Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium

KAUST Repository

Katuri, Krishna; Albertsen, Mads; Saikaly, Pascal

2017-01-01

Here, we report the draft genome sequence of Desulfuromonas acetexigens strain 2873, which was originally isolated from digester sludge from a sewage treatment plant in Germany. This bacterium is capable of anode respiration with high electrochemical activity in microbial electrochemical systems. The draft genome contains 3,376 predicted protein-coding genes and putative multiheme c-type cytochromes.

Draft genome sequences of Streptococcus bovis strains ATCC 33317 and JB1

Science.gov (United States)

We report the draft genome sequences of Streptococcus bovis type strain ATTC 33317 (CVM42251) isolated from cow dung and strain JB1 (CVM42252) isolated from a cow rumen in 1977. Strains were subjected to Next Generation sequencing and the genome sizes are approximately 2 MB and 2.2 MB, respectively....

Draft Genome Sequence of Escherichia coli K-12 (ATCC 10798)

OpenAIRE

Dimitrova, Daniela; Engelbrecht, Kathleen C.; Putonti, Catherine; Koenig, David W.; Wolfe, Alan J.

2017-01-01

ABSTRACT Here, we present the draft genome sequence of Escherichia coli ATCC 10798. E.?coli ATCC 10798 is a K-12 strain, one of the most well-studied model microorganisms. The size of the genome was 4,685,496?bp, with a G+C content of 50.70%. This assembly consists of 62 contigs and the F plasmid.

Draft Genome Sequence of "Terrisporobacter othiniensis" Isolated from a Blood Culture from a Human Patient

DEFF Research Database (Denmark)

Lund, Lars Christian; Sydenham, Thomas Vognbjerg; Høgh, Silje Vermedal

2015-01-01

"Terrisporobacter othiniensis" (proposed species) was isolated from a blood culture. Genomic DNA was sequenced using a MiSeq benchtop sequencer (Illumina) and assembled using the SPAdes genome assembler. This resulted in a draft genome sequence comprising 3,980,019 bp in 167 contigs containing 3...

Draft genome sequence of Acidithiobacillus ferrooxidans YQH-1

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Lei Yan

2015-12-01

Full Text Available Acidithiobacillus ferrooxidans YQH-1 is a moderate acidophilic bacterium isolated from a river in a volcano of Northeast China. Here, we describe the draft genome of strain YQH-1, which was assembled into 123 contigs containing 3,111,222 bp with a G + C content of 58.63%. A large number of genes related to carbon dioxide fixation, dinitrogen fixation, pH tolerance, heavy metal detoxification, and oxidative stress defense were detected. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LJBT00000000.

Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1

NARCIS (Netherlands)

Wawrzyniak, Ivan; Courtine, Damien; Osman, Marwan; Hubans-Pierlot, Christine; Cian, Amandine; Nourrisson, Céline; Chabe, Magali; Poirier, Philippe; Bart, Aldert; Polonais, Valérie; Delgado-Viscogliosi, Pilar; El Alaoui, Hicham; Belkorchia, Abdel; van Gool, Tom; Tan, Kevin S. W.; Ferreira, Stéphanie; Viscogliosi, Eric; Delbac, Frédéric

2015-01-01

(ST1-ST17) described to date. Only the whole genome of a human ST7 isolate was previously sequenced. Here we report the draft genome sequence of Blastocystis ST4-WR1 isolated from a laboratory rodent at Singapore. (C) 2015 The Authors. Published by Elsevier Inc

Draft Genome Sequence of Bacillus mycoides M2E15, a Strain Isolated from the Endosphere of Potato

NARCIS (Netherlands)

Yi, Yanglei; de Jong, Anne; Spoelder, Jan; Elzenga, J Theo M; van Elsas, Jan Dirk; Kuipers, Oscar P

2016-01-01

We present the draft genome sequence of Bacillus mycoides M2E15, a bacterium isolated from potato endosphere. Analysis of the 6.08-Mbp draft genome sequence identified 6,386 protein-encoding sequences, including potential plant growth promoting genes. Specifically, genes for proteins involved in

Draft genome sequences of seven isolates of Phytophthora ramorum EU2 from Northern Ireland

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Lourdes de la Mata Saez

2015-12-01

Full Text Available Here we present draft-quality genome sequence assemblies for the oomycete Phytophthora ramorum genetic lineage EU2. We sequenced genomes of seven isolates collected in Northern Ireland between 2010 and 2012. Multiple genome sequences from P. ramorum EU2 will be valuable for identifying genetic variation within the clonal lineage that can be useful for tracking its spread.

Draft Genome Sequence of the Yeast Pachysolen tannophilus CBS 4044/NRRL Y-2460

DEFF Research Database (Denmark)

Liu, Xiaoying; Kaas, Rolf Sommer; Jensen, Peter Ruhdal

2012-01-01

A draft genome sequence of the yeast Pachysolen tannophilus CBS 4044/NRRL Y-2460 is presented. The organism has the potential to be developed as a cell factory for biorefineries due to its ability to utilize waste feedstocks. The sequenced genome size was 12,238,196 bp, consisting of 34 scaffolds...

Draft Genome Sequences of Three β-Lactam-Catabolizing Soil Proteobacteria

DEFF Research Database (Denmark)

Crofts, Terence S.; Wang, Bin; Spivak, Aaron

2017-01-01

Most antibiotics are derived from the soil, but their catabolism there, which is necessary to close the antibiotic carbon cycle, remains uncharacterized. We report the first draft genome sequences of soil Proteobacteria identified for subsisting solely on β-lactams as their carbon sources...

Draft Genome Sequences of Actinobacillus pleuropneumoniae Serotypes 2 and 6

DEFF Research Database (Denmark)

Zhan, Bujie; Angen, Øystein; Hedegaard, Jakob

2010-01-01

Actinobacillus pleuropneumoniae is a bacterial pathogen that causes highly contagious respiratory infection in pigs and has a serious impact on the production economy and animal welfare. As clear differences in virulence between serotypes have been observed, the genetic basis should be investigat...... at the genomic level. Here, we present the draft genome sequences of the A. pleuropneumoniae serotypes 2 (strain 4226) and 6 (strain Femo)....

Draft Genome Sequence of Escherichia coli K-12 (ATCC 10798).

Science.gov (United States)

Dimitrova, Daniela; Engelbrecht, Kathleen C; Putonti, Catherine; Koenig, David W; Wolfe, Alan J

2017-07-06

Here, we present the draft genome sequence of Escherichia coli ATCC 10798. E. coli ATCC 10798 is a K-12 strain, one of the most well-studied model microorganisms. The size of the genome was 4,685,496 bp, with a G+C content of 50.70%. This assembly consists of 62 contigs and the F plasmid. Copyright © 2017 Dimitrova et al.

Draft genome sequence of the rubber tree Hevea brasiliensis

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Rahman Ahmad Yamin Abdul

2013-02-01

Full Text Available Abstract Background Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR. NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876. Results Here, we report the draft genome sequence of H. brasiliensis. The assembly spans ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. Gene prediction shows 68,955 gene models, of which 12.7% are unique to Hevea. Most of the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity have been identified. Conclusions The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever increasing need for natural rubber.

Draft Genome Sequence of Mycobacterium chimaera Type ...

Science.gov (United States)

We report the draft genome sequence of the type strain Mycobacterium chimaera Fl-0169T, a member of the Mycobacterium avium complex (MAC). M. chimaera Fl-0169T was isolated from a patient in Italy and is highly similar to strains of M. chimaera isolated in Ireland, though Fl-0169T possesses unique virulence genes. Evidence suggests that M. avium, M. intracellulare, and M. chimaera are differently virulent and a comparative genomic analysis is critically needed to identify diagnostic targets that reliably differentiate species of MAC. With treatment costs for Mycobacterium infections estimated to be >$1.8 B annually in the U.S., correct species identification will result in improved treatment selection, lower costs, and improved patient outcomes.

Draft genome sequence of the silver pomfret fish, Pampus argenteus.

Science.gov (United States)

AlMomin, Sabah; Kumar, Vinod; Al-Amad, Sami; Al-Hussaini, Mohsen; Dashti, Talal; Al-Enezi, Khaznah; Akbar, Abrar

2016-01-01

Silver pomfret, Pampus argenteus, is a fish species from coastal waters. Despite its high commercial value, this edible fish has not been sequenced. Hence, its genetic and genomic studies have been limited. We report the first draft genome sequence of the silver pomfret obtained using a Next Generation Sequencing (NGS) technology. We assembled 38.7 Gb of nucleotides into scaffolds of 350 Mb with N50 of about 1.5 kb, using high quality paired end reads. These scaffolds represent 63.7% of the estimated silver pomfret genome length. The newly sequenced and assembled genome has 11.06% repetitive DNA regions, and this percentage is comparable to that of the tilapia genome. The genome analysis predicted 16 322 genes. About 91% of these genes showed homology with known proteins. Many gene clusters were annotated to protein and fatty-acid metabolism pathways that may be important in the context of the meat texture and immune system developmental processes. The reference genome can pave the way for the identification of many other genomic features that could improve breeding and population-management strategies, and it can also help characterize the genetic diversity of P. argenteus.

Draft genome sequence of Phomopsis longicolla isolate MSPL 10-6

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Shuxian Li

2015-03-01

Full Text Available Phomopsis longicolla is the primary cause of Phomopsis seed decay in soybean. This disease severely affects soybean seed quality by reducing seed viability and oil content, altering seed composition, and increasing frequencies of moldy and/or split beans. It is one of the most economically important soybean diseases. Here, we report the de novo assembled draft genome sequence of the P. longicolla isolate MSPL10-6, which was isolated from field-grown soybean seed in Mississippi, USA. This study represents the first reported genome sequence of a seedborne fungal pathogen in the Diaporthe–Phomopsis complex. The P. longicolla genome sequence will enable research into the genetic basis of fungal infection of soybean seed and provide information for the study of soybean–fungal interactions. The genome sequence will also be valuable for molecular genetic marker development, manipulation of pathogenicity-related genes and development of new control strategies for this pathogen.

Draft genome sequence of Xylella fastidiosa pear leaf scorch strain in Taiwan

Science.gov (United States)

The draft genome sequence of Xylella fastidiosa pear leaf scorch strain (PLS229) isolated from pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan is reported. The bacterium has a genome size of 2,733,013 bp with a G+C content of 53.1%. The PLS229 strain genome was annotated to have 3,259 open readin...

Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1

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Ivan Wawrzyniak

2015-06-01

Full Text Available The intestinal protistan parasite Blastocystis is characterized by an extensive genetic variability with 17 subtypes (ST1–ST17 described to date. Only the whole genome of a human ST7 isolate was previously sequenced. Here we report the draft genome sequence of Blastocystis ST4-WR1 isolated from a laboratory rodent at Singapore.

Draft Genome Sequence and Gene Annotation of the Entomopathogenic Fungus Verticillium hemipterigenum

OpenAIRE

Horn, Fabian; Habel, Andreas; Scharf, Daniel H.; Dworschak, Jan; Brakhage, Axel A.; Guthke, Reinhard; Hertweck, Christian; Linde, J?rg

2015-01-01

Verticillium hemipterigenum (anamorph Torrubiella hemipterigena) is an entomopathogenic fungus and produces a broad range of secondary metabolites. Here, we present the draft genome sequence of the fungus, including gene structure and functional annotation. Genes were predicted incorporating RNA-Seq data and functionally annotated to provide the basis for further genome studies.

Draft Genome Sequence of the Microbispora sp. Strain ATCC-PTA-5024, Producing the Lantibiotic NAI-107

DEFF Research Database (Denmark)

Sosio, M.; Gallo, G.; Pozzi, R.

2014-01-01

We report the draft genome sequence of Microbispora sp. strain ATCC-PTA-5024, a soil isolate that produces NAI-107, a new lantibiotic with the potential to treat life-threatening infections caused by multidrug-resistant Gram-positive pathogens. The draft genome of strain Microbispora sp. ATCC...

Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169

Science.gov (United States)

We report the draft genome sequence of the type strain Mycobacterium chimaera Fl-0169T, a member of the Mycobacterium avium complex (MAC). M. chimaera Fl-0169T was isolated from a patient in Italy and is highly similar to strains of M. chimaera isolated in Ireland, though Fl-016...

Draft genome sequence of Francisella tularensis subsp. holarctica BD11-00177

NARCIS (Netherlands)

Coolen, J.P.M.; Sjödin, A.; Maraha, B.; Hajer, G.F.; Forsman, M.; Verspui, E.; Frenay, H.M.E.; Notermans, D.W.; Vries, M.C. de; Reubsaet, F.A.G.; Paauw, A.; Roeselers, G.

2013-01-01

Francisella tularensis is a facultative intracellular bacterium in the class Gammaproteobacteria. This strain is of interest because it is the etiologic agent of tularemia and a highly virulent category A biothreat agent. Here we describe the draft genome sequence and annotation of Francisella

Draft Genome Sequence of Hoeflea sp. Strain BAL378, a Potential Producer of Bioactive Compounds

DEFF Research Database (Denmark)

Bentzon-Tilia, Mikkel; Riemann, Lasse; Gram, Lone

2014-01-01

Some phytoplankton-associated marine bacteria produce bioactive compounds. Members of the genus Hoeflea may be examples of such bacteria; however, data describing their metabolisms are scarce. Here, we report the draft genome sequence of Hoeflea sp. strain BAL378, a putative producer of bacterioc......Some phytoplankton-associated marine bacteria produce bioactive compounds. Members of the genus Hoeflea may be examples of such bacteria; however, data describing their metabolisms are scarce. Here, we report the draft genome sequence of Hoeflea sp. strain BAL378, a putative producer...

Human genetics and genomics a decade after the release of the draft sequence of the human genome

Science.gov (United States)

2011-01-01

Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with respect to advances in genotyping technologies. These developments are vital for the emergence of genome-wide association studies in the investigation of complex diseases and traits. In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing studies such as the 1000 Genomes Project and the International Cancer Genome Consortium. The high-throughput sequencing and sequence-capture technologies are also providing new opportunities to study Mendelian disorders through exome sequencing and whole-genome sequencing. This paper reviews these major developments in human genetics and genomics over the past decade. PMID:22155605

Draft Genome Sequences of the Black Rock Fungus Knufia petricola and Its Spontaneous Nonmelanized Mutant

OpenAIRE

Tesei, Donatella; Tafer, Hakim; Poyntner, Caroline; Piñar, Guadalupe; Lopandic, Ksenija; Sterflinger, Katja

2017-01-01

ABSTRACT The fungal genus Knufia mostly comprises extremotolerant species from environmental sources, especially rock surfaces. The draft genome sequence of the rock fungus Knufia petricola presented here is the first whole-genome sequence of the only species among black fungi known to have a nonmelanized spontaneous mutant.

The draft genome sequence of Mangrovibacter sp. strain MP23, an endophyte isolated from the roots of Phragmites karka

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Pratiksha Behera

2016-09-01

Full Text Available Till date, only one draft genome has been reported within the genus Mangrovibacter. Here, we report the second draft genome shotgun sequence of a Mangrovibacter sp. strain MP23 that was isolated from the roots of Phargmites karka (P. karka, an invasive weed growing in the Chilika Lagoon, Odisha, India. Strain MP23 is a facultative anaerobic, nitrogen-fixing endophytic bacteria that grows optimally at 37 °C, 7.0 pH, and 1% NaCl concentration. The draft genome sequence of strain MP23 contains 4,947,475 bp with an estimated G + C content of 49.9% and total 4392 protein coding genes. The genome sequence has provided information on putative genes that code for proteins involved in oxidative stress, uptake of nutrients, and nitrogen fixation that might offer niche specific ecological fitness and explain the invasive success of P. karka in Chilika Lagoon. The draft genome sequence and annotation have been deposited at DDBJ/EMBL/GenBank under the accession number LYRP00000000.

Draft Genome Sequence of Antimicrobial-Producing Clostridium sp. JC272, Isolated from Marine Sediment

OpenAIRE

Tushar, L.; Sasi Jyothsna, T. S.; Sasikala, C.; Ramana, C. V.

2015-01-01

We announce the draft genome sequence of Clostridium sp. JC272, isolated from a sediment sample collected from marine habitats of Gujarat, India. Clostridium sp. JC272 is an obligate anaerobe and has the ability to produce antimicrobial compounds. The genome sequence indicates the strain?s capability of producing small peptides (microcins), which are potential novel antibiotics.

Draft genome sequence of a multidrug-resistant Chryseobacterium indologenes isolate from Malaysia

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Choo Yee Yu

2016-03-01

Full Text Available Chryseobacterium indologenes is an emerging pathogen which poses a threat in clinical healthcare setting due to its multidrug-resistant phenotype and its common association with nosocomial infections. Here, we report the draft genome of a multidrug-resistant C. indologenes CI_885 isolated in 2014 from Malaysia. The 908,704-kb genome harbors a repertoire of putative antibiotic resistance determinants which may elucidate the molecular basis and underlying mechanisms of its resistant to various classes of antibiotics. The genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession number LJOD00000000. Keywords: Chryseobacterium indologenes, Genome, Multi-drug resistant, blaIND, Next generation sequencing

Draft Genome Sequences of Historical Listeria monocytogenes from Human Listeriosis, 1933

Science.gov (United States)

We report here the draft genome sequences of two Listeria monocytogenes strains from some of the earliest reported cases of human listeriosis in North America. The strains were isolated in 1933 from patients in Massachusetts and Connecticut, USA, and belong to the widely disseminated hypervirulent c...

Draft genome sequence of Xylella fastidiosa subsp. fastidiosa strain Stag’s Leap

Science.gov (United States)

Xylella fastidiosa subsp. fastidiosa causes Pierce’s disease of grapevine. Presented here is the draft genome sequence of the Stag’s Leap strain, previously used in pathogenicity/virulence assays to evaluate grapevine germplasm bearing Pierce’s disease....

Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich.

Science.gov (United States)

Luan, Ming-Bao; Jian, Jian-Bo; Chen, Ping; Chen, Jun-Hui; Chen, Jian-Hua; Gao, Qiang; Gao, Gang; Zhou, Ju-Hong; Chen, Kun-Mei; Guang, Xuan-Min; Chen, Ji-Kang; Zhang, Qian-Qian; Wang, Xiao-Fei; Fang, Long; Sun, Zhi-Min; Bai, Ming-Zhou; Fang, Xiao-Dong; Zhao, Shan-Cen; Xiong, He-Ping; Yu, Chun-Ming; Zhu, Ai-Guo

2018-05-01

Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fibre crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fibre quality, protein content and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach. The highly heterozygous B. nivea genome was assembled using the Platanus Genome Assembler, which is an effective tool for the assembly of highly heterozygous genome sequences. The final length of the draft genome of this species was approximately 341.9 Mb (contig N50 = 22.62 kb, scaffold N50 = 1,126.36 kb). Based on ramie genome annotations, 30,237 protein-coding genes were predicted, and the repetitive element content was 46.3%. The completeness of the final assembly was evaluated by benchmarking universal single-copy orthologous genes (BUSCO); 90.5% of the 1,440 expected embryophytic genes were identified as complete, and 4.9% were identified as fragmented. Phylogenetic analysis based on single-copy gene families and one-to-one orthologous genes placed ramie with mulberry and cannabis, within the clade of urticalean rosids. Genome information of ramie will be a valuable resource for the conservation of endangered Boehmeria species and for future studies on the biogeography and characteristic evolution of members of Urticaceae. © 2018 John Wiley & Sons Ltd.

Draft Genome Sequences of Three Novel Low-Abundance Species Strains Isolated from Kefir Grain.

Science.gov (United States)

Kim, Yongkyu; Blasche, Sonja; Patil, Kiran R

2017-09-28

We report here the genome sequences of three novel bacterial species strains- Bacillus kefirresidentii Opo, Rothia kefirresidentii KRP, and Streptococcus kefirresidentii YK-isolated from kefir grains collected in Germany. The draft genomes of these isolates were remarkably dissimilar (average nucleotide identities, 77.80%, 89.01%, and 92.10%, respectively) to those of the previously sequenced strains. Copyright © 2017 Kim et al.

Draft Genome Sequence of Corynebacterium kefirresidentii SB, Isolated from Kefir.

Science.gov (United States)

Blasche, Sonja; Kim, Yongkyu; Patil, Kiran R

2017-09-14

The genus Corynebacterium includes Gram-positive species with a high G+C content. We report here a novel species, Corynebacterium kefirresidentii SB, isolated from kefir grains collected in Germany. Its draft genome sequence was remarkably dissimilar (average nucleotide identity, 76.54%) to those of other Corynebacterium spp., confirming that this is a unique novel species. Copyright © 2017 Blasche et al.

Draft Genome Sequence of a Highly Flagellated, Fast-Swimming Archaeon, Methanocaldococcus villosus Strain KIN24-T80 (DSM 22612)

KAUST Repository

Thennarasu, Sugumar; Poli Reddy, Dinesh Reddy; Antony, Aju; Yada, Madhava; Alqarawi, Sami; Neelamegam, Sivakumar

2013-01-01

We report the draft genome sequence of a hyperthermophilic Methanocaldococcus villosus strain, KIN24-T80. The gene associated with its heavy flagellum formation was annotated in the 1.2-Mb draft genome sequence, and this strain may be a good model system to study the extensive functional role of flagella and their fast motor activity.

Draft Genome Sequence of a Highly Flagellated, Fast-Swimming Archaeon, Methanocaldococcus villosus Strain KIN24-T80 (DSM 22612)

KAUST Repository

Thennarasu, Sugumar

2013-07-11

We report the draft genome sequence of a hyperthermophilic Methanocaldococcus villosus strain, KIN24-T80. The gene associated with its heavy flagellum formation was annotated in the 1.2-Mb draft genome sequence, and this strain may be a good model system to study the extensive functional role of flagella and their fast motor activity.

Draft genome sequence of Bacillus oleronius DSM 9356 isolated from the termite Reticulitermes santonensis

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Rodney Owusu-Darko

2017-06-01

Full Text Available Bacillus oleronius strain DSM 9356 isolated from the termite Reticulitermes santonensis was sequenced to gain insights in relation to its closest phylogenetic neighbor Bacillus sporothermodurans. The draft genome of strain DSM 9356 contains 5,083,966 bp with an estimated G + C content of 35%, 4899 protein-coding genes, 116 tRNAs and 18 rRNAs. The RAST annotation assigned these genes into 462 subsystems, with the maximum number of genes associated with amino acids and derivatives metabolism (14.84%, followed by carbohydrates (13.89% and protein metabolism subsystems (9.10%. The draft genome sequence and annotation has been deposited at NCBI under the accession number MTLA00000000.

Draft Genome Sequence of a Chitinase-producing Biocontrol Bacterium Serratia sp. C-1

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Seur Kee Park

2015-09-01

Full Text Available The chitinase-producing bacterial strain C-1 is one of the key chitinase-producing biocontrol agents used for effective bioformulations for biological control. These bioformulations are mixed cultures of various chitinolytic bacteria. However, the precise identification, biocontrol activity, and the underlying mechanisms of the strain C-1 have not been investigated so far. Therefore, we evaluated in planta biocontrol efficacies of C-1 and determined the draft genome sequence of the strain in this study. The bacterial C-1 strain was identified as a novel Serratia sp. by a phylogenic analysis of its 16S rRNA sequence. The Serratia sp. C-1 bacterial cultures showed strong in planta biocontrol efficacies against some major phytopathogenic fungal diseases. The draft genome sequence of Serratia sp. C-1 indicated that the C-1 strain is a novel strain harboring a subset of genes that may be involved in its biocontrol activities.

Draft genome sequence of the Algerian bee Apis mellifera intermissa

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Nizar Jamal Haddad

2015-06-01

Full Text Available Apis mellifera intermissa is the native honeybee subspecies of Algeria. A. m. intermissa occurs in Tunisia, Algeria and Morocco, between the Atlas and the Mediterranean and Atlantic coasts. This bee is very important due to its high ability to adapt to great variations in climatic conditions and due to its preferable cleaning behavior. Here we report the draft genome sequence of this honey bee, its Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JSUV00000000. The 240-Mb genome is being annotated and analyzed. Comparison with the genome of other Apis mellifera sub-species promises to yield insights into the evolution of adaptations to high temperature and resistance to Varroa parasite infestation.

Draft Genome Sequences of Vibrio alginolyticus Strains V1 and V2, Opportunistic Marine Pathogens

DEFF Research Database (Denmark)

Castillo, Daniel; D'Alvise, Paul; Kalatzis, Panos G.

2015-01-01

We announce the draft genome sequences of Vibrio alginolyticus strains V1 and V2, isolated from juvenile Sparus aurata and Dentex dentex, respectively, during outbreaks of vibriosis. The genome sequences are 5,257,950 bp with a G+C content of 44.5% for V. alginolyticus V1 and 5,068,299 bp with a G...

SEQUENCING AND DE NOVO DRAFT ASSEMBLIES OF A FATHEAD MINNOW (Pimpehales promelas) reference genome

Data.gov (United States)

U.S. Environmental Protection Agency — The dataset provides the URLs for accessing the genome sequence data and two draft assemblies as well as fathead minnow genotyping data associated with estimating...

Draft genome sequence of “Candidatus Liberibacter asiaticus” from Diaphorina citri in Guangdong, China

Science.gov (United States)

The draft genome sequence of “Candidatus Liberibacter asiaticus” strain YCPsy from an Asian citrus psyllid (Diaphorina citri) in Guangdong of China is reported. The YCPsy strain has a genome size of 1,233,647 bp, 36.5% G+C content, 1,171 open reading frames (ORFs), and 53 RNAs....

Draft genome sequence of the docosahexaenoic acid producing thraustochytrid Aurantiochytrium sp. T66

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Bin Liu

2016-06-01

Full Text Available Thraustochytrids are unicellular, marine protists, and there is a growing industrial interest in these organisms, particularly because some species, including strains belonging to the genus Aurantiochytrium, accumulate high levels of docosahexaenoic acid (DHA. Here, we report the draft genome sequence of Aurantiochytrium sp. T66 (ATCC PRA-276, with a size of 43 Mbp, and 11,683 predicted protein-coding sequences. The data has been deposited at DDBJ/EMBL/Genbank under the accession LNGJ00000000. The genome sequence will contribute new insight into DHA biosynthesis and regulation, providing a basis for metabolic engineering of thraustochytrids.

Draft Genome Sequence of Xylella fastidiosa subsp. fastidiosa Strain Stag?s Leap

OpenAIRE

Chen, J.; Wu, F.; Zheng, Z.; Deng, X.; Burbank, L. P.; Stenger, D. C.

2016-01-01

Xylella fastidiosa subsp. fastidiosa causes Pierce?s disease of grapevine. Presented here is the draft genome sequence of the Stag?s Leap strain, previously used in pathogenicity/virulence assays to evaluate grapevine germplasm bearing Pierce?s disease resistance and a phenotypic assessment of knockout mutants to determine gene function.

Draft Genome Sequence of Photobacterium halotolerans S2753, Producer of Bioactive Secondary Metabolites

DEFF Research Database (Denmark)

Machado, Henrique; Månsson, Maria; Gram, Lone

2014-01-01

We report here the whole draft genome sequence of marine isolate Photobacterium halotolerans S2753, which produces the known antibiotic holomycin and also ngercheumicins and solonamides A and B, which interfere with virulence of methicillin-resistant Staphylococcus aureus strains by interacting...

Draft Genome Sequence of Lactobacillus plantarum XJ25 Isolated from Chinese Red Wine.

Science.gov (United States)

Zhao, Meijing; Liu, Shuwen; He, Ling; Tian, Yu

2016-11-17

Here, we present the draft genome sequence of Lactobacillus plantarum XJ25, isolated from Chinese red wine that had undergone spontaneous malolactic fermentation, which consists of 25 contigs and is 3,218,018 bp long. Copyright © 2016 Zhao et al.

Draft Genome Sequence of the Antagonistic Rhizosphere Bacterium Serratia plymuthica Strain PRI-2C

NARCIS (Netherlands)

Garbeva, P.; van Elsas, J.D.; de Boer, W.

Serratia plymuthica strain PRI-2C is a rhizosphere bacterial strain with antagonistic activity against different plant pathogens. Here we present the 5.39-Mb (G+C content, 55.67%) draft genome sequence of S. plymuthica strain PRI-2C with the aim of providing insight into the genomic basis of its

Draft Genome Sequence of a Biosurfactant-Producing Bacillus subtilis UMX-103 Isolated from Hydrocarbon-Contaminated Soil in Terengganu, Malaysia.

Science.gov (United States)

Abdelhafiz, Yousri Abdelmutalab; Manaharan, Thamilvaani; BinMohamad, Saharuddin; Merican, Amir Feisal

2017-07-01

The draft genome here presents the sequence of Bacillus subtilis UMX-103. The bacterial strain was isolated from hydrocarbon-contaminated soil from Terengganu, Malaysia. The whole genome of the bacterium was sequenced using Illumina HiSeq 2000 sequencing platform. The genome was assembled using de novo approach. The genome size of UMX-103 is 4,234,627 bp with 4399 genes comprising 4301 protein-coding genes and 98 RNA genes. The analysis of assembled genes revealed the presence of 25 genes involved in biosurfactant production, where 14 of the genes are related to biosynthesis and 11 of the genes are in the regulation of biosurfactant productions. This draft genome will provide insights into the genetic bases of its biosurfactant-producing capabilities.

