. oryzae enquanto a variedade Branco Tardão foi a mais suscetível nos dois períodos de armazenamento.

  12. DNA Microarray and Gene Ontology Enrichment Analysis Reveals That a Mutation in opsX Affects Virulence and Chemotaxis in Xanthomonas oryzae pv. oryzae

    Directory of Open Access Journals (Sweden)

    Hong-Il Kim

    2016-06-01

    Full Text Available Xanthomonas oryzae pv. oryzae (Xoo causes bacterial leaf blight (BLB in rice (Oryza sativa L.. In this study, we investigated the effect of a mutation in opsX (XOO1056, which encodes a saccharide biosynthesis regulatory protein, on the virulence and bacterial chemotaxis of Xoo. We performed DNA microarray analysis, which showed that 63 of 2,678 genes, including genes related to bacterial motility (flagellar and chemotaxis proteins were significantly downregulated (<−2 log₂ fold changes by the mutation in opsX. Indeed, motility assays showed that the mutant strain was nonmotile on semisolid agar swarm plates. In addition, a mutant strain (opsX::Tn5 showed decreased virulence against the susceptible rice cultivar, IR24. Quantitative real-time RT-PCR reaction was performed to confirm the expression levels of these genes, including those related to flagella and chemotaxis, in the opsX mutant. Our findings revealed that mutation of opsX affects both virulence and bacterial motility. These results will help to improve our understanding of Xoo and provide insight into Xoo-rice interactions.

  13. AAS 228: Day 3 morning

    Science.gov (United States)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Plenary Session 2015 Newton Lacy Pierce Prize Lecture: The Elephant in the Room: Effects of Distant, Massive Companions on Planetary System Architectures (by Leonardo dos Santos)The first session on Wednesday at 228th AAS Meeting was the Newton Lacy Pierce Prize Lecture by Heather Knutson (California Institute of Technology). This talk featured a broad range of research efforts on exoplanets, with the main focus on how we study the composition of their atmospheres, and how multi-body interactions carve the structure of the planetary systems we observe.One of her first points is the well-known idea that the Solar System is an oddball, compared to the exoplanet systems we have found so far: most of these systems contain hot Jupiters and mini-Neptunes at very close-in orbits around their host stars. Moreover, even when studying their transmission spectra, it is difficult to know the exact composition of their atmospheres.Knutson: it is difficult to constrain atmospheric composition of exoplanets (H-poor or H-rich+clouds?) #aas228pic.twitter.com/LdyN4o9RC7 astrobites (@astrobites) June 15, 2016The main proposal on how these systems formed is the migration scenario. In order to validate this idea, Dr. Knutson and her group The Friends of Hot Jupiters study systems with close-in gas giants and their frequency of binary companions, which are supposed to be the main culprits causing gas-giant migration. They found that approximately half of the observed systems have long-distance companions, providing strong validation of the migration scenario. Moreover, Dr. Knutson speculates that wide binaries have more

  14. Negative Affect, Relapse, and Alcoholics Anonymous (AA): Does AA Work by Reducing Anger?*

    Science.gov (United States)

    Kelly, John F.; Stout, Robert L.; Tonigan, J. Scott; Magill, Molly; Pagano, Maria E.

    2010-01-01

    Objective: Anger and other indices of negative affect have been implicated in a stress-induced pathway to relapse. The Alcoholics Anonymous (AA) literature states that reduction of anger is critical to recovery, yet this proposed mechanism has rarely been investigated. Using lagged, controlled hierarchical linear modeling analyses, this study investigated whether AA attendance mobilized changes in anger and whether such changes explained AA-related benefit. Method: Alcohol-dependent adults (N = 1,706) receiving treatment as part of a clinical trial were assessed at intake and at 3, 6, 9, 12, and 15 months. Results: Findings revealed substantially elevated levels of anger compared with the general population (98th percentile) that decreased over 15-month follow-up but remained high (89th percentile). AA attendance was associated with better drinking outcomes, and higher levels of anger were associated with heavier drinking. However, AA attendance was unrelated to changes in anger. Conclusions: Although support was not found for anger as a mediator, there was strong convergence between AA's explicit emphasis on anger and the present findings: Anger appears to be a serious, enduring problem related to relapse and heavy alcohol consumption. Methodological factors may have contributed to the lack of association between AA and anger, but results suggest that AA attendance alone may be insufficient to alleviate the suffering and alcohol-related risks specifically associated with anger. PMID:20409438

  15. Negative affect, relapse, and Alcoholics Anonymous (AA): does AA work by reducing anger?

    Science.gov (United States)

    Kelly, John F; Stout, Robert L; Tonigan, J Scott; Magill, Molly; Pagano, Maria E

    2010-05-01

    Anger and other indices of negative affect have been implicated in a stress-induced pathway to relapse. The Alcoholics Anonymous (AA) literature states that reduction of anger is critical to recovery, yet this proposed mechanism has rarely been investigated. Using lagged, controlled hierarchical linear modeling analyses, this study investigated whether AA attendance mobilized changes in anger and whether such changes explained AA-related benefit. Alcohol-dependent adults (N = 1,706) receiving treatment as part of a clinical trial were assessed at intake and at 3, 6, 9, 12, and 15 months. Findings revealed substantially elevated levels of anger compared with the general population (98th percentile) that decreased over 15-month follow-up but remained high (89th percentile). AA attendance was associated with better drinking outcomes, and higher levels of anger were associated with heavier drinking. However, AA attendance was unrelated to changes in anger. Although support was not found for anger as a mediator, there was strong convergence between AA's explicit emphasis on anger and the present findings: Anger appears to be a serious, enduring problem related to relapse and heavy alcohol consumption. Methodological factors may have contributed to the lack of association between AA and anger, but results suggest that AA attendance alone may be insufficient to alleviate the suffering and alcohol-related risks specifically associated with anger.

  16. Toxic effects of essential plant oils in adult Sitophilus oryzae (Linnaeus (Coleoptera, Curculionidae

    Directory of Open Access Journals (Sweden)

    Andréa Roveré Franz

    2011-03-01

    Full Text Available Toxic effects of essential plant oils in adult Sitophilus oryzae (Linnaeus (Coleoptera, Curculionidae. Stored grains are subject to losses in quality nutritional value and in sanitation from the time they are stored to the time they are consumed. Botanical insecticides may offer an alternative solution for pest control. The objective was to test the insecticidal properties of the essential oils of Cymbopogon citratus (leaf, Zingiber officinale (root and Mentha sp. (leaf. The efficacy of these oils was tested to control the rice weevil, S. oryzae, using hydrodistillation. Chemical analysis of the essential oils was carried out by gas chromatography. Major components of C. citratus were geranial (48% and neral (31%, of Z. officinale were α-zingibereno (13%, geranial (16%, neral (10% and α-farneseno (5% and of Mentha sp. was menthol (92%. Bioassays were carried out by fumigation and topical application. In topical application assays, the essential oil of C. citratus had greater toxicity (LC50 0.027 µL mL-1 and shorter exposure time than the oils of the other two plants. After 24 h and 48 h, 70% and 100% mortality of S. oryzae occurred, respectively. In fumigation assays, essential oil of Z. officinale had a lower LC50 (1.18 µL cm-2 and 70% mortality after 24 h exposure. Therefore, we recommend the use of essential oils of C. citratus and Z. officinale to control the rice weevil S. oryzae.

  17. Change in hyphal morphology of Aspergillus Oryzae during fed-batch cultivation

    DEFF Research Database (Denmark)

    Haack, Martin Brian; Olsson, Lisbeth; Hansen, K

    2006-01-01

    Industrial enzymes are often produced by filamentous fungi in fed-batch cultivations. During cultivation, the different morphological forms displayed by the fungi have an impact on the overall production. The morphology of a recombinant lipase producing Aspergillus oryzae strain was investigated...

  18. An unusual ulcer: A case of cutaneous mucormycosis caused by Rhizopus oryzae

    Directory of Open Access Journals (Sweden)

    Bradley J. Gardiner

    2015-03-01

    Full Text Available Mucormycoses are high-mortality infections feared by clinicians worldwide. They predominantly affect immunocompromised hosts and are associated with a spectrum of disease. We describe a case of cutaneous mucormycosis caused by Rhizopus oryzae in a patient with multiple risk factors cured with complete surgical excision and a short course of antifungal therapy.

  19. Morphological characterization of recombinant strains of Aspergillus oryzae producing alpha-amylase during batch cultivations

    DEFF Research Database (Denmark)

    Spohr, Anders Bendsen; Carlsen, Morten; Nielsen, Jens Bredal;

    1997-01-01

    Three alpha-amylase producing strains of Aspergillus oryzae used for recombinant protein production have been studied with respect to growth and protein production. By comparing the three strains with respect to morphology and protein production it is shown that a morphological mutant with a more...... dense mycelium is more efficient in producing alpha-amylase....

  20. A New Eudesmane Sesquiterpene from Nigrospora oryzae, an Endophytic Fungus of Aquilaria sinensis

    Directory of Open Access Journals (Sweden)

    Dongli Li

    2014-07-01

    Full Text Available A new eudesmane-type sesquiterpene, 11 -hydroxy capitulatin B (1 , along with a known related sesquiterpene, capitulatin B (2, was isolated from the endophytic fungus Nigrospora oryzae A8 from Aquilaria sinensis, the only plant resource for agarwood production in China. This research demonstrates that the endophytic fungi from A. sinensis might play a role in the formation of agarwood.

  1. Metabolic engineering of Rhizopus oryzae for the production of platform chemicals

    NARCIS (Netherlands)

    Meussen, B.J.; Graaff, de L.H.; Sanders, J.P.M.; Weusthuis, R.A.

    2012-01-01

    Rhizopus oryzae is a filamentous fungus belonging to the Zygomycetes. It is among others known for its ability to produce the sustainable platform chemicals L-(+)-lactic acid, fumaric acid, and ethanol. During glycolysis, all fermentable carbon sources are metabolized to pyruvate and subsequently di

  2. Identification of a RAPD marker linked to a blast resistance gene in Oryza sativa L.

    Institute of Scientific and Technical Information of China (English)

    LUJun; ZHUANGJieyun; LINHongxuan; ZHENGKangle

    1994-01-01

    Marker-aided selection has received more attention in recent years. This relies on the exploitation of close linkage between molecular markers and target gene(s). We report here a randomly amplified polymorphic DNA (RAID) marker tightly linked to the blast resistance gene Pi-11(t) derived from Hongjiaozhan, which confers the resistante to race ZBI of Pyricularia oryzae Car.

  3. Construction of six Oryza sativa x O. rufipogon Chromosome Segment Substitution Line (CSSL) Libraries

    Science.gov (United States)

    Transgressive variation has been observed in rice (Oryza sativa) as an increase in grain yield and attributed to the ancestral parent, O. rufipogon, in mapping populations developed from several adapted rice varieties crossed with a single O. rufipogon accession. To explore this phenomenon of transg...

  4. Polyol accumulation by Aspergillus oryzae at low water activity in solid-state fermentation

    NARCIS (Netherlands)

    Ruijter, G.J.G.; Visser, J.; Rinzema, A.

    2004-01-01

    Polyol accumulation and metabolism were examined in Aspergillus oryzae cultured on whole wheat grains or on wheat dough as a model for solid-state culture. In solid-state fermentation (SSF), water activity (a(w)) is typically low resulting in osmotic stress. In addition to a high level of mannitol,

  5. Basil oil fumigation increases radiation sensitivity in adult Sitophilus oryzae (Coleoptera: Curculionidae).

    Science.gov (United States)

    The biological activity of basil (Ocimum basilicum L.) oil was tested against the stored product pest rice weevil, Sitophilus oryzae(L.). Adult weevils were exposed to seven different concentrations of basil oil ranging from 0.12 µl/ml-0.60 µl/ml in Petri dishes and mortality was assessed at 3,4 and...

  6. Modulation of Isoflavonoid Composition of Rhizopus oryzae Elicited Soybean (Glycine max) Seedlings by Light and Wounding

    NARCIS (Netherlands)

    Aisyah, S.; Gruppen, H.; Madzora, B.; Vincken, J.P.

    2013-01-01

    The isoflavonoid profile of soybean was altered in different ways by stimulation of defense response upon germination. The combination of simultaneous germination and induction by Rhizopus oryzae increased the total isoflavonoid content of soybeans over 2-fold. Pterocarpans became the predominant

  7. Early senescence of rice and Drechslera oryzae in the Wageningen polder, Surinam

    NARCIS (Netherlands)

    Klomp, A.O.

    1977-01-01

    Rice is grown in monoculture in the Wageningen Polder, Surinam, South America, which comprises 10 000 ha of heavy clay soil. Fungal diseases caused appreciable losses of the rice crop in several years. Drechslera oryzae van Breda de Haan was found to be the major pathogen of rice. Its most conspicuo

  8. Natural variation of rice blast resistant gene Pi-ta in Oryza species

    Science.gov (United States)

    The Pi-ta gene in rice is a putative NBS type cytoplasmic receptor conferring resistance to races of Magnaporthe oryzae in a gene-for-gene manner. A Functional Nucleotide Polymorphism (FNP) change resulting in an amino acid substitution of Alanine to Serine at position 918 (nucleotide G to T at posi...

  9. Transcriptome Analysis of Early Responsive Genes in Rice during Magnaporthe oryzae Infection

    Directory of Open Access Journals (Sweden)

    Yiming Wang

    2014-12-01

    Full Text Available Rice blast disease caused by Magnaporthe oryzae is one of the most serious diseases of cultivated rice (Oryza sativa L. in most rice-growing regions of the world. In order to investigate early response genes in rice, we utilized the transcriptome analysis approach using a 300 K tilling microarray to rice leaves infected with compatible and incompatible M. oryzae strains. Prior to the microarray experiment, total RNA was validated by measuring the differential expression of rice defense-related marker genes (chitinase 2, barwin, PBZ1, and PR-10 by RT-PCR, and phytoalexins (sakuranetin and momilactone A with HPLC. Microarray analysis revealed that 231 genes were up-regulated (>2 fold change, p < 0.05 in the incompatible interaction compared to the compatible one. Highly expressed genes were functionally characterized into metabolic processes and oxidation-reduction categories. The oxidative stress response was induced in both early and later infection stages. Biotic stress overview from MapMan analysis revealed that the phytohormone ethylene as well as signaling molecules jasmonic acid and salicylic acid is important for defense gene regulation. WRKY and Myb transcription factors were also involved in signal transduction processes. Additionally, receptor-like kinases were more likely associated with the defense response, and their expression patterns were validated by RT-PCR. Our results suggest that candidate genes, including receptor-like protein kinases, may play a key role in disease resistance against M. oryzae attack.

  10. Identification of molecular markers linked to rice bacterial blight resistance genes from Oryza meyeriana

    Directory of Open Access Journals (Sweden)

    Jing WANG,Chen CHENG,Yanru ZHOU,Yong YANG,Qiong MEI,Junmin LI,Ye CHENG,Chengqi YAN,Jianping CHEN

    2015-09-01

    Full Text Available Y73 is a progeny of asymmetric somatic hybridization between Oryza sativa cv. Dalixiang and the wild rice species Oryza meyeriana. Inoculation with a range of strains of Xanthomonas oryzae pv. oryzae showed that Y73 had inherited a high level of resistance to rice bacterial blight (BB from its wild parent. An F2 population of 7125 individuals was constructed from the cross between Y73 and a BB-susceptible cultivar IR24. After testing 615 SSR and STS markers covering the 12 rice chromosomes, 186 markers were selected that showed polymorphism between Y73 and IR24. Molecular markers linked to the BB resistance genes in Y73 were scanned using the F2 population and the polymorphic markers. The SSR marker RM128 on chromosome 1, the STS marker R03D159 on chromosome 3 and the STS marker R05D104 on chromosome 5 were found to be linked to the rice BB resistance genes in Y73.

  11. Synthesis of quarternary ammonium salts with dithiocarbamate moiety and their antifungal activities against Helminthosporium oryzae

    Indian Academy of Sciences (India)

    Mandeep Singh; Anita Garg; Anjali Sidhu; Vineet Kumar

    2013-05-01

    Quaternary ammonium salts containing dithiocarbamate moiety were synthesized and evaluated for their antifungal activities against Helminthosporium oryzae. All the synthesized compounds showed moderate to promising fungitoxicity against the test. Some of the synthesized compounds inflicted antifungal activity greater than the standard fungicide.

  12. Physiological changes promoted by a strobilurin fungicide in the rice-Bipolaris oryzae interaction.

    Science.gov (United States)

    Debona, D; Nascimento, K J T; Gomes, J G O; Aucique-Perez, C E; Rodrigues, F A

    2016-06-01

    Strobilurins are among the most important fungicides that are used for plant disease control worldwide. In addition to their fungicide effect, strobilurins can also improve crop physiology. Nonetheless, the impact of azoxystrobin (Az), the main marketed strobilurin, on rice physiology is still unknown. Detailed gas exchange measurements and chlorophyll a fluorescence analysis were used to examine the Az effects on the photosynthetic performance of rice plants (cultivar Metica-1) either challenged or not with Bipolaris oryzae, the causal agent of brown spot. Az impaired carbon (C) fixation in the non-inoculated plants in a manner that was not related to photochemical or biochemical limitations, but rather to decreased stomatal conductance that limited the CO2 influx into the mesophyll cells. The photosynthesis of rice plants that were not sprayed with Az dramatically decreased upon B. oryzae infection, which was chiefly governed by photochemical and biochemical limitations. The energy surplus that was caused by limited C fixation in the rice plants that were treated with Az and inoculated with B. oryzae was thermally and effectively dissipated until 72h after inoculation. In Az absence, however, this mechanism was not sufficient to prevent chronic photoinhibition to photosynthesis. The inoculated plants were not able to fully capture and exploit the collected light energy, but these constraints were greatly limited in the presence of Az. In conclusion, Az impaired the photosynthetic performance of non-infected plants by diffusive constraints, but prevented, to a greater extent, the damage to the photosynthetic apparatus during the infection process of B. oryzae.

  13. Measurement and analysis on optical characteristics of Aspergillus oryzae spores in infrared band

    Science.gov (United States)

    Li, Le; Hu, Yihua; Gu, Youlin; Chen, Wei; Xu, Shilong; Zhao, Xinying

    2015-10-01

    Spore is an important part of bioaerosols. The optical characteristics of spore is a crucial parameter for study on bioaerosols. The reflection within the waveband of 2.5 to15μm were measured by squash method. Based on the measured data, Complex refractive index of Aspergillus oryzae spores within the waveband of 3 to 5μm and 8 to 14 μm were calculated by using Krames-Kronig (K-K) relationship. Then,the mass extinction coefficient of Aspergillus oryzae spores within the waveband of 3 to 5μm and 8 to 14μm were obtained by utilizing Mie scattering theory, and the results were analyzed and discussed. The average mass extinction coefficient of Aspergillus oryzae spores is 0.51 m2/g in the range of 3 to 5μm and 0.48m2/g in the range of 8 to 14μm. Compared with common inorganic compounds, Aspergillus oryzae spores possesses a good extinction performance in infrared band.

  14. Interesterification of Milk Fat with Oleic Acid Catalyzed by Immobilized Rhizopus oryzae Lipase

    NARCIS (Netherlands)

    OBA, T; Witholt, B.

    1994-01-01

    Milk fat was interesterified with oleic acid by catalysis of an immobilized lipase in a microaqueous two-phase system. A commercial lipase from Rhizopus oryzae and a controlled pore glass carrier were selected for preparation of an immobilized lipase. The prepared immobilized lipase showed a Michael

  15. Identification and toxigenic potential of the industrially important fungi, Aspergillus oryzae and Aspergillus sojae

    DEFF Research Database (Denmark)

    Jørgensen, Thomas R

    2007-01-01

    are associated with the carcinogenic aflatoxins. Thus, reliable identification of individual strains is very important for application purposes. This review considers the pheno- and genotypic markers used in the classification of A. flavus group strains and specifically in the identification of A. oryzae and A...

  16. Organic anion exudation by lowland rice (Oryza sativa L.) at zinc and phosphorus deficiency

    NARCIS (Netherlands)

    Hoffland, E.; Wei, C.Z.; Wissuwa, M.

    2006-01-01

    The objectives of this paper were to determine (1) if lowland rice (Oryza sativa L.) plants respond similarly to low zinc (Zn) and phosphorus (P) availability by increased root exudation of low-molecular weight organic anions (LMWOAs) and (2) if genotypic variation in tolerance to low soil supply of

  17. Studying Pellet Formation of a Filamentous Fungus Rhizopus oryzae to Enhance Organic Acid Production

    Science.gov (United States)

    Liao, Wei; Liu, Yan; Chen, Shulin

    Using pelletized fungal biomass can effectively improve the fermentation performance for most of fugal strains. This article studied the effects of inoculum and medium compositions such as potato dextrose broth (PDB) as carbon source, soybean peptone, calcium carbonate, and metal ions on pellet formation of Rhizopus oryzae. It has been found that metal ions had significantly negative effects on pellet formation whereas soybean peptone had positive effects. In addition PDB and calcium carbonate were beneficial to R. oryzae for growing small smooth pellets during the culture. The study also demonstrated that an inoculum size of less than 1.5×109 spores/L had no significant influence on pellet formation. Thus, a new approach to form pellets has been developed using only PDB, soybean peptone, and calcium carbonate. Meanwhile, palletized fungal fermentation significantly enhanced organic acid production. Lactic acid concentration reached 65.0 g/L in 30 h using pelletized R. oryzae NRRL 395, and fumeric acid concentration reached 31.0 g/L in 96 h using pelletized R. oryzae ATCC 20344.