Draft genome sequence of Vitellibacter aquimaris D-24T isolated from seawater

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Suganthi Thevarajoo

Full Text Available ABSTRACT Vitellibacter aquimaris D-24T (=KCTC 42708T = DSM 101732T, a halophilic marine bacterium, was isolated from seawater collected from Desaru beach, Malaysia. Here, we present the draft genome sequence of D-24T with a genome size of approximately 3.1 Mbp and G + C content of 39.93%. The genome of D-24T contains genes involved in reducing a potent greenhouse gas (N2O in the environment and the degradation of proteinaceous compounds. Genome availability will provide insights into potential biotechnological and environmental applications of this bacterium.

Draft Genome Sequence of Serratia sp. Strain DD3, Isolated from the Guts of Daphnia magna

OpenAIRE

Poehlein, Anja; Freese, Heike M.; Daniel, Rolf; Simeonova, Diliana D.

2014-01-01

We report the draft genome sequence of Serratia sp. strain DD3, a gammaproteobacterium from the family Enterobacteriaceae. It was isolated from homogenized guts of Daphnia magna. The genome size is 5,274 Mb. peerReviewed

Draft genome sequence of Streptomyces sp. strain F1, a potential source for glycoside hydrolases isolated from Brazilian soil

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Ricardo Rodrigues de Melo

Full Text Available ABSTRACT Here, we show the draft genome sequence of Streptomyces sp. F1, a strain isolated from soil with great potential for secretion of hydrolytic enzymes used to deconstruct cellulosic biomass. The draft genome assembly of Streptomyces sp. strain F1 has 69 contigs with a total genome size of 8,142,296 bp and G + C 72.65%. Preliminary genome analysis identified 175 proteins as Carbohydrate-Active Enzymes, being 85 glycoside hydrolases organized in 33 distinct families. This draft genome information provides new insights on the key genes encoding hydrolytic enzymes involved in biomass deconstruction employed by soil bacteria.

Draft Genome Sequences of Pseudomonas aeruginosa B3 Strains Isolated from a Cystic Fibrosis Patient Undergoing Antibiotic Chemotherapy

DEFF Research Database (Denmark)

Marvig, Rasmus Lykke; Jochumsen, Nicholas; Johansen, Helle Krogh

2013-01-01

Pseudomonas aeruginosa frequently establishes chronic infections in the airways of patients suffering from cystic fibrosis (CF). Here, we report the draft genome sequences of four P. aeruginosa B3 strains isolated from a chronically infected CF patient undergoing antibiotic chemotherapy.......Pseudomonas aeruginosa frequently establishes chronic infections in the airways of patients suffering from cystic fibrosis (CF). Here, we report the draft genome sequences of four P. aeruginosa B3 strains isolated from a chronically infected CF patient undergoing antibiotic chemotherapy....

Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila

OpenAIRE

Hammer, Austin J.; Walters, Amber; Carroll, Courtney; Newell, Peter D.; Chaston, John M.

2017-01-01

ABSTRACT The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate from wild Drosophila flies, is reported here. Strain DmW181 possesses genes for sialic acid and mannose metabolism. The assembled genome is 3,201,429?bp, with 3,454 predicted genes.

Draft Genome Sequence of Ezakiella peruensis Strain M6.X2, a Human Gut Gram-Positive Anaerobic Coccus.

Science.gov (United States)

Diop, Awa; Diop, Khoudia; Tomei, Enora; Raoult, Didier; Fenollar, Florence; Fournier, Pierre-Edouard

2018-03-01

We report here the draft genome sequence of Ezakiella peruensis strain M6.X2 T The draft genome is 1,672,788 bp long and harbors 1,589 predicted protein-encoding genes, including 26 antibiotic resistance genes with 1 gene encoding vancomycin resistance. The genome also exhibits 1 clustered regularly interspaced short palindromic repeat region and 333 genes acquired by horizontal gene transfer. Copyright © 2018 Diop et al.

Draft Genome Sequence of an Obligately Methylotrophic Methanogen, Methanococcoides methylutens, Isolated from Marine Sediment

KAUST Repository

Guan, Yue

2014-11-20

Methanococcoides methylutens, the type species of the genus Methanococcoides, is a slightly halophilic methanogenic archaeon with a methylotrophic metabolism. Here, we present the annotated draft genome sequence of M. methylutens, which comprises 2,508,511 bp with 2,482 coding sequences, 51 tRNA genes, and a G+C content of 42.5%.

Draft Genome Sequence of an Obligately Methylotrophic Methanogen, Methanococcoides methylutens, Isolated from Marine Sediment

KAUST Repository

Guan, Yue; Ngugi, David; Blom, J.; Ali, Shahjahan; Ferry, J. G.; Stingl, Ulrich

2014-01-01

Methanococcoides methylutens, the type species of the genus Methanococcoides, is a slightly halophilic methanogenic archaeon with a methylotrophic metabolism. Here, we present the annotated draft genome sequence of M. methylutens, which comprises 2,508,511 bp with 2,482 coding sequences, 51 tRNA genes, and a G+C content of 42.5%.

Draft Genome Sequence of Methylocella silvestris TVC, a Facultative Methanotroph Isolated from Permafrost

OpenAIRE

Wang, Jing; Geng, Kan; Farhan Ul Haque, Muhammad; Crombie, Andrew; Street, Lorna E.; Wookey, Philip A.; Ma, Ke; Murrell, J. Colin; Pratscher, Jennifer

2018-01-01

Permafrost environments play a crucial role in global carbon and methane cycling. We report here the draft genome sequence of Methylocella silvestris TVC, a new facultative methanotroph strain, isolated from the Siksik Creek catchment in the continuous permafrost zone of Inuvik (Northwest Territories, Canada).

Draft Genome Sequence of a Picorna-Like Virus Associated with Gill Tissue in Clinically Normal Brook Trout, Salvelinus fontinalis

OpenAIRE

Iwanowicz, Luke R.; Iwanowicz, Deborah D.; Adams, Cynthia R.; Galbraith, Heather; Aunins, Aaron; Cornman, Robert S.

2017-01-01

ABSTRACT Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis, gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates.

Draft Genome Sequence of a Picorna-Like Virus Associated with Gill Tissue in Clinically Normal Brook Trout, Salvelinus fontinalis.

Science.gov (United States)

Iwanowicz, Luke R; Iwanowicz, Deborah D; Adams, Cynthia R; Galbraith, Heather; Aunins, Aaron; Cornman, Robert S

2017-10-12

Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis , gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates.

Draft Genome Sequence of Lactobacillus salivarius L28 Isolated from Ground Beef.

Science.gov (United States)

Ayala, Diana I; Cook, Peter W; Campos, David L; Brashears, Mindy M; den Bakker, Henk; Nightingale, Kendra K

2017-09-28

In this report, we describe the draft genome sequence of a newly discovered probiotic strain, Lactobacillus salivarius L28. L. salivarius L28 demonstrates antagonistic effects against human foodborne pathogens, including Escherichia coli O157:H7, Salmonella spp., and Listeria monocytogenes , in coculture experiments and food matrices. Copyright © 2017 Ayala et al.

Draft Genome Sequence of Catellicoccus marimammalium, a Novel Species Commonly Found in Gull Feces

Science.gov (United States)

Catellicoccus marimammalium is a relatively uncharacterized Gram-positive, facultative anaerobe with potential utility as an indicator of waterfowl fecal contamination. Here we report an annotated draft genome sequence that suggests this organism may be a symbiotic gut microbe.

The draft genome sequence of the American mink (Neovison vison) opens new opportunities of genomic research in mink

DEFF Research Database (Denmark)

Cai, Zexi; Panitz, Frank; Petersen, Bent

2016-01-01

The American mink (Neovison vison) is a semiaquatic mustelid native to North America. It is an important animal for the fur industry. Although many efforts have been made to locate genes influencing fur quality and color, the lack of a reference genome impedes the search. American mink has...... of Carnivora. Here we present the draft genome sequence of American mink. In our study, a male inbred pearl mink was sequenced by Illumina paired-end and mate pair sequencing. The reads were assembled, which lead to 22,419 scaffolds with an N50 (shortest sequence length at 50% of the genome) of 646,304 bp...

Draft genome sequence of Sclerospora graminicola, the pearl millet downy mildew pathogen

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S. Chandra Nayaka

2017-12-01

Full Text Available Sclerospora graminicola pathogen is the most important biotic production constraints of pearl millet in India, Africa and other parts of the world. We report a de novo whole genome assembly and analysis of pathotype 1, one of the most virulent pathotypes of S. graminicola from India. The draft genome assembly contained 299,901,251 bp with 65,404 genes. This study may help understand the evolutionary pattern of pathogen and aid elucidation of effector evolution for devising effective durable resistance breeding strategies in pearl millet. Keywords: Sclerospora graminicola, Pathotype 1, Pearl millet, Downy mildew, Whole genome sequence

Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila.

Science.gov (United States)

Hammer, Austin J; Walters, Amber; Carroll, Courtney; Newell, Peter D; Chaston, John M

2017-07-06

The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate from wild Drosophila flies, is reported here. Strain DmW181 possesses genes for sialic acid and mannose metabolism. The assembled genome is 3,201,429 bp, with 3,454 predicted genes. Copyright © 2017 Hammer et al.

Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana.

Science.gov (United States)

Radakovits, Randor; Jinkerson, Robert E; Fuerstenberg, Susan I; Tae, Hongseok; Settlage, Robert E; Boore, Jeffrey L; Posewitz, Matthew C

2012-02-21

The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a genetic transformation method for the marine microalga Nannochloropsis gaditana CCMP526. We show that N. gaditana has highly favourable lipid yields, and is a promising production organism. The genome assembly includes nuclear (~29 Mb) and organellar genomes, and contains 9,052 gene models. We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis. Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed. The availability of a genome sequence and transformation methods will facilitate investigations into N. gaditana lipid biosynthesis and permit genetic engineering strategies to further improve this naturally productive alga.

Draft genome sequence of Sclerospora graminicola, the pearl millet downy mildew pathogen

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Navajeet Chakravartty

2017-12-01

Full Text Available Sclerospora graminicola pathogen is the most important biotic production constraints of pearl millet in India, Africa and other parts of the world. We report a de novo whole genome assembly and analysis of pathotype 1, one of the most virulent pathotypes of S. graminicola from India. The whole genome sequencing was performed by sequencing of 7.38 Gb with 73,889,924 paired end reads from the paired-end library, and 1.15 Gb with 3,851,788 reads from the mate pair library generated from Illumina HiSeq 2500 and Illumina MiSeq, respectively. A total 597,293 filtered sub reads with average read length of 6.39 Kb was generated on PACBIO RSII with P6-C4 chemistry. Assembled draft genome sequence of S. graminicola pathotype 1 was 299,901,251 bp in length, N50 of 17,909 bp with a minimum of 1 Kb scaffold size. The GC content was 47.2 % consisting of 26,786 scaffolds with longest scaffold size of 238,843 bp. The overall coverage was 40X. The draft genome sequence was used for gene prediction using AUGUSTUS which resulted in 65,404 genes using Saccharomyces cerevisiae as a model. A total of 52,285 predicted genes found homology using BLASTX against nr database and 38,120 genes were observed with a significant BLASTX match with E-value cutoff of 1e-5 and 40% identity percentage. Out of 38,120 genes annotated a set of 11,873 genes had UniProt entries, while 7,248 were GO terms and 9,686 with KEGG IDs. Of the 7,248 GO terms, 2,724 were associated with the biological processes. The genome information of downy mildew pathogen is available in the NCBI GenBank database. The Sclerospora graminicola whole genome shotgun (WGS project has the project accession MIQA00000000. This version of the project (02 has the accession number MIQA02000000, and consists of sequences MIQA02000001-MIQA02026786, with BioProject ID PRJNA325098 and BioSample ID SAMN05219233. This study may help understand the evolutionary pattern of pathogen and aid elucidation of effector evolution for

Draft genome sequence of Streptomyces sp. strain F1, a potential source for glycoside hydrolases isolated from Brazilian soil.

Science.gov (United States)

Melo, Ricardo Rodrigues de; Persinoti, Gabriela Felix; Paixão, Douglas Antonio Alvaredo; Squina, Fábio Márcio; Ruller, Roberto; Sato, Helia Harumi

Here, we show the draft genome sequence of Streptomyces sp. F1, a strain isolated from soil with great potential for secretion of hydrolytic enzymes used to deconstruct cellulosic biomass. The draft genome assembly of Streptomyces sp. strain F1 has 69 contigs with a total genome size of 8,142,296bp and G+C 72.65%. Preliminary genome analysis identified 175 proteins as Carbohydrate-Active Enzymes, being 85 glycoside hydrolases organized in 33 distinct families. This draft genome information provides new insights on the key genes encoding hydrolytic enzymes involved in biomass deconstruction employed by soil bacteria. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Draft Genome Sequence of Methylocella silvestris TVC, a Facultative Methanotroph Isolated from Permafrost.

Science.gov (United States)

Wang, Jing; Geng, Kan; Farhan Ul Haque, Muhammad; Crombie, Andrew; Street, Lorna E; Wookey, Philip A; Ma, Ke; Murrell, J Colin; Pratscher, Jennifer

2018-02-22

Permafrost environments play a crucial role in global carbon and methane cycling. We report here the draft genome sequence of Methylocella silvestris TVC, a new facultative methanotroph strain, isolated from the Siksik Creek catchment in the continuous permafrost zone of Inuvik (Northwest Territories, Canada). Copyright © 2018 Wang et al.

Draft Genome Sequence of Lactobacillus salivarius SGL 03, a Novel Potential Probiotic Strain.

Science.gov (United States)

Federici, Federica; Manna, Laura; Rizzi, Eleonora; Galantini, Elena; Marini, Umberto

2017-12-07

In this work, we report the draft genome sequence of Lactobacillus salivarius SGL 03, a novel potential probiotic strain isolated from healthy infant stools. Antibiotic resistance analysis revealed the presence of a tetracycline resistance gene without elements potentially responsible for interspecific horizontal gene transfer. Copyright © 2017 Federici et al.

Sequencing and De novo Draft Assemblies of the Fathead Minnow (Pimphales promelas)Reference Genome

Science.gov (United States)

This study was undertaken to develop genome-scale resources for the fathead minnow (Pimphales promelas) an important model organism widely used in both aquatic ecotoxicology research and in regulatory toxicity testing. We report on the first sequencing and two draft assemblies fo...

Draft Genome Sequence of the Model Naphthalene-Utilizing Organism Pseudomonas putida OUS82

DEFF Research Database (Denmark)

Tay, Martin; Roizman, Dan; Cohen, Yehuda

2014-01-01

Pseudomonas putida OUS82 was isolated from petrol- and oil-contaminated soil in 1992, and ever since, it has been used as a model organism to study the microbial assimilation of naphthalene and phenanthrene. Here, we report the 6.7-Mb draft genome sequence of P. putida OUS82 and analyze its...

Draft genome sequence of Bizionia argentinensis, isolated from antarctic surface water

OpenAIRE

Lanzarotti, E.; Pellizza, L.; Bercovich, A.; Foti, M.; Coria, S.H.; Vazquez, S.C.; Ruberto, L.; Hernández, E.A.; Dias, R.L.; Mac Cormack, W.P.; Cicero, D.O.; Smal, C.; Nicolas, M.F.; Vasconcelos, A.T.R.; Marti, M.A.

2011-01-01

A psychrotolerant marine bacterial strain, designated JUB59 T, was isolated from Antarctic surface seawater and classified as a new species of the genus Bizionia. Here, we present the first draft genome sequence for this genus, which suggests interesting features such as UV resistance, hydrolytic exoenzymes, and nitrogen metabolism. © 2011, American Society for Microbiology. Fil:Pellizza, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Mac Cormac...

Draft genome sequence of a caprolactam degrader bacterium: Pseudomonas taiwanensis strain SJ9

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Sung-Jun Hong

Full Text Available Abstract Pseudomonas taiwanensis strain SJ9 is a caprolactam degrader, isolated from industrial wastewater in South Korea and considered to have the potential for caprolactam bioremediation. The genome of this strain is approximately 6.2 Mb (G + C content, 61.75% with 6,010 protein-coding sequences (CDS, of which 46% are assigned to recognized functional genes. This draft genome of strain SJ9 will provide insights into the genetic basis of its caprolactam-degradation ability.

Draft genome sequence of Mycobacterium tuberculosis strain B9741 of Beijing B0/W lineage from HIV positive patient from Siberia

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K.V. Shur

2016-12-01

Full Text Available We report a draft genome sequence of Mycobacterium tuberculosis strain B9741 belonging to Beijing B0/W lineage isolated from a HIV patient from Siberia, Russia. This clinical isolate showed MDR phenotype and resistance to isoniazid, rifampin, streptomycin and pyrazinamide. We analyzed SNPs associated with virulence and resistance. The draft genome sequence and annotation have been deposited at GenBank under the accession NZ_LVJJ00000000.

Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium

KAUST Repository

Lafi, Feras Fawzi; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2017-01-01

Ochrobactrum intermedium strain SA148 is a plant growth-promoting bacterium isolated from sandy soil in the Jizan area of Saudi Arabia. Here, we report the 4.9-Mb draft genome sequence of this strain, highlighting different pathways characteristic

Draft genome sequence of the yeast Starmerella bacillaris (syn., Candida zemplinina) FRI751 isolated from fermenting must of dried Raboso grapes

DEFF Research Database (Denmark)

Lemos Junior, Wilson Jose Fernandes; Treu, Laura; da Silva Duarte, Vinicius

2017-01-01

Starmerella bacillaris is an ascomycetous yeast commonly present in enological environments. Here, we report the first draft genome sequence of S. bacillaris FRI751, which will facilitate the study of the characteristics of this interesting enological yeast.......Starmerella bacillaris is an ascomycetous yeast commonly present in enological environments. Here, we report the first draft genome sequence of S. bacillaris FRI751, which will facilitate the study of the characteristics of this interesting enological yeast....

Draft genome sequence of Streptomyces coelicoflavus ZG0656 reveals the putative biosynthetic gene cluster of acarviostatin family α-amylase inhibitors.

Science.gov (United States)

Guo, X; Geng, P; Bai, F; Bai, G; Sun, T; Li, X; Shi, L; Zhong, Q

2012-08-01

The aims of this study are to obtain the draft genome sequence of Streptomyces coelicoflavus ZG0656, which produces novel acarviostatin family α-amylase inhibitors, and then to reveal the putative acarviostatin-related gene cluster and the biosynthetic pathway. The draft genome sequence of S. coelicoflavus ZG0656 was generated using a shotgun approach employing a combination of 454 and Solexa sequencing technologies. Genome analysis revealed a putative gene cluster for acarviostatin biosynthesis, termed sct-cluster. The cluster contains 13 acarviostatin synthetic genes, six transporter genes, four starch degrading or transglycosylation enzyme genes and two regulator genes. On the basis of bioinformatic analysis, we proposed a putative biosynthetic pathway of acarviostatins. The intracellular steps produce a structural core, acarviostatin I00-7-P, and the extracellular assemblies lead to diverse acarviostatin end products. The draft genome sequence of S. coelicoflavus ZG0656 revealed the putative biosynthetic gene cluster of acarviostatins and a putative pathway of acarviostatin production. To our knowledge, S. coelicoflavus ZG0656 is the first strain in this species for which a genome sequence has been reported. The analysis of sct-cluster provided important insights into the biosynthesis of acarviostatins. This work will be a platform for producing novel variants and yield improvement. © 2012 The Authors. Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

Draft Genome Sequence of Leuconostoc mesenteroides P45 Isolated from Pulque, a Traditional Mexican Alcoholic Fermented Beverage.

Science.gov (United States)

Riveros-Mckay, Fernando; Campos, Itzia; Giles-Gómez, Martha; Bolívar, Francisco; Escalante, Adelfo

2014-11-06

Leuconostoc mesenteroides P45 was isolated from the traditional Mexican pulque beverage. We report its draft genome sequence, assembled in 6 contigs consisting of 1,874,188 bp and no plasmids. Genome annotation predicted a total of 1,800 genes, 1,687 coding sequences, 52 pseudogenes, 9 rRNAs, 51 tRNAs, 1 noncoding RNA, and 44 frameshifted genes. Copyright © 2014 Riveros-Mckay et al.

Draft genome sequence of Bradyrhizobium manausense strain BR 3351T, an effective symbiont isolated from Amazon rainforest.

Science.gov (United States)

Simões-Araújo, Jean Luiz; Rumjanek, Norma Gouvêa; Xavier, Gustavo Ribeiro; Zilli, Jerri Édson

The strain BR 3351 T (Bradyrhizobium manausense) was obtained from nodules of cowpea (Vigna unguiculata L. Walp) growing in soil collected from Amazon rainforest. Furthermore, it was observed that the strain has high capacity to fix nitrogen symbiotically in symbioses with cowpea. We report here the draft genome sequence of strain BR 3351 T . The information presented will be important for comparative analysis of nodulation and nitrogen fixation for diazotrophic bacteria. A draft genome with 9,145,311bp and 62.9% of GC content was assembled in 127 scaffolds using 100bp pair-end Illumina MiSeq system. The RAST annotation identified 8603 coding sequences, 51 RNAs genes, classified in 504 subsystems. Published by Elsevier Editora Ltda.

Draft genome sequence of Bradyrhizobium manausense strain BR 3351T, an effective symbiont isolated from Amazon rainforest

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Jean Luiz Simões-Araújo

Full Text Available ABSTRACT The strain BR 3351T (Bradyrhizobium manausense was obtained from nodules of cowpea (Vigna unguiculata L. Walp growing in soil collected from Amazon rainforest. Furthermore, it was observed that the strain has high capacity to fix nitrogen symbiotically in symbioses with cowpea. We report here the draft genome sequence of strain BR 3351T. The information presented will be important for comparative analysis of nodulation and nitrogen fixation for diazotrophic bacteria. A draft genome with 9,145,311 bp and 62.9% of GC content was assembled in 127 scaffolds using 100 bp pair-end Illumina MiSeq system. The RAST annotation identified 8603 coding sequences, 51 RNAs genes, classified in 504 subsystems.

Draft genome and sequence variant data of the oomycete Pythium insidiosum strain Pi45 from the phylogenetically-distinct Clade-III

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Weerayuth Kittichotirat

2017-12-01

Full Text Available Pythium insidiosum is a unique oomycete microorganism, capable of infecting humans and animals. The organism can be phylogenetically categorized into three distinct clades: Clade-I (strains from the Americas; Clade-II (strains from Asia and Australia, and Clade–III (strains from Thailand and the United States. Two draft genomes of the P. insidiosum Clade-I strain CDC-B5653 and Clade-II strain Pi-S are available in the public domain. The genome of P. insidiosum from the distinct Clade-III, which is distantly-related to the other two clades, is lacking. Here, we report the draft genome sequence of the P. insidiosum strain Pi45 (also known as MCC13; isolated from a Thai patient with pythiosis; accession numbers BCFM01000001-BCFM01017277 as a representative strain of the phylogenetically-distinct Clade-III. We also report a genome-scale data set of sequence variants (i.e., SNPs and INDELs found in P. insidiosum (accessible online at the Mendeley database: http://dx.doi.org/10.17632/r75799jy6c.1. Keywords: Pythium insidiosum, Pythiosis, Draft genome, Sequence variant

Draft Genome Sequence of Lactobacillus casei Lbs2.

Science.gov (United States)

Bhowmick, Swati; Malar, Mathu; Das, Abhishek; Kumar Thakur, Bhupesh; Saha, Piu; Das, Santasabuj; Rashmi, H M; Batish, Virender K; Grover, Sunita; Tripathy, Sucheta

2014-12-24

We report here a 3.2-Mb draft assembled genome of Lactobacillus casei Lbs2. The bacterium shows probiotic and immunomodulatory activities. The genome assembly and annotation will help to identify molecules and pathways responsible for interaction between the host immune system and the microbe. Copyright © 2014 Bhowmick et al.

Draft genome sequence of Streptococcus equi subsp. zooepidemicus strain S31A1, isolated from equine infectious endometritis

DEFF Research Database (Denmark)

da Piedade, Isabelle; Skive, Bolette; Christensen, Henrik

2013-01-01

We present the draft genome sequence of Streptococcus equi subsp. zooepidemicus S31A1, a strain isolated from equine infectious endometritis in Denmark. Comparative analyses of this genome were done with four published reference genomes: S. zooepidemicus strains MGCS10565, ATCC 35246, and H70 and S...

Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria

OpenAIRE

da Silva, F?bio Daniel Flor?ncio; Lima, Alex Ranieri Jer?nimo; Moraes, Pablo Henrique Gon?alves; Siqueira, Andrei Santos; Dall?Agnol, Leonardo Teixeira; Bara?na, Anna Rafaella Ferreira; Martins, Luisa Car?cio; Oliveira, Karol Guimar?es; de Lima, Clayton Pereira Silva; Nunes, M?rcio Roberto Teixeira; Vianez-J?nior, Jo?o L?dio Silva Gon?alves; Gon?alves, Evonnildo Costa

2016-01-01

Ecological interactions between cyanobacteria and heterotrophic prokaryotes are poorly known. To improve the genomic studies of heterotrophic bacterium-cyanobacterium associations, the draft genome sequence (3.2 Mbp) of Limnobacter sp. strain CACIAM 66H1, found in a nonaxenic culture of Synechococcus sp. (cyanobacteria), is presented here.

Draft Genome Sequence of Lactobacillus farciminis NBRC 111452, Isolated from K?so, a Japanese Sugar-Vegetable Fermented Beverage

OpenAIRE

Chiou, Tai-Ying; Oshima, Kenshiro; Suda, Wataru; Hattori, Masahira; Takahashi, Tomoya

2016-01-01

Here, we report the draft genome sequence of the Lactobacillus farciminis strain NBRC 111452, isolated from k?so, a Japanese sugar-vegetable fermented beverage. This genome information is of potential use in studies of Lactobacillus farciminis as a probiotic.

Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions.

Science.gov (United States)

Urasaki, Naoya; Takagi, Hiroki; Natsume, Satoshi; Uemura, Aiko; Taniai, Naoki; Miyagi, Norimichi; Fukushima, Mai; Suzuki, Shouta; Tarora, Kazuhiko; Tamaki, Moritoshi; Sakamoto, Moriaki; Terauchi, Ryohei; Matsumura, Hideo

2017-02-01

Bitter gourd (Momordica charantia) is an important vegetable and medicinal plant in tropical and subtropical regions globally. In this study, the draft genome sequence of a monoecious bitter gourd inbred line, OHB3-1, was analyzed. Through Illumina sequencing and de novo assembly, scaffolds of 285.5 Mb in length were generated, corresponding to ∼84% of the estimated genome size of bitter gourd (339 Mb). In this draft genome sequence, 45,859 protein-coding gene loci were identified, and transposable elements accounted for 15.3% of the whole genome. According to synteny mapping and phylogenetic analysis of conserved genes, bitter gourd was more related to watermelon (Citrullus lanatus) than to cucumber (Cucumis sativus) or melon (C. melo). Using RAD-seq analysis, 1507 marker loci were genotyped in an F2 progeny of two bitter gourd lines, resulting in an improved linkage map, comprising 11 linkage groups. By anchoring RAD tag markers, 255 scaffolds were assigned to the linkage map. Comparative analysis of genome sequences and predicted genes determined that putative trypsin-inhibitor and ribosome-inactivating genes were distinctive in the bitter gourd genome. These genes could characterize the bitter gourd as a medicinal plant. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Draft genome sequence of Bacillus okhensis Kh10-101T, a halo-alkali tolerant bacterium from Indian saltpan

Directory of Open Access Journals (Sweden)

Pilla Sankara Krishna

2015-12-01

Full Text Available We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali tolerant rod shaped bacterium isolated from a salt pan near port of Okha, India. This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions. The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs. Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000.

Draft Genome Sequence of the Putrescine-Producing Strain Lactococcus lactis subsp. lactis 1AA59

Science.gov (United States)

del Rio, Beatriz; Linares, Daniel M.; Fernandez, María; Mayo, Baltasar; Martín, M. Cruz

2015-01-01

We report here the 2,576,542-bp genome annotated draft assembly sequence of Lactococcus lactis subsp. lactis 1AA59. This strain—isolated from a traditional cheese—produces putrescine, one of the most frequently biogenic amines found in dairy products. PMID:26089428

Draft Genome Sequence of Lactobacillus sp. Strain TCF032-E4, Isolated from Fermented Radish.

Science.gov (United States)

Mao, Yuejian; Chen, Meng; Horvath, Philippe

2015-07-30

Here, we report the draft genome sequence of Lactobacillus sp. strain TCF032-E4 (= CCTCC AB2015090 = DSM 100358), isolated from a Chinese fermented radish. The total length of the 57 contigs is about 2.9 Mb, with a G+C content of 43.5 mol% and 2,797 predicted coding sequences (CDSs). Copyright © 2015 Mao et al.

Draft Genome Sequence of Bacillus velezensis B6, a Rhizobacterium That Can Control Plant Diseases.