  18. Hydrogen Production by Co-cultures of Rhizopus oryzae and a Photosynthetic Bacterium, Rhodobacter sphaeroides RV

    Science.gov (United States)

    Asada, Yasuo; Ishimi, Katsuhiro; Nagata, Yoko; Wakayama, Tatsuki; Miyake, Jun; Kohno, Hideki

    Hydrogen production with glucose by using co-immobilized cultures of a fungus, Rhizopus oryzae NBRC5384, and a photosynthetic bacterium, Rhodobacter sphaeroides RV, in agar gels was studied. The co-immobilized cultures converted glucose to hydrogen via lactate in a high molar yield of about 8moles of hydrogen per glucose at a maximum under illuminated conditions.

  19. The ultrasound-enhanced bioscouring performance of four polygalacturonase enzymes obtained from rhizopus oryzae

    Science.gov (United States)

    An analytical and statistical method has been developed to measure the ultrasound-enhanced bioscouring performance of milligram quantities of endo- and exo-polygalacturonase enzymes obtained from Rhizopus oryzae fungi. UV-Vis spectrophotometric data and a general linear mixed models procedure indic...

  20. Kinetic properties of Rhizopus oryzae RPG1 endo-polygalacturonase hydrolyzing galacturonic acid oligomers

    Science.gov (United States)

    Future fuel and specialty chemical production will benefit from the use of agricultural biomass. Efficient and effective use of agricultural biomass requires conversion to simple sugars by chemical pre-treatments and enzymes into simple sugars. Rhizopus oryzae, a filamentous fungus, makes enzymes ca...

  1. Expression and characterization of fifteen Rhizopus oryzae 99-880 polygalacturonase enzymes in Pichia pastoris

    Science.gov (United States)

    Polygalacturonase enzymes hydrolyze the long polygalacturonic acid chains found in the smooth regions of pectin. Interest in this enzyme class continues due to their ability to macerate tissues of economically important crops and their use in a number of industrial processes. Rhizopus oryzae has a l...

  2. Production of Ammonium Lactate by Fed-batch Fermentation of Rhizopus oryzae from Corncob Hydrolysate

    Institute of Scientific and Technical Information of China (English)

    BAI Dong-mei; LI Shi-zhong; LIN Fang-qian

    2004-01-01

    L- (+)-Lactic acid production from corncob hydrolysate as a cheap carbohydrate source by fed-batch fermentation of Rhizopus oryzae HZS6 was studied. After 96 h of fermentation in a 5 L fermentor, the final concentration of ammonium L-(+)-lactate, average productivity(based on initial xylose concentration) and max(+)-lactate was 98.8%.

  3. The High Affinity Iron Permease is a Key Virulence Factor Required for Rhizopus oryzae Pathogenesis

    Science.gov (United States)

    Rhizopus oryzae is the most common cause of mucormycosis, an angioinvasive fungal infection that causes a >/=50% mortality rate despite first-line therapy. Clinical and animal model data clearly demonstrate that the presence of elevated available serum iron predisposes the host to mucormycosis. Th...

  4. INTERESTERIFICATION OF MILK-FAT WITH OLEIC-ACID CATALYZED BY IMMOBILIZED RHIZOPUS-ORYZAE LIPASE

    NARCIS (Netherlands)

    OBA, T; WITHOLT, B

    1994-01-01

    Milk fat was interesterified with oleic acid by catalysis of an immobilized lipase in a microaqueous two-phase system. A commercial lipase from Rhizopus oryzae and a controlled pore glass carrier were selected for preparation of an immobilized lipase. The prepared immobilized lipase showed a Michael

  5. Construction of an insecticidal baculovirus expressing insect-specific neurotoxin AaIT

    Institute of Scientific and Technical Information of China (English)

    姚斌; 庞义; 范云六; 赵荣敏; 杨应昌; 王天原

    1996-01-01

    Considering the factors which affect gene transcription, translation and the stability of mRNA, without changing the amino acid composition of the encoded polypeptide, AaIT gene encoding insect-specific neurotoxin was designed and synthesized according to bias in codon choice, overall G+C content and G + C content of bases at the third position in codons of polyhedrin genes of baculovirus and of plant genes as well. AaIT gene was fused behind a synthetic gp67 signal sequence and then recombined into the genome of Trichoplusia ni nuclear polyhedrosis virus (TnNPV) by transfer vector pSXIV VI+X3. The recombinant virus TnNPV-AalT (occ+-gal-) was screened. The results of Southern blotting and SDS-PAGE demonstrated that AaIT gene had integrated into the genome of virus and expressed. Bioassays on the 3rd-instar Trichoplusia ni larvae showed that recombinant viruses TnNPV-AalT could shorten the time of killing insect and improve the efficiency of killing agronomically important insects.

  6. AAS 228: Day 1 afternoon

    Science.gov (United States)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Plenary Session: From Space Archeology to Serving the World Today: A 20-year Journey from the Jungles of Guatemala to a Network of Satellite Remote Sensing Facilities Around the World(by Michael Zevin)In the conferences second plenary session, NASAs Daniel Irwin turned the eyes of the conference back to Earth by highlighting the huge impact that NASA missions play in protecting and developing our own planet.Daniel Irwin: using satellite imagery to detect differences in vegetation and find ancient Mayan cities. #aas228 pic.twitter.com/9LFPQdCHTM astrobites (@astrobites) June 13, 2016Irwin came to be involved in NASA through his work mapping Guatemalan jungles, where he would spend 22 days at a time exploring the treacherous jungles on foot armed with a 1st generation GPS, a compass, and a machete. A colleague introduced Irwin to the satellite imagery thathe was exploring, demonstratinghow these images are a strong complement to field work. The sharing of this satellite data with nearby villages helped to show the encroachment of agriculture and the necessity of connecting space to the village. Satellite imagery also played a role in archeological endeavors, uncovering dozens of Mayan cities that have been buried for over a millennia by vegetation, and it provided evidence that the fall of the Mayan civilization may have been due to massive deforestation that ledto drought.Glacial retreat in Chile imaged by ISERV.Irwin displayed the constellation of NASAs Earth-monitoring satellites that have played an integral role in conserving our planet and alerting the world of natural disasters. He also showed

  7. Applications of the double-barreled data in whole-genome shotgun sequence assembly and analysis

    Institute of Scientific and Technical Information of China (English)

    HAN Yujun; WANG Jing; GU Xiaocheng; YU Jun; LI Songgang; NI Peixiang; L(U) Hong; YE Jia; HU Jianfei; CHEN Chen; HUANG Xiangang; CONG Lijuan; LI Guangyuan

    2005-01-01

    Double-barreled (DB) data have been widely used for the assembly of large genomes. Based on the experience of building the whole-genome working draft of Oryza sativa L.ssp. Indica, we present here the prevailing and improved uses of DB data in the assembly procedure and report on novel applications during the following data-mining processes such as acquiring precise insert fragment information of each clone across the genome, and a new kind of Iow-cost whole-genome microarray. With the increasing number of organisms being sequenced,we believe that DB data will play an important role both in other assembly procedures and infuture genomic studies.

  8. Bioremoval of heavy metals and nutrients from sewage plant by Anabaena oryzae and Cyanosarcina fontana.

    Science.gov (United States)

    Fawzy, Mustafa A; Issa, Ahmed A

    2016-01-01

    The present study demonstrated the growth of two species of cyanobacteria on wastewater isolated from sewage plant in Aswan, Egypt. We evaluated their efficiency for eliminating nitrogen, phosphorus, chemical oxygen demand (COD) and heavy metals (Fe(2+), Pb(2+), Cu(2+), and Mn(2+)). The growth of Cyanosarcina fontana has supported wastewater as a growth medium than Anabaena oryzae compared to standard medium. The nutrients concentration such as COD, NO3-N and PO4-P were decreased by the growth of A. oryzae and C. fontana in the wastewater after primary settling and centrate. However, the reduction of COD was less efficient than the other nutrients. The reduction percentage of COD, NO3-N and PO4-P reached 39.3, 84.1 and 90.7% as well as 54.6, 83.1, and 89.8%, in cultures of A. oryzae and C. fontana grown in the wastewater after primary settling, respectively. The reduction amounted to 10.1, 76.8, and 63.0% by A. oryzae and 43.2, 62.1, and 74.8% by C. fontana, grown in the centrate, respectively. Cyanobacteria species have the ability to accumulate the heavy metals from the wastewater to level far than the exceeding metal level in the water. Whereas, the heavy metals biosorption performance of C. fontana was higher in accumulating Fe(2+) (93.95%), Pb(2+) (81.21%), Cu(2+) (63.9%), and Mn(2+) (48.49%) compared to A. oryzae. The biosorption ability is dependent on the nature of the adsorbent studied and the type of wastewater treated. Therefore, removal of heavy metals and nutrients by the tested algae is strongly recommended as a powerful technique for the removal of pollutants from wastewater.

  9. The AA disappearing under concrete shielding

    CERN Multimedia

    CERN PhotoLab

    1982-01-01

    When the AA started up in July 1980, the machine stood freely in its hall, providing visitors with a view through the large window in the AA Control Room. The target area, in which the high-intensity 26 GeV/c proton beam from the PS hit the production target, was heavily shielded, not only towards the outside but also towards the AA-Hall. However, electrons and pions emanating from the target with the same momentum as the antiprotons, but much more numerous, accompanied these through the injection line into the AA ring. The pions decayed with a half-time corresponding to approximately a revolution period (540 ns), whereas the electrons lost energy through synchrotron radiation and ended up on the vacuum chamber wall. Electrons and pions produced the dominant component of the radiation level in the hall and the control room. With operation times far exceeding original expectations, the AA had to be buried under concrete shielding in order to reduce the radiation level by an order of magnitude.

  10. Genomic behavior of hybrid combinations between elephant grass and pearl millet

    OpenAIRE

    Fernando Ferreira Leão; Lisete Chamma Davide; José Marcello Salabert de Campos; Antonio Vander Pereira; Fernanda de Oliveira Bustamante

    2011-01-01

    The objective of this work was to evaluate the genomic behavior of hybrid combinations between elephant grass (Pennisetum purpureum) and pearl millet (P. glaucum). Tetraploid (AAA'B) and pentaploid (AA'A'BB) chromosome races resulting from the backcross of the hexaploid hybrid to its parents elephant grass (A'A'BB) and pearl millet (AA) were analyzed as to chromosome number and DNA content. Genotypes of elephant grass, millet, and triploid and hexaploid induced hybrids were compared. Pentaplo...

  11. Genome-wide characterization of soybean P 1B -ATPases gene family provides functional implications in cadmium responses

    OpenAIRE

    Fang, Xiaolong; Wang, Lei; Deng, Xiaojuan; Wang, Peng; Ma, Qibin; Nian, Hai; Wang, Yingxiang; Yang, Cunyi

    2016-01-01

    Background The P1B-ATPase subfamily is an important group involved in transporting heavy metals and has been extensively studied in model plants, such as Arabidopsis thaliana and Oryza sativa. Emerging evidence indicates that one homolog in Glycine max is also involved in cadmium (Cd) stress, but the gene family has not been fully investigated in soybean. Results Here, we identified 20 heavy metal ATPase (HMA) family members in the soybean genome, presented as 10 paralogous pairs, which is si...

  12. Genetic and physical mapping of AvrPi7, a novel avirulence gene of Magnaporthe oryzae using physical position-ready markers

    Institute of Scientific and Technical Information of China (English)

    FENG ShuJie; WANG Ling; MA JunHong; LIN Fei; PAN QingHua

    2007-01-01

    Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating crop diseases worldwide. The avirulence gene corresponding to rice blast resistance gene Pi7 in field isolate CHL346 was inherited as a single gene, designated AvrPi7, in a segregating population consisting of 189 ascospore progenies derived from a cross between field isolates CHL346 and CHL42. In order to determine the chromosomal location of the AvrPi7 locus, a total of 121 simple sequence repeat (SSR) markers were developed based on the whole-genome sequence of reference isolate 70-15 of M. oryzae.Linkage analysis of the locus with these SSR markers showed that eight SSR markers on chromosome1 were linked to the locus, among which the closest flanking markers MS1-9 and MS1-15 were 3.2 and 16.4 cM from the locus, respectively. For fine mapping, additional PCR-based makers including eight SSR markers and three candidate avirulence gene (CAG) markers were developed in the region flanking both markers. The AvrPi7 locus was genetically delimited within a 1.6-cM region flanked by markers MS1-21 and MS1-22, and co-segregated with the marker CAG2. To construct a physical map of the AvrPi7 locus, molecular markers linked to the Avr gene were mapped on the supercontigs of the reference isolate 70-15 through bioinformation analysis (BIA). Consequently, the AvrPi7 locus was delimited to a 75-kb interval flanked by markers MS1-21 and MS1-22 based on the reference sequence.Merodiploids observed in this study are also discussed.

  13. Characterization of soybean fermented by aflatoxin non-producing Aspergillus oryzae and γ-aminobutyric acid producing Lactobacillus brevis

    National Research Council Canada - National Science Library

    Kim, Nam Yeun; Ji, Geun Eog

    2014-01-01

    .... The aim of the present study was to develop and characterize fermented soybean products with enhanced safety and bioactive compound using aflatoxin non-producing Aspergillus oryzae FMB S46471 and γ-aminobutyric acid (GABA...

  14. Improved production of raw starch degrading enzyme by Aspergillus oryzae F-30 using methyl glucoside sesqui-stearate.

    Science.gov (United States)

    Sun, Hai-Yan; Wang, Lu; Liu, Jian-Wen; Peng, Ming

    2009-10-01

    The effect of methyl glucoside sesqui-stearate (MGS) on the production of raw starch degrading enzyme (RSDE) by Aspergillus oryzae F-30 was studied in this paper. The activity of RSDE formed by Aspergillus oryzae F-30 was enhanced dramatically by the addition of MGS to the medium. As a result, with the addition of 1.5 g MGS in 1 L basal medium, RSDE activity and productivity were 107 U mL(-1) and 1.49 U mL(-1) h(-1), 4.3-fold and 7.1-fold greater than the values obtained in the basal medium, respectively. The effect of MGS on the synthesis of RSDE by Aspergillus oryzae F-30 was also studied on a molecular level. It was observed that the regulation of RSDE synthesis in Aspergillus oryzae F-30 occurs at both transcriptional and translational level and the enzyme synthesis was provoked by the addition of MGS at transcriptional level.

  15. Structure-function analysis of Rgs1 in Magnaporthe oryzae: role of DEP domains in subcellular targeting

    National Research Council Canada - National Science Library

    Ramanujam, Ravikrishna; Yishi, Xu; Liu, Hao; Naqvi, Naweed I

    2012-01-01

    Rgs1, a prototypical Regulator of G protein Signaling, negatively modulates the cyclic AMP pathway thereby influencing various aspects of asexual development and pathogenesis in the rice-blast fungus Magnaporthe oryzae...

  16. The late endosomal HOPS complex anchors active G-protein signaling essential for pathogenesis in magnaporthe oryzae

    National Research Council Canada - National Science Library

    Ramanujam, Ravikrishna; Calvert, Meredith E; Selvaraj, Poonguzhali; Naqvi, Naweed I

    2013-01-01

    In Magnaporthe oryzae, the causal ascomycete of the devastating rice blast disease, the conidial germ tube tip must sense and respond to a wide array of requisite cues from the host in order to switch...

  17. Complete Genome Sequence of Bacillus thuringiensis subsp. chinensis Strain CT-43▿

    Science.gov (United States)

    He, Jin; Wang, Jieping; Yin, Wen; Shao, Xiaohu; Zheng, Huajun; Li, Mingshun; Zhao, Youwen; Sun, Ming; Wang, Shengyue; Yu, Ziniu

    2011-01-01

    Bacillus thuringiensis has been widely used as an agricultural biopesticide for a long time. As a producing strain, B. thuringiensis subsp. chinensis strain CT-43 is highly toxic to lepidopterous and dipterous insects. It can form various parasporal crystals consisting of Cry1Aa3, Cry1Ba1, Cry1Ia14, Cry2Aa9, and Cry2Ab1. During fermentation, it simultaneously generates vegetative insecticidal protein Vip3Aa10 and the insecticidal nucleotide analogue thuringiensin. Here, we report the finished, annotated genome sequence of B. thuringiensis strain CT-43. PMID:21551307

  18. Complete genome sequence of Bacillus thuringiensis subsp. chinensis strain CT-43.

    Science.gov (United States)

    He, Jin; Wang, Jieping; Yin, Wen; Shao, Xiaohu; Zheng, Huajun; Li, Mingshun; Zhao, Youwen; Sun, Ming; Wang, Shengyue; Yu, Ziniu

    2011-07-01

    Bacillus thuringiensis has been widely used as an agricultural biopesticide for a long time. As a producing strain, B. thuringiensis subsp. chinensis strain CT-43 is highly toxic to lepidopterous and dipterous insects. It can form various parasporal crystals consisting of Cry1Aa3, Cry1Ba1, Cry1Ia14, Cry2Aa9, and Cry2Ab1. During fermentation, it simultaneously generates vegetative insecticidal protein Vip3Aa10 and the insecticidal nucleotide analogue thuringiensin. Here, we report the finished, annotated genome sequence of B. thuringiensis strain CT-43.

  19. Purification, characterization and antiproliferative activity of l-asparaginase from Aspergillus oryzae CCT 3940 with no glutaminase activity

    Directory of Open Access Journals (Sweden)

    Fernanda Furlan Gonçalves Dias

    2016-09-01

    Conclusions: The sensitivity of the cells lines to purified l-asparaginase from A. oryzae CCT 3940 appeared to be concentration dependent affording a more significant decrease in cell growth than that observed for the commercial l-asparaginase from Escherichia coli. The l-asparaginase from A. oryzae CCT 3940 has a high potential for pharmaceutical exploitation in the treatment of leukemia.

  20. POTENSI DARI KAPANG Aspergilus niger, Rhizophus oryzae DAN Neurospora sitophila SEBAGAI PENGHASIL EZIM FITASE DAN AMILASE PADA SUBSTRATE AMPAS TAHU

    Directory of Open Access Journals (Sweden)

    Atit - Kanti

    2017-02-01

    Full Text Available Penambahan enzim hidrolisis untuk pakan ternak dapat meningkatkan nilai nutrisi pakan. Penelitian bertujuan untuk mendapatkan kondisi optimal untuk produksi enzim amilase dan fitase pada media ampas tahu menggunakan Aspergilus niger, Rhizophus oryzae dan Neurospora sitophila. Uji kemampuan produksi enzim fitase dan amilase oleh Aspergilus niger, Rhizophus oryzae dan Neurospora sitophila dilakukan menggunakan media ampas tahu yang disterilisasi. Pemilihan ketiga isolat ini diawali dengan uji produksi enzim amilase pada kultur cair yang mengandung 2 % pati, dan uji fitase dilakukan pada media yang mengandung 0.5 % sodium fitat. Hasil uji pada medium cair selanjutnya digunakan untuk uji produksi enzim fitase dan fitase pada sistem fermentasi padat (SSF menggunakan ampas tahu sebagai media fermentasi. Untuk mendapatkan produksi enzim yang tinggi dilakukan melalui optimasi waktu inkubasi, suhu inkubasi dan pH media. Fitase dan amilase dapat diproduksi dengan media ampas tahu oleh R. oryzae, A. niger dan N. sitophila. Kondisi optimum untuk produksi fitase, yaitu waktu inkubasi pada hari keempat untuk ketiga kapang, suhu 25 °C untuk R. oryzae dan A. niger, suhu 30°C untuk N. sitophila, pH 8 untuk R. oryzae, pH 6 untuk Aspergillus niger dan N. Sitophila. Neurospora sitophila menghasilkan amilase optimum pada suhu 35°C, sedangkan Aspergillus niger dan Rhizopus oryzae optimum pada suhu 30°C. Penurunan aktivitas produksi amilase menurun oleh R. oryzae pada suhu 40°C. Amilase diproduksi optimal pada pH 6-7. Pakan ternak yang mengandung asam fitat mampu dihidrolisis oleh fitase pada kondisi optimum. Ketiga kapang juga menghasilkan enzim amilase pada media ampas tahu mengindikasikan bahwa ampas tahu merupakan susbtrat yang baik untuk produksi enzim hidrolisis yang berguna untuk meningkatkan nilai nutrisi pakan ternak. (Kata kunci: Amilase, Aspergilus niger, Neurospora sitophila, phytase, Rhizophus oryzae

  1. AAS Nova and Astrobites: Making current astronomy research accessible

    Science.gov (United States)

    Kohler, Susanna; Astrobites Team

    2016-10-01

    AAS Nova and Astrobites are two resources available for astronomers, astronomy students, and astronomy enthusiasts to keep up with some of the most recent research published across the field of astronomy. Both supported by the AAS, these two daily astrophysical literature blogs provide accessible summaries of recent publications on the arXiv and in AAS journals. We present the goals, content, and readership of AAS Nova and Astrobites, and discuss how they might be used as tools in the undergraduate classroom.