Science.gov (United States)

Gao, Yu-Han; Guo, Rong-Jun; Li, Shi-Dong

2018-03-22

The draft genome of Bacillus velezensis strain B6, a rhizobacterium with good biocontrol performance isolated from soil in China, was sequenced. The assembly comprises 32 scaffolds with a total size of 3.88 Mb. Gene clusters coding either ribosomally encoded bacteriocins or nonribosomally encoded antimicrobial polyketides and lipopeptides in the genome may contribute to plant disease control. Copyright © 2018 Gao et al.

Draft genome sequence of Pseudomonas corrugata, a phytopathogenic bacterium with potential industrial applications.

Science.gov (United States)

Licciardello, G; Jackson, R W; Bella, P; Strano, C P; Catara, A F; Arnold, D L; Venturi, V; Silby, M W; Catara, V

2014-04-10

Pseudomonas corrugata was first described as the causal agent of a tomato disease called 'pith necrosis' yet it is considered as a biological resource in various fields such as biocontrol of plant diseases and production of industrially promising microbial biopolymers (mcl-PHA). Here we report the first draft genome sequence of this species. Copyright © 2014 Elsevier B.V. All rights reserved.

Draft Genome Sequence of Staphylococcus cohnii subsp. urealyticus Isolated from a Healthy Dog.

Science.gov (United States)

Bean, David C; Wigmore, Sarah M; Wareham, David W

2017-02-16

Staphylococcus cohnii subsp. urealyticus strain SW120 was isolated from the ear swab of a healthy dog. The isolate is resistant to methicillin and fusidic acid. The SW120 draft genome is 2,805,064 bp and contains 2,667 coding sequences, including 58 tRNAs and nine complete rRNA coding regions. Copyright © 2017 Bean et al.

Draft Genome Sequences of Two Novel Acidimicrobiaceae Members from an Acid Mine Drainage Biofilm Metagenome

OpenAIRE

Pinto, Ameet J.; Sharp, Jonathan O.; Yoder, Michael J.; Almstrand, Robert

2016-01-01

Bacteria belonging to the family Acidimicrobiaceae are frequently encountered in heavy metal-contaminated acidic environments. However, their phylogenetic and metabolic diversity is poorly resolved. We present draft genome sequences of two novel and phylogenetically distinct Acidimicrobiaceae members assembled from an acid mine drainage biofilm metagenome.

Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9

Science.gov (United States)

Liu, Jin-liang; Hu, Xiao-min

2013-01-01

Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a soil sample, and is pale pink-pigmented, aerobic, and Gram-positive. Here, we report the draft genome sequence and the initial findings from a preliminary analysis of strain A9, which is a novel species of Paenibacillus. PMID:23618713

Draft Genome Sequence of Leptolyngbya sp. KIOST-1, a Filamentous Cyanobacterium with Biotechnological Potential for Alimentary Purposes.

Science.gov (United States)

Kim, Ji Hyung; Kang, Do-Hyung

2016-09-15

Here, we report the draft genome of cyanobacterium Leptolyngbya sp. KIOST-1 isolated from a microalgal culture pond in South Korea. The genome consists of 13 contigs containing 6,320,172 bp, and a total of 5,327 coding sequences were predicted. This genomic information will allow further exploitation of its biotechnological potential for alimentary purposes. Copyright © 2016 Kim and Kang.

Draft Genome Sequence of Clostridium mangenotii TR, Isolated from the Fecal Material of a Timber Rattlesnake

Science.gov (United States)

Cochran, Philip A.; Dowd, Scot E.; Andersen, Kylie; Anderson, Nichole; Brennan, Rachel; Brook, Nicole; Callaway, Tracie; Diamante, Kimberly; Duberstine, Annie; Fitch, Karla; Freiheit, Heidi; Godlewski, Chantel; Gorman, Kelly; Haubrich, Mark; Hernandez, Mercedes; Hirtreiter, Amber; Ivanoski, Beth; Jaminet, Xochitl; Kirkpatrick, Travis; Kratowicz, Jennifer; Latus, Casey; Leable, Tiegen; Lingafelt, Nicole; Lowe, DeAnna; Lowrance, Holly; Malsack, Latiffa; Mazurkiewicz, Julie; Merlos, Persida; Messley, Jamie; Montemurro, Dawn; Nakitare, Samora; Nelson, Christine; Nye, Amber; Pazera, Valerie; Pierangeli, Gina; Rellora, Ashley; Reyes, Angelica; Roberts, Jennifer; Robins, Shadara; Robinson, Jeshannah; Schultz, Alissa; Seifert, Sara; Sigler, Elona; Spangler, Julie; Swift, Ebony; TenCate, Rebecca; Thurber, Jessica; Vallee, Kristin; Wamboldt, Jennifer; Whitten, Shannon; Woods, De’andrea; Wright, Amanda; Yankunas, Darin

2014-01-01

Here, we report the draft genome sequence of Clostridium mangenotii strain TR, which was isolated from the fecal material of a timber rattlesnake. This bacterium is nonpathogenic but contains 68 genes involved in virulence, disease, and defense. PMID:24407632

Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome

KAUST Repository

Haroon, Mohamed

2016-02-11

A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface water sample from the Red Sea, Saudi Arabia. The genome is more complete and has a higher G+C content than that of previously sequenced SAR324 representatives. Its genomic information shows a versatile metabolism that confers an advantage to SAR324, which is reflected in its distribution throughout different depths of the marine water column.

Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome

KAUST Repository

Haroon, Mohamed; Thompson, Luke R.; Stingl, Ulrich

2016-01-01

A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface water sample from the Red Sea, Saudi Arabia. The genome is more complete and has a higher G+C content than that of previously sequenced SAR324 representatives. Its genomic information shows a versatile metabolism that confers an advantage to SAR324, which is reflected in its distribution throughout different depths of the marine water column.

Draft Genome Sequence of Pontibacter sp. nov. BAB1700, a Halotolerant, Industrially Important Bacterium

Science.gov (United States)

Joshi, M. N.; Sharma, A. C.; Pandya, R. V.; Patel, R. P.; Saiyed, Z. M.; Saxena, A. K.

2012-01-01

Pontibacter sp. nov. BAB1700 is a halotolerant, Gram-negative, rod-shaped, pink-pigmented, menaquinone-7-producing bacterium isolated from sediments of a drilling well. The draft genome sequence of the strain, consisting of one chromosome of 4.5 Mb, revealed vital gene clusters involved in vitamin biosynthesis and resistance against various metals and antibiotics. PMID:23105068

Draft Genome Sequence of the Psychrophilic and Alkaliphilic Rhodonellum psychrophilum Strain GCM71T.

Science.gov (United States)

Hauptmann, Aviaja L; Glaring, Mikkel A; Hallin, Peter F; Priemé, Anders; Stougaard, Peter

2013-12-05

Rhodonellum psychrophilum GCM71(T), isolated from the cold and alkaline submarine ikaite columns in the Ikka Fjord in Greenland, displays optimal growth at 5 to 10°C and pH 10. Here, we report the draft genome sequence of this strain, which may provide insight into the mechanisms of adaptation to these extreme conditions.

Draft Genome Sequence of a Novel Desulfobacteraceae Member from a Sulfate-Reducing Bioreactor Metagenome

OpenAIRE

Almstrand, Robert; Pinto, Ameet J.; Figueroa, Linda A.; Sharp, Jonathan O.

2016-01-01

Sulfate-reducing bacteria are important players in the global sulfur cycle and of considerable commercial interest. The draft genome sequence of a sulfate-reducing bacterium of the family Desulfobacteraceae, assembled from a sulfate-reducing bioreactor metagenome, indicates that heavy-metal? and acid-resistance traits of this organism may be of importance for its application in acid mine drainage mitigation.

Draft Genome Sequence of an Isolate of Colletotrichum fructicola, a Causal Agent of Mango Anthracnose.

Science.gov (United States)

Li, Qili; Bu, Junyan; Yu, Zhihe; Tang, Lihua; Huang, Suiping; Guo, Tangxun; Mo, Jianyou; Hsiang, Tom

2018-02-22

Here, we present a draft genome sequence of isolate 15060 of Colletotrichum fructicola , a causal agent of mango anthracnose. The final assembly consists of 1,048 scaffolds totaling 56,493,063 bp (G+C content, 53.38%) and 15,180 predicted genes. Copyright © 2018 Li et al.

Draft genomic sequencing of six potential extraintestinal pathogenic Escherichia coli isolates from retail chicken meat.

Science.gov (United States)

Potential Extraintestinal pathogenic Escherichia coli isolates DP254, WH333, WH398, F356, FEX675 and FEX725 were isolated from retail chicken meat products. Here, we report the draft genome sequences for these six E. coli isolates, which are currently being used in food safety research....

Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria.

Science.gov (United States)

da Silva, Fábio Daniel Florêncio; Lima, Alex Ranieri Jerônimo; Moraes, Pablo Henrique Gonçalves; Siqueira, Andrei Santos; Dall'Agnol, Leonardo Teixeira; Baraúna, Anna Rafaella Ferreira; Martins, Luisa Carício; Oliveira, Karol Guimarães; de Lima, Clayton Pereira Silva; Nunes, Márcio Roberto Teixeira; Vianez-Júnior, João Lídio Silva Gonçalves; Gonçalves, Evonnildo Costa

2016-05-19

Ecological interactions between cyanobacteria and heterotrophic prokaryotes are poorly known. To improve the genomic studies of heterotrophic bacterium-cyanobacterium associations, the draft genome sequence (3.2 Mbp) of Limnobacter sp. strain CACIAM 66H1, found in a nonaxenic culture of Synechococcus sp. (cyanobacteria), is presented here. Copyright © 2016 da Silva et al.

Draft genome sequence of the arsenite-oxidizing strain Aliihoeflea sp. 2WW, isolated from arsenic-contaminated groundwater

NARCIS (Netherlands)

Cavalca, L.; Corsini, A.; Andreoni, V.; Muyzer, G.

2013-01-01

Here, we report the draft genome sequence of the arsenite-oxidizing bacterium Aliihoeflea sp. strain 2WW, which consists of a 4.15-Mb chromosome and contains different genes that are involved in arsenic transformations.

Draft Genome Sequence of a Sequence Type 398 Methicillin-Resistant Staphylococcus aureus Isolate from a Danish Dairy Cow with Mastitis

DEFF Research Database (Denmark)

Ronco, Troels; Stegger, Marc; Pedersen, Karl

2017-01-01

Livestock-associated (LA) methicillin-resistant Staphylococcus aureus (MRSA) strains of sequence type 398 (ST398) colonize both humans and various livestock species. In 2016, an ST398 LA-MRSA isolate (Sa52) was collected from a Danish dairy cow with mastitis, and here, we report the draft genome...

Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium

KAUST Repository

Lafi, Feras Fawzi

2017-03-03

Ochrobactrum intermedium strain SA148 is a plant growth-promoting bacterium isolated from sandy soil in the Jizan area of Saudi Arabia. Here, we report the 4.9-Mb draft genome sequence of this strain, highlighting different pathways characteristic of plant growth promotion activity and environmental adaptation of SA148.

Draft Genome Sequence of Staphylococcus carnosus subsp. utilis LTH 7013, Isolated from South Tyrolean Ham

OpenAIRE

M?ller, Anne; Huptas, Christopher; Wenning, Mareike; Schmidt, Herbert; Weiss, Agnes

2015-01-01

Staphylococcus carnosus is used as a starter culture in meat fermentation, where it contributes to color formation and produces aromatic compounds. Here, we report the first draft genome sequence of an S.?carnosus subsp. utilis strain, LTH 7013, isolated from South Tyrolean ham, with potential application as a starter culture.

Draft Genome Sequence of Cupriavidus pauculus Strain KF709, a Biphenyl-Utilizing Bacterium Isolated from Biphenyl-Contaminated Soil

OpenAIRE

Watanabe, Takahito; Yamazoe, Atsushi; Hosoyama, Akira; Fujihara, Hidehiko; Suenaga, Hikaru; Hirose, Jun; Futagami, Taiki; Goto, Masatoshi; Kimura, Nobutada; Furukawa, Kensuke

2015-01-01

We report the draft genome sequence of Cupriavidus pauculus strain KF709, which comprises 6,826,799 bp with 6,272 coding sequences. The strain KF709 utilizes biphenyl and degrades low-chlorinated biphenyls; however, it possesses fewer coding sequences involved in the degradation of aromatic compounds than other strains belonging to the Betaproteobacteria.

Draft genome sequence of Bradyrhizobium sp. strain BR 3267, an elite strain recommended for cowpea inoculation in Brazil

Directory of Open Access Journals (Sweden)

Jean Luiz Simões-Araújo

Full Text Available Abstract The strain BR 3267 is a nitrogen-fixing symbiotic bacteria isolated from soil of semi-arid area of Brazilian Northeast using cowpea as the trap plant. This strain is used as commercial inoculant for cowpea and presents high efficient in nitrogen fixation as consequence of its adaptation potential to semi-arid conditions. We report here the draft genome sequence of Bradyrhizobium sp. strain BR 3267, an elite bacterium used as inoculant for cowpea. Whole genome sequencing of BR 3267 using Illumina MiSeq sequencing technology has 55 scaffolds with a total genome size of 7,904,309 bp and C+G 63%. Annotation was added by the RAST prokaryotic genome annotation service and has shown 7314 coding sequences and 52 RNA genes.

Genome Sequence Databases (Overview): Sequencing and Assembly

Energy Technology Data Exchange (ETDEWEB)

Lapidus, Alla L.

2009-01-01

From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

Draft Genome Sequence of Bacillus coagulans GBI-30, 6086, a Widely Used Spore-Forming Probiotic Strain

OpenAIRE

Orrù, Luigi; Salvetti, Elisa; Cattivelli, Luigi; Lamontanara, Antonella; Michelotti, Vania; Capozzi, Vittorio; Spano, Giuseppe; Keller, David; Cash, Howard; Martina, Alessia; Torriani, Sandra; Felis, Giovanna E.

2014-01-01

Bacillus coagulans GBI-30, 6086 is a safe strain, already available on the market, and characterized by certified beneficial effects. The draft genome sequence presented here constitutes the first pillar toward the identification of the molecular mechanisms responsible for its positive features and safety.

Draft genome sequence of the first human isolate of the ruminant pathogen Mycoplasma capricolum subsp. capricolum

DEFF Research Database (Denmark)

Seersholm, Frederik Valeur; Fischer, Anne; Heller, Martin

2015-01-01

Mycoplasma capricolum subsp. capricolum is a well-known pathogen of small ruminants. A recent human case of septicemia involving this agent raised the question of its potential pathogenicity to humans. We present the first draft genome sequence of a human Mycoplasma capricolum subsp. capricolum...

Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome.

Science.gov (United States)

Verwaaijen, Bart; Wibberg, Daniel; Nelkner, Johanna; Gordin, Miriam; Rupp, Oliver; Winkler, Anika; Bremges, Andreas; Blom, Jochen; Grosch, Rita; Pühler, Alfred; Schlüter, Andreas

2018-02-10

Lettuce (Lactuca sativa, L.) is an important annual plant of the family Asteraceae (Compositae). The commercial lettuce cultivar Tizian has been used in various scientific studies investigating the interaction of the plant with phytopathogens or biological control agents. Here, we present the de novo draft genome sequencing and gene prediction for this specific cultivar derived from transcriptome sequence data. The assembled scaffolds amount to a size of 2.22 Gb. Based on RNAseq data, 31,112 transcript isoforms were identified. Functional predictions for these transcripts were determined within the GenDBE annotation platform. Comparison with the cv. Salinas reference genome revealed a high degree of sequence similarity on genome and transcriptome levels, with an average amino acid identity of 99%. Furthermore, it was observed that two large regions are either missing or are highly divergent within the cv. Tizian genome compared to cv. Salinas. One of these regions covers the major resistance complex 1 region of cv. Salinas. The cv. Tizian draft genome sequence provides a valuable resource for future functional and transcriptome analyses focused on this lettuce cultivar. Copyright © 2017 Elsevier B.V. All rights reserved.

Draft Genome Sequence of the Phytopathogenic Fungus Ganoderma boninense, the Causal Agent of Basal Stem Rot Disease on Oil Palm.

Science.gov (United States)

Utomo, Condro; Tanjung, Zulfikar Achmad; Aditama, Redi; Buana, Rika Fithri Nurani; Pratomo, Antonius Dony Madu; Tryono, Reno; Liwang, Tony

2018-04-26

Ganoderma boninense is the dominant fungal pathogen of basal stem rot (BSR) disease on Elaeis guineensis We sequenced the nuclear genome of mycelia using both Illumina and Pacific Biosciences platforms for assembly of scaffolds. The draft genome comprised 79.24 Mb, 495 scaffolds, and 26,226 predicted coding sequences. Copyright © 2018 Utomo et al.

Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome.

Science.gov (United States)

Durham, Bryndan P; Grote, Jana; Whittaker, Kerry A; Bender, Sara J; Luo, Haiwei; Grim, Sharon L; Brown, Julia M; Casey, John R; Dron, Antony; Florez-Leiva, Lennin; Krupke, Andreas; Luria, Catherine M; Mine, Aric H; Nigro, Olivia D; Pather, Santhiska; Talarmin, Agathe; Wear, Emma K; Weber, Thomas S; Wilson, Jesse M; Church, Matthew J; DeLong, Edward F; Karl, David M; Steward, Grieg F; Eppley, John M; Kyrpides, Nikos C; Schuster, Stephan; Rappé, Michael S

2014-06-15

Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.

Draft Genome Sequences of Six Mycobacterium immunogenum, Strains Obtained from a Chloraminated Drinking Water Distribution System Simulator

Science.gov (United States)

We report the draft genome sequences of six Mycobacterium immunogenum isolated from a chloraminated drinking water distribution system simulator subjected to changes in operational parameters. M. immunogenum, a rapidly growing mycobacteria previously reported as the cause of hyp...

Draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659

Science.gov (United States)

This work reports the draft genome of Agrobacterium rhizogenes strain NCPPB2659 (also known as strain K599). The assembled genome contains 5,277,347 bp, and is composed of 1 circular chromosome, the Ri virulence plasmid, and 17 scaffolds pertaining to the linear chromosome. The wild type strain cau...

Genome sequencing and annotation of Stenotrophomonas sp. SAM8

Directory of Open Access Journals (Sweden)

Samy Selim

2015-12-01

Full Text Available We report draft genome sequence of Stenotrophomonas sp. strain SAM8, isolated from environmental water. The draft genome size is 3,665,538 bp with a G + C content of 67.2% and contains 6 rRNA sequence (single copies of 5S, 16S & 23S rRNA. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LDAV00000000.

Draft Genome Sequence of Bacillus coagulans GBI-30, 6086, a Widely Used Spore-Forming Probiotic Strain

Science.gov (United States)

Orrù, Luigi; Salvetti, Elisa; Cattivelli, Luigi; Lamontanara, Antonella; Michelotti, Vania; Capozzi, Vittorio; Spano, Giuseppe; Keller, David; Cash, Howard; Martina, Alessia; Felis, Giovanna E.

2014-01-01

Bacillus coagulans GBI-30, 6086 is a safe strain, already available on the market, and characterized by certified beneficial effects. The draft genome sequence presented here constitutes the first pillar toward the identification of the molecular mechanisms responsible for its positive features and safety. PMID:25377698

Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium

Science.gov (United States)

Jin, Decai; Zhou, Lisha; Wu, Liang; An, Wei; Zhao, Lin

2014-01-01

Advenella kashmirensis strain W13003 is a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from PAH-contaminated marine sediments. Here, we report the 4.8-Mb draft genome sequence of this strain, which will provide insights into the diversity of A. kashmirensis and the mechanism of PAH degradation in the marine environment. PMID:24482505

Draft Genome Sequence of Bacillus velezensis GF610, a Producer of Potent Anti-Listeria Agents.

Science.gov (United States)

Gerst, Michelle M; Dudley, Edward G; Xiaoli, Lingzi; Yousef, Ahmed E

2017-10-12

Bacillus velezensis GF610 was isolated from soil in Illinois, USA, and found to produce amyloliquecidin GF610, a potent two-component antimicrobial peptide. We report here the GF610 strain draft genome sequence, which contains 4.29 Mb and an overall GC content of 45.91%. Copyright © 2017 Gerst et al.

Draft Genome Sequence of Sphingomonas sp. Strain Sph1(2015), Isolated from a Fouled Membrane Filter Used To Produce Drinking Water.

Science.gov (United States)

de Vries, Hendrik J; Marshall, Ian P G; Schreiber, Lars; Plugge, Caroline M

2017-06-15

We report here the high-quality draft genome sequence of Sphingomonas sp. strain Sph1(2015), isolated from a fouled reverse osmosis membrane used for the production of high-quality drinking water. The draft sequence provides insights into the modus operandi of this strain to form biofilms on membrane surfaces. This knowledge offers tools to develop novel antifouling strategies. Copyright © 2017 de Vries et al.

Draft genome sequences of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from human patients

OpenAIRE

Mendoza-Olazar?n, Soraya; Garcia-Mazcorro, Jos? F.; Morf?n-Otero, Rayo; Villarreal-Trevi?o, Licet; Camacho-Ortiz, Adri?n; Rodr?guez-Noriega, Eduardo; Bocanegra-Ibarias, Paola; Maldonado-Garza, H?ctor J.; Dowd, Scot E.; Garza-Gonz?lez, Elvira

2017-01-01

Herein, we report the draft-genome sequences and annotation of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from humans. One strain (SC-57) was isolated from blood from a male patient in May 2006 and the other (SC-532) from a catheter from a male patient in June 2006. Similar to other genomes of Staphylococcus species, most genes (42%) of both strains are involved in metabolism of amino acids and derivatives, carbohydrates and proteins. Eighty (4%) genes are involved...

Draft Genome Sequence of Cupriavidus pauculus Strain KF709, a Biphenyl-Utilizing Bacterium Isolated from Biphenyl-Contaminated Soil.

Science.gov (United States)

Watanabe, Takahito; Yamazoe, Atsushi; Hosoyama, Akira; Fujihara, Hidehiko; Suenaga, Hikaru; Hirose, Jun; Futagami, Taiki; Goto, Masatoshi; Kimura, Nobutada; Furukawa, Kensuke

2015-03-26

We report the draft genome sequence of Cupriavidus pauculus strain KF709, which comprises 6,826,799 bp with 6,272 coding sequences. The strain KF709 utilizes biphenyl and degrades low-chlorinated biphenyls; however, it possesses fewer coding sequences involved in the degradation of aromatic compounds than other strains belonging to the Betaproteobacteria. Copyright © 2015 Watanabe et al.

Draft Genome Sequence of Komagataeibacter rhaeticus Strain AF1, a High Producer of Cellulose, Isolated from Kombucha Tea.

Science.gov (United States)

Dos Santos, Renato Augusto Corrêa; Berretta, Andresa A; Barud, Hernane da Silva; Ribeiro, Sidney José Lima; González-García, Laura Natalia; Zucchi, Tiago Domingues; Goldman, Gustavo H; Riaño-Pachón, Diego M

2014-07-24

Here, we present the draft genome sequence of Komagatabaeicter rhaeticus strain AF1, which was isolated from Kombucha tea and is capable of producing high levels of cellulose. Copyright © 2014 dos Santos et al.

Draft Genome Sequence of Sphingopyxis sp. Strain MWB1, a Crude-Oil-Degrading Marine Bacterium

Science.gov (United States)

Kim, Jonghyun; Kim, Soo Jung; Kim, Seon Hee; Kim, Seung Il; Moon, Yoon-Jung; Park, Sung-Joon

2014-01-01

Sphingopyxis sp. strain MWB1, which is capable of degrading crude oil, diesel, and kerosene, was isolated from crude oil–contaminated seashore in Tae-an, South Korea. Here, we report the draft genome sequence of this strain, which comprises 3,118,428 bp with a G+C content of 62.85 mol%. PMID:25477411

Draft Genome Sequence of Staphylococcus carnosus subsp. utilis LTH 7013, Isolated from South Tyrolean Ham.

Science.gov (United States)

Müller, Anne; Huptas, Christopher; Wenning, Mareike; Schmidt, Herbert; Weiss, Agnes

2015-05-14

Staphylococcus carnosus is used as a starter culture in meat fermentation, where it contributes to color formation and produces aromatic compounds. Here, we report the first draft genome sequence of an S. carnosus subsp. utilis strain, LTH 7013, isolated from South Tyrolean ham, with potential application as a starter culture. Copyright © 2015 Müller et al.

Draft Genome Sequence of Vibrio parahaemolyticus VH3, Isolated from an Aquaculture Environment in Greece

DEFF Research Database (Denmark)

Castillo, Daniel; Jun, Jin Woo; D'Alvise, Paul

2015-01-01

Vibrio parahaemolyticus is an important foodborne pathogen responsible for gastroenteritis outbreaks globally. It has also been identified as an important pathogen in aquatic organisms. Here, we report a draft genome sequence of V. parahaemolyticus, strain VH3, isolated from farmed juvenile greater...

Draft genome sequences of the oomycete Pythium insidiosum strain CBS 573.85 from a horse with pythiosis and strain CR02 from the environment

Directory of Open Access Journals (Sweden)

Preecha Patumcharoenpol

2018-02-01

Full Text Available Pythium insidiosum is an aquatic oomycete microorganism that causes the fatal infectious disease, pythiosis, in humans and animals. The organism has been successfully isolated from the environment worldwide. Diagnosis and treatment of pythiosis is difficult and challenging. Genome sequences of P. insidiosum, isolated from humans, are available and accessible in public databases. To further facilitate biology-, pathogenicity-, and evolution-related genomic and genetic studies of P. insidiosum, we report two additional draft genome sequences of the P. insidiosum strain CBS 573.85 (35.6 Mb in size; accession number, BCFO00000000.1 isolated from a horse with pythiosis, and strain CR02 (37.7 Mb in size; accession number, BCFR00000000.1 isolated from the environment. Keywords: Pythium insidiosum, Pythiosis, Draft genome sequence

Draft genome sequence of a human-associated isolate of Haloferax alexandrinus strain Arc-hr, an extremely halophilic archaea.

Science.gov (United States)

Khelaifia, S; Caputo, A; Djossou, F; Raoult, D

2017-01-01

We report the draft genome sequence of Haloferax alexandrinus strain Arc-hr (CSUR P798), isolated from the human gut of a 10-year-old Amazonian individual. Its 3 893 626 bp genome exhibits a 66.00% GC content. The genome of the strain Arc-hr contains 37 genes identified as ORFans, seven genes associated to halocin and 11 genes associated with polyketide synthases or nonribosomal peptide synthetases.

Draft genome sequence of an endophytic bacterium, Paenibacillus tyrfis strain SUK123, isolated from Santiria apiculata stem

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Emmanuel Haruna

2017-12-01

Full Text Available Here we report the draft genome sequence of an endophytic Paenibacillus tyrfis strain isolated from the Universiti Kebangsaan Malaysia reserve forest, Malaysia. The genome size was approximately 8.04 Mb, and the assembly consisted of 107 scaffolds with 168 contigs, and had a G + C content of 53%. Phylogenetic analysis of strain SUK123 using the 16S rRNA gene revealed that it belonged to the family Paenibacillaceae with the highest similarity to Paenibacillus elgii SDT (99%. Whole genome comparison of SUK123 with related species using average nucleotide identity (ANI analysis revealed a similarity of 98% to Paenibacillus tyrfis Mst1T, 94% to Paenibacillus elgii B69T, 91% to Paenibacillus ehimensis A2T, 68% to Paenibacillus polymyxa SC2T and 69% to Paenibacillus alvei DMS29T. The draft genome was deposited at the European Nucleotide Archive (PRJEB21373.

Genome sequencing and annotation of Proteus sp. SAS71

Directory of Open Access Journals (Sweden)

Samy Selim

2015-12-01

Full Text Available We report draft genome sequence of Proteus sp. strain SAS71, isolated from water spring in Aljouf region, Saudi Arabia. The draft genome size is 3,037,704 bp with a G + C content of 39.3% and contains 6 rRNA sequence (single copies of 5S, 16S & 23S rRNA. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LDIU00000000.

Draft genome sequence and annotation of Lactobacillus acetotolerans BM-LA14527, a beer-spoilage bacteria.

Science.gov (United States)

Liu, Junyan; Li, Lin; Peters, Brian M; Li, Bing; Deng, Yang; Xu, Zhenbo; Shirtliff, Mark E

2016-09-01

Lactobacillus acetotolerans is a hard-to-culture beer-spoilage bacterium capable of entering into the viable putative nonculturable (VPNC) state. As part of an initial strategy to investigate the phenotypic behavior of L. acetotolerans, draft genome sequencing was performed. Results demonstrated a total of 1824 predicted annotated genes, with several potential VPNC- and beer-spoilage-associated genes identified. Importantly, this is the first genome sequence of L. acetotolerans as beer-spoilage bacteria and it may aid in further analysis of L. acetotolerans and other beer-spoilage bacteria, with direct implications for food safety control in the beer brewing industry. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Draft Genome Sequence of the Biocontrol Strain Serratia plymuthica A30, Isolated from Rotting Potato Tuber Tissue

NARCIS (Netherlands)

Czajkowski, R.L.; Wolf, van der J.M.

2012-01-01

Serratia plymuthica A30 is a Gram-negative bacterium expressing antagonistic activity toward blackleg- and soft rot-causing Dickeya sp. biovar 3 (“Dickeya solani”). Here, we present the draft genome sequence of strain A30, which has been isolated from rotten potato tuber tissue

Draft Genome Sequence of Leuconostoc mesenteroides 406 Isolated from the Traditional Fermented Mare Milk Airag in Tuv Aimag, Mongolia

OpenAIRE

Morita, Hidetoshi; Toh, Hidehiro; Oshima, Kenshiro; Nakano, Akiyo; Hano, Chihiro; Yoshida, Saki; Nguyen, Tien Thi Thuy; Wulijideligen,; Tashiro, Kosuke; Arakawa, Kensuke; Miyamoto, Taku

2016-01-01

Leuconostoc mesenteroides 406 was isolated from the traditional fermented mare milk airag in Tuv Aimag, Mongolia. This strain produces an antilisterial bacteriocin. Here, we report the draft genome sequence of this organism.

Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

KAUST Repository

Harjes, Janno; Ryu, Tae Woo; Abdelmohsen, Usama Ramadan; Moitinho-Silva, Lucas; Horn, Hannes; Ravasi, Timothy; Hentschel, Ute

2014-01-01

The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.

Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

KAUST Repository

Harjes, Janno

2014-03-06

The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.

Draft Whole-Genome Sequence of Bacillus altitudinis Strain B-388, a Producer of Extracellular RNase.

Science.gov (United States)

Shah Mahmud, Raihan; Ulyanova, Vera; Malanin, Sergey; Dudkina, Elena; Vershinina, Valentina; Ilinskaya, Olga

2015-01-29

Here, we present a draft genome sequence of Bacillus altitudinis strain B-388, including a putative plasmid. The strain was isolated from the intestine of Indian meal moth, a common pest of stored grains, and it is characterized by the production of extracellular RNase, similar to binase, which is of interest for comparative studies and biotechnology. Copyright © 2015 Shah Mahmud et al.

Draft Genome Sequence of an Invasive Multidrug-Resistant Strain, Pseudomonas aeruginosa BK1, Isolated from a Keratitis Patient

KAUST Repository

Jeganathan, Lakshmi Priya; Prakash, Logambiga; Neelamegam, Sivakumar; Antony, Aju; Alqarawi, Sami; Prajna, Lalitha; Devarajan, Bharanidharan; Mohankumar, Vidyarani

2014-01-01

Pseudomonas aeruginosa infections are difficult to treat due to the presence of a multitude of virulence factors and antibiotic resistance. Here, we report the draft genome sequence of P. aeruginosa BK1, an invasive and multidrug-resistant strain

Draft Genome Sequence of the Biocontrol Strain Serratia plymuthica A30, Isolated from Rotting Potato Tuber Tissue

NARCIS (Netherlands)

Czajkowski, R.L.; Van der Wolf, J.M.

2012-01-01

Serratia plymuthica A30 is a Gram-negative bacterium expressing antagonistic activity toward blackleg- and soft rot-causing Dickeya sp. biovar 3 ("Dickeya solani"). Here, we present the draft genome sequence of strain A30, which has been isolated from rotten potato tuber tissue. [KEYWORDS: biovar 3

Draft genome sequences of two protease-producing strains of Arsukibacterium, isolated from two cold and alkaline environments

DEFF Research Database (Denmark)

Lylloff, Jeanette Eva; Hansen, Lea Benedicte Skov; Jepsen, Morten

2015-01-01

Arsukibacterium ikkense GCM72(T) and a close relative, Arsukibacterium sp. MJ3, were isolated from two cold and alkaline environments as producers of extracellular proteolytic enzymes active at high pH and low temperature. This report describes the two draft genome sequences, which may serve...

Draft genome sequences of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from human patients.

Science.gov (United States)

Mendoza-Olazarán, Soraya; Garcia-Mazcorro, José F; Morfín-Otero, Rayo; Villarreal-Treviño, Licet; Camacho-Ortiz, Adrián; Rodríguez-Noriega, Eduardo; Bocanegra-Ibarias, Paola; Maldonado-Garza, Héctor J; Dowd, Scot E; Garza-González, Elvira

2017-01-01

Herein, we report the draft-genome sequences and annotation of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from humans. One strain (SC-57) was isolated from blood from a male patient in May 2006 and the other (SC-532) from a catheter from a male patient in June 2006. Similar to other genomes of Staphylococcus species, most genes (42%) of both strains are involved in metabolism of amino acids and derivatives, carbohydrates and proteins. Eighty (4%) genes are involved in virulence, disease, and defense and both species show phenotypic low biofilm production and evidence of increased antibiotic resistance associated to biofilm production. From both isolates, a new Staphylococcal Cassette Chromosome mec was detected: mec class A, ccr type 1. This is the first report of whole genome sequences of opportunistic S. cohnii isolated from human patients.

Draft Genome Sequences of the Fish Pathogen Vibrio harveyi Strains VH2 and VH5

DEFF Research Database (Denmark)

Castillo, Daniel; D'Alvise, Paul; Middelboe, Mathias

2015-01-01

Vibrio harveyi is an important marine pathogen that is responsible for vibriosis outbreaks in cultured fish and invertebrates worldwide. Here, we announce the draft genome sequences of V. harveyi strains VH2 and VH5, isolated from farmed juvenile Seriola dumerili during outbreaks of vibriosis...... in Crete, Greece....

Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208.

Science.gov (United States)

Nissimov, Jozef I; Worthy, Charlotte A; Rooks, Paul; Napier, Johnathan A; Kimmance, Susan A; Henn, Matthew R; Ogata, Hiroyuki; Allen, Michael J

2012-03-01

The Coccolithoviridae are a group of viruses which infect the marine coccolithophorid microalga Emiliania huxleyi. The Emiliania huxleyi viruses (known as EhVs) described herein have 160- to 180-nm diameter icosahedral structures, have genomes of approximately 400 kbp, and consist of more than 450 predicted coding sequences (CDSs). Here, we describe the genomic features of four newly sequenced coccolithoviruses (EhV-88, EhV-201, EhV-207, and EhV-208) together with their draft genome sequences and their annotations, highlighting the homology and heterogeneity of these genomes to the EhV-86 model reference genome.

Draft Genome Sequences of 116 Campylobacter jejuni Strains Isolated from Humans, Animals, Food, and the Environment in Brazil.

Science.gov (United States)

Frazão, Miliane Rodrigues; Cao, Guojie; Medeiros, Marta Inês Cazentini; Duque, Sheila da Silva; Leon, Maria Sanchez; Allard, Marc William; Falcão, Juliana Pfrimer

2018-04-19

Campylobacter jejuni is a major zoonotic pathogen that causes foodborne gastroenteritis worldwide. However, clinical cases of campylobacteriosis have been underreported and underdiagnosed in Brazil. Herein, we describe the draft genome sequences of 116 C. jejuni strains isolated from diverse sources in Brazil.

Permanent draft genome of Rhodopirellula sallentina SM41.

Science.gov (United States)

Wegner, Carl-Eric; Richter, Michael; Richter-Heitmann, Tim; Klindworth, Anna; Frank, Carsten S; Glöckner, Frank Oliver; Harder, Jens

2014-02-01

The genome of Rhodopirellula sallentina SM41 was sequenced as a permanent draft to supplement the full genome sequence of the type strain Rhodopirellula baltica SH1(T). This isolate is part of a larger study to gain insights into the biogeography of Rhodopirellula species in European marine waters, as well as to amend the genus description of R. baltica. This genomics resource article is the third of a series of five publications reporting in total eight new permanent daft genomes of Rhodopirellula species. Copyright © 2013 Elsevier B.V. All rights reserved.

Draft Genome Sequence of Exiguobacterium sp. Strain BMC-KP, an Environmental Isolate from Bryn Mawr, Pennsylvania.

Science.gov (United States)

Hyson, Peter; Shapiro, Joshua A; Wien, Michelle W

2015-10-08

Exiguobacterium sp. strain BMC-KP was isolated as part of a student environmental sampling project at Bryn Mawr College, PA. Sequencing of bacterial DNA assembled a 3.32-Mb draft genome. Analysis suggests the presence of genes for tolerance to cold and toxic metals, broad carbohydrate metabolism, and genes derived from phage. Copyright © 2015 Hyson et al.

Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.

Science.gov (United States)

Wang, Guojun; Barrett, Nolan H; McCarthy, Peter J

2017-02-02

The proteobacterium Alteromonas sp. strain V450 was isolated from the Atlantic deep-sea sponge Leiodermatium sp. Here, we report the draft genome sequence of this strain, with a genome size of approx. 4.39 Mb and a G+C content of 44.01%. The results will aid deep-sea microbial ecology, evolution, and sponge-microbe association studies. Copyright © 2017 Wang et al.

Draft Genome Sequence of a Novel Chitinophaga sp. Strain, MD30, Isolated from a Biofilm in an Air Conditioner Condensate Pipe.

Science.gov (United States)

Wan, Xuehua; Darris, Maxwell; Hou, Shaobin; Donachie, Stuart P

2017-10-19

Most of the 24 known Chitinophaga species were originally isolated from soils. We report the draft genome sequence of a putatively novel Chitinophaga sp. from a biofilm in an air conditioner condensate pipe. The genome comprises 7,661,303 bp in one scaffold, 5,694 predicted protein-coding sequences, and a G+C content of 47.6%. Copyright © 2017 Wan et al.

Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China)

OpenAIRE

Poltaraus, Andrey B.; Sokolova, Diyana S.; Grouzdev, Denis S.; Ivanov, Timophey M.; Malakho, Sophia G.; Korshunova, Alena V.; Rozanov, Aleksey S.; Tourova, Tatiyana P.; Nazina, Tamara N.

2016-01-01

The draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic aerobic oil-oxidizing bacterium isolated from production water from the Dagang high-temperature oil field, China, is presented here. The genome is annotated to provide insights into the genomic and phenotypic diversity of the genus Aeribacillus.

Draft Genome Sequence of Methyloferula stellata AR4, an Obligate Methanotroph Possessing Only a Soluble Methane Monooxygenase

OpenAIRE

Dedysh, Svetlana N.; Naumoff, Daniil G.; Vorobev, Alexey V.; Kyrpides, Nikos; Woyke, Tanja; Shapiro, Nicole; Crombie, Andrew T.; Murrell, J. Colin; Kalyuzhnaya, Marina G.; Smirnova, Angela V.; Dunfield, Peter F.

2015-01-01

Methyloferula stellata AR4 is an aerobic acidophilic methanotroph, which, in contrast to most known methanotrophs but similar to Methylocella spp., possesses only a soluble methane monooxygenase. However, it differs from Methylocella spp. by its inability to grow on multicarbon substrates. Here, we report the draft genome sequence of this bacterium.

Draft Genome Sequences of Two Propionibacterium acnes Strains Isolated from Progressive Macular Hypomelanosis Lesions of Human Skin

DEFF Research Database (Denmark)

Petersen, Rolf; Lomholt, Hans B.; Scholz, Christian F. P.

2015-01-01

Propionibacterium acnes is a Gram-positive bacterium that is prevalent on human skin. It has been associated with skin disorders such as acne vulgaris and progressive macular hypomelanosis (PMH). Here, we report draft genome sequences of two type III P. acnes strains, PMH5 and PMH7, isolated from...

Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea.

Science.gov (United States)

Dos Santos, Renato Augusto Corrêa; Berretta, Andresa Aparecida; Barud, Hernane da Silva; Ribeiro, Sidney José Lima; González-García, Laura Natalia; Zucchi, Tiago Domingues; Goldman, Gustavo H; Riaño-Pachón, Diego M

2015-12-03

Here, we present the draft genome sequence of Komagataeibacter intermedius strain AF2, which was isolated from Kombucha tea and is capable of producing cellulose, although at lower levels compared to another bacterium from the same environment, K. rhaeticus strain AF1. Copyright © 2015 dos Santos et al.

Extensive error in the number of genes inferred from draft genome assemblies.

Directory of Open Access Journals (Sweden)

James F Denton

2014-12-01

Full Text Available Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.

Draft Genome Sequence of Leuconostoc mesenteroides 406 Isolated from the Traditional Fermented Mare Milk Airag in Tuv Aimag, Mongolia.

Science.gov (United States)

Morita, Hidetoshi; Toh, Hidehiro; Oshima, Kenshiro; Nakano, Akiyo; Hano, Chihiro; Yoshida, Saki; Nguyen, Tien Thi Thuy; Wulijideligen; Tashiro, Kosuke; Arakawa, Kensuke; Miyamoto, Taku

2016-03-24

Leuconostoc mesenteroides406 was isolated from the traditional fermented mare milk airag in Tuv Aimag, Mongolia. This strain produces an antilisterial bacteriocin. Here, we report the draft genome sequence of this organism. Copyright © 2016 Morita et al.

Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces (Pseudogymnoascus) destructans

OpenAIRE

Chibucos, Marcus C.; Crabtree, Jonathan; Nagaraj, Sushma; Chaturvedi, Sudha; Chaturvedi, Vishnu

2013-01-01

We report the draft genome sequences of Geomyces pannorum sensu lato and Geomyces (Pseudogymnoascus) destructans. G.?pannorum has a larger proteome than G.?destructans, containing more proteins with ascribed enzymatic functions. This dichotomy in the genomes of related psychrophilic fungi is a valuable target for defining their distinct saprobic and pathogenic attributes.

Draft Genome Sequence of Staphylococcus chromogenes Strain MU 970, Isolated from a Case of Chronic Bovine Mastitis

OpenAIRE

Fry, Pamela R.; Calcutt, Michael J.; Foecking, Mark F.; Hsieh, Hsin-Yeh; Suntrup, Douglas G.; Perry, Jeanette; Stewart, George C.; Middleton, John R.

2014-01-01

Coagulase-negative staphylococcal species are a common cause of subclinical bovine mastitis, with Staphylococcus chromogenes being one of the most frequently identified species in these cases. The draft genome sequence of an S. chromogenes isolate (MU 970) recovered from the milk of a cow with a chronic intramammary infection is reported here.

Draft Genome Sequences of Klebsiella oxytoca Isolates Originating from a Highly Contaminated Liquid Hand Soap Product

OpenAIRE

Hammerl, J. A.; Lasch, P.; Nitsche, A.; Dabrowski, P. W.; Hahmann, H.; Wicke, A.; Kleta, S.; Dahouk, S. Al; Dieckmann, R.

2015-01-01

In 2013, contaminated liquid soap was detected by routine microbiological monitoring of consumer products through state health authorities. Because of its high load of Klebsiella oxytoca, the liquid soap was notified via the European Union Rapid Alert System for Dangerous Non-Food Products (EU-RAPEX) and recalled. Here, we present two draft genome sequences and a summary of their general features.

Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces (Pseudogymnoascus) destructans.

Science.gov (United States)

Chibucos, Marcus C; Crabtree, Jonathan; Nagaraj, Sushma; Chaturvedi, Sudha; Chaturvedi, Vishnu

2013-12-19

We report the draft genome sequences of Geomyces pannorum sensu lato and Geomyces (Pseudogymnoascus) destructans. G. pannorum has a larger proteome than G. destructans, containing more proteins with ascribed enzymatic functions. This dichotomy in the genomes of related psychrophilic fungi is a valuable target for defining their distinct saprobic and pathogenic attributes.

Draft genomes and reference transcriptomes extend the coding potential of the fish pathogen Piscirickettsia salmonis

Directory of Open Access Journals (Sweden)

Angela D. Millar

2018-05-01

Full Text Available Background: Draft and complete genome sequences from bacteria are key tools to understand genetic determinants involved in pathogenesis in several disease models. Piscirickettsia salmonis is a Gram-negative bacterium responsible for the Salmon Rickettsial Syndrome (SRS, a bacterial disease that threatens the sustainability of the Chilean salmon industry. In previous reports, complete and draft genome sequences have been generated and annotated. However, the lack of transcriptome data underestimates the genetic potential, does not provide information about transcriptional units and contributes to disseminate annotation errors. Results: Here we present the draft genome and transcriptome sequences of four P. salmonis strains. We have identified the transcriptional architecture of previously characterized virulence factors and trait-specific genes associated to cation uptake, metal efflux, antibiotic resistance, secretion systems and other virulence factors. Conclusions: This data has provided a refined genome annotation and also new insights on the transcriptional structures and coding potential of this fish pathogen.How to cite: Millar AD, Tapia P, Gomez FA, et al. Draft genomes and reference transcriptomes extend the coding potential of the fish pathogen Piscirickettsia salmonis. Electron J Biotechnol 2018;33. https://doi.org/10.1016/j.ejbt.2018.04.002. Keywords: Bacterial genomes, Coding potential, Comparative analysis, Draft genome, Piscirickettsia salmonis, Reference transcriptome, Refined annotation, Salmon Rickettsial Syndrome, Salmonids

Draft Genome Sequence of Staphylococcus chromogenes Strain MU 970, Isolated from a Case of Chronic Bovine Mastitis

Science.gov (United States)

Fry, Pamela R.; Calcutt, Michael J.; Foecking, Mark F.; Hsieh, Hsin-Yeh; Suntrup, Douglas G.; Perry, Jeanette; Stewart, George C.

2014-01-01

Coagulase-negative staphylococcal species are a common cause of subclinical bovine mastitis, with Staphylococcus chromogenes being one of the most frequently identified species in these cases. The draft genome sequence of an S. chromogenes isolate (MU 970) recovered from the milk of a cow with a chronic intramammary infection is reported here. PMID:25125652

Draft Genome Sequence of Leuconostoc mesenteroides 213M0, Isolated from Traditional Fermented Mare Milk Airag in Bulgan Aimag, Mongolia

OpenAIRE

Morita, Hidetoshi; Toh, Hidehiro; Oshima, Kenshiro; Nakano, Akiyo; Hano, Chihiro; Yoshida, Saki; Bolormaa, Tsognemekh; Burenjargal, Sedkhuu; Nguyen, Co Thi Kim; Tashiro, Kosuke; Arakawa, Kensuke; Miyamoto, Taku

2016-01-01

Leuconostoc mesenteroides 213M0 was isolated from traditional fermented mare milk airag in Bulgan Aimag, Mongolia. This strain produces a listericidal bacteriocin-like inhibitory substance. Here, we report the draft genome sequence of this organism.

Draft Genome Sequence of an Invasive Multidrug-Resistant Strain, Pseudomonas aeruginosa BK1, Isolated from a Keratitis Patient

KAUST Repository

Jeganathan, Lakshmi Priya

2014-03-27

Pseudomonas aeruginosa infections are difficult to treat due to the presence of a multitude of virulence factors and antibiotic resistance. Here, we report the draft genome sequence of P. aeruginosa BK1, an invasive and multidrug-resistant strain, isolated from a bacterial keratitis patient in southern India.

Draft genome sequences of four uropathogenic escherichia coli 04:H5 isolates (ATCC 700414,700415,700416 and 700417)

Science.gov (United States)

Uropathogenic Escherichia coli O4: H5 isolates ATCC 700414, 700415, 700416, and 700417 were recovered from women with first-time urinary tract infections. Here, we report the draft genome sequences for these four E. coli isolates, which are currently being used to validate food safety processing tec...

Draft genome sequences of three Escherichia coli strains with different In Vivo pathogenicities in an avian (Ascending) infection model of the oviduct

DEFF Research Database (Denmark)

Olsen, Rikke Heidemann; Thøfner, Ida; Pors, Susanne Elisabeth

2015-01-01

Here, we present three draft genome sequences of Escherichia coli strains that experimentally were proven to possess low (strain D2-2), intermediate (Chronic_salp), or high virulence (Cp6salp3) in an avian (ascending) infection model of the oviduct.......Here, we present three draft genome sequences of Escherichia coli strains that experimentally were proven to possess low (strain D2-2), intermediate (Chronic_salp), or high virulence (Cp6salp3) in an avian (ascending) infection model of the oviduct....

Draft Genome Sequence of Leptospira interrogans Serovar Bataviae Strain LepIMR 22 Isolated from a Rodent in Johor, Malaysia

NARCIS (Netherlands)

Amran, Fairuz; Mohd Khalid, Mohd Khairul Nizam; Mohamad, Saharuddin; Mat Ripen, Adiratna; Ahmad, Norazah; Goris, Marga G. A.; Muhammad, Ayu Haslin; Noor Halim, Nurul Atiqah

2016-01-01

Leptospira interrogans serovar Bataviae was recently identified as one of the persistent Leptospira serovars in Malaysia. Here, we report the draft genome sequence of the L. interrogans serovar Bataviae strain LepIMR 22 isolated from kidney of a rodent in Johor, Malaysia

Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China).

Science.gov (United States)

Poltaraus, Andrey B; Sokolova, Diyana S; Grouzdev, Denis S; Ivanov, Timophey M; Malakho, Sophia G; Korshunova, Alena V; Rozanov, Aleksey S; Tourova, Tatiyana P; Nazina, Tamara N

2016-06-09

The draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic aerobic oil-oxidizing bacterium isolated from production water from the Dagang high-temperature oil field, China, is presented here. The genome is annotated to provide insights into the genomic and phenotypic diversity of the genus Aeribacillus. Copyright © 2016 Poltaraus et al.

Draft Genome Sequences of Staphylococcus aureus AMRF1 (ST22) and AMRF2 (ST672), Ocular Methicillin-Resistant Isolates

KAUST Repository

Velusamy, Nithya

2014-03-20

Sequence type 22 (ST22) and ST672 are the two major emerging clones of community-acquired methicillin-resistant Staphylococcus aureus in India. ST672 strains were found to cause severe ocular infections. We report the draft genome sequences of two emerging strains of methicillin-resistant S. aureus, AMRF1 (ST22) and AMRF2 (ST672), isolated from patients with ocular infections.

Draft Genome Sequences of Staphylococcus aureus AMRF1 (ST22) and AMRF2 (ST672), Ocular Methicillin-Resistant Isolates

KAUST Repository

Velusamy, Nithya; Prakash, Logambiga; Neelamegam, Sivakumar; Antony, Aju; Prajna, Lalitha; Mohankumar, Vidyarani; Devarajan, Bharanidharan

2014-01-01

Sequence type 22 (ST22) and ST672 are the two major emerging clones of community-acquired methicillin-resistant Staphylococcus aureus in India. ST672 strains were found to cause severe ocular infections. We report the draft genome sequences of two emerging strains of methicillin-resistant S. aureus, AMRF1 (ST22) and AMRF2 (ST672), isolated from patients with ocular infections.

First draft genome sequencing of indole acetic acid producing and plant growth promoting fungus Preussia sp. BSL10.

Science.gov (United States)

Khan, Abdul Latif; Asaf, Sajjad; Khan, Abdur Rahim; Al-Harrasi, Ahmed; Al-Rawahi, Ahmed; Lee, In-Jung

2016-05-10

Preussia sp. BSL10, family Sporormiaceae, was actively producing phytohormone (indole-3-acetic acid) and extra-cellular enzymes (phosphatases and glucosidases). The fungus was also promoting the growth of arid-land tree-Boswellia sacra. Looking at such prospects of this fungus, we sequenced its draft genome for the first time. The Illumina based sequence analysis reveals an approximate genome size of 31.4Mbp for Preussia sp. BSL10. Based on ab initio gene prediction, total 32,312 coding sequences were annotated consisting of 11,967 coding genes, pseudogenes, and 221 tRNA genes. Furthermore, 321 carbohydrate-active enzymes were predicted and classified into many functional families. Copyright © 2016 Elsevier B.V. All rights reserved.

Draft Genome Sequence of Methyloferula stellata AR4, an Obligate Methanotroph Possessing Only a Soluble Methane Monooxygenase.

Science.gov (United States)

Dedysh, Svetlana N; Naumoff, Daniil G; Vorobev, Alexey V; Kyrpides, Nikos; Woyke, Tanja; Shapiro, Nicole; Crombie, Andrew T; Murrell, J Colin; Kalyuzhnaya, Marina G; Smirnova, Angela V; Dunfield, Peter F

2015-03-05

Methyloferula stellata AR4 is an aerobic acidophilic methanotroph, which, in contrast to most known methanotrophs but similar to Methylocella spp., possesses only a soluble methane monooxygenase. However, it differs from Methylocella spp. by its inability to grow on multicarbon substrates. Here, we report the draft genome sequence of this bacterium. Copyright © 2015 Dedysh et al.

Draft Genome Sequence of Staphylococcus chromogenes Strain MU 970, Isolated from a Case of Chronic Bovine Mastitis.

Science.gov (United States)

Fry, Pamela R; Calcutt, Michael J; Foecking, Mark F; Hsieh, Hsin-Yeh; Suntrup, Douglas G; Perry, Jeanette; Stewart, George C; Middleton, John R

2014-08-14

Coagulase-negative staphylococcal species are a common cause of subclinical bovine mastitis, with Staphylococcus chromogenes being one of the most frequently identified species in these cases. The draft genome sequence of an S. chromogenes isolate (MU 970) recovered from the milk of a cow with a chronic intramammary infection is reported here. Copyright © 2014 Fry et al.

Draft Genome of the Marine Gammaproteobacterium Halomonas titanicae

Science.gov (United States)

Sánchez-Porro, Cristina; de la Haba, Rafael R.; Cruz-Hernández, Norge; González, Juan M.; Reyes-Guirao, Cristina; Navarro-Sampedro, Laura; Carballo, Modesto

2013-01-01

Halomonas titanicae strain BH1 is a heterotrophic, aerobic marine bacterium which was isolated from rusticles of the RMS Titanic wreck. Here we report the draft genome sequence of this halophilic gammaproteobacterium. PMID:23516210

Draft Genome Sequences of Klebsiella oxytoca Isolates Originating from a Highly Contaminated Liquid Hand Soap Product.

Science.gov (United States)

Hammerl, J A; Lasch, P; Nitsche, A; Dabrowski, P W; Hahmann, H; Wicke, A; Kleta, S; Al Dahouk, S; Dieckmann, R

2015-07-23

In 2013, contaminated liquid soap was detected by routine microbiological monitoring of consumer products through state health authorities. Because of its high load of Klebsiella oxytoca, the liquid soap was notified via the European Union Rapid Alert System for Dangerous Non-Food Products (EU-RAPEX) and recalled. Here, we present two draft genome sequences and a summary of their general features. Copyright © 2015 Hammerl et al.

Draft Genome Sequences of the Probiotic Enterococcus faecalis Symbioflor 1 Clones DSM16430 and DSM16434

OpenAIRE

Fritzenwanker, Moritz; Chakraborty, Anindita; Hain, Torsten; Zimmermann, Kurt; Domann, Eugen

2016-01-01

The probiotic Symbioflor 1 is a historical concoction of 10 isolates of Enterococcus faecalis. Pulsed-field gel electrophoresis revealed two groups: one comprising eight identical clones (DSM16430, DSM16432, DSM16433, DSM16435 to DSM16439) and a further two isolates (DSM16431, DSM16434) with marginally different profiles. Here, we report a comparative analysis of the draft genome sequences of representative isolates.

Draft genome sequence of Bradyrhizobium sp. strain BR 3262, an effective microsymbiont recommended for cowpea inoculation in Brazil.

Science.gov (United States)

Simões-Araújo, Jean Luiz; Leite, Jakson; Marie Rouws, Luc Felicianus; Passos, Samuel Ribeiro; Xavier, Gustavo Ribeiro; Rumjanek, Norma Gouvêa; Zilli, Jerri Édson

The strain BR 3262 was isolated from nodule of cowpea (Vigna unguiculata L. Walp) growing in soil of the Atlantic Forest area in Brazil and it is reported as an efficient nitrogen fixing bacterium associated to cowpea. Firstly, this strain was assigned as Bradyrhizobium elkanii, however, recently a more detailed genetic and molecular characterization has indicated it could be a Bradyrhizobium pachyrhizi species. We report here the draft genome sequence of B. pachyrhizi strain BR 3262, an elite bacterium used as inoculant for cowpea. The whole genome with 116 scaffolds, 8,965,178bp and 63.8% of C+G content for BR 3262 was obtained using Illumina MiSeq sequencing technology. Annotation was added by the RAST prokaryotic genome annotation service and shown 8369 coding sequences, 52 RNAs genes, classified in 504 subsystems. Published by Elsevier Editora Ltda.

Draft genome sequence of Bradyrhizobium sp. strain BR 3262, an effective microsymbiont recommended for cowpea inoculation in Brazil

Directory of Open Access Journals (Sweden)

Jean Luiz Simões-Araújo

Full Text Available Abstract The strain BR 3262 was isolated from nodule of cowpea (Vigna unguiculata L. Walp growing in soil of the Atlantic Forest area in Brazil and it is reported as an efficient nitrogen fixing bacterium associated to cowpea. Firstly, this strain was assigned as Bradyrhizobium elkanii, however, recently a more detailed genetic and molecular characterization has indicated it could be a Bradyrhizobium pachyrhizi species. We report here the draft genome sequence of B. pachyrhizi strain BR 3262, an elite bacterium used as inoculant for cowpea. The whole genome with 116 scaffolds, 8,965,178 bp and 63.8% of C+G content for BR 3262 was obtained using Illumina MiSeq sequencing technology. Annotation was added by the RAST prokaryotic genome annotation service and shown 8369 coding sequences, 52 RNAs genes, classified in 504 subsystems.