  2. Comparative study on the antifungal activity of hydroalcoholic extract of Iranian Propolis and Royal jelly against Rhizopus oryzae

    Directory of Open Access Journals (Sweden)

    Moghim Hassan

    2015-07-01

    Full Text Available Introduction: Mucormycosis is an opportunistic fungal infection. Rhizopus oryzae is major cause of mucormycosis in humans. This disease is the most common form of the acute fungal infection with rapid progress. Iranian Propolis extract and Royal jelly are honey bee products which have been used by human over the past centuries in traditional medicine. In this study the effects of Iranian Propolis and Royal jelly were investigated against Rhizopus oryzae and Candida albicans. Methods: The used method in this study was microdilution. To perform it, the prepared dilutions of Royal jelly and alcoholic extract of Iranian Propolis were added to tubes containing Sabouraud dextrose broth culture media except to control group and then Rhizopus oryzae suspension was added to all microtubes. In the next stage, microtubes were maintained in incubator at 25oC for 48 hours and then 10 ml of the content of each microtube was transferred to Sabouraud dextrose agar media. The minimum inhibitory concentration (MIC and minimum fungicidal concentration (MFC of the agents were calculated. Results: In this study, the MIC and MFC of Iranian Propolis alcoholic extract on Rhizopus oryzae were respectively 0.1 and 0.25 mg/ml and the MFC of Royal jelly on Rhizopus oryzae were respectively 100 ± 34 and 133 ± 46 mg/ml. Conclusion: The results indicate that Propolis might be used as an ideal combination for the treatment of fungal infections like Rhizopus oryzae. However, clinical studies are needed to confirm the effects of these drugs.

  3. Transcriptome and Proteome Expression Analysis of the Metabolism of Amino Acids by the Fungus Aspergillus oryzae in Fermented Soy Sauce

    Directory of Open Access Journals (Sweden)

    Guozhong Zhao

    2015-01-01

    Full Text Available Amino acids comprise the majority of the flavor compounds in soy sauce. A portion of these amino acids are formed from the biosynthesis and metabolism of the fungus Aspergillus oryzae; however, the metabolic pathways leading to the formation of these amino acids in A. oryzae remain largely unknown. We sequenced the transcriptomes of A. oryzae 100-8 and A. oryzae 3.042 under similar soy sauce fermentation conditions. 2D gel electrophoresis was also used to find some differences in protein expression. We found that many amino acid hydrolases (endopeptidases, aminopeptidases, and X-pro-dipeptidyl aminopeptidase were expressed at much higher levels (mostly greater than double in A. oryzae 100-8 than in A. oryzae 3.042. Our results indicated that glutamate dehydrogenase may activate the metabolism of amino acids. We also found that the expression levels of some genes changed simultaneously in the metabolic pathways of tyrosine and leucine and that these conserved genes may modulate the function of the metabolic pathway. Such variation in the metabolic pathways of amino acids is important as it can significantly alter the flavor of fermented soy sauce.

  4. AAS 228: Day 2 afternoon

    Science.gov (United States)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.The Limits of Scientific Cosmology: Setting the Stage: Accepted Facts, and Testing Limitations in Theory and Data (by Gourav Khullar)With a stellar lineup of speakers to talk about current and future prospects of cosmology and its limits (or lack thereof), the first session kicked off with talks by Risa Wechsler, Joseph Silk, and Sean Carroll (his talk on Multiverses is described below, by Nathan Sanders). Risa set the stage with an elaborate description of the current accepted facts in the era of precision cosmology including the standard model of concordance cosmology, described by seven parameters and an accepted Lambda-CDM paradigm (with a cosmological constant and cold dark matter). The talk stressed on the fact that all these parameters are understood to a percent order precision, which is a remarkable deviation from the time in 1990s when according to Risa, Alan Guth never thought that any of these numbers could be measured precisely!Risa Wechsler describing our current constraints on what Dark Matter could constitute.Joseph Silk discussing limits on cosmological parameters.The CMB measurements, Big Bang Nucleosynthesis estimates and galaxy clustering statistics all contribute to locking down the description of our universe. She emphasized on the tensions between different probes to measure expansion rate H0 of the universe, and small scale predictions of cold dark matter simulations, but she is hopeful that these shall be resolved eventually. Joe Silk followed this up with his interpretation of trying to understand our place in the universe and placing limits on different parameters and

  5. 水稻和拟南芥中几丁质酶的分析%Chitinases in Oryza sativa ssp. japonica and Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    许凤华; 范成明; 何月秋

    2007-01-01

    Chitinases (EC3.2.1.14), found in a wide range of organisms, catalyze the hydrolysis of chitin and play a major role in defense mechanisms against fungal pathogens. The alignment and typical domains were analyzed using basic local alignment search tool (BLAST) and simple modular architecture research tool (SMART), respectively. On the basis of the annotations of rice (Oryza sativa L.) and Arabidopsis genomic sequences and using the bio-software SignalP3.0, TMHMM2.0, TargetPl.1, and big-Pi Predictor, 25 out of 37 and 16 out of 24 open reading frames (ORFs) with chitinase activity from rice and Arabidopsis, respectively, were predicted to have signal peptides (SPs), which have an average of 24.8 amino acids at the N-terminal region. Some of the chitinases were secreted extracellularly, whereas some were located in the vacuole. The phylogenic relationship was analyzed with 61 ORFs and 25 known chitinases and they were classified into 6 clusters using Clustal X and MEGA3.1. This classification is not completely consistent when compared with the traditional system that classifies the chitinases into 7 classes. The frequency of distribution of amino acid residues was distinct in different clusters. The contents of alanine, glycine, serine, and leucine were very high in each cluster, whereas the contents of methionine, histidine, tryptophan, and cysteine were lower than 20%. Each cluster had distinct amino acid characteristics. Alanine, valine, leucine, cysteine, serine, and lysine were rich in Clusters Ⅰ to Ⅵ, respectively.%几丁质酶(EC3.2.1.14)是一种降解几丁质的糖苷酶,广泛存在于各种生物体中,并在植物中对病原真菌起重要抗性作用.首先通过BLAST在GenBank中对其同源性进行搜索,用SMART分析其结构.基于水稻和拟南芥的基因组注释,借助4个生物学软件(SignalP3.0,TMHMM2.0,TargetP1.1 and big-Pi Predictor),分析了水稻所有37条和拟南芥所有24条几丁质酶序列,发现有些几丁质酶都分

  6. AAS 228: Day 2 morning

    Science.gov (United States)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Plenary Session (Day 1) The Galaxy Zoo(by Benny Tsang)Galaxy Zoo was so hot that the servers hosting the galaxy images got melted down soon after being launched.Kevin Schawinski from ETH Zurich took us on a tour ofhis wonderful Galaxy Zoo. It is a huge zoo with about a quarter million zookeepers, they are citizen astronomers who collaboratively classify galaxies by their looks as an attempt to understand galaxy evolution. The big question that is being answered is: how do blue, actively star-forming galaxies evolve into red, quiescent (non-star-forming) galaxies? The Zoo helped reveal that blue galaxies turn into red galaxies via two possible paths galaxies might run out of supply of gas and shut off star formation slowly; or they could merge with one another and turn off star formation by destroying the gas reservoir rapidly!The Galaxy Zoo project also led to the discoveries of:Green Peas: they are the living fossils of galaxy evolution; compact, bright, green galaxies that are actively forming starsOverlapping galaxies: they are pairs of galaxies that are separated physically but happen to lie on the same line of sight; they provide excellent laboratories for studying dust extinctionHannys Voorwerp: an unusual object named after Hanny the discoverer, which is believed to be the first detection of quasar light echoThe idea of Galaxy Zoo in getting help from citizen scientists was further extended into an award-winningproject known as the Zooniverse, which is an online platform for streamlined crowd-sourcing for scientific research that requires human input. The future of astronomy is going to be

  7. Activity of vegetative insecticidal proteins Vip3Aa58 and Vip3Aa59 of Bacillus thuringiensis against lepidopteran pests.

    Science.gov (United States)

    Baranek, Jakub; Kaznowski, Adam; Konecka, Edyta; Naimov, Samir

    2015-09-01

    Vegetative insecticidal proteins (Vips) secreted by some isolates of Bacillus thuringiensis show activity against insects and are regarded as insecticides against pests. A number of B. thuringiensis strains harbouring vip3A genes were isolated from different sources and identified by using a PCR based approach. The isolates with the highest insecticidal activity were indicated in screening tests, and their vip genes were cloned and sequenced. The analysis revealed two polymorphic Vip protein forms, which were classified as Vip3Aa58 and Vip3Aa59. After expression of the vip genes, the proteins were isolated and characterized. The activity of both toxins was estimated against economically important lepidopteran pests of woodlands (Dendrolimus pini), orchards (Cydia pomonella) and field crops (Spodoptera exigua). Vip3Aa58 and Vip3Aa59 were highly toxic and their potency surpassed those of many Cry proteins used in commercial bioinsecticides. Vip3Aa59 revealed similar larvicidal activity as Vip3Aa58 against S. exigua and C. pomonella. Despite 98% similarity of amino acid sequences of both proteins, Vip3Aa59 was significantly more active against D. pini. Additionally the effect of proteolytic activation of Vip58Aa and Vip3Aa59 on toxicity of D. pini and S. exigua was studied. Both Vip3Aa proteins did not show any activity against Tenebrio molitor (Coleoptera) larvae. The results suggest that the Vip3Aa58 and Vip3Aa59 toxins might be useful for controlling populations of insect pests of crops and forests.

  8. Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa

    Science.gov (United States)

    Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania

    2016-01-01

    Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica. PMID:27077002

  9. Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa

    Directory of Open Access Journals (Sweden)

    Eric J. Fuchs

    2016-04-01

    Full Text Available Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001 among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

  10. Polyamine oxidase 7 is a terminal catabolism-type enzyme in Oryza sativa and is specifically expressed in anthers.

    Science.gov (United States)

    Liu, Taibo; Kim, Dong Wook; Niitsu, Masaru; Maeda, Shunsuke; Watanabe, Masao; Kamio, Yoshiyuki; Berberich, Thomas; Kusano, Tomonobu

    2014-06-01

    Polyamine oxidase (PAO), which requires FAD as a cofactor, functions in polyamine catabolism. Plant PAOs are classified into two groups based on their reaction modes. The terminal catabolism (TC) reaction always produces 1,3-diaminopropane (DAP), H2O2, and the respective aldehydes, while the back-conversion (BC) reaction produces spermidine (Spd) from tetraamines, spermine (Spm) and thermospermine (T-Spm) and/or putrescine from Spd, along with 3-aminopropanal and H2O2. The Oryza sativa genome contains seven PAO-encoded genes termed OsPAO1-OsPAO7. To date, we have characterized four OsPAO genes. The products of these genes, i.e. OsPAO1, OsPAO3, OsPAO4 and OsPAO5, catalyze BC-type reactions. Whereas OsPAO1 remains in the cytoplasm, the other three PAOs localize to peroxisomes. Here, we examined OsPAO7 and its gene product. OsPAO7 shows high identity to maize ZmPAO1, the best characterized plant PAO having TC-type activity. OsPAO7 seems to remain in a peripheral layer of the plant cell with the aid of its predicted signal peptide and transmembrane domain. Recombinant OsPAO7 prefers Spm and Spd as substrates, and it produces DAP from both substrates in a time-dependent manner, indicating that OsPAO7 is the first TC-type enzyme identified in O. sativa. The results clearly show that two types of PAOs co-exist in O. sativa. Furthermore, OsPAO7 is specifically expressed in anthers, with an expressional peak at the bicellular pollen stage. The physiological function of OsPAO7 in anthers is discussed.

  11. Transgenerational inheritance of modified DNA methylation patterns and enhanced tolerance induced by heavy metal stress in rice (Oryza sativa L..

    Directory of Open Access Journals (Sweden)

    Xiufang Ou

    Full Text Available BACKGROUND: DNA methylation is sensitive and responsive to stressful environmental conditions. Nonetheless, the extent to which condition-induced somatic methylation modifications can impose transgenerational effects remains to be fully understood. Even less is known about the biological relevance of the induced epigenetic changes for potentially altered well-being of the organismal progenies regarding adaptation to the specific condition their progenitors experienced. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed DNA methylation pattern by gel-blotting at genomic loci representing transposable elements and protein-coding genes in leaf-tissue of heavy metal-treated rice (Oryza sativa plants (S0, and its three successive organismal generations. We assessed expression of putative genes involved in establishing and/or maintaining DNA methylation patterns by reverse transcription (RT-PCR. We measured growth of the stressed plants and their unstressed progenies vs. the control plants. We found (1 relative to control, DNA methylation patterns were modified in leaf-tissue of the immediately treated plants, and the modifications were exclusively confined to CHG hypomethylation; (2 the CHG-demethylated states were heritable via both maternal and paternal germline, albeit often accompanying further hypomethylation; (3 altered expression of genes encoding for DNA methyltransferases, DNA glycosylase and SWI/SNF chromatin remodeling factor (DDM1 were induced by the stress; (4 progenies of the stressed plants exhibited enhanced tolerance to the same stress their progenitor experienced, and this transgenerational inheritance of the effect of condition accompanying heritability of modified methylation patterns. CONCLUSIONS/SIGNIFICANCE: Our findings suggest that stressful environmental condition can produce transgenerational epigenetic modifications. Progenies of stressed plants may develop enhanced adaptability to the condition, and this acquired trait is

  12. Association Mapping for Drought Tolerance of Rice (Oryza sativa L.) at Vegetative Stage

    Institute of Scientific and Technical Information of China (English)

    Yulong XIAO; Chuanyuan YU; Jianguo LEI; Quirino D; DELA CRUZ; Jonalyn M.YABES; Dindo A.TABANAo

    2012-01-01

    [Objective] This study aimed to identify possible quantitative trait loci (QTL) for vegetative drought tolerance traits of rice (Oryza sativa L.). [Method] A total of 184 rice genotypes were field screened and 156 SSR markers randomly distributed at each 3 Mb bin were used through genome-wide scanning method and association analysis to detect QTLs for vegetative drought tolerance traits leaf rolling (LER), leaf drying (LED) and drought recovery rate (DRR). [Result] The experimental rice geno- types showed varied response under vegetative drought, LER, LED and DRR were highly correlated. Population structure was detected at K=3 and K=7, certain extent of admixture existed in the experimental rice genotypes, relative kinship of the rice genotypes ranged from 0 to 0.924 5. Significant linkage disequilibrium among SSR markers was detected. Sixteen SSR markers have been detected to be associated with vegetative drought tolerance traits, four for LER, eight for LED and four for DDR. Most of the markers were associated with more than one trait, indicating a single mechanism might involve in expression of several related traits, i.e. osmotic adjustment. RM107 (Chr.9) was associated with all the three traits and fell exactly within or closely nearby to previous reported regions, was a major QTL for vegeta- tive drought tolerance, RM477 (Chr.8) was significantly associated with DRR and ex- tremely significantly associated with LER was probably another major QTL for vege- tative drought tolerance. [Conclusion] Association mapping is a very effective method for describing complex traits like drought tolerance.

  13. Antarctic Genomics

    Directory of Open Access Journals (Sweden)

    Alex D. Rogers

    2006-03-01

    Full Text Available With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

  14. AA, sandwich line with magnetic horn

    CERN Document Server

    1980-01-01

    Continuation from 8010293: Finally, the sandwich line with the horn is placed on the ground, for the horn to be inspected and, if needed, exchanged for a new one. The whole procedure was trained with several members of the AA team, for quick and safe handling, and to share the radiation dose amongst them.

  15. AA, vacuum tank for stochastic precooling

    CERN Multimedia

    1979-01-01

    The vaccum tank in which the fast stochastic precooling kicker was installed. It is clad with heating jackets for bake-out to 200 deg C, indispensable for reaching the operational vacuum of 7E-11 Torr. Alain Poncet, responsible for AA vacuum, is looking on. See also 7910268, 8002234.

  16. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

    Directory of Open Access Journals (Sweden)

    Ma Hong

    2010-02-01

    Full Text Available Abstract Background Although the overwhelming majority of genes found in angiosperms are members of gene families, and both gene- and genome-duplication are pervasive forces in plant genomes, some genes are sufficiently distinct from all other genes in a genome that they can be operationally defined as 'single copy'. Using the gene clustering algorithm MCL-tribe, we have identified a set of 959 single copy genes that are shared single copy genes in the genomes of Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa. To characterize these genes, we have performed a number of analyses examining GO annotations, coding sequence length, number of exons, number of domains, presence in distant lineages, such as Selaginella and Physcomitrella, and phylogenetic analysis to estimate copy number in other seed plants and to demonstrate their phylogenetic utility. We then provide examples of how these genes may be used in phylogenetic analyses to reconstruct organismal history, both by using extant coverage in EST databases for seed plants and de novo amplification via RT-PCR in the family Brassicaceae. Results There are 959 single copy nuclear genes shared in Arabidopsis, Populus, Vitis and Oryza ["APVO SSC genes"]. The majority of these genes are also present in the Selaginella and Physcomitrella genomes. Public EST sets for 197 species suggest that most of these genes are present across a diverse collection of seed plants, and appear to exist as single or very low copy genes, though exceptions are seen in recently polyploid taxa and in lineages where there is significant evidence for a shared large-scale duplication event. Genes encoding proteins localized in organelles are more commonly single copy than expected by chance, but the evolutionary forces responsible for this bias are unknown. Regardless of the evolutionary mechanisms responsible for the large number of shared single copy genes in diverse flowering plant lineages, these

  17. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

    Science.gov (United States)

    2010-01-01

    Background Although the overwhelming majority of genes found in angiosperms are members of gene families, and both gene- and genome-duplication are pervasive forces in plant genomes, some genes are sufficiently distinct from all other genes in a genome that they can be operationally defined as 'single copy'. Using the gene clustering algorithm MCL-tribe, we have identified a set of 959 single copy genes that are shared single copy genes in the genomes of Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa. To characterize these genes, we have performed a number of analyses examining GO annotations, coding sequence length, number of exons, number of domains, presence in distant lineages, such as Selaginella and Physcomitrella, and phylogenetic analysis to estimate copy number in other seed plants and to demonstrate their phylogenetic utility. We then provide examples of how these genes may be used in phylogenetic analyses to reconstruct organismal history, both by using extant coverage in EST databases for seed plants and de novo amplification via RT-PCR in the family Brassicaceae. Results There are 959 single copy nuclear genes shared in Arabidopsis, Populus, Vitis and Oryza ["APVO SSC genes"]. The majority of these genes are also present in the Selaginella and Physcomitrella genomes. Public EST sets for 197 species suggest that most of these genes are present across a diverse collection of seed plants, and appear to exist as single or very low copy genes, though exceptions are seen in recently polyploid taxa and in lineages where there is significant evidence for a shared large-scale duplication event. Genes encoding proteins localized in organelles are more commonly single copy than expected by chance, but the evolutionary forces responsible for this bias are unknown. Regardless of the evolutionary mechanisms responsible for the large number of shared single copy genes in diverse flowering plant lineages, these genes are valuable for

  18. Genome-wide patterns of nucleotide polymorphism in domesticated rice

    DEFF Research Database (Denmark)

    Caicedo, Ana L; Williamson, Scott H; Hernandez, Ryan D

    2007-01-01

    Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments......, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models...... explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection...

  19. Investigating the biology of plant infection by the rice blast fungus Magnaporthe oryzae.

    Science.gov (United States)

    Martin-Urdiroz, Magdalena; Oses-Ruiz, Miriam; Ryder, Lauren S; Talbot, Nicholas J

    2016-05-01

    The rice blast fungus, Magnaporthe oryzae, is responsible for the most serious disease of rice and is a continuing threat to ensuring global food security. The fungus has also, however, emerged as a model experimental organism for understanding plant infection processes by pathogenic fungi. This is largely due to its amenability to both classical and molecular genetics, coupled with the efforts of a very large international research community. This review, which is based on a plenary presentation at the 28th Fungal Genetics Conference in Asilomar, California in March 2015, describes recent progress in understanding how M. oryzae uses specialised cell called appressoria to bring about plant infection and the underlying biology of this developmental process. We also review how the fungus is then able to proliferate within rice tissue, deploying effector proteins to facilitate its spread by suppressing plant immunity and promoting growth and development of the fungus.

  20. Expression and characterization of recombinant Rhizopus oryzae lipase for enzymatic biodiesel production.

    Science.gov (United States)

    Li, Zhilin; Li, Xun; Wang, Ye; Wang, Youdong; Wang, Fei; Jiang, Jianchun

    2011-10-01

    The Rhizopus oryzae lipase containing prosequence was expressed in Pichia pastoris. Recombinant lipase subunit showed a molecular mass of 32 kDa. The maximum activity of recombinant lipase obtained from Mut(s) recombinant was 90 IU/ml. The enzyme was stable in broad ranges of temperatures and pH, with the optimal temperature at 35 °C and pH 7.0. The crude recombinant R. oryzae lipase can be directly used for the transesterification of plant oils at high-water content of 60-100% (w/w) based on oil weight. The addition of 80% water to the transesterification systems resulted in the yield of methyl ester of 95%, 94% and 92% after 72 h using soybean oil, Jatropha curcas seed raw oil and Pistacia chinensis seed raw oil as raw material, respectively. These results indicate that the recombinant lipase is an effective biocatalyst for enzymatic biodiesel production.