Draft Genome Sequence of Bacillus velezensis OSY-S3, a Producer of Potent Antimicrobial Agents Active against Bacteria and Fungi

OpenAIRE

Gerst, Michelle M.; Yesil, Mustafa; Yousef, Ahmed E.

2018-01-01

ABSTRACT Bacillus velezensis OSY-S3 produces anti-Listeria, anti-Escherichia coli, and antifungal compounds. Additionally, fermentate of B. velezensis OSY-S3 culture removes Staphylococcus aureus biofilms effectively. The draft genome sequence of B. velezensis OSY-S3 reported here had a genome size of ~3.90 Mb and a G+C content of 46.5%.

Draft Genome Sequence of Bacillus aryabhattai Strain PHB10, a Poly(3-Hydroxybutyrate)-Accumulating Bacterium Isolated from Domestic Sewerage.

Science.gov (United States)

Balakrishna Pillai, Aneesh; Jaya Kumar, Arjun; Thulasi, Kavitha; Reghunathan, Dinesh; Prasannakumar, Manoj; Kumarapillai, Harikrishnan

2017-10-12

Bacillus aryabhattai PHB10 is a poly(3-hydroxybutyrate) (PHB)-accumulating bacterium isolated from domestic sewerage. Here, we report the 4.19-Mb draft genome sequence, with 4,050 protein-coding genes and a G+C content of 37.5%. This sequence will be helpful in the study of the high-level PHB accumulation mechanism of the strain. Copyright © 2017 Balakrishna Pillai et al.

Draft Genome Sequences of Two Isolates of Colletotrichum lindemuthianum, the Causal Agent of Anthracnose in Common Beans.

Science.gov (United States)

de Queiroz, Casley Borges; Correia, Hilberty L Nunes; Menicucci, Renato Pedrozo; Vidigal, Pedro M Pereira; de Queiroz, Marisa Vieira

2017-05-04

Colletotrichum lindemuthianum is the causal agent of anthracnose in common beans, one of the main limiting factors of their culture. Here, we report for the first time, to our knowledge, a draft of the complete genome sequences of two isolates belonging to 83.501 and 89 A 2 2-3 of C. lindemutuianum . Copyright © 2017 de Queiroz et al.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Science.gov (United States)

Ming, Ray; Hou, Shaobin; Feng, Yun; Yu, Qingyi; Dionne-Laporte, Alexandre; Saw, Jimmy H; Senin, Pavel; Wang, Wei; Ly, Benjamin V; Lewis, Kanako L T; Salzberg, Steven L; Feng, Lu; Jones, Meghan R; Skelton, Rachel L; Murray, Jan E; Chen, Cuixia; Qian, Wubin; Shen, Junguo; Du, Peng; Eustice, Moriah; Tong, Eric; Tang, Haibao; Lyons, Eric; Paull, Robert E; Michael, Todd P; Wall, Kerr; Rice, Danny W; Albert, Henrik; Wang, Ming-Li; Zhu, Yun J; Schatz, Michael; Nagarajan, Niranjan; Acob, Ricelle A; Guan, Peizhu; Blas, Andrea; Wai, Ching Man; Ackerman, Christine M; Ren, Yan; Liu, Chao; Wang, Jianmei; Wang, Jianping; Na, Jong-Kuk; Shakirov, Eugene V; Haas, Brian; Thimmapuram, Jyothi; Nelson, David; Wang, Xiyin; Bowers, John E; Gschwend, Andrea R; Delcher, Arthur L; Singh, Ratnesh; Suzuki, Jon Y; Tripathi, Savarni; Neupane, Kabi; Wei, Hairong; Irikura, Beth; Paidi, Maya; Jiang, Ning; Zhang, Wenli; Presting, Gernot; Windsor, Aaron; Navajas-Pérez, Rafael; Torres, Manuel J; Feltus, F Alex; Porter, Brad; Li, Yingjun; Burroughs, A Max; Luo, Ming-Cheng; Liu, Lei; Christopher, David A; Mount, Stephen M; Moore, Paul H; Sugimura, Tak; Jiang, Jiming; Schuler, Mary A; Friedman, Vikki; Mitchell-Olds, Thomas; Shippen, Dorothy E; dePamphilis, Claude W; Palmer, Jeffrey D; Freeling, Michael; Paterson, Andrew H; Gonsalves, Dennis; Wang, Lei; Alam, Maqsudul

2008-04-24

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.

Draft Genome Sequence of Pseudomonas sp. EpS/L25, Isolated from the Medicinal Plant Echinacea purpurea and Able To Synthesize Antimicrobial Compounds.

Science.gov (United States)

Presta, Luana; Bosi, Emanuele; Fondi, Marco; Maida, Isabel; Perrin, Elena; Miceli, Elisangela; Maggini, Valentina; Bogani, Patrizia; Firenzuoli, Fabio; Di Pilato, Vincenzo; Rossolini, Gian Maria; Mengoni, Alessio; Fani, Renato

2016-05-05

We announce here the draft genome sequence of Pseudomonas sp. strain EpS/L25, isolated from the stem/leaves of the medicinal plant Echinacea purpurea This genome will allow for comparative genomics in order to identify genes associated with the production of bioactive compounds and antibiotic resistance. Copyright © 2016 Presta et al.

Draft genome sequence of two Shingopyxis sp. strains H107 and H115 isolated from a chloraminated drinking water distriburion system simulator

Data.gov (United States)

U.S. Environmental Protection Agency — Draft genome sequence of two Shingopyxis sp. strains H107 and H115 isolated from a chloraminated drinking water distriburion system simulator. This dataset is...

Draft Genome Sequence of Caenibacillus caldisaponilyticus B157T, a Thermophilic and Phospholipase-Producing Bacterium Isolated from Acidulocompost

Science.gov (United States)

Tsujimoto, Yoshiyuki; Saito, Ryo; Sahara, Takehiko; Kimura, Nobutada; Tsuruoka, Naoki; Shigeri, Yasushi

2017-01-01

ABSTRACT Caenibacillus caldisaponilyticus B157T (= NBRC 111400T = DSM 101100T), in the family Sporolactobacillaceae, was isolated from acidulocompost as a thermophilic and phospholipid-degrading bacterium. Here, we report the 3.36-Mb draft genome sequence, with a G+C content of 51.8%, to provide the genetic information coding for phospholipases. PMID:28360164

Snake Genome Sequencing: Results and Future Prospects.

Science.gov (United States)

Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

2016-12-01

Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

Snake Genome Sequencing: Results and Future Prospects

Directory of Open Access Journals (Sweden)

Harald M. I. Kerkkamp

2016-12-01

Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

Draft Genome Sequences of TwoThiomicrospiraStrains Isolated from the Brine-Seawater Interface of Kebrit Deep in the Red Sea

KAUST Repository

Zhang, Guishan

2016-03-11

Two Thiomicrospira strains, WB1 and XS5, were isolated from the Kebrit Deep brine-seawater interface in the Red Sea, Saudi Arabia. Here, we present the draft genome sequences of these gammaproteobacteria, which both produce sulfuric acid from thiosulfate in culture.

Draft Genome Sequences of TwoThiomicrospiraStrains Isolated from the Brine-Seawater Interface of Kebrit Deep in the Red Sea

KAUST Repository

Zhang, Guishan; Haroon, Mohamed; Zhang, Ruifu; Hikmawan, Tyas I.; Stingl, Ulrich

2016-01-01

Two Thiomicrospira strains, WB1 and XS5, were isolated from the Kebrit Deep brine-seawater interface in the Red Sea, Saudi Arabia. Here, we present the draft genome sequences of these gammaproteobacteria, which both produce sulfuric acid from thiosulfate in culture.

Draft Genome Sequence of Leuconostoc mesenteroides 213M0, Isolated from Traditional Fermented Mare Milk Airag in Bulgan Aimag, Mongolia.

Science.gov (United States)

Morita, Hidetoshi; Toh, Hidehiro; Oshima, Kenshiro; Nakano, Akiyo; Hano, Chihiro; Yoshida, Saki; Bolormaa, Tsognemekh; Burenjargal, Sedkhuu; Nguyen, Co Thi Kim; Tashiro, Kosuke; Arakawa, Kensuke; Miyamoto, Taku

2016-03-31

Leuconostoc mesenteroides213M0 was isolated from traditional fermented mare milk airag in Bulgan Aimag, Mongolia. This strain produces a listericidal bacteriocin-like inhibitory substance. Here, we report the draft genome sequence of this organism. Copyright © 2016 Morita et al.

Draft Genome Sequence of Leptospira interrogans Serovar Bataviae Strain LepIMR 22 Isolated from a Rodent in Johor, Malaysia.

Science.gov (United States)

Amran, Fairuz; Mohd Khalid, Mohd Khairul Nizam; Mohamad, Saharuddin; Mat Ripen, Adiratna; Ahmad, Norazah; Goris, Marga G A; Muhammad, Ayu Haslin; Noor Halim, Nurul Atiqah

2016-09-08

Leptospira interrogans serovar Bataviae was recently identified as one of the persistent Leptospira serovars in Malaysia. Here, we report the draft genome sequence of the L. interrogans serovar Bataviae strain LepIMR 22 isolated from kidney of a rodent in Johor, Malaysia. Copyright © 2016 Amran et al.

Draft Genome Sequence of a “Candidatus Liberibacter europaeus” Strain Assembled from Broom Psyllids (Arytainilla spartiophila) from New Zealand

Science.gov (United States)

Thompson, Sarah M.; Kalamorz, Falk; David, Charles; Addison, Shea M.; Smith, Grant R.

2018-01-01

ABSTRACT Here, we report the draft genome sequence of “Candidatus Liberibacter europaeus” ASNZ1, assembled from broom psyllids (Arytainilla spartiophila) from New Zealand. The assembly comprises 15 contigs, with a total length of 1.33 Mb and a G+C content of 33.5%. PMID:29773636

Draft Genome Sequence of Bacillus velezensis OSY-S3, a Producer of Potent Antimicrobial Agents Active against Bacteria and Fungi.

Science.gov (United States)

Gerst, Michelle M; Yesil, Mustafa; Yousef, Ahmed E

2018-01-18

Bacillus velezensis OSY-S3 produces anti- Listeria , anti- Escherichia coli , and antifungal compounds. Additionally, fermentate of B. velezensis OSY-S3 culture removes Staphylococcus aureus biofilms effectively. The draft genome sequence of B. velezensis OSY-S3 reported here had a genome size of ~3.90 Mb and a G+C content of 46.5%. Copyright © 2018 Gerst et al.

Genome sequence of carboxylesterase, carboxylase and xylose isomerase producing alkaliphilic haloarchaeon Haloterrigena turkmenica WANU15

Directory of Open Access Journals (Sweden)

Samy Selim

2016-03-01

Full Text Available We report draft genome sequence of Haloterrigena turkmenica strain WANU15, isolated from Soda Lake. The draft genome size is 2,950,899 bp with a G + C content of 64% and contains 49 RNA sequence. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LKCV00000000. Keywords: Soda Lake, Haloterrigena turkmenica, Carboxylesterase, Carboxylase, Xylose isomerase, Whole genome sequencing

Draft genome sequence of Serratia sp. strain M24T3, isolated from pinewood disease nematode Bursaphelenchus xylophilus.

Science.gov (United States)

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor; Morais, Paula V

2012-07-01

Here we report the draft genome sequence of Serratia sp. strain M24T3, which is associated with pinewood nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease. Serratia sp. strain M24T3 has been identified as a bionematocide for B. xylophilus in vitro, and multiple genes potentially involved in virulence and nematotoxity were identified.

Draft Genome Sequence of Serratia sp. Strain M24T3, Isolated from Pinewood Disease Nematode Bursaphelenchus xylophilus

OpenAIRE

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor; Morais, Paula V.

2012-01-01

Here we report the draft genome sequence of Serratia sp. strain M24T3, which is associated with pinewood nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease. Serratia sp. strain M24T3 has been identified as a bionematocide for B. xylophilus in vitro, and multiple genes potentially involved in virulence and nematotoxity were identified.

Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station

NARCIS (Netherlands)

Venkateswaran, Kasthuri; Checinska Sielaff, Aleksandra; Ratnayake, Shashikala; Pope, Robert K; Blank, Thomas E; Stepanov, Victor G; Fox, George E; van Tongeren, Sandra P; Torres, Clinton; Allen, Jonathan; Jaing, Crystal; Pierson, Duane; Perry, Jay; Koren, Sergey; Phillippy, Adam; Klubnik, Joy; Treangen, Todd J; Rosovitz, M J; Bergman, Nicholas H

2017-01-01

The draft genome sequences of six Bacillus strains, isolated from the International Space Station and belonging to the Bacillus anthracis-B. cereus-B. thuringiensis group, are presented here. These strains were isolated from the Japanese Experiment Module (one strain), U.S. Harmony Node 2 (three

Draft Genome Sequence of Halomonas elongata Strain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity Tolerance In Planta

KAUST Repository

Lafi, Feras Fawzi; Ramirez Prado, Juan Sebastian; Alam, Intikhab; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2016-01-01

Halomonas elongata strain K4 is an endophytic bacterial strain that was isolated from roots of Cyperus conglomeratus collected at the Red Sea coast in Thuwal, Saudi Arabia. Here, we present a draft genome sequence of this strain, highlighting a number of pathways involved in plant growth promotion under salt stress.

Draft Genome Sequence of Halomonas elongata Strain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity Tolerance In Planta

KAUST Repository

Lafi, Feras Fawzi

2016-11-04

Halomonas elongata strain K4 is an endophytic bacterial strain that was isolated from roots of Cyperus conglomeratus collected at the Red Sea coast in Thuwal, Saudi Arabia. Here, we present a draft genome sequence of this strain, highlighting a number of pathways involved in plant growth promotion under salt stress.

Draft genome sequence of Bacillus thuringiensis strain BrMgv02-JM63, a chitinolytic bacterium isolated from oil-contaminated mangrove soil in Brazil

NARCIS (Netherlands)

Marcon, Joelma; Taketani, Rodrigo Gouvêa; Dini-Andreote, Francisco; Mazzero, Giulia Inocêncio; Soares Junior, Fabio Lino; Melo, Itamar Soares; Azevedo, João Lúcio; Andreote, Fernando Dini

2014-01-01

Here, we report the draft genome sequence and the automatic annotation of Bacillus thuringiensis strain BrMgv02-JM63. This genome comprises a set of genes involved in the metabolism of chitin and N-acetylglucosamine utilization, thus suggesting the possible role of this strain in the cycling of

Draft Genome Sequence of a Clostridium botulinum Isolate from Water Used for Cooling at a Plant Producing Low-Acid Canned Foods.

Science.gov (United States)

Basavanna, Uma; Gonzalez-Escalona, Narjol; Timme, Ruth; Datta, Shomik; Schoen, Brianna; Brown, Eric W; Zink, Donald; Sharma, Shashi K

2013-01-01

Clostridium botulinum is a pathogen of concern for low-acid canned foods. Here we report draft genomes of a neurotoxin-producing C. botulinum strain isolated from water samples used for cooling low-acid canned foods at a canning facility. The genome sequence confirmed that this strain belonged to C. botulinum serotype B1, albeit with major differences, including thousands of unique single nucleotide polymorphisms (SNPs) compared to other genomes of the same serotype.

Draft Genome Sequence of a Clostridium botulinum Isolate from Water Used for Cooling at a Plant Producing Low-Acid Canned Foods

OpenAIRE

Basavanna, Uma; Gonzalez-Escalona, Narjol; Timme, Ruth; Datta, Shomik; Schoen, Brianna; Brown, Eric W.; Zink, Donald; Sharma, Shashi K.

2013-01-01

Clostridium botulinum is a pathogen of concern for low-acid canned foods. Here we report draft genomes of a neurotoxin-producing C.?botulinum strain isolated from water samples used for cooling low-acid canned foods at a canning facility. The genome sequence confirmed that this strain belonged to C.?botulinum serotype B1, albeit with major differences, including thousands of unique single nucleotide polymorphisms (SNPs) compared to other genomes of the same serotype.

Permanent draft genomes of the Rhodopirellula maiorica strain SM1.

Science.gov (United States)

Richter, Michael; Richter-Heitmann, Tim; Klindworth, Anna; Wegner, Carl-Eric; Frank, Carsten S; Harder, Jens; Glöckner, Frank Oliver

2014-02-01

The genome of Rhodopirellula maiorica strain SM1 was sequenced as a permanent draft to complement the full genome sequence of the type strain Rhodopirellula baltica SH1(T). This isolate is part of a larger study to infer the biogeography of Rhodopirellula species in European marine waters, as well as to amend the genus description of R. baltica. This genomics resource article is the fifth of a series of five publications reporting in total eight new permanent daft genomes of Rhodopirellula species. Copyright © 2013 Elsevier B.V. All rights reserved.

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana.

Science.gov (United States)

Nowell, Reuben W; Elsworth, Ben; Oostra, Vicencio; Zwaan, Bas J; Wheat, Christopher W; Saastamoinen, Marjo; Saccheri, Ilik J; Van't Hof, Arjen E; Wasik, Bethany R; Connahs, Heidi; Aslam, Muhammad L; Kumar, Sujai; Challis, Richard J; Monteiro, Antónia; Brakefield, Paul M; Blaxter, Mark

2017-07-01

The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (∼×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html). © The Authors 2017. Published by Oxford University Press.

Draft Genome Sequence of Plant Growth–Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia

KAUST Repository

Lafi, Feras Fawzi; Ramirez Prado, Juan Sebastian; Alam, Intikhab; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2017-01-01

Micrococcus luteus strain K39 is an endophyte bacterium isolated from roots of the desert plant Cyperus conglomeratus collected from the Red Sea shore, Thuwal, Saudi Arabia. The draft genome sequence of strain K39 revealed a number of enzymes involved in salinity and oxidative stress tolerance or having herbicide-resistance activity.

Draft Genome Sequence of Plant Growth–Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia

KAUST Repository

Lafi, Feras Fawzi

2017-01-27

Micrococcus luteus strain K39 is an endophyte bacterium isolated from roots of the desert plant Cyperus conglomeratus collected from the Red Sea shore, Thuwal, Saudi Arabia. The draft genome sequence of strain K39 revealed a number of enzymes involved in salinity and oxidative stress tolerance or having herbicide-resistance activity.

Draft genome sequences of Escherichia coli O113:H21 strains recovered from a major produce-production region in California

Science.gov (United States)

Shiga toxin-producing Escherichia coli is a foodborne and waterborne pathogen and is responsible for outbreaks of human gastroenteritis. This report documents the draft genome sequences of seven O113:H21 strains recovered from livestock, wildlife, and soil samples collected in a major agricultural r...

Draft genome sequence of Pseudomonas sp. strain M47T1, carried by Bursaphelenchus xylophilus isolated from Pinus pinaster.

Science.gov (United States)

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor; Morais, Paula V

2012-09-01

The draft genome sequence of Pseudomonas sp. strain M47T1, carried by the Bursaphelenchus xylophilus pinewood nematode, the causative agent of pine wilt disease, is presented. In Pseudomonas sp. strain M47T1, genes that make this a plant growth-promoting bacterium, as well as genes potentially involved in nematotoxicity, were identified.

Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Infantis Strain SPE101, Isolated from a Chronic Human Infection.

Science.gov (United States)

Iriarte, Andrés; Giner-Lamia, Joaquín; Silva, Claudia; Betancor, Laura; Astocondor, Lizeth; Cestero, Juan J; Ochoa, Theresa; García, Coralith; Puente, José L; Chabalgoity, José A; García-Del Portillo, Francisco

2017-07-20

We report a 4.99-Mb draft genome sequence of Salmonella enterica subsp. enterica serovar Infantis strain SPE101, isolated from feces of a 5-month-old breast-fed female showing diarrhea associated with severe dehydration and malnutrition. The infection prolonged for 6 months despite antibiotic treatment. Copyright © 2017 Iriarte et al.

Draft genome sequence of the fungus associated with oak-wilt mortality in South Korea, Raffaelea quercus-mongolicae KACC44405

Science.gov (United States)

Jongbum Jeon; Ki-Tae Kim; Hyeunjeong Song; Gir-Won Lee; Kyeongchae Cheong; Hyunbin Kim; Gobong Choi; Yong-Hwan Lee; Jane E. Stewart; Ned B. Klopfenstein; Mee-Sook Kim

2017-01-01

The fungus Raffaelea quercus-mongolicae is the causal agent of Korean oak wilt, a disease associated with mass mortality of oak trees (e.g., Quercus spp.). The fungus is vectored and dispersed by the ambrosia beetle, Platypus koryoensis. Here, we present the 27.0-Mb draft genome sequence of R. quercus-mongolicae strain KACC44405.

Draft Genome Sequence of Paenibacillus sp. Strain DMB20, Isolated from Alang Ship-Breaking Yard, Which Harbors Genes for Xenobiotic Degradation.

Science.gov (United States)

Shah, Binal; Jain, Kunal; Patel, Namrata; Pandit, Ramesh; Patel, Anand; Joshi, Chaitanya G; Madamwar, Datta

2015-06-11

Paenibacillus sp. strain DMB20, in cometabolism with other Proteobacteria and Firmicutes, exhibits azoreduction of textile dyes. Here, we report the draft genome sequence of this bacterium, consisting of 6,647,181 bp with 7,668 coding sequences (CDSs). The data presented highlight multiple sets of functional genes associated with xenobiotic compound degradation. Copyright © 2015 Shah et al.

Value of a newly sequenced bacterial genome

DEFF Research Database (Denmark)

Barbosa, Eudes; Aburjaile, Flavia F; Ramos, Rommel Tj

2014-01-01

and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses...... heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting...

Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling.

Science.gov (United States)

Hausmann, Bela; Pjevac, Petra; Schreck, Katharina; Herbold, Craig W; Daims, Holger; Wagner, Michael; Loy, Alexander

2018-01-25

The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum siberiense 26-4b1 was isolated from a Siberian peatland. We report here a 6.20-Mbp near-complete high-quality draft genome sequence of T. siberiense that reveals expected and novel metabolic potential for the genus Telmatospirillum , including genes for sulfur oxidation. Copyright © 2018 Hausmann et al.

Draft Genome Sequence of Isoproturon-Mineralizing Sphingomonas sp. SRS2, Isolated from an Agricultural Field in the United Kingdom.

Science.gov (United States)

Nielsen, Tue Kjærgaard; Sørensen, Sebastian R; Hansen, Lars Hestbjerg

2015-05-28

Sphingomonas sp. SRS2 was the first described pure strain that is capable of mineralizing the phenylurea herbicide isoproturon and some of its related compounds. This strain has been studied thoroughly and shows potential for bioremediation purposes. We present the draft genome sequence of this bacterium, which will aid future studies. Copyright © 2015 Nielsen et al.

Draft Genome Sequence of a Multidrug-Resistant Klebsiella quasipneumoniae subsp. similipneumoniae Isolate from a Clinical Source

Energy Technology Data Exchange (ETDEWEB)

Ozer, Egon A.; Morris, Andrew R.; Krapp, Fiorella; Henry, Christopher S.; Tyo, Keith E.; Lathem, Wyndham W.; Hauser, Alan R.

2016-05-26

We report here the draft genome sequence of a multidrug-resistant clinical isolate ofKlebsiella quasipneumoniaesubsp.similipneumoniae, KP_Z4175. This strain, isolated as part of a hospital infection-control screening program, is resistant to multiple β-lactam antibiotics, aminoglycosides, and trimethoprim-sulfamethoxazole.

Draft Genome Sequence of Bacillus thuringiensis Strain BrMgv02-JM63, a Chitinolytic Bacterium Isolated from Oil-Contaminated Mangrove Soil in Brazil.

Science.gov (United States)

Marcon, Joelma; Taketani, Rodrigo Gouvêa; Dini-Andreote, Francisco; Mazzero, Giulia Inocêncio; Soares, Fabio Lino; Melo, Itamar Soares; Azevedo, João Lúcio; Andreote, Fernando Dini

2014-01-30

Here, we report the draft genome sequence and the automatic annotation of Bacillus thuringiensis strain BrMgv02-JM63. This genome comprises a set of genes involved in the metabolism of chitin and N-acetylglucosamine utilization, thus suggesting the possible role of this strain in the cycling of organic matter in mangrove soils.

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

DEFF Research Database (Denmark)

Lewis, Nathan E; Liu, Xin; Li, Yuxiang

2013-01-01

stymied by the lack of a unifying genomic resource for CHO cells. Here we report a 2.4-Gb draft genome sequence of a female Chinese hamster, Cricetulus griseus, harboring 24,044 genes. We also resequenced and analyzed the genomes of six CHO cell lines from the CHO-K1, DG44 and CHO-S lineages...

Identification of a haemolysin-like peptide with antibacterial activity using the draft genome sequence of Staphylococcus epidermidis strain A487.

Science.gov (United States)

Al-Mahrous, Mohammed M; Jack, Ralph W; Sandiford, Stephanie K; Tagg, John R; Beatson, Scott A; Upton, Mathew

2011-08-01

Our interest in Staphylococcus epidermidis strain A487 was prompted by the unusual nature of its inhibitory activity in screening tests against methicillin-resistant Staphylococcus aureus isolates. The inhibitory activity was detected in deferred antagonism tests only if the agar plate was preheated for at least 35 min at ≥ 55 °C before inoculation of the indicator bacteria, this phenomenon indicating possible involvement of a heat-labile immunity agent or protease. The inhibitor was purified to homogeneity by ammonium sulphate precipitation, followed by cation-exchange and reversed-phase chromatography. Tandem MS revealed a novel peptide of molecular weight 2588.4 Da. The draft genome sequence of strain A487 was determined using 454 GS FLX technology, allowing the identification of the structural gene (hlp) encoding the mature peptide MQFITDLIKKAVDFFKGLFGNK. The deduced amino acid sequence of peptide 487 exhibited 70.8% similarity to that of a putative haemolysin from Staphylococcus cohnii. Analysis of the genome of strain A487 showed several additional inhibitor-encoding genes, including hld, the determinant for staphylococcal δ-lysin. This work indicates that potentially useful inhibitors could be overlooked in agar-based inhibitor screening programmes lacking a heat pretreatment step and also highlights the utility of draft genome sequence examination in antibacterial agent discovery. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Draft genome sequence of Paraburkholderia tropica Ppe8 strain, a sugarcane endophytic diazotrophic bacterium.

Science.gov (United States)

Silva, Paula Renata Alves da; Simões-Araújo, Jean Luiz; Vidal, Márcia Soares; Cruz, Leonardo Magalhães; Souza, Emanuel Maltempi de; Baldani, José Ivo

Paraburkholderia tropica (syn Burkholderia tropica) are nitrogen-fixing bacteria commonly found in sugarcane. The Paraburkholderia tropica strain Ppe8 is part of the sugarcane inoculant consortium that has a beneficial effect on yield. Here, we report a draft genome sequence of this strain elucidating the mechanisms involved in its interaction mainly with Poaceae. A genome size of approximately 8.75Mb containing 7844 protein coding genes distributed in 526 subsystems was de novo assembled with ABySS and annotated by RAST. Genes related to the nitrogen fixation process, the secretion systems (I, II, III, IV, and VI), and related to a variety of metabolic traits, such as metabolism of carbohydrates, amino acids, vitamins, and proteins, were detected, suggesting a broad metabolic capacity and possible adaptation to plant association. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Draft genome sequence of a novel marine bacterium, Paraglaciecola sp. strain S66, with hydrolytic activity against seaweed polysaccharides

DEFF Research Database (Denmark)

Schultz-Johansen, Mikkel; Glaring, Mikkel Andreas; Bech, Pernille Kjersgaard

2016-01-01

A novel agarolytic gammaproteobacterium, ITALIC! Paraglaciecolasp. S66, was isolated from marine samples of eelgrass ( ITALIC! Zosterasp.) and sequenced. The draft genome contains a large number of enzyme-encoding genes with predicted function against several complex polysaccharides found in the ...... in the cell walls of algae....

Phenotypic, molecular characterization, antimicrobial susceptibility and draft genome sequence of Corynebacterium argentoratense strains isolated from clinical samples

Directory of Open Access Journals (Sweden)

I. Fernández-Natal

2016-03-01

Full Text Available During a 12-year period we isolated five Corynebacterium argentoratense strains identified by phenotypic methods, including the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF and 16S rRNA gene sequencing. In addition, antimicrobial susceptibility was determined, and genome sequencing for the detection of antibiotic resistance genes was performed. The organisms were isolated from blood and throat cultures and could be identified by all methods used. All strains were resistant to cotrimoxazole, and resistance to β-lactams was partly present. Two strains were resistant to erythromycin and clindamycin. The draft genome sequences of theses isolates revealed the presence of the erm(X resistance gene that is embedded in the genetic structure of the transposable element Tn5423. Although rarely reported as a human pathogen, C. argentoratense can be involved in bacteraemia and probably in other infections. Our results also show that horizontal transfer of genes responsible for antibiotic resistance is occurring in this species.

Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts

KAUST Repository

An, Ran; Lin, Pengpeng; Bougouffa, Salim; Essack, Magbubah; Boxrud, David; Bajic, Vladimir B.; Vidovic, Sinisa

2018-01-01

Salmonella enterica subsp. enterica serovar Enteritidis is a wide-host-range pathogen. Occasionally, it is involved in invasive infections, leading to a high mortality rate. Here, we present the draft genome sequences of four S Enteritidis strains obtained from human and avian hosts that had been involved in bacteremia, gastroenteritis, and primary infections.

Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts

KAUST Repository

An, Ran

2018-01-24

Salmonella enterica subsp. enterica serovar Enteritidis is a wide-host-range pathogen. Occasionally, it is involved in invasive infections, leading to a high mortality rate. Here, we present the draft genome sequences of four S Enteritidis strains obtained from human and avian hosts that had been involved in bacteremia, gastroenteritis, and primary infections.

Draft Genome Sequence of the Plant Growth-Promoting Cupriavidus gilardii Strain JZ4 Isolated from the Desert Plant Tribulus terrestris

KAUST Repository

Lafi, Feras Fawzi; Bokhari, Ameerah; Alam, Intikhab; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2016-01-01

We isolated the plant endophytic bacterium Cupriavidus gilardii strain JZ4 from the roots of the desert plant Tribulus terrestris, collected from the Jizan region, Saudi Arabia. We report here the draft genome sequence of JZ4, together with several enzymes related to plant growth-promoting activity, environmental adaption, and antifungal activity.

Draft Genome Sequence of the Plant Growth-Promoting Cupriavidus gilardii Strain JZ4 Isolated from the Desert Plant Tribulus terrestris

KAUST Repository

Lafi, Feras Fawzi

2016-07-28

We isolated the plant endophytic bacterium Cupriavidus gilardii strain JZ4 from the roots of the desert plant Tribulus terrestris, collected from the Jizan region, Saudi Arabia. We report here the draft genome sequence of JZ4, together with several enzymes related to plant growth-promoting activity, environmental adaption, and antifungal activity.

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana

NARCIS (Netherlands)

Nowell, Reuben W.; Elsworth, Ben; Oostra, Vicencio; Zwaan, Bas J.; Wheat, Christopher W.; Saastamoinen, Marjo; Saccheri, Ilik J.; Hof, van 't Arjen E.; Wasik, Bethany R.; Connahs, Heidi; Aslam, Muhammad L.; Kumar, Sujai; Challis, Richard J.; Monteiro, Antónia; Brakefield, Paul M.; Blaxter, Mark

2017-01-01

The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important

Draft genome sequence of Therminicola potens strain JR

Energy Technology Data Exchange (ETDEWEB)

Byrne-Bailey, K.G.; Wrighton, K.C.; Melnyk, R.A.; Agbo, P.; Hazen, T.C.; Coates, J.D.

2010-07-01

'Thermincola potens' strain JR is one of the first Gram-positive dissimilatory metal-reducing bacteria (DMRB) for which there is a complete genome sequence. Consistent with the physiology of this organism, preliminary annotation revealed an abundance of multiheme c-type cytochromes that are putatively associated with the periplasm and cell surface in a Gram-positive bacterium. Here we report the complete genome sequence of strain JR.

The first draft reference genome of the American mink ( Neovison vison )

DEFF Research Database (Denmark)

Cai, Zexi; Petersen, Bent; Sahana, Goutam

2017-01-01

The American mink (Neovison vison) is a semiaquatic species of mustelid native to North America. It’s an important animal for the fur industry. Many efforts have been made to locate genes influencing fur quality and color, but this search has been impeded by the lack of a reference genome. Here we...... present the first draft genome of mink. In our study, two mink individuals were sequenced by Illumina sequencing with 797 Gb sequence generated. Assembly yielded 7,175 scaffolds with an N50 of 6.3 Mb and length of 2.4 Gb including gaps. Repeat sequences constitute around 31% of the genome, which is lower...

The draft genome of Corchorus olitorius cv. JRO-524 (Navin

Directory of Open Access Journals (Sweden)

Debabrata Sarkar

2017-06-01

Full Text Available Here, we present the draft genome (377.3 Mbp of Corchorus olitorious cv. JRO-524 (Navin, which is a leading dark jute variety developed from a cross between African (cv. Sudan Green and indigenous (cv. JRO-632 types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii. Seven chromosome-scale genetically anchored pseudomolecules were constructed with a total size of 8.53 Mbp and used for synteny analyses with the cocoa and cotton genomes. Like other plant species, gypsy and copia retrotransposons were the most abundant classes of repeat elements in jute. The raw data of our study are available in SRA database of NCBI with accession number SRX1506532. The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000.

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

Science.gov (United States)

Pilkington, Sarah M; Crowhurst, Ross; Hilario, Elena; Nardozza, Simona; Fraser, Lena; Peng, Yongyan; Gunaseelan, Kularajathevan; Simpson, Robert; Tahir, Jibran; Deroles, Simon C; Templeton, Kerry; Luo, Zhiwei; Davy, Marcus; Cheng, Canhong; McNeilage, Mark; Scaglione, Davide; Liu, Yifei; Zhang, Qiong; Datson, Paul; De Silva, Nihal; Gardiner, Susan E; Bassett, Heather; Chagné, David; McCallum, John; Dzierzon, Helge; Deng, Cecilia; Wang, Yen-Yi; Barron, Lorna; Manako, Kelvina; Bowen, Judith; Foster, Toshi M; Erridge, Zoe A; Tiffin, Heather; Waite, Chethi N; Davies, Kevin M; Grierson, Ella P; Laing, William A; Kirk, Rebecca; Chen, Xiuyin; Wood, Marion; Montefiori, Mirco; Brummell, David A; Schwinn, Kathy E; Catanach, Andrew; Fullerton, Christina; Li, Dawei; Meiyalaghan, Sathiyamoorthy; Nieuwenhuizen, Niels; Read, Nicola; Prakash, Roneel; Hunter, Don; Zhang, Huaibi; McKenzie, Marian; Knäbel, Mareike; Harris, Alastair; Allan, Andrew C; Gleave, Andrew; Chen, Angela; Janssen, Bart J; Plunkett, Blue; Ampomah-Dwamena, Charles; Voogd, Charlotte; Leif, Davin; Lafferty, Declan; Souleyre, Edwige J F; Varkonyi-Gasic, Erika; Gambi, Francesco; Hanley, Jenny; Yao, Jia-Long; Cheung, Joey; David, Karine M; Warren, Ben; Marsh, Ken; Snowden, Kimberley C; Lin-Wang, Kui; Brian, Lara; Martinez-Sanchez, Marcela; Wang, Mindy; Ileperuma, Nadeesha; Macnee, Nikolai; Campin, Robert; McAtee, Peter; Drummond, Revel S M; Espley, Richard V; Ireland, Hilary S; Wu, Rongmei; Atkinson, Ross G; Karunairetnam, Sakuntala; Bulley, Sean; Chunkath, Shayhan; Hanley, Zac; Storey, Roy; Thrimawithana, Amali H; Thomson, Susan; David, Charles; Testolin, Raffaele; Huang, Hongwen; Hellens, Roger P; Schaffer, Robert J

2018-04-16

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and

Approaches for in silico finishing of microbial genome sequences.

Science.gov (United States)

Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva

The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as "drafts", incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing.

Draft Genome Sequence of Pseudoalteromonas sp. Strain XI10 Isolated from the Brine-Seawater Interface of Erba Deep in the Red Sea

KAUST Repository

Zhang, Guishan; Haroon, Mohamed; Zhang, Ruifu; Hikmawan, Tyas I.; Stingl, Ulrich

2016-01-01

Pseudoalteromonas sp. strain XI10 was isolated from the brine-seawater interface of Erba Deep in the Red Sea, Saudi Arabia. Here, we present the draft genome sequence of strain XI10, a gammaproteobacterium that synthesizes polysaccharides for biofilm formation when grown in liquid culture.

Draft Genome Sequence of Pseudoalteromonas sp. Strain XI10 Isolated from the Brine-Seawater Interface of Erba Deep in the Red Sea

KAUST Repository

Zhang, Guishan

2016-03-10

Pseudoalteromonas sp. strain XI10 was isolated from the brine-seawater interface of Erba Deep in the Red Sea, Saudi Arabia. Here, we present the draft genome sequence of strain XI10, a gammaproteobacterium that synthesizes polysaccharides for biofilm formation when grown in liquid culture.

The draft genome of a diploid cotton Gossypium raimondii

DEFF Research Database (Denmark)

Wang, Kunbo; Wang, Zhiwen; Li, Fuguang

2012-01-01

We have sequenced and assembled a draft genome of G. raimondii, whose progenitor is the putative contributor of the D subgenome to the economically important fiber-producing cotton species Gossypium hirsutum and Gossypium barbadense. Over 73% of the assembled sequences were anchored on 13 G. raim...

Draft Genome Sequence of Hymenobacter sp. Strain AT01-02, Isolated from a Surface Soil Sample in the Atacama Desert, Chile

DEFF Research Database (Denmark)

Hansen, Anders Cai Holm; Paulino-Lima, Ivan Glaucio; Fujishima, Kosuke

2016-01-01

Here, we report the 5.09-Mb draft genome sequence of Hymenobacter sp. strain AT01-02, which was isolated from a surface soil sample in the Atacama Desert, Chile. The isolate is extremely resistant to UV-C radiation and is able to accumulate high intracellular levels of Mn/Fe....

Draft Genome Sequence of the Plant Growth–Promoting Rhizobacterium Acinetobacter radioresistens Strain SA188 Isolated from the Desert Plant Indigofera argentea

KAUST Repository

Lafi, Feras Fawzi; Alam, Intikhab; Bisseling, Ton; Geurts, Rene; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2017-01-01

Acinetobacter radioresistens strain SA188 is a plant endophytic bacterium, isolated from root nodules of the desert plants Indigofera spp., collected in Jizan, Saudi Arabia. Here, we report the 3.2-Mb draft genome sequence of strain SA188, highlighting characteristic pathways for plant growth–promoting activity and environmental adaptation.

Draft Genome Sequence of the Plant Growth–Promoting Rhizobacterium Acinetobacter radioresistens Strain SA188 Isolated from the Desert Plant Indigofera argentea

KAUST Repository

Lafi, Feras Fawzi

2017-03-03

Acinetobacter radioresistens strain SA188 is a plant endophytic bacterium, isolated from root nodules of the desert plants Indigofera spp., collected in Jizan, Saudi Arabia. Here, we report the 3.2-Mb draft genome sequence of strain SA188, highlighting characteristic pathways for plant growth–promoting activity and environmental adaptation.

Draft Genome Sequences of 12 Dry-Heat-Resistant Bacillus Strains Isolated from the Cleanrooms Where the Viking Spacecraft Were Assembled.

Science.gov (United States)

Seuylemezian, Arman; Cooper, Kerry; Schubert, Wayne; Vaishampayan, Parag

2018-03-22

Spore-forming microorganisms are of concern for forward contamination because they can survive harsh interplanetary travel. Here, we report the draft genome sequences of 12 spore-forming strains isolated from the Manned Spacecraft Operations Building (MSOB) and the Vehicle Assembly Building (VAB) in Cape Canaveral, FL, where the Viking spacecraft were assembled. Copyright © 2018 Seuylemezian et al.

Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides.

Science.gov (United States)

Brown, Steven D; Utturkar, Sagar M; Klingeman, Dawn M; Johnson, Courtney M; Martin, Stanton L; Land, Miriam L; Lu, Tse-Yuan S; Schadt, Christopher W; Doktycz, Mitchel J; Pelletier, Dale A

2012-11-01

To aid in the investigation of the Populus deltoides microbiome, we generated draft genome sequences for 21 Pseudomonas strains and 19 other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium, and Variovorax were generated.

Draft genome sequence of the extremely halophilic Halorubrum sp. SAH-A6 isolated from rock salts of the Danakil depression, Ethiopia

Directory of Open Access Journals (Sweden)

Ashagrie Gibtan

2016-12-01

Full Text Available The draft genome sequence of Halorubrum sp. SAH-A6, isolated from commercial rock salts of the Danakil depression, Ethiopia. The genome comprised 3,325,770 bp, with the G + C content of 68.0%. The strain has many genes which are responsible for secondary metabolites biosynthesis, transport and catabolism as compared to other Halorubrum archaea members. Abundant genes responsible for numerous transport systems, solute accumulation, and aromatic/sulfur decomposition were detected. The first genomic analysis encourages further research on comparative genomics, and biotechnological applications. The NCBI accession number for this genome is SAMN04278861 and ID: 4278861 and strain deposited with accession number KCTC 43215.

The draft genome of MD-2 pineapple using hybrid error correction of long reads

Science.gov (United States)

Redwan, Raimi M.; Saidin, Akzam; Kumar, S. Vijay

2016-01-01

The introduction of the elite pineapple variety, MD-2, has caused a significant market shift in the pineapple industry. Better productivity, overall increased in fruit quality and taste, resilience to chilled storage and resistance to internal browning are among the key advantages of the MD-2 as compared with its previous predecessor, the Smooth Cayenne. Here, we present the genome sequence of the MD-2 pineapple (Ananas comosus (L.) Merr.) by using the hybrid sequencing technology from two highly reputable platforms, i.e. the PacBio long sequencing reads and the accurate Illumina short reads. Our draft genome achieved 99.6% genome coverage with 27,017 predicted protein-coding genes while 45.21% of the genome was identified as repetitive elements. Furthermore, differential expression of ripening RNASeq library of pineapple fruits revealed ethylene-related transcripts, believed to be involved in regulating the process of non-climacteric pineapple fruit ripening. The MD-2 pineapple draft genome serves as an example of how a complex heterozygous genome is amenable to whole genome sequencing by using a hybrid technology that is both economical and accurate. The genome will make genomic applications more feasible as a medium to understand complex biological processes specific to pineapple. PMID:27374615

Genome Sequence of Lactobacillus plantarum Strain UCMA 3037

OpenAIRE

Naz, Saima; Tareb, Raouf; Bernardeau, Marion; Vaisse, Melissa; Lucchetti-Miganeh, Celine; Rechenmann, Mathias; Vernoux, Jean-Paul

2013-01-01

Nucleic acid of the strain Lactobacillus plantarum UCMA 3037, isolated from raw milk camembert cheese in our laboratory, was sequenced. We present its draft genome sequence with the aim of studying its functional properties and relationship to the cheese ecosystem.

Genome Sequence of Lactobacillus plantarum Strain UCMA 3037.

Science.gov (United States)

Naz, Saima; Tareb, Raouf; Bernardeau, Marion; Vaisse, Melissa; Lucchetti-Miganeh, Celine; Rechenmann, Mathias; Vernoux, Jean-Paul

2013-05-23

Nucleic acid of the strain Lactobacillus plantarum UCMA 3037, isolated from raw milk camembert cheese in our laboratory, was sequenced. We present its draft genome sequence with the aim of studying its functional properties and relationship to the cheese ecosystem.

Draft Genome Sequences of Three Escherichia coli Strains with Different In Vivo Pathogenicities in an Avian (Ascending) Infection Model of the Oviduct.

Science.gov (United States)

Olsen, Rikke Heidemann; Thøfner, Ida Cecilie Naundrup; Pors, Susanne Elisabeth; Christensen, Henrik; Bisgaard, Magne; Christensen, Jens Peter

2015-05-07

Here, we present three draft genome sequences of Escherichia coli strains that experimentally were proven to possess low (strain D2-2), intermediate (Chronic_salp), or high virulence (Cp6salp3) in an avian (ascending) infection model of the oviduct. Copyright © 2015 Olsen et al.

Complete and draft genome sequences of six members of the aquificales

Science.gov (United States)

Reysenbach, A.-L.; Hamamura, N.; Podar, M.; Griffiths, E.; Ferreira, S.; Hochstein, R.; Heidelberg, J.; Johnson, J.; Mead, D.; Pohorille, A.; Sarmiento, M.; Sehweighofer, K.; Seshadri, R.; Voytek, M.A.

2009-01-01

The Aquificales are widespread in marine and terrestrial hydrothermal environments. Here, we report the complete and draft genome sequences of six new members of the Aquificales: two marine species, Persephonella marina strain EX-H1 and Hydrogenivirga strain 128-5-R1 (from the East Pacific Rise, 9??50.3???N, 104??17.5???W, and the Eastern Lau Spreading Center, 176??11.5???W, 20??45.8???S, respectively), and four terrestrial isolates, Sulfuri-hydrogenibium azorense strain Az-Ful, Sulfurihydrogenibium yellowstonense strain SS-5, and Sulfurihydro-genibium strain Y03AOP1 (from Furnas, Azores, Portugal, and Calcite Springs and Obsidian Pool in Yellowstone National Park, United States, respectively), and the only thermoacidophilic isolate, Hydrogenobaculum strain Y04AAS1 (from a stream adjacent to Obsidian Pool). Significant differences among the different species exist that include nitrogen metabolism, hydrogen utilization, Chemotaxis, and signal transduction, providing insights into their ecological niche adaptations. Copyright ?? 2009, American Society for Microbiology. All Rights Reserved.

Complete and draft genome sequences of six members of the Aquificales.

Science.gov (United States)

Reysenbach, Anna-Louise; Hamamura, N; Podar, M; Griffiths, E; Ferreira, S; Hochstein, R; Heidelberg, J; Johnson, J; Mead, D; Pohorille, A; Sarmiento, M; Schweighofer, K; Seshadri, R; Voytek, M A

2009-03-01

The Aquificales are widespread in marine and terrestrial hydrothermal environments. Here, we report the complete and draft genome sequences of six new members of the Aquificales: two marine species, Persephonella marina strain EX-H1 and Hydrogenivirga strain 128-5-R1 (from the East Pacific Rise, 9 degrees 50.3'N, 104 degrees 17.5'W, and the Eastern Lau Spreading Center, 176 degrees 11.5'W, 20 degrees 45.8'S, respectively), and four terrestrial isolates, Sulfurihydrogenibium azorense strain Az-Fu1, Sulfurihydrogenibium yellowstonense strain SS-5, and Sulfurihydrogenibium strain Y03AOP1 (from Furnas, Azores, Portugal, and Calcite Springs and Obsidian Pool in Yellowstone National Park, United States, respectively), and the only thermoacidophilic isolate, Hydrogenobaculum strain Y04AAS1 (from a stream adjacent to Obsidian Pool). Significant differences among the different species exist that include nitrogen metabolism, hydrogen utilization, chemotaxis, and signal transduction, providing insights into their ecological niche adaptations.

Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides

Energy Technology Data Exchange (ETDEWEB)

Brown, Steven D [ORNL; Utturkar, Sagar M [ORNL; Klingeman, Dawn Marie [ORNL; Johnson, Courtney M [ORNL; Martin, Stanton [ORNL; Land, Miriam L [ORNL; Lu, Tse-Yuan [ORNL; Schadt, Christopher Warren [ORNL; Doktycz, Mitchel John [ORNL; Pelletier, Dale A [ORNL

2012-01-01

To aid in the investigation of the Populus deltoides microbiome we generated draft genome sequences for twenty one Pseudomonas and twenty one other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Burkholderia, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium and Variovorax were generated.

Draft genome sequences of three Aeromonas hybrophila isolates from catfish and tilapia

Science.gov (United States)

Aeromonas hydrophila is a Gram-negative bacteria that is particularly adapted to freshwater environments and can cause severe infections in fish and humans. Here we report the draft genomes of three A. hydrophila catfish and tilapia isolates....

Draft Genome Sequences of Three Multiantibiotic-Resistant Campylobacter jejuni Strains (2865, 2868, and 2871) Isolated from Poultry at Retail Outlets in Malaysia

OpenAIRE

Teh, Amy Huei Teen; Lee, Sui Mae; Dykes, Gary A.

2016-01-01

Campylobacter jejuni is a frequent cause of human bacterial gastrointestinal foodborne disease worldwide. Antibiotic resistance in this species is of public health concern. The draft genome sequences of three multiantibiotic-resistant C.?jejuni strains (2865, 2868, and 2871) isolated from poultry at retail outlets in Malaysia are presented here.

Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean Sea

KAUST Repository

Barbato, Marta

2015-12-10

We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5.

Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean Sea

KAUST Repository

Barbato, Marta; Mapelli, Francesca; Chouaia, Bessem; Crotti, Elena; Daffonchio, Daniele; Borin, Sara

2015-01-01

We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5.

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana

OpenAIRE

Nowell, RW; Elsworth, B; Oostra, Vicencio; Zwaan, Bas J.; Wheat, Christopher West; Saastamoinen, Marjo Anna Kaarina; Saccheri, Ilik; Van't Hof, AE; Wasik, BR; Connahs, H; Kumar, S; Challis, RJ; Aslam, L; Monteiro, Antonia; Brakefield, Paul M.

2017-01-01

Background: The mycalesine butterfly Bicyclus anynana, the 'Squinting bush brown', is a model organism in the study of lepidopteran ecology, development and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Findings: Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology...

Draft Whole-Genome Sequence of Serratia sp. Strain TEL, Associated with Oscheius sp. TEL-2014 (Nematoda: Rhabditidae) Isolated from a Grassland in South Africa

OpenAIRE

Lephoto, Tiisetso E.; Featherston, Jonathan; Gray, Vincent M.

2015-01-01

Here, we report on the draft genome sequence of Serratia sp. strain TEL, associated with Oscheius sp. TEL-2014 (Nematoda: Rhabditidae, KM492926) isolated from a grassland in Suikerbosrand Nature Reserve near Johannesburg in South Africa. Serratia sp. strain TEL has a genome size of 5,000,541 bp with 4,647 genes and a G+C content of 59.1%.

Draft genome of the medaka fish: a comprehensive resource for medaka developmental genetics and vertebrate evolutionary biology.

Science.gov (United States)

Takeda, Hiroyuki

2008-06-01

The medaka Oryzias latipes is a small egg-laying freshwater teleost, and has become an excellent model system for developmental genetics and evolutionary biology. The medaka genome is relatively small in size, approximately 800 Mb, and the genome sequencing project was recently completed by Japanese research groups, providing a high-quality draft genome sequence of the inbred Hd-rR strain of medaka. In this review, I present an overview of the medaka genome project including genome resources, followed by specific findings obtained with the medaka draft genome. In particular, I focus on the analysis that was done by taking advantage of the medaka system, such as the sex chromosome differentiation and the regional history of medaka species using single nucleotide polymorphisms as genomic markers.

Draft genome sequence of Halorubrum tropicale strain V5, a novel halophilic archaeon isolated from the solar salterns of Cabo Rojo, Puerto Rico.

Science.gov (United States)

Sánchez-Nieves, Rubén; Facciotti, Marc T; Saavedra-Collado, Sofía; Dávila-Santiago, Lizbeth; Rodríguez-Carrero, Roy; Montalvo-Rodríguez, Rafael

2016-03-01

The genus Halorubrum is a member of the family Halobacteriaceae which currently has the highest number of described species (31) of all the haloarchaea. Here we report the draft genome sequence of strain V5, a new species within this genus that was isolated from the solar salterns of Cabo Rojo, Puerto Rico. Assembly was performed and rendered the genome into 17 contigs (N50 = 515,834 bp), the largest of which contains 1,031,026 bp. The genome consists of 3.57 MB in length with G + C content of 67.6%. In general, the genome includes 4 rRNAs, 52 tRNAs, and 3246 protein-coding sequences. The NCBI accession number for this genome is LIST00000000 and the strain deposit number is CECT9000.

Draft Genome Sequences of Dickeya sp. Isolates B16 (NIB Z 2098) and S1 (NIB Z 2099) Causing Soft Rot of Phalaenopsis Orchids.

Science.gov (United States)

Alič, Špela; Naglič, Tina; Llop, Pablo; Toplak, Nataša; Koren, Simon; Ravnikar, Maja; Dreo, Tanja

2015-09-10

The genus Dickeya contains bacteria causing soft rot of economically important crops and ornamental plants. Here, we report the draft genome sequences of two Dickeya sp. isolates from rotted leaves of Phalaenopsis orchids. Copyright © 2015 Alič et al.

Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology

Science.gov (United States)

Takeuchi, Takeshi; Kawashima, Takeshi; Koyanagi, Ryo; Gyoja, Fuki; Tanaka, Makiko; Ikuta, Tetsuro; Shoguchi, Eiichi; Fujiwara, Mayuki; Shinzato, Chuya; Hisata, Kanako; Fujie, Manabu; Usami, Takeshi; Nagai, Kiyohito; Maeyama, Kaoru; Okamoto, Kikuhiko; Aoki, Hideo; Ishikawa, Takashi; Masaoka, Tetsuji; Fujiwara, Atushi; Endo, Kazuyoshi; Endo, Hirotoshi; Nagasawa, Hiromichi; Kinoshita, Shigeharu; Asakawa, Shuichi; Watabe, Shugo; Satoh, Nori

2012-01-01

The study of the pearl oyster Pinctada fucata is key to increasing our understanding of the molecular mechanisms involved in pearl biosynthesis and biology of bivalve molluscs. We sequenced ∼1150-Mb genome at ∼40-fold coverage using the Roche 454 GS-FLX and Illumina GAIIx sequencers. The sequences were assembled into contigs with N50 = 1.6 kb (total contig assembly reached to 1024 Mb) and scaffolds with N50 = 14.5 kb. The pearl oyster genome is AT-rich, with a GC content of 34%. DNA transposons, retrotransposons, and tandem repeat elements occupied 0.4, 1.5, and 7.9% of the genome, respectively (a total of 9.8%). Version 1.0 of the P. fucata draft genome contains 23 257 complete gene models, 70% of which are supported by the corresponding expressed sequence tags. The genes include those reported to have an association with bio-mineralization. Genes encoding transcription factors and signal transduction molecules are present in numbers comparable with genomes of other metazoans. Genome-wide molecular phylogeny suggests that the lophotrochozoan represents a distinct clade from ecdysozoans. Our draft genome of the pearl oyster thus provides a platform for the identification of selection markers and genes for calcification, knowledge of which will be important in the pearl industry. PMID:22315334

Genome sequencing and annotation of Serratia sp. strain TEL.

Science.gov (United States)

Lephoto, Tiisetso E; Gray, Vincent M

2015-12-01

We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410). This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926) collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000.

Genome sequencing and annotation of Serratia sp. strain TEL

Directory of Open Access Journals (Sweden)

Tiisetso E. Lephoto

2015-12-01

Full Text Available We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410. This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926 collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000.

Genome sequencing and annotation of Serratia sp. strain TEL

OpenAIRE

Lephoto, Tiisetso E.; Gray, Vincent M.

2015-01-01

We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410). This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926) collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000.

Draft genome sequence and transcriptional analysis of Rosellinia necatrix infected with a virulent mycovirus.

Science.gov (United States)

Shimizu, Takeo; Kanematsu, Satoko; Yaegashi, Hajime

2018-04-24

Understanding the molecular mechanisms of pathogenesis is useful in developing effective control methods for fungal diseases. The white root rot fungus Rosellinia necatrix is a soil-borne pathogen that causes serious economic losses in various crops, including fruit trees, worldwide. Here, using next-generation sequencing techniques, we first produced a 44-Mb draft genome sequence of R. necatrix strain W97, an isolate from Japan, in which 12,444 protein-coding genes were predicted. To survey differentially expressed genes (DEGs) associated with the pathogenesis of the fungus, the hypovirulent W97 strain infected with Rosellinia necatrix megabirnavirus 1 (RnMBV1) was used for a comprehensive transcriptome analysis. In total, 545 and 615 genes are up- and down-regulated, respectively, in R. necatrix infected with RnMBV1. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the DEGs suggested that primary and secondary metabolism would be greatly disturbed in R. necatrix infected with RnMBV1. The genes encoding transcriptional regulators, plant cell wall-degrading enzymes, and toxin production, such as cytochalasin E, were also found in the DEGs. The genetic resources provided in this study will accelerate the discovery of genes associated with pathogenesis and other biological characteristics of R. necatrix, thus contributing to disease control.

Draft genome of bagasse-degrading bacteria Bacillus aryabhattai GZ03 from deep sea water.

Science.gov (United States)

Wen, Jian; Ren, Chong; Huang, Nan; Liu, Yang; Zeng, Runying

2015-02-01

Bacillus aryabhattai GZ03 was isolated from deep sea water of the South China Sea, which can produce glucose and fructose by degrading bagasse at 25 °C. Here we report the draft genome sequence of Bacillus aryabhattai GZ03. The data obtained revealed 37 contigs with genome size of 5,105,129 bp and G+C content of 38.09%. The draft genome of B. aryabhattai GZ03 may provide insights into the mechanism of microbial carbohydrate and lignocellulosic material degradation. Copyright © 2014 Elsevier B.V. All rights reserved.

High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond.

Science.gov (United States)

Gong, Xianzhe; Skrivergaard, Stig; Korsgaard, Benjamin Smed; Schreiber, Lars; Marshall, Ian P G; Finster, Kai; Schramm, Andreas

2017-01-01

Strain S3-2 T , isolated from sediment of a frozen freshwater pond, shares 99% 16S rRNA gene sequence identity with strains of the genus Janthinobacterium . Strain S3-2 T is a facultative anaerobe that lacks the ability to produce violacein but shows antibiotic resistance, psychrotolerance, incomplete denitrification, and fermentation. The draft genome of strain S3-2 T has a size of ~5.8 Mbp and contains 5,297 genes, including 115 RNA genes. Based on the phenotypic properties of the strain, the low in silico DNA-DNA hybridization (DDH) values with related genomes (<35%), and the low whole genome-based average nucleotide identity (ANI) (<86%) with other strains within the genus Janthinobacterium, we propose that strain S3-2 T is the type strain (= DSM 102223 = LMG 29653) of a new species within this genus. We propose the name Janthinobacterium psychrotolerans sp. nov. to emphasize the capability of the strain to grow at low temperatures.

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

DEFF Research Database (Denmark)

Carlton, Jane M.; Hirt, Robert P.; Silva, Joana C.

2007-01-01

We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion...... environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria....

Draft Whole-Genome Sequence of Serratia sp. Strain TEL, Associated with Oscheius sp. TEL-2014 (Nematoda: Rhabditidae) Isolated from a Grassland in South Africa.

Science.gov (United States)

Lephoto, Tiisetso E; Featherston, Jonathan; Gray, Vincent M

2015-07-09

Here, we report on the draft genome sequence of Serratia sp. strain TEL, associated with Oscheius sp. TEL-2014 (Nematoda: Rhabditidae, KM492926) isolated from a grassland in Suikerbosrand Nature Reserve near Johannesburg in South Africa. Serratia sp. strain TEL has a genome size of 5,000,541 bp with 4,647 genes and a G+C content of 59.1%. Copyright © 2015 Lephoto et al.

Permanent draft genome of the malachite-green-tolerant bacterium Rhizobium sp. MGL06.

Science.gov (United States)

Liu, Yang; Wang, Runping; Zeng, Runying

2014-12-01

Rhizobium sp. MGL06, the first Rhizobium isolate from a marine environment, is a malachite-green-tolerant bacterium with a broader salinity tolerance (range: 0.5% to 9%) than other rhizobia. This study sequences and annotates the draft genome sequence of this strain. Genome sequence information provides a basis for analyzing the malachite green tolerance, broad salinity adaptation, nitrogen fixation properties, and taxonomic classification of the isolate. Copyright © 2014 Elsevier B.V. All rights reserved.

Draft Genome Sequence of the Polyextremophilic Halorubrum sp. Strain AJ67, Isolated from Hyperarsenic Lakes in the Argentinian Puna

OpenAIRE

Burguener, Germán Federico; Maldonado, Marcos Javier; Revale, Santiago; Fernández Do Porto, Darío Augusto; Rascovan, Nicolas; Vazquez, Martin Pablo; Farias, Maria Eugenia; Marti, Marcelo Adrian; Turjanski, Adrian

2016-01-01

Halorubrum sp. AJ67, an extreme halophilic, UV resistant archae that was isolated from Laguna Antofalla in the Argentinean Puna. The draft genome sequence suggests potent enzyme candidates that are essential to survive in multiple environmental extreme conditions, as high UV radiation, elevated salinity and the presence of critical arsenic concentration. Fil: Burguener, Germán Federico. Facultad de Ciencias Exactas y Naturales. Instituto de Cálculo. Plataforma de Bioinformática Argentina; ...

Draft Genome Sequences of 12 Clinical and Environmental Methicillin-Resistant Strains of Staphylococcus pseudintermedius Isolated from a Veterinary Teaching Hospital in Washington State

Science.gov (United States)

Shah, Devendra H.; Jones, Lisa P.; Paul, Narayan

2018-01-01

ABSTRACT Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a globally emergent multidrug-resistant pathogen of dogs associated with nosocomial transmission in dogs and with potential zoonotic impacts. Here, we report the draft whole-genome sequences of 12 hospital-associated MRSP strains and their resistance genotypes and phenotypes. PMID:29650582

Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement.

Science.gov (United States)

Gupta, Sonal; Nawaz, Kashif; Parween, Sabiha; Roy, Riti; Sahu, Kamlesh; Kumar Pole, Anil; Khandal, Hitaishi; Srivastava, Rishi; Kumar Parida, Swarup; Chattopadhyay, Debasis

2017-02-01

Cicer reticulatum L. is the wild progenitor of the fourth most important legume crop chickpea (C. arietinum L.). We assembled short-read sequences into 416 Mb draft genome of C. reticulatum and anchored 78% (327 Mb) of this assembly to eight linkage groups. Genome annotation predicted 25,680 protein-coding genes covering more than 90% of predicted gene space. The genome assembly shared a substantial synteny and conservation of gene orders with the genome of the model legume Medicago truncatula. Resistance gene homologs of wild and domesticated chickpeas showed high sequence homology and conserved synteny. Comparison of gene sequences and nucleotide diversity using 66 wild and domesticated chickpea accessions suggested that the desi type chickpea was genetically closer to the wild species than the kabuli type. Comparative analyses predicted gene flow between the wild and the cultivated species during domestication. Molecular diversity and population genetic structure determination using 15,096 genome-wide single nucleotide polymorphisms revealed an admixed domestication pattern among cultivated (desi and kabuli) and wild chickpea accessions belonging to three population groups reflecting significant influence of parentage or geographical origin for their cultivar-specific population classification. The assembly and the polymorphic sequence resources presented here would facilitate the study of chickpea domestication and targeted use of wild Cicer germplasms for agronomic trait improvement in chickpea. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Draft genome sequence of Thalassobius mediterraneus CECT 5383T, a poly-beta-hydroxybutyrate producer

Directory of Open Access Journals (Sweden)

Lidia Rodrigo-Torres

2016-03-01

Full Text Available Thalassobius mediterraneus is the type species of the genus Thalassobius and a member of the Roseobacter clade, an abundant representative of marine bacteria. T. mediterraneus XSM19T (=CECT 5383T was isolated from the Western Mediterranean coast near Valencia (Spain in 1989. We present here the draft genome sequence and annotation of this strain (ENA/DDBJ/NCBI accession number CYSF00000000, which is comprised of 3,431,658 bp distributed in 19 contigs and encodes 10 rRNA genes, 51 tRNA genes and 3276 protein coding genes. Relevant findings are commented, including the complete set of genes required for poly-beta-hydroxybutyrate (PHB synthesis and genes related to degradation of aromatic compounds. Keywords: Rhodobacteraceae, Roseobacter clade, PHB, Aromatic compounds

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana

OpenAIRE

Nowell, R. W.; Elsworth, B.; Oostra, V.; Zwaan, B. J.; Wheat, C. W.; Saastamoinen, M.; Saccheri, I. J.; Van t Hof, A. E.; Wasik, B. R.; Connahs, H.; Aslam, M. L.; Kumar, S.; Challis, R. J.; Monteiro, A.; Brakefield, P. M.

2017-01-01

The mycalesine butterfly Bicyclus anynana, the “Squinting bush brown,” is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illum...

Draft Genome Sequence of Pseudomonas sp. Strain Ep R1 Isolated from Echinacea purpurea Roots and Effective in the Growth Inhibition of Human Opportunistic Pathogens Belonging to the Burkholderia cepacia Complex.

Science.gov (United States)

Maggini, Valentina; Presta, Luana; Miceli, Elisangela; Fondi, Marco; Bosi, Emanuele; Chiellini, Carolina; Fagorzi, Camilla; Bogani, Patrizia; Di Pilato, Vincenzo; Rossolini, Gian Maria; Mengoni, Alessio; Firenzuoli, Fabio; Perrin, Elena; Fani, Renato

2017-05-18

In this announcement, we detail the draft genome sequence of the Pseudomonas sp. strain Ep R1, isolated from the roots of the medicinal plant Echinacea purpurea The elucidation of this genome sequence may allow the identification of genes associated with the production of antimicrobial compounds. Copyright © 2017 Maggini et al.

Genome Sequences of Two Copper-Resistant Escherichia coli Strains Isolated from Copper-Fed Pigs

DEFF Research Database (Denmark)

Lüthje, Freja L.; Hasman, Henrik; Aarestrup, Frank Møller

2014-01-01

The draft genome sequences of two copper-resistant Escherichia coli strains were determined. These had been isolated from copper-fed pigs and contained additional putative operons conferring copper and other metal and metalloid resistances.......The draft genome sequences of two copper-resistant Escherichia coli strains were determined. These had been isolated from copper-fed pigs and contained additional putative operons conferring copper and other metal and metalloid resistances....

Draft Genome Sequences of Three Multiantibiotic-Resistant Campylobacter jejuni Strains (2865, 2868, and 2871) Isolated from Poultry at Retail Outlets in Malaysia.

Science.gov (United States)

Teh, Amy Huei Teen; Lee, Sui Mae; Dykes, Gary A

2016-05-05

Campylobacter jejuni is a frequent cause of human bacterial gastrointestinal foodborne disease worldwide. Antibiotic resistance in this species is of public health concern. The draft genome sequences of three multiantibiotic-resistant C. jejuni strains (2865, 2868, and 2871) isolated from poultry at retail outlets in Malaysia are presented here. Copyright © 2016 Teh et al.

Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria.

Science.gov (United States)

Useh, Nicodemus M; Ngbede, Emmanuel O; Akange, Nguavese; Thomas, Milton; Foley, Andrew; Keena, Mitchel Chan; Nelson, Eric; Christopher-Hennings, Jane; Tomita, Masaru; Suzuki, Haruo; Scaria, Joy

2016-05-05

Here, we report the availability of draft genomes of several Salmonella serotypes, isolated from poultry sources from Nigeria. These genomes will help to further understand the biological diversity of S. enterica and will serve as references in microbial trace-back studies to improve food safety. Copyright © 2016 Useh et al.

Genome sequencing and annotation of multidrug resistant Mycobacterium tuberculosis (MDR-TB PR10 strain

Directory of Open Access Journals (Sweden)

Mohd Zakihalani A. Halim

2016-03-01

Full Text Available Here, we report the draft genome sequence and annotation of a multidrug resistant Mycobacterium tuberculosis strain PR10 (MDR-TB PR10 isolated from a patient diagnosed with tuberculosis. The size of the draft genome MDR-TB PR10 is 4.34 Mbp with 65.6% of G + C content and consists of 4637 predicted genes. The determinants were categorized by RAST into 400 subsystems with 4286 coding sequences and 50 RNAs. The whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number CP010968. Keywords: Mycobacterium tuberculosis, Genome, MDR, Extrapulmonary

Genome sequences of Listeria monocytogenes strains with resistance to arsenic

Science.gov (United States)

Listeria monocytogenes frequently exhibits resistance to arsenic. We report here the draft genome sequences of eight genetically diverse arsenic-resistant L. monocytogenes strains from human listeriosis and food-associated environments. Availability of these genomes would help to elucidate the role ...

Reducing assembly complexity of microbial genomes with single-molecule sequencing

Science.gov (United States)

Genome assembly algorithms cannot fully reconstruct microbial chromosomes from the DNA reads output by first or second-generation sequencing instruments. Therefore, most genomes are left unfinished due to the significant resources required to manually close gaps left in the draft assemblies. Single-...

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

Science.gov (United States)

2004-12-09

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile.

Science.gov (United States)

Issotta, Francisco; Galleguillos, Pedro A; Moya-Beltrán, Ana; Davis-Belmar, Carol S; Rautenbach, George; Covarrubias, Paulo C; Acosta, Mauricio; Ossandon, Francisco J; Contador, Yasna; Holmes, David S; Marín-Eliantonio, Sabrina; Quatrini, Raquel; Demergasso, Cecilia

2016-01-01

Leptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod-shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations.

Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CRL871, a Folate-Producing Strain Isolated from a Northwestern Argentinian Yogurt.

Science.gov (United States)

Laiño, Jonathan Emiliano; Hebert, Elvira María; Savoy de Giori, Graciela; LeBlanc, Jean Guy

2015-06-25

Lactobacillus delbrueckii subsp. bulgaricus CRL871 is the first strain of L. delbrueckii subsp. bulgaricus reported as a folate-producing strain. We report the draft genome sequence of L. delbrueckii subsp. bulgaricus CRL871 (2,063,981 bp, G+C content of 49.1%). This strain is of great biotechnological importance to the dairy industry because it constitutes an alternative to folic acid fortification. Copyright © 2015 Laiño et al.

Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the Poly-?-d-Glutamic Acid Anthrax Capsule

OpenAIRE

Stabler, Richard A.; Negus, David; Pain, Arnab; Taylor, Peter W.

2013-01-01

A mixed culture of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8 degraded poly-?-d-glutamic acid; when the 2 strains were cultured separately, no hydrolytic activity was apparent. Here we report the draft genome sequences of both soil isolates.

Genome Sequence of the Palaeopolyploid soybean

Energy Technology Data Exchange (ETDEWEB)

Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica; Ma, Jianxin; Mitros, Therese; Nelson, William; Hyten, David L.; Song, Qijian; Thelen, Jay J.; Cheng, Jianlin; Xu, Dong; Hellsten, Uffe; May, Gregory D.; Yu, Yeisoo; Sakura, Tetsuya; Umezawa, Taishi; Bhattacharyya, Madan K.; Sandhu, Devinder; Valliyodan, Babu; Lindquist, Erika; Peto, Myron; Grant, David; Shu, Shengqiang; Goodstein, David; Barry, Kerrie; Futrell-Griggs, Montona; Abernathy, Brian; Du, Jianchang; Tian, Zhixi; Zhu, Liucun; Gill, Navdeep; Joshi, Trupti; Libault, Marc; Sethuraman, Anand; Zhang, Xue-Cheng; Shinozaki, Kazuo; Nguyen, Henry T.; Wing, Rod A.; Cregan, Perry; Specht, James; Grimwood, Jane; Rokhsar, Dan; Stacey, Gary; Shoemaker, Randy C.; Jackson, Scott A.

2009-08-03

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70percent more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78percent of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75percent of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

Draft Genome Sequence of a Novel Lactobacillus salivarius Strain Isolated from Piglet.

Science.gov (United States)

Mackenzie, Donald A; McLay, Kirsten; Roos, Stefan; Walter, Jens; Swarbreck, David; Drou, Nizar; Crossman, Lisa C; Juge, Nathalie

2014-02-13

Lactobacillus salivarius is part of the vertebrate indigenous microbiota of the gastrointestinal tract, oral cavity, and milk. The properties associated with some L. salivarius strains have led to their use as probiotics. Here we describe the draft genome of the pig isolate L. salivarius cp400, providing insights into host-niche specialization.

Draft Genome Sequence of Acinetobacter johnsonii C6, an Environmental Isolate Engaging in Interspecific Metabolic Interactions

DEFF Research Database (Denmark)

Kaas, Rolf Sommer; Mordhorst, Hanne; Leekitcharoenphon, Pimlapas

2017-01-01

Acinetobacter johnsonii C6 originates from creosote-polluted groundwater and performs ecological and evolutionary interactions with Pseudomonas putida in biofilms. The draft genome of A. johnsonii C6 is 3.7 Mbp and was shaped by mobile genetic elements. It reveals genes facilitating the biodegrad......Acinetobacter johnsonii C6 originates from creosote-polluted groundwater and performs ecological and evolutionary interactions with Pseudomonas putida in biofilms. The draft genome of A. johnsonii C6 is 3.7 Mbp and was shaped by mobile genetic elements. It reveals genes facilitating...

Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties.

Science.gov (United States)

Yasui, Yasuo; Hirakawa, Hideki; Oikawa, Tetsuo; Toyoshima, Masami; Matsuzaki, Chiaki; Ueno, Mariko; Mizuno, Nobuyuki; Nagatoshi, Yukari; Imamura, Tomohiro; Miyago, Manami; Tanaka, Kojiro; Mise, Kazuyuki; Tanaka, Tsutomu; Mizukoshi, Hiroharu; Mori, Masashi; Fujita, Yasunari

2016-12-01

Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Draft Genome Sequence of Lactobacillus delbrueckii Strain #22 Isolated from a Patient with Short Bowel Syndrome and Previous d-Lactic Acidosis and Encephalopathy.

Science.gov (United States)

Domann, Eugen; Fischer, Florence; Glowatzki, Fabian; Fritzenwanker, Moritz; Hain, Torsten; Zechel-Gran, Silke; Giffhorn-Katz, Susanne; Neubauer, Bernd A

2016-07-28

d-Lactic acidosis with associated encephalopathy caused by overgrowth of intestinal lactic acid bacteria is a rarely diagnosed neurological complication of patients with short bowel syndrome. Here, we report the draft genome sequence of Lactobacillus delbrueckii strain #22 isolated from a patient with short bowel syndrome and previous d-lactic acidosis/encephalopathy. Copyright © 2016 Domann et al.

Draft Genome Sequences of Two Salmonella enterica Serotype Infantis Strains Isolated from a Captive Western Lowland Gorilla (Gorilla gorilla gorilla) and a Cohabitant Black and White Tegu (Tupinambis merianae) in Brazil.

Science.gov (United States)

Paixão, Tatiane A; Coura, Fernanda M; Malta, Marcelo C C; Tinoco, Herlandes P; Pessanha, Angela T; Pereira, Felipe L; Leal, Carlos A G; Heinemann, Marcos B; Figueiredo, Henrique C P; Santos, Renato L

2016-01-21

The draft genome sequences of two Salmonella enterica serotype Infantis isolates are reported here. One of the strains was isolated from a western lowland gorilla (Gorilla gorilla gorilla) with colitis. The second strain was isolated from a reptile that inhabited the same premises. Whole-genome sequencing demonstrated that these isolates were not clonal. Copyright © 2016 Paixão et al.

Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms

Science.gov (United States)

Bertolini, Francesca; Scimone, Concetta; Geraci, Claudia; Schiavo, Giuseppina; Utzeri, Valerio Joe; Chiofalo, Vincenzo; Fontanesi, Luca

2015-01-01

Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources. PMID:26151450

Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms.

Directory of Open Access Journals (Sweden)

Francesca Bertolini

Full Text Available Few studies investigated the donkey (Equus asinus at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca. The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing and Ion Torrent (RRL runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

Draft Genome Sequence of the Tyramine Producer Enterococcus durans Strain IPLA 655

Science.gov (United States)

Ladero, Victor; Linares, Daniel M.; del Rio, Beatriz; Fernandez, Maria; Martin, M. Cruz

2013-01-01

We here report a 3.059-Mbp draft assembly for the genome of Enterococcus durans strain IPLA 655. This dairy isolate provides a model for studying the regulation of the biosynthesis of tyramine (a toxic compound). These results should aid our understanding of tyramine production and allow tyramine accumulation in food to be reduced. PMID:23682153

Draft Genome Sequence of Lactobacillus kunkeei AR114 Isolated from Honey Bee Gut.

Science.gov (United States)

Porcellato, Davide; Frantzen, Cyril; Rangberg, Anbjørg; Umu, Ozgun C; Gabrielsen, Christina; Nes, Ingolf F; Amdam, Gro V; Diep, Dzung B

2015-03-19

Lactobacillus kunkeei is a common inhabitant in honey bee gut, being present in several parts of the world. Here, we describe the draft genome of L. kunkeei AR114, an isolate from late foraging season in Norway. Copyright © 2015 Porcellato et al.

Draft genome sequences of six neonatal meningitis-causing escherichia coli isolates (SP-4, SP-5, SP-13, SP-16, SP-46, and SP-65)

Science.gov (United States)

Neonatal meningitis Escherichia coli isolates (SP-4, SP-5, SP-13, SP-16, SP-46, and SP-65) were recovered from infants in the Netherlands from 1989 to 1997. Here, we report the draft genome sequences for these six E. coli isolates, which are currently being used to validate food safety processing te...

Acetone utilization by sulfate-reducing bacteria: draft genome sequence of Desulfococcus biacutus and a proteomic survey of acetone-inducible proteins

OpenAIRE

Gutiérrez Acosta, Olga B; Schleheck, David; Schink, Bernhard

2014-01-01

Background The sulfate-reducing bacterium Desulfococcus biacutus is able to utilize acetone for growth by an inducible degradation pathway that involves a novel activation reaction for acetone with CO as a co-substrate. The mechanism, enzyme(s) and gene(s) involved in this acetone activation reaction are of great interest because they represent a novel and yet undefined type of activation reaction under strictly anoxic conditions. Results In this study, a draft genome sequence of D. biacutus ...

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

Directory of Open Access Journals (Sweden)

Lincoln D Stein

2003-11-01

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

Nothing special in the specialist? Draft genome sequence of Cryomyces antarcticus, the most extremophilic fungus from Antarctica.

Directory of Open Access Journals (Sweden)

Katja Sterflinger

Full Text Available The draft genome of the Antarctic endemic fungus Cryomyces antarcticus is presented. This rock inhabiting, microcolonial fungus is extremely stress tolerant and it is a model organism for exobiology and studies on stress resistance in Eukaryots. Since this fungus is a specialist in the most extreme environment of the Earth, the analysis of its genome is of important value for the understanding of fungal genome evolution and stress adaptation. A comparison with Neurospora crassa as well as with other microcolonial fungi shows that the fungus has a genome size of 24 Mbp, which is the average in the fungal kingdom. Although sexual reproduction was never observed in this fungus, 34 mating genes are present with protein homologs in the classes Eurotiomycetes, Sordariomycetes and Dothideomycetes. The first analysis of the draft genome did not reveal any significant deviations of this genome from comparative species and mesophilic hyphomycetes.

Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis).

Science.gov (United States)

Miller, Joshua M; Moore, Stephen S; Stothard, Paul; Liao, Xiaoping; Coltman, David W

2015-05-20

Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction of a genome sequence necessitates de novo assembly which may be beyond the ability of many labs due to the large volumes of raw sequence data and extensive bioinformatics required. In contrast, the presence of a reference WGS allows for alignment which is more tractable than assembly. Recent work has highlighted that the reference need not come from the same species, potentially enabling a wide array of species WGS to be constructed using cross-species alignment. Here we report on the creation a draft WGS from a single bighorn sheep (Ovis canadensis) using alignment to the closely related domestic sheep (Ovis aries). Two sequencing libraries on SOLiD platforms yielded over 865 million reads, and combined alignment to the domestic sheep reference resulted in a nearly complete sequence (95% coverage of the reference) at an average of 12x read depth (104 SD). From this we discovered over 15 million variants and annotated them relative to the domestic sheep reference. We then conducted an enrichment analysis of those SNPs showing fixed differences between the reference and sequenced individual and found significant differences in a number of gene ontology (GO) terms, including those associated with reproduction, muscle properties, and bone deposition. Our results demonstrate that cross-species alignment enables the creation of novel WGS for non-model organisms. The bighorn sheep WGS will provide a resource for future resequencing studies or comparative genomics.

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

DEFF Research Database (Denmark)

Guo, Shaogui; Zhang, Jianguo; Sun, Honghe

2013-01-01

Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolut...

Draft Genome Sequences of 17 Isolates of the Plant Pathogenic Bacterium Dickeya

OpenAIRE

Pritchard, Leighton; Humphris, Sonia; Saddler, Gerry S.; Elphinstone, John G.; Pirhonen, Minna; Toth, Ian K.

2013-01-01

Dickeya (formerly Erwinia chrysanthemi) species cause diseases on a wide range of crops and ornamental plants worldwide. Here we present the draft sequences of 17 Dickeya isolates spanning four Dickeya species, including five isolates that are currently unassigned to a species.

Draft genome sequences of 17 isolates of the plant pathogenic bacterium dickeya.

Science.gov (United States)

Pritchard, Leighton; Humphris, Sonia; Saddler, Gerry S; Elphinstone, John G; Pirhonen, Minna; Toth, Ian K

2013-11-21

Dickeya (formerly Erwinia chrysanthemi) species cause diseases on a wide range of crops and ornamental plants worldwide. Here we present the draft sequences of 17 Dickeya isolates spanning four Dickeya species, including five isolates that are currently unassigned to a species.

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.

Science.gov (United States)

Agrawal, Sonia; Arze, Cesar; Adkins, Ricky S; Crabtree, Jonathan; Riley, David; Vangala, Mahesh; Galens, Kevin; Fraser, Claire M; Tettelin, Hervé; White, Owen; Angiuoli, Samuel V; Mahurkar, Anup; Fricke, W Florian

2017-04-27

The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in genomics projects, while eliminating the need for on-site computational resources and expertise.

Genome Sequence of the Freshwater Yangtze Finless Porpoise.

Science.gov (United States)

Yuan, Yuan; Zhang, Peijun; Wang, Kun; Liu, Mingzhong; Li, Jing; Zheng, Jingsong; Wang, Ding; Xu, Wenjie; Lin, Mingli; Dong, Lijun; Zhu, Chenglong; Qiu, Qiang; Li, Songhai

2018-04-16

The Yangtze finless porpoise ( Neophocaena asiaeorientalis ssp. asiaeorientalis ) is a subspecies of the narrow-ridged finless porpoise ( N. asiaeorientalis ). In total, 714.28 gigabases (Gb) of raw reads were generated by whole-genome sequencing of the Yangtze finless porpoise, using an Illumina HiSeq 2000 platform. After filtering the low-quality and duplicated reads, we assembled a draft genome of 2.22 Gb, with contig N50 and scaffold N50 values of 46.69 kilobases (kb) and 1.71 megabases (Mb), respectively. We identified 887.63 Mb of repetitive sequences and predicted 18,479 protein-coding genes in the assembled genome. The phylogenetic tree showed a relationship between the Yangtze finless porpoise and the Yangtze River dolphin, which diverged approximately 20.84 million years ago. In comparisons with the genomes of 10 other mammals, we detected 44 species-specific gene families, 164 expanded gene families, and 313 positively selected genes in the Yangtze finless porpoise genome. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information under BioProject accession number PRJNA433603.

Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the Poly- -D-Glutamic Acid Anthrax Capsule

KAUST Repository

Stabler, R. A.

2013-01-24

A mixed culture of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8 degraded poly-γ-d-glutamic acid; when the 2 strains were cultured separately, no hydrolytic activity was apparent. Here we report the draft genome sequences of both soil isolates.

Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the Poly-γ-d-Glutamic Acid Anthrax Capsule.

Science.gov (United States)

Stabler, Richard A; Negus, David; Pain, Arnab; Taylor, Peter W

2013-01-01

A mixed culture of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8 degraded poly-γ-d-glutamic acid; when the 2 strains were cultured separately, no hydrolytic activity was apparent. Here we report the draft genome sequences of both soil isolates.

Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the Poly- -D-Glutamic Acid Anthrax Capsule

KAUST Repository

Stabler, R. A.; Negus, D.; Pain, Arnab; Taylor, P. W.

2013-01-01

A mixed culture of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8 degraded poly-γ-d-glutamic acid; when the 2 strains were cultured separately, no hydrolytic activity was apparent. Here we report the draft genome sequences of both soil isolates.

Single molecule sequencing-guided scaffolding and correction of draft assemblies.

Science.gov (United States)

Zhu, Shenglong; Chen, Danny Z; Emrich, Scott J

2017-12-06

Although single molecule sequencing is still improving, the lengths of the generated sequences are inevitably an advantage in genome assembly. Prior work that utilizes long reads to conduct genome assembly has mostly focused on correcting sequencing errors and improving contiguity of de novo assemblies. We propose a disassembling-reassembling approach for both correcting structural errors in the draft assembly and scaffolding a target assembly based on error-corrected single molecule sequences. To achieve this goal, we formulate a maximum alternating path cover problem. We prove that this problem is NP-hard, and solve it by a 2-approximation algorithm. Our experimental results show that our approach can improve the structural correctness of target assemblies in the cost of some contiguity, even with smaller amounts of long reads. In addition, our reassembling process can also serve as a competitive scaffolder relative to well-established assembly benchmarks.

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line

DEFF Research Database (Denmark)

Xu, Xun; Pan, Shengkai; Liu, Xin

2011-01-01

Chinese hamster ovary (CHO)-derived cell lines are the preferred host cells for the production of therapeutic proteins. Here we present a draft genomic sequence of the CHO-K1 ancestral cell line. The assembly comprises 2.45 Gb of genomic sequence, with 24,383 predicted genes. We associate most of...

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence.

Directory of Open Access Journals (Sweden)

Atteyet F Yassin

Full Text Available The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM systems, type II toxin-antitoxin (TA, CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA and topisomerase IV (ParC enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

Science.gov (United States)

Mavromatis, Konstantinos; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, Alex; Clum, Alicia; Goodwin, Lynne; Woyke, Tanja; Lapidus, Alla; Klenk, Hans Peter; Cottingham, Robert W; Kyrpides, Nikos C

2012-01-01

The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

Draft Genome Sequence of Marine Sponge Symbiont Pseudoalteromonas luteoviolacea IPB1, Isolated from Hilo, Hawaii.

Science.gov (United States)

Sakai-Kawada, Francis E; Yakym, Christopher J; Helmkampf, Martin; Hagiwara, Kehau; Ip, Courtney G; Antonio, Brandi J; Armstrong, Ellie; Ulloa, Wesley J; Awaya, Jonathan D

2016-09-22

We report here the 6.0-Mb draft genome assembly of Pseudoalteromonas luteoviolacea strain IPB1 that was isolated from the Hawaiian marine sponge Iotrochota protea Genome mining complemented with bioassay studies will elucidate secondary metabolite biosynthetic pathways and will help explain the ecological interaction between host sponge and microorganism. Copyright © 2016 Sakai-Kawada et al.

Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata.

Science.gov (United States)

Meyer, Julie L; Dillard, Brian A; Rodgers, John M; Ritchie, Kim B; Paul, Valerie J; Teplitski, Max

2015-01-01

Members of the gammaproteobacterial genus Halomonas are common in marine environments. Halomonas and other members of the Oceanospirillales have recently been identified as prominent members of the surface microbiota of reef-building corals. Halomonas meridiana strain R1t3 was isolated from the surface mucus layer of the scleractinian coral Acropora palmata in 2005 from the Florida Keys. This strain was chosen for genome sequencing to provide insight into the role of commensal heterotrophic bacteria in the coral holobiont. The draft genome consists of 290 scaffolds, totaling 3.5 Mbp in length and contains 3397 protein-coding genes.