  1. Rmg8, a New Gene for Resistance to Triticum Isolates of Pyricularia oryzae in Hexaploid Wheat.

    Science.gov (United States)

    Anh, Vu Lan; Anh, Nguyen Tuan; Tagle, Analiza Grubanzo; Vy, Trinh Thi Phuong; Inoue, Yoshihiro; Takumi, Shigeo; Chuma, Izumi; Tosa, Yukio

    2015-12-01

    Blast, caused by Pyricularia oryzae, is one of the major diseases of wheat in South America. We identified a new gene for resistance to Triticum isolates of P. oryzae in common wheat 'S-615', and designated it "resistance to Magnaporthe grisea 8" (Rmg8). Rmg8 was assigned to chromosome 2B through molecular mapping with simple-sequence repeat markers. To identify an avirulence gene corresponding to Rmg8, Triticum isolate Br48 (avirulent on S-615) was crossed with 200R29 (virulent on S-615), an F1 progeny derived from a cross between an Eleusine isolate (MZ5-1-6) and Br48. Segregation analysis of their progeny revealed that avirulence of Br48 on S-615 was conditioned by a single gene, which was designated AVR-Rmg8. AVR-Rmg8 was closely linked to AVR-Rmg7, which corresponded to Rmg7 located on chromosome 2A of tetraploid wheat.

  2. Gene Expression Proifling Related to Hyphal Growth in a Temperature- Sensitive Mutant ofMagnaporthe oryzae

    Institute of Scientific and Technical Information of China (English)

    LI Xue-song; XU Fei; WANG Hong-kai; and LIN Fu-cheng

    2013-01-01

    The rice blast, caused by fungusMagnaporthe oryzae, is a major constraint to the world food security. Hyphal growth is the foundation of fungal development and proliferation of fungi. To investigate genes involved in hyphal growth of this fungus, digital gene expression tag proifling was used to compare a previously generated temperature-sensitive mutant which defect at hyphae growth and reduction on pathogenicity, with its related wildtype strain. 416 genes were detected as differential expression, 178 of which were speciifcally expressed in Guy-11 but down-regulated expression in the mutant. Functional classiifcation analysis revealed the phenotype mutation may be mainly caused by a defection in translational and vacuole-related processes. The results and the protocol used will improve our knowledge on morphogenesis and promote the further study onM. oryzae pathogenesis.

  3. Physicochemical and technological characterization of whole soybean flour fermented by Aspergillus oryzae

    OpenAIRE

    Leomar Hackbart da Silva; Paula Fernanda Pinto da Costa; Gabriela Wakayama Nomiyama; Ingrid Paula de Souza; Yoon Kil Chang

    2012-01-01

    Neste trabalho, estudou-se o efeito das condições de fermentação da farinha de soja integral, utilizando-se o fungo Aspergillus oryzae, sobre as características físico-químicas e as propriedades tecnológicas da farinha de soja integral autoclavada fermentada. A farinha de soja integral autoclavada foi fermentada com o fungo Aspergillus oryzae CCT 4359, incubada às temperaturas de 30 °C e 40 °C por 24 horas e 48 horas, e seca em estufa a vácuo, a 60 °C, até 10% de umidade final, obtendo-se a f...

  4. Insular organization of gene space in grass genomes.

    Science.gov (United States)

    Gottlieb, Andrea; Müller, Hans-Georg; Massa, Alicia N; Wanjugi, Humphrey; Deal, Karin R; You, Frank M; Xu, Xiangyang; Gu, Yong Q; Luo, Ming-Cheng; Anderson, Olin D; Chan, Agnes P; Rabinowicz, Pablo; Devos, Katrien M; Dvorak, Jan

    2013-01-01

    Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands "gene insulae" to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschii chromosomes is shown to be primarily caused by shortening of inter-insular distances. The comparison of the four grass genomes suggests that gene locations are largely a function of a homogeneous Poisson process in small genomes. Nonrandom insertions of LTR retroelements during genome expansion creates gene insulae, which become less dense and further apart with the increase in genome size. High concordance in relative lengths of orthologous intergenic distances among the investigated genomes including the maize genome suggests functional constraints on gene distribution in the grass genomes.

  5. Insular organization of gene space in grass genomes.

    Directory of Open Access Journals (Sweden)

    Andrea Gottlieb

    Full Text Available Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands "gene insulae" to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschii chromosomes is shown to be primarily caused by shortening of inter-insular distances. The comparison of the four grass genomes suggests that gene locations are largely a function of a homogeneous Poisson process in small genomes. Nonrandom insertions of LTR retroelements during genome expansion creates gene insulae, which become less dense and further apart with the increase in genome size. High concordance in relative lengths of orthologous intergenic distances among the investigated genomes including the maize genome suggests functional constraints on gene distribution in the grass genomes.

  6. Processing and Optimization of Dissimilar Friction Stir Welding of AA 2219 and AA 7039 Alloys

    Science.gov (United States)

    Venkateswarlu, D.; Nageswara rao, P.; Mahapatra, M. M.; Harsha, S. P.; Mandal, N. R.

    2015-12-01

    The present paper discusses the optimization of dissimilar friction stir welding of AA 2219 and AA 7039 alloys with respect to tool design issues including microstructural study of weld. The optimized ultimate tensile strength was ~280 MPa, and % elongation was ~11.5. It was observed that the extent of tool shoulder flat surface and tool rotational speed influenced the weld quality significantly. A mathematical model was also developed using response surface regression analysis to predict the effects of tool geometry and process variables on dissimilar AA 2219 and AA 7039 alloys welds. The microstructure evolution and mechanical properties were investigated by employing electron backscatter diffraction technique, Vickers microhardness, and tensile testing, respectively. The microstructural observations indicated that the grain size obtained at advancing side (AA 2219 alloy side) was much finer compared to the retreating side (AA 7039 alloy side). Hardness distribution in the stir zone was inhomogeneous, which might be due to inadequate mixing of weld zone material. The hardness values observed at the weld zone were lower than that in the base materials.

  7. Genomic and transcriptomic alterations following hybridisation and genome doubling in trigenomic allohexaploid Brassica carinata × Brassica rapa.

    Science.gov (United States)

    Xu, Y; Zhao, Q; Mei, S; Wang, J

    2012-09-01

    Allopolyploidisation is a prominent evolutionary force that involves two major events: interspecific hybridisation and genome doubling. Both events have important functional consequences in shaping the genomic architecture of the neo-allopolyploids. The respective effects of hybridisation and genome doubling upon genomic and transcriptomic changes in Brassica allopolyploids are unresolved. In this study, amplified fragment length polymorphism (AFLP), methylation-sensitive amplification polymorphism (MSAP) and cDNA-AFLP approaches were used to track genetic, epigenetic and transcriptional changes in both allohexaploid Brassica (ArArBcBcCcCc genome) and triploid hybrids (ArBcCc genome). Results from these groups were compared with each other and also to their parents Brassica carinata (BBCC genome) and Brassica rapa (AA genome). Rapid and dramatic genetic, DNA methylation and gene expression changes were detected in the triploid hybrids. During the shift from triploidy to allohexaploidy, some of the hybridisation-induced alterations underwent reversion. Additionally, novel genetic, epigenetic and transcriptional alterations were also detected. The proportions of A-genome-specific DNA methylation and gene expression alterations were significantly greater than those of BC-genome-specific alterations in the triploid hybrids. However, the two parental genomes were equally affected during the ploidy shift. Hemi-CCG methylation changes induced by hybridisation were recovered after genome doubling. Full-CG methylation changes were a more general process initiated in the hybrid and continued after genome doubling. These results indicate that genome doubling could ameliorate genomic and transcriptomic alterations induced by hybridisation and instigate additional alterations in trigenomic Brassica allohexaploids. Moreover, genome doubling also modified hybridisation-induced progenitor genome-biased alterations and epigenetic alteration characteristics.

  8. Application of EST Data of Siderophore Regulation Protein-like Gene of Aspergillus oryzae RIB40

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Objective: To acquire the new clear color phenotype of Aspergillus oryzae b y th e antisense strategy of siderophore regulation protein (SREP)-like gene. Method s: Construct the cDNA library of Aspergillus oryzae RIB40 and amplify the fr agme nt ac7336f from the every EST clone, which had high homology with SREP gene of o ther species, then construct the eukaryotic expression vector with SREP-like ge ne using antisense strategy. Results: The sequence of this SREP-like gene was a cquired, the vector was successfully constructed. Conclusion: The deduced amino acid sequence of SREP-like gene of Aspergillus oryzae indicated that there is t he high homology with those of SREP genes of Penicillium chrysogenum, Neur ospora crassa and Schizosaccharomyces pombe.%目的:通过反义RNA技术获取稻属曲霉(Aspergillus oryzae)新的表现型.方法:应用BLAST网络服务对稻属曲霉EST数据进行同源性比较,PCR扩增与其它种属铁配体调节蛋白基因(SREP)具有高度同源性的ac7336f片段并反向插入pUSA真核表达载体.结果:测得铁配体调节蛋白类似基因的序列,完成反义表达载体构建.结论:由铁配体调节蛋白类似基因的DNA序列推出的氨基酸序列与Penicillium chrysogenum, Neurospora crassa和Schizosaccharomyces pombe等种属铁配体调节蛋白基因的氨基酸序列具有高度同源性.

  9. Ehd4 encodes a novel and Oryza-genus-specific regulator of photoperiodic flowering in rice.

    Directory of Open Access Journals (Sweden)

    He Gao

    Full Text Available Land plants have evolved increasingly complex regulatory modes of their flowering time (or heading date in crops. Rice (Oryza sativa L. is a short-day plant that flowers more rapidly in short-day but delays under long-day conditions. Previous studies have shown that the CO-FT module initially identified in long-day plants (Arabidopsis is evolutionary conserved in short-day plants (Hd1-Hd3a in rice. However, in rice, there is a unique Ehd1-dependent flowering pathway that is Hd1-independent. Here, we report isolation and characterization of a positive regulator of Ehd1, Early heading date 4 (Ehd4. ehd4 mutants showed a never flowering phenotype under natural long-day conditions. Map-based cloning revealed that Ehd4 encodes a novel CCCH-type zinc finger protein, which is localized to the nucleus and is able to bind to nucleic acids in vitro and transactivate transcription in yeast, suggesting that it likely functions as a transcriptional regulator. Ehd4 expression is most active in young leaves with a diurnal expression pattern similar to that of Ehd1 under both short-day and long-day conditions. We show that Ehd4 up-regulates the expression of the "florigen" genes Hd3a and RFT1 through Ehd1, but it acts independently of other known Ehd1 regulators. Strikingly, Ehd4 is highly conserved in the Oryza genus including wild and cultivated rice, but has no homologs in other species, suggesting that Ehd4 is originated along with the diversification of the Oryza genus from the grass family during evolution. We conclude that Ehd4 is a novel Oryza-genus-specific regulator of Ehd1, and it plays an essential role in photoperiodic control of flowering time in rice.

  10. Diazotrophic bacteria isolated from wild rice Oryza glumaepatula (Poaceae) in the Brazilian Amazon

    OpenAIRE

    Fernandes Júnior,Paulo Ivan; Duarte Pereira, Gilmara Maria; Perin, Liamara; da Silva, Luana Mesquita; Cardoso Baraúna, Alexandre; Muniz Alves, Francilene; Ribeiro Passos, Samuel; Édson Zilli, Jerri

    2013-01-01

    The association of wild grasses with diazotrophic bacteria in Brazilian biomes is poorly understood. The isolation and characterization of bacteria associated with wild grasses can contribute to understand the diazotrophic ecology as well as to identify bacteria with biotechnological applications. In this study, we isolated and characterized diazotrophic bacterial isolates from Oryza glumaepatula collected in Cerrado and Forest areas of the Amazon in Roraima State, Brazil. Healthy O. glumepat...

  11. Genetic Conservation of Phosphine Resistance in the Rice Weevil Sitophilus oryzae (L.).

    Science.gov (United States)

    Nguyen, Tam T; Collins, Patrick J; Duong, Tu M; Schlipalius, David I; Ebert, Paul R

    2016-05-01

    High levels of resistance to phosphine in the rice weevil Sitophilus oryzae have been detected in Asian countries including China and Vietnam, however there is limited knowledge of the genetic mechanism of resistance in these strains. We find that the genetic basis of strong phosphine resistance is conserved between strains of S. oryzae from China, Vietnam, and Australia. Each of 4 strongly resistant strains has an identical amino acid variant in the encoded dihydrolipoamide dehydrogenase (DLD) enzyme that was previously identified as a resistance factor in Rhyzopertha dominica and Tribolium castaneum. The unique amino acid substitution, Asparagine > Threonine (N505T) of all strongly resistant S. oryzae corresponds to the position of an Asparagine > Histidine variant (N506H) that was previously reported in strongly resistant R. dominica. Progeny (F16 and F18) from 2 independent crosses showed absolute linkage of N505T to the strong resistance phenotype, indicating that if N505T was not itself the resistance variant that it resided within 1 or 2 genes of the resistance factor. Non-complementation between the strains confirmed the shared genetic basis of strong resistance, which was supported by the very similar level of resistance between the strains, with LC50 values ranging from 0.20 to 0.36 mg L(-1) for a 48-h exposure at 25 °C. Thus, the mechanism of high-level resistance to phosphine is strongly conserved between R. dominica, T. castaneum and S. oryzae. A fitness cost associated with strongly resistant allele was observed in segregating populations in the absence of selection.

  12. Esterase as molecular marker for salt tolerance in regenerated plants of rice, Oryza sativa L.

    Science.gov (United States)

    Swapna, T S

    2002-09-01

    Esterase variation was studied in plants regenerated from callus cultures of four rice (Oryza sativa) varieties, viz. pokkali, which is a moderately salt tolerant variety and three salt sensitive varieties MI 48, annapoorna and jyothi. Variation was studied at tillering stage of plants regenerated from callus culture and germinated from seeds. Somaclonal variants for salt tolerance could be detected using variation in esterase banding pattern and activity.

  13. Tanggap Pertumbuhan dan Produksi Padi (Oryza sativa L.) Varietas Ciherang Terhadap Pemberian Pupuk Organik

    OpenAIRE

    Sari, Vira Irma

    2011-01-01

    VIRA IRMA SARI. Response of Growth and Production of Rice (Oryza sativa L.) Variety Ciherang to The Application of Organic Fertilizer. Scarcity of inorganic fertilizer and the negative effect caused by inorganic fertilizer continuing to make organic fertilizer as a solution to overcome these problems. The availability of organic fertilizers is expected that the farmers can get the optimal production and profit, because the organic fertilizer is cheaper and easy ...

  14. ALIMENTARY PREFERENCE OF SITOPHILUS ORYZAE (COLEOPTERA: CURCULIONIDAE TO BRANDS OF COMMERCIAL RICE FROM PERU

    Directory of Open Access Journals (Sweden)

    Velez-Azañero, Armando

    2013-07-01

    Full Text Available Between February and April 2012 were evaluated the feeding preferences of S. oryzae on four brands of commercial rice from Peru: criollo rendidor®, Chulucanas®, Costeño® and Samán®. It was found that the "rice weevil" showed a food preference for costeño brand. However, oviposition levels were variable, with a larger population of adults in the Saman® brand.

  15. A New Sesquiterpene from Caragana intermediia and Its Anti-Pyricularia oryzae P-2b Activity

    Institute of Scientific and Technical Information of China (English)

    SUN Zhi-Hua; HU Chang-Qi; WANG Jin-Yi

    2008-01-01

    A new aromadendrane-type sesquiterpene,(-)-alloaromadendrane-4β,10β-diol(1),has been isolated from the aerial part of Caragana intermediia,the structure of which was established by spectroscopic methods,including X-ray analysis that provided its relative stereochemistry.Bioassay showed that 1 possessed anti-Pyricularia oryzae P-2b activity with an MIC(minimum inhibitory concentration)value of 10μg/mL.

  16. Enzymatic Modification of Poly (ethylene terephthalate) Fiber with Lipase from Aspergillus oryzae

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-hua; LU Da-nian; SHAO Zhi-yu; HONG Feng

    2007-01-01

    Lipase preparation from Aspergiilus oryzae could act on ester bonds on the surface of poly (ethylene terephthalate) fibers and a possible hydrolytic product mono (2-hydroxyethyl) terephthalate was released. After the iipase modification, there were more carboxyl groups on the treated poly (ethylene terephthalate) fabric surface that resulted in binding with mote cationic dyes. Increased hydrophilicity and antistatic ability of poly (ethylene terephthalate) samples were found based on moisture regain, water contact angle and static half decay time.

  17. Hyperthermia sensitizes Rhizopus oryzae to posaconazole and itraconazole action through apoptosis.

    Science.gov (United States)

    Shirazi, Fazal; Pontikos, Michael A; Walsh, Thomas J; Albert, Nathaniel; Lewis, Russell E; Kontoyiannis, Dimitrios P

    2013-09-01

    The high mortality rate of mucormycosis with currently available monotherapy has created interest in studying novel strategies for antifungal agents. With the exception of amphotericin B (AMB), the triazoles (posaconazole [PCZ] and itraconazole [ICZ]) are fungistatic in vitro against Rhizopus oryzae . We hypothesized that growth at a high temperature (42°C) results in fungicidal activity of PCZ and ICZ that is mediated through apoptosis. R. oryzae had high MIC values for PCZ and ICZ (16 to 64 μg/ml) at 25°C; in contrast, the MICs for PCZ and ICZ were significantly lower at 37°C (8 to 16 μg/ml) and 42°C (0.25 to 1 μg/ml). Furthermore, PCZ and ICZ dose-dependent inhibition of germination was more pronounced at 42°C than at 37°C. In addition, intracellular reactive oxygen species (ROS) increased significantly when fungi were exposed to antifungals at 42°C. Characteristic cellular changes of apoptosis in R. oryzae were induced by the accumulation of intracellular reactive oxygen species. Cells treated with PCZ or ICZ in combination with hyperthermia (42°C) exhibited characteristic markers of early apoptosis: phosphatidylserine externalization visualized by annexin V staining, membrane depolarization visualized by bis-[1,3-dibutylbarbituric acid] trimethine oxonol (DiBAC) staining, and increased metacaspase activity. Moreover, terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) assay and DAPI (4',6-diamidino-2-phenylindole) staining demonstrated DNA fragmentation and condensation, respectively. The addition of N-acetylcysteine increased fungal survival, prevented apoptosis, reduced ROS accumulation, and decreased metacaspase activation. We concluded that hyperthermia, either alone or in the presence of PCZ or ICZ, induces apoptosis in R. oryzae. Local thermal delivery could be a therapeutically useful adjunct strategy for these refractory infections.

  18. Amylolytic enzyme production byRhizopus oryzae grown on agricultural commodities.

    Science.gov (United States)

    Yu, R C; Hang, Y D

    1990-03-01

    The amylolytic enzyme production byRhizopus oryzae NRRL 395 grown on different agricultural commodities was datermined. The mould produced much higher enzyme activity from barley, corn, bats, and rice than from cassava. The optimal temperature for enzyme production was 30°C. Neutralization with CaCO3 greatly enhanced the rate of enzyme production. Nitrogen supplementation of cassava resulted in higher enzyme yields.

  19. Two evolutionary histories in the genome of rice: the roles of domestication genes.

    Science.gov (United States)

    He, Ziwen; Zhai, Weiwei; Wen, Haijun; Tang, Tian; Wang, Yu; Lu, Xuemei; Greenberg, Anthony J; Hudson, Richard R; Wu, Chung-I; Shi, Suhua

    2011-06-01

    Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) shared by both cultivars. We found that the genealogical histories of these overlapping LDRs are distinct from the genomic background. While indica and japonica genomes generally appear to be of independent origin, many overlapping LDRs may have originated only once, as a result of selection and subsequent introgression. Interestingly, many such LDRs contain only one candidate gene of rice domestication, and several known domestication genes have indeed been "rediscovered" by this approach. In summary, we identified 13 additional candidate genes of domestication.

  20. NCBI nr-aa BLAST: CBRC-OSAT-06-0012 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-OSAT-06-0012 ref|NP_001057075.1| Os06g0201200 [Oryza sativa (japonica cultivar...-group)] dbj|BAD35589.1| unknown protein [Oryza sativa (japonica cultivar-group)] dbj|BAD36659.1| unknown protein [Oryza sativa... (japonica cultivar-group)] dbj|BAF18989.1| Os06g0201200 [Oryza sativa (japonica cultivar...-group)] gb|EAZ00057.1| hypothetical protein OsI_021289 [Oryza sativa (indica cultiva...r-group)] gb|EAZ36177.1| hypothetical protein OsJ_019660 [Oryza sativa (japonica cultivar-group)] NP_001057075.1 3e-12 41% ...