The genome sequence of the model ascomycete fungus Podospora anserina

NARCIS (Netherlands)

Espagne, Eric; Lespinet, Olivier; Malagnac, Fabienne; Da Silva, Corinne; Jaillon, Olivier; Porcel, Betina M; Couloux, Arnaud; Aury, Jean-Marc; Ségurens, Béatrice; Poulain, Julie; Anthouard, Véronique; Grossetete, Sandrine; Khalili, Hamid; Coppin, Evelyne; Déquard-Chablat, Michelle; Picard, Marguerite; Contamine, Véronique; Arnaise, Sylvie; Bourdais, Anne; Berteaux-Lecellier, Véronique; Gautheret, Daniel; de Vries, Ronald P; Battaglia, Evy; Coutinho, Pedro M; Danchin, Etienne Gj; Henrissat, Bernard; Khoury, Riyad El; Sainsard-Chanet, Annie; Boivin, Antoine; Pinan-Lucarré, Bérangère; Sellem, Carole H; Debuchy, Robert; Wincker, Patrick; Weissenbach, Jean; Silar, Philippe

2008-01-01

BACKGROUND: The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development. RESULTS: We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed

Draft genome of the fungus-growing termite pathogenic fungus Ophiocordyceps bispora (Ophiocordycipitaceae, Hypocreales, Ascomycota

Directory of Open Access Journals (Sweden)

Benjamin H. Conlon

2017-04-01

Full Text Available This article documents the public availability of genome sequence data and assembled contigs representing the partial draft genome of Ophiocordyceps bispora. As one of the few known pathogens of fungus-farming termites, a draft genome of O. bispora represents the opportunity to further the understanding of disease and resistance in these complex termite societies. With the ongoing attempts to resolve the taxonomy of the Hypocralaean family, more genetic data will also help to shed light on the phylogenetic relationship between sexual and asexual life stages. Next generation sequence data is available from the European Nucleotide Archive (ENA under accession PRJEB13655; run numbers: ERR1368522, ERR1368523, and ERR1368524. Genome assembly available from ENA under accession numbers: FKNF01000001–FKNF01000302. Gene prediction available as protein fasta, nucleotide fasta and GFF file from Mendeley Data with accession doi:10.17632/r99fd6g3s4.2 (http://dx.doi.org/10.17632/r99fd6g3s4.2.

Draft genomes of the corallimorpharians Amplexidiscus fenestrafer and Discosoma sp

KAUST Repository

Wang, Xin

2017-04-13

Corallimorpharia are the closest non-calcifying relatives of reef-building corals. Aside from their popularity among aquarium hobbyists, their evolutionary position between the Actiniaria (sea anemones) and the Scleractinia (hard corals) makes them ideal candidates for comparative studies aiming at understanding the evolution of hexacorallian orders in general and reef-building corals in particular. Here we have sequenced and assembled two draft genomes for the Corallimorpharia species Amplexidiscus fenestrafer and Discosoma sp.. The draft genomes encompass 370 Mbp and 445 Mbp respectively and encode for 21,372 and 23,199 genes. To facilitate future studies using these resources, we provide annotations for the predicted gene models-not only at gene level, by annotating gene models with the function of the best-matching homolog, and GO terms when available; but also at protein domain level, where gene function can be better verified through the conservation of the sequence and order of protein domains. Further, we provide an online platform (http://corallimorpharia.reefgenomics.org), which includes a BLAST interface as well as a genome browser to facilitate the use of these resources. We believe that these two genomes are important resources for future studies on hexacorallian systematics and the evolutionary basis of their specific traits such as the symbiotic relationship with dinoflagellates of the genus Symbiodinium or the evolution of calcification in reef-building corals. This article is protected by copyright. All rights reserved.

Getting complete genomes from complex samples using nanopore sequencing

DEFF Research Database (Denmark)

Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Albertsen, Mads

Background Short read DNA sequencing and metagenomic binning workflows have made it possible to extract bacterial genome bins from environmental microbial samples containing hundreds to thousands of different species. However, these genome bins often do not represent complete genomes......, as they are mostly fragmented, incomplete and often contaminated with foreign DNA. The value of these `draft genomes` have limited, lasting value to the scientific community, as gene synteny is broken and there is some uncertainty of what is missing1. The genetic material most often missed is important multi......-copy and/or conserved marker genes such as the 16S rRNA gene, as sequence micro-heterogeneity prevents assembly of these genes in the de novo assembly. However, long read sequencing technologies are emerging promising an end to fragmented genome assemblies2. Experimental design We extracted DNA from a full...

The draft genome sequence of multidrug-resistant Pseudomonas aeruginosa strain CCBH4851, a nosocomial isolate belonging to clone SP (ST277 that is prevalent in Brazil

Directory of Open Access Journals (Sweden)

Melise Silveira

2014-12-01

Full Text Available The high occurrence of nosocomial multidrug-resistant (MDR microorganisms is considered a global health problem. Here, we report the draft genome sequence of a MDR Pseudomonas aeruginosa strain isolated in Brazil that belongs to the endemic clone ST277. The genome encodes important resistance determinant genes and consists of 6.7 Mb with a G+C content of 66.86% and 6,347 predicted coding regions including 60 RNAs.

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

OpenAIRE

Agrawal, Sonia; Arze, Cesar; Adkins, Ricky S.; Crabtree, Jonathan; Riley, David; Vangala, Mahesh; Galens, Kevin; Fraser, Claire M.; Tettelin, Herv?; White, Owen; Angiuoli, Samuel V.; Mahurkar, Anup; Fricke, W. Florian

2017-01-01

Background The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. Results CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. ...

Draft genome sequences of Phytophthora kernoviae and Phytophthora ramorum lineage EU2 from Scotland

Directory of Open Access Journals (Sweden)

Christine Sambles

2015-12-01

Full Text Available Newly discovered Phytophthora species include invasive pathogens that threaten trees and shrubs. We present draft genome assemblies for three isolates of Phytophthora kernoviae and one isolate of the EU2 lineage of Phytophthora ramorum, collected from outbreak sites in Scotland.

High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain.

Science.gov (United States)

Osman, Wan Adnawani Meor; van Berkum, Peter; León-Barrios, Milagros; Velázquez, Encarna; Elia, Patrick; Tian, Rui; Ardley, Julie; Gollagher, Margaret; Seshadri, Rekha; Reddy, T B K; Ivanova, Natalia; Woyke, Tanja; Pati, Amrita; Markowitz, Victor; Baeshen, Mohamed N; Baeshen, Naseebh Nabeeh; Kyrpides, Nikos; Reeve, Wayne

2017-01-01

10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata . This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T , 10.1601/nm.1334 A 321 T and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T , based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata -nodulating 10.1601/nm.1328 strains, but ≤93% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic

High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond

DEFF Research Database (Denmark)

Gong, Xianzhe; Skrivergaard, Stig; Korsgaard, Benjamin

2017-01-01

denitrification, and fermentation. The draft genome of strain S3-2T has a size of ~5.8 Mbp and contains 5,297 genes, including 115 RNA genes. Based on the phenotypic properties of the strain, the low in silico DNA-DNA hybridization (DDH) values with related genomes (

The draft genome of tropical fruit durian (Durio zibethinus).

Science.gov (United States)

Teh, Bin Tean; Lim, Kevin; Yong, Chern Han; Ng, Cedric Chuan Young; Rao, Sushma Ramesh; Rajasegaran, Vikneswari; Lim, Weng Khong; Ong, Choon Kiat; Chan, Ki; Cheng, Vincent Kin Yuen; Soh, Poh Sheng; Swarup, Sanjay; Rozen, Steven G; Nagarajan, Niranjan; Tan, Patrick

2017-11-01

Durian (Durio zibethinus) is a Southeast Asian tropical plant known for its hefty, spine-covered fruit and sulfury and onion-like odor. Here we present a draft genome assembly of D. zibethinus, representing the third plant genus in the Malvales order and first in the Helicteroideae subfamily to be sequenced. Single-molecule sequencing and chromosome contact maps enabled assembly of the highly heterozygous durian genome at chromosome-scale resolution. Transcriptomic analysis showed upregulation of sulfur-, ethylene-, and lipid-related pathways in durian fruits. We observed paleopolyploidization events shared by durian and cotton and durian-specific gene expansions in MGL (methionine γ-lyase), associated with production of volatile sulfur compounds (VSCs). MGL and the ethylene-related gene ACS (aminocyclopropane-1-carboxylic acid synthase) were upregulated in fruits concomitantly with their downstream metabolites (VSCs and ethylene), suggesting a potential association between ethylene biosynthesis and methionine regeneration via the Yang cycle. The durian genome provides a resource for tropical fruit biology and agronomy.

Permanent draft genomes of the three Rhodopirellula baltica strains SH28, SWK14 and WH47.

Science.gov (United States)

Richter, Michael; Richter-Heitmann, Tim; Klindworth, Anna; Wegner, Carl-Eric; Frank, Carsten S; Harder, Jens; Glöckner, Frank Oliver

2014-02-01

The genomes of three Rhodopirellula baltica strains were sequenced as permanent drafts to complement the full genome sequence of the type strain R. baltica SH1(T). The isolates are part of a larger study to infer the biogeography of Rhodopirellula species in European marine waters, as well as to amend the genus description of R. baltica. This genomics resource article is the first of a series of five publications reporting in total eight new permanent daft genomes of Rhodopirellula species. Copyright © 2013 Elsevier B.V. All rights reserved.

The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species.

Science.gov (United States)

Gilchrist, Anthony Stuart; Shearman, Deborah C A; Frommer, Marianne; Raphael, Kathryn A; Deshpande, Nandan P; Wilkins, Marc R; Sherwin, William B; Sved, John A

2014-12-20

The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. In Australia, there exists a triad of closely-related, sympatric Bactrocera species which do not mate in the wild but which, despite distinct morphologies and behaviours, can be force-mated in the laboratory to produce fertile hybrid offspring. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations. We produced a draft de novo genome assembly of Australia's major tephritid pest species, Bactrocera tryoni. The male genome (650-700 Mbp) includes approximately 150 Mb of interspersed repetitive DNA sequences and 60 Mb of satellite DNA. Assessment using conserved core eukaryotic sequences indicated 98% completeness. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. The sequence of the ribosomal RNA transcribed unit was also determined. Unscaffolded assemblies of B. neohumeralis and B. jarvisi were then produced; comparison with B. tryoni showed that the species are more closely related than any Drosophila species pair. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions. This first draft B. tryoni genome resembles other dipteran genomes in terms of size and putative coding sequences. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA

Genome sequence of a urease-positive Campylobacter lari strain

Science.gov (United States)

Campylobacter lari is frequently isolated from shore birds and can cause illness in humans. Here we report the draft whole genome sequence of an urease-positive strain of C. lari that was isolated in estuarial water on the coast of Delaware, USA....

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

Science.gov (United States)

Aversano, Riccardo; Contaldi, Felice; Ercolano, Maria Raffaella; Grosso, Valentina; Iorizzo, Massimo; Tatino, Filippo; Xumerle, Luciano; Dal Molin, Alessandra; Avanzato, Carla; Ferrarini, Alberto; Delledonne, Massimo; Sanseverino, Walter; Cigliano, Riccardo Aiese; Capella-Gutierrez, Salvador; Gabaldón, Toni; Frusciante, Luigi; Bradeen, James M.; Carputo, Domenico

2015-01-01

Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes. PMID:25873387

Draft Genome Sequence of Halostagnicola sp. A56, an Extremely Halophilic Archaeon Isolated from the Andaman Islands

Science.gov (United States)

Kanekar, Sagar P.; Saxena, Neha; Pore, Soham D.; Arora, Preeti; Kanekar, P. P.

2015-01-01

The first draft genome of Halostagnicola sp. A56, isolated from the Andaman Islands is reported here. The A56 genome comprises 3,178,490 bp in 26 contigs with a G+C content of 60.8%. The genome annotation revealed that A56 could have potential applications for the production of polyhydroxyalkanoate or bioplastics. PMID:26564049

Draft Genome Sequence of the Nicotinate-Metabolizing Soil Bacterium Bacillus niacini DSM 2923.

Science.gov (United States)

Harvey, Zachary H; Snider, Mark J

2014-12-04

Bacillus niacini is a member of a small yet diverse group of bacteria able to catabolize nicotinic acid. We report here the availability of a draft genome for B. niacini, which we will use to understand the evolution of its namesake phenotype, which appears to be unique among the species in its phylogenetic neighborhood. Copyright © 2014 Harvey and Snider.

Draft Genome Sequences of Two Avian Pathogenic Escherichia coli Strains of Clinical Importance, E44 and E51

DEFF Research Database (Denmark)

Ronco, Troels; Stegger, Marc; Andersen, Paal S

2016-01-01

Avian pathogenic Escherichia coli strains have remarkable impacts on animal welfare and the production economy in the poultry industry worldwide. Here, we present the draft genomes of two isolates from chickens (E44 and E51) obtained from field outbreaks and subsequently investigated for their po......Avian pathogenic Escherichia coli strains have remarkable impacts on animal welfare and the production economy in the poultry industry worldwide. Here, we present the draft genomes of two isolates from chickens (E44 and E51) obtained from field outbreaks and subsequently investigated...

The genome sequence of four isolates from the family Lichtheimiaceae.

Science.gov (United States)

Chibucos, Marcus C; Etienne, Kizee A; Orvis, Joshua; Lee, Hongkyu; Daugherty, Sean; Lockhart, Shawn R; Ibrahim, Ashraf S; Bruno, Vincent M

2015-07-01

This study reports the release of draft genome sequences of two isolates of Lichtheimia corymbifera and two isolates of L. ramosa. Phylogenetic analyses indicate that the two L. corymbifera strains (CDC-B2541 and 008-049) are closely related to the previously sequenced L. corymbifera isolate (FSU 9682) while our two L. ramosa strains CDC-B5399 and CDC-B5792 cluster apart from them. These genome sequences will further the understanding of intraspecies and interspecies genetic variation within the Mucoraceae family of pathogenic fungi. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Draft Genome Sequence of Clostridium sp. Strain NJ4, a Bacterium Capable of Producing Butanol from Inulin Through Consolidated Bioprocessing.

Science.gov (United States)

Jiang, Yujia; Lu, Jiasheng; Chen, Tianpeng; Yan, Wei; Dong, Weiliang; Zhou, Jie; Zhang, Wenming; Ma, Jiangfeng; Jiang, Min; Xin, Fengxue

2018-05-23

A novel butanogenic Clostridium sp. NJ4 was successfully isolated and characterized, which could directly produce relatively high titer of butanol from inulin through consolidated bioprocessing (CBP). The assembled draft genome of strain NJ4 is 4.09 Mp, containing 3891 encoded protein sequences with G+C content of 30.73%. Among these annotated genes, a levanase, a hypothetical inulinase, and two bifunctional alcohol/aldehyde dehydrogenases (AdhE) were found to play key roles in the achievement of ABE production from inulin through CBP.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

DEFF Research Database (Denmark)

Gibbs, Richard A; Weinstock, George M; Metzker, Michael L

2004-01-01

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering ove...

Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4

OpenAIRE

Masuda, Shinji; Hori, Koichi; Maruyama, Fumito; Ren, Shukun; Sugimoto, Saori; Yamamoto, Nozomi; Mori, Hiroshi; Yamada, Takuji; Sato, Shusei; Tabata, Satoshi; Ohta, Hiroyuki; Kurokawa, Ken

2013-01-01

We report the draft genome sequence of the purple photosynthetic bacterium Rhodovulum sulfidophilum. The photosynthesis gene cluster comprises two segments?a unique feature among photosynthesis gene clusters of purple bacteria. The genome information will be useful for further analysis of bacterial photosynthesis.

Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598.

Science.gov (United States)

Ardley, Julie; Tian, Rui; Howieson, John; Yates, Ron; Bräu, Lambert; Han, James; Lobos, Elizabeth; Huntemann, Marcel; Chen, Amy; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Pati, Amrita; Goodwin, Lynne; Woyke, Tanja; Kyrpides, Nikos; Reeve, Wayne

2014-01-01

Strains of a pink-pigmented Methylobacterium sp. are effective nitrogen- (N2) fixing microsymbionts of species of the African crotalarioid genus Listia. Strain WSM2598 is an aerobic, motile, Gram-negative, non-spore-forming rod isolated in 2002 from a Listia bainesii root nodule collected at Estcourt Research Station in South Africa. Here we describe the features of Methylobacterium sp. WSM2598, together with information and annotation of a high-quality draft genome sequence. The 7,669,765 bp draft genome is arranged in 5 scaffolds of 83 contigs, contains 7,236 protein-coding genes and 18 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 G enomic E ncyclopedia for B acteria and A rchaea- R oot N odule B acteria (GEBA-RNB) project.

Genome Sequence of Antibiotic-Producing Bacillus amyloliquefaciens Strain KCTC 13012.

Science.gov (United States)

Jeong, Haeyoung; Park, Seung-Hwan; Choi, Soo-Keun

2015-10-01

We report the 4.0-Mb draft genome sequence of Bacillus amyloliquefaciens (syn. Bacillus velezensis) KCTC 13012, which exhibits a broad spectrum of antagonistic activity against bacteria and fungi and promotes plant growth as well. The genome contains an array of biosynthetic gene clusters for secondary metabolites that are comparable to those in Bacillus amyloliquefaciens subsp. plantarum FZB42(T). Copyright © 2015 Jeong et al.

Getting complete genomes from complex samples using nanopore sequencing

DEFF Research Database (Denmark)

Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Albertsen, Mads

Short read sequencing and metagenomic binning workflows have made it possible to extract bacterial genome bins from environmental microbial samples containing hundreds to thousands of different species. However, these genome bins often do not represent complete genomes, as they are mostly...... fragmented, incomplete and often contaminated with foreign DNA and with no robust strategies to validate the quality. The value of these `draft genomes` have limited, lasting value to the scientific community, as gene synteny is broken and the uncertainty of what is missing. The genetic material most often...... missed is important multi-copy and/or conserved marker genes such as the 16S rRNA gene, as sequence micro-heterogeneity prevents assembly of these genes in the de novo assembly. We demonstrate that using nanopore long reads it is now possible to overcome these issues and make complete genomes from...

Draft genome sequence of Bacillus toyonensis VU-DES13, isolated from Folsomia candida (Collembola: Entomobryidae)

NARCIS (Netherlands)

Janssens, T.K.S.; de Boer, T.E.; Agamennone, V.; Zaagman, N.; van Straalen, N.M.; Roelofs, T.F.M.

2017-01-01

We present here the draft genome of Bacillus toyonensis VU-DES13, which was isolated from the midgut of the soil-living springtail Folsomia candida. Previous research revealed the presence of gene clusters for the biosynthesis of various secondary metabolites, including -lactam antibiotics, in the

High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain hu-01.

Science.gov (United States)

Hu, XinJun; Li, Ang; Lv, LongXian; Yuan, Chunhui; Guo, Lihua; Jiang, Xiawei; Jiang, Haiyin; Qian, GuiRong; Zheng, BeiWen; Guo, Jing; Li, LanJuan

2014-06-15

Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order Bacillales, class Bacilli and phylum Firmicutes. The increasing relevance of S. cohnii to human health prompted us to determine the genomic sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a multidrug-resistant isolate from a hospital in China. Here we describe the features of S. cohnii subsp. cohnii strain hu-01, together with the genome sequence and its annotation. This is the first genome sequence of the species Staphylococcus cohnii.

Permanent draft genomes of the two Rhodopirellula europaea strains 6C and SH398.

Science.gov (United States)

Richter-Heitmann, Tim; Richter, Michael; Klindworth, Anna; Wegner, Carl-Eric; Frank, Carsten S; Glöckner, Frank Oliver; Harder, Jens

2014-02-01

The genomes of two Rhodopirellula europaea strains were sequenced as permanent drafts to study the genomic diversity within this genus, especially in comparison with the closed genome of the type strain Rhodopirellula baltica SH1(T). The isolates are part of a larger study to infer the biogeography of Rhodopirellula species in European marine waters, as well as to amend the genus description of R. baltica. This genomics resource article is the second of a series of five publications describing a total of eight new permanent daft genomes of Rhodopirellula species. Copyright © 2013 Elsevier B.V. All rights reserved.

Draft genome of the lined seahorse, Hippocampus erectus.

Science.gov (United States)

Lin, Qiang; Qiu, Ying; Gu, Ruobo; Xu, Meng; Li, Jia; Bian, Chao; Zhang, Huixian; Qin, Geng; Zhang, Yanhong; Luo, Wei; Chen, Jieming; You, Xinxin; Fan, Mingjun; Sun, Min; Xu, Pao; Venkatesh, Byrappa; Xu, Junming; Fu, Hongtuo; Shi, Qiong

2017-06-01

The lined seahorse, Hippocampus erectus , is an Atlantic species and mainly inhabits shallow sea beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly, and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding. A total of 174.6 Gb (Gigabase) raw DNA sequences were generated by the Illumina Hiseq2500 platform. The final assembly of the lined seahorse genome is around 458 Mb, representing 94% of the estimated genome size (489 Mb by k-mer analysis). The contig N50 and scaffold N50 reached 14.57 kb and 1.97 Mb, respectively. Quality of the assembled genome was assessed by BUSCO with prediction of 85% of the known vertebrate genes and evaluated using the de novo assembled RNA-seq transcripts to prove a high mapping ratio (more than 99% transcripts could be mapped to the assembly). Using homology-based, de novo and transcriptome-based prediction methods, we predicted 20 788 protein-coding genes in the generated assembly, which is less than our previously reported gene number (23 458) of the tiger tail seahorse ( H. comes ). We report a draft genome of the lined seahorse. These generated genomic data are going to enrich genome resource of this economically important fish, and also provide insights into the genetic mechanisms of its iconic morphology and male pregnancy behavior. © The Authors 2017. Published by Oxford University Press.

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

NARCIS (Netherlands)

Abad, P.; Gouzy, J.; Aury, J.M.; Tytgat, T.O.G.; Smant, G.

2008-01-01

Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the

Draft Genome Sequence of Rhizobium sp. Strain TBD182, an Antagonist of the Plant-Pathogenic Fungus Fusarium oxysporum, Isolated from a Novel Hydroponics System Using Organic Fertilizer.

Science.gov (United States)

Iida, Yuichiro; Fujiwara, Kazuki; Someya, Nobutaka; Shinohara, Makoto

2017-03-16

Rhizobium sp. strain TBD182, isolated from a novel hydroponics system, is an antagonistic bacterium that inhibits the mycelial growth of Fusarium oxysporum but does not eliminate the pathogen. We report the draft genome sequence of TBD182, which may contribute to elucidation of the molecular mechanisms of its fungistatic activity. Copyright © 2017 Iida et al.

Acetone utilization by sulfate-reducing bacteria: draft genome sequence of Desulfococcus biacutus and a proteomic survey of acetone-inducible proteins.

Science.gov (United States)

Gutiérrez Acosta, Olga B; Schleheck, David; Schink, Bernhard

2014-07-11

The sulfate-reducing bacterium Desulfococcus biacutus is able to utilize acetone for growth by an inducible degradation pathway that involves a novel activation reaction for acetone with CO as a co-substrate. The mechanism, enzyme(s) and gene(s) involved in this acetone activation reaction are of great interest because they represent a novel and yet undefined type of activation reaction under strictly anoxic conditions. In this study, a draft genome sequence of D. biacutus was established. Sequencing, assembly and annotation resulted in 159 contigs with 5,242,029 base pairs and 4773 predicted genes; 4708 were predicted protein-encoding genes, and 3520 of these had a functional prediction. Proteins and genes were identified that are specifically induced during growth with acetone. A thiamine diphosphate-requiring enzyme appeared to be highly induced during growth with acetone and is probably involved in the activation reaction. Moreover, a coenzyme B12- dependent enzyme and proteins that are involved in redox reactions were also induced during growth with acetone. We present for the first time the genome of a sulfate reducer that is able to grow with acetone. The genome information of this organism represents an important tool for the elucidation of a novel reaction mechanism that is employed by a sulfate reducer in acetone activation.

Genome sequence of the olive tree, Olea europaea.

Science.gov (United States)

Cruz, Fernando; Julca, Irene; Gómez-Garrido, Jèssica; Loska, Damian; Marcet-Houben, Marina; Cano, Emilio; Galán, Beatriz; Frias, Leonor; Ribeca, Paolo; Derdak, Sophia; Gut, Marta; Sánchez-Fernández, Manuel; García, Jose Luis; Gut, Ivo G; Vargas, Pablo; Alioto, Tyler S; Gabaldón, Toni

2016-06-27

The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line

DEFF Research Database (Denmark)

Xu, Xun; Pan, Shengkai; Liu, Xin

2011-01-01

Chinese hamster ovary (CHO)-derived cell lines are the preferred host cells for the production of therapeutic proteins. Here we present a draft genomic sequence of the CHO-K1 ancestral cell line. The assembly comprises 2.45 Gb of genomic sequence, with 24,383 predicted genes. We associate most....... Homologs of most human glycosylation-associated genes are present in the CHO-K1 genome, although 141 of these homologs are not expressed under exponential growth conditions. Many important viral entry genes are also present in the genome but not expressed, which may explain the unusual viral resistance...... property of CHO cell lines. We discuss how the availability of this genome sequence may facilitate genome-scale science for the optimization of biopharmaceutical protein production....

Draft genome analysis of Dietzia sp. 111N12-1, isolated from the South China Sea with bioremediation activity.

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Yang, Shanjun; Yu, Mingjia; Chen, Jianming

Dietzia sp. 111N12-1, isolated from the seawater of South China Sea, shows strong petroleum hydrocarbons degradation activity. Here, we report the draft sequence of approximately 3.7-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Dietzia strain isolated from the sea. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of hydrocarbons degradation in this strain. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing

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Muammar eMansor

2015-08-01

Full Text Available Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cultured or sequenced using environmental genomics approaches to date. We utilized single-cell genomic sequencing to obtain one incomplete and two nearly complete draft genomes for Achromatium collected at Warm Mineral Springs, FL. Based on 16S rRNA gene sequences, the three cells represent distinct and relatively distant Achromatium populations (91-92% identity. The draft genomes encode key genes involved in sulfur and hydrogen oxidation; oxygen, nitrogen and polysulfide respiration; carbon and nitrogen fixation; organic carbon assimilation and storage; chemotaxis; twitching motility; antibiotic resistance; and membrane transport. Known genes for iron and manganese energy metabolism were not detected. The presence of pyrophosphatase and vacuolar (V-type ATPases, which are generally rare in bacterial genomes, suggests a role for these enzymes in calcium transport, proton pumping, and/or energy generation in the membranes of calcite-containing inclusions.

Draft Genome Sequence of Bacillus sp. FMQ74, a Dairy-contaminating Isolate from Raw Milk

DEFF Research Database (Denmark)

Okshevsky, Mira Ursula; Regina, Viduthalai R.; Marshall, Ian

2017-01-01

Representatives of the genus Bacillus are common milk contaminants that cause spoilage and flavor alterations of dairy products. Bacillus sp. FMQ74 was isolated from raw milk on a Danish dairy farm. To elucidate the genomic basis of this strain’s survival in the dairy industry, a high-quality draft...

Three draft genomes of Vibrio coralliilyticus strains isolated from bivalve hatcheries

Science.gov (United States)

Reported here are the draft genomes of three Vibrio coralliilyticus isolates RE87, AIC-7, and 080116A. Each strain was isolated in association with diseased oyster larvae in commercial aquaculture systems. These draft genomes will be useful for further studies in understanding the genomic features...

Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

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Xu Xiangming

2010-12-01

Full Text Available Abstract Background Determining the position and order of contigs and scaffolds from a genome assembly within an organism's genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method. Results The strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for V. inaequalis and F. vesca, respectively, to genetic linkage maps. Conclusions We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.

Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti.

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Ahn, Do-Hwan; Shin, Seung Chul; Kim, Bo-Mi; Kang, Seunghyun; Kim, Jin-Hyoung; Ahn, Inhye; Park, Joonho; Park, Hyun

2017-08-01

The Antarctic bathydraconid dragonfish, Parachaenichthys charcoti, is an Antarctic notothenioid teleost endemic to the Southern Ocean. The Southern Ocean has cooled to -1.8ºC over the past 30 million years, and the seawater had retained this cold temperature and isolated oceanic environment because of the Antarctic Circumpolar Current. Notothenioids dominate Antarctic fish, making up 90% of the biomass, and all notothenioids have undergone molecular and ecological diversification to survive in this cold environment. Therefore, they are considered an attractive Antarctic fish model for evolutionary and ancestral genomic studies. Bathydraconidae is a speciose family of the Notothenioidei, the dominant taxonomic component of Antarctic teleosts. To understand the process of evolution of Antarctic fish, we select a typical Antarctic bathydraconid dragonfish, P. charcoti. Here, we have sequenced, de novo assembled, and annotated a comprehensive genome from P. charcoti. The draft genome of P. charcoti is 709 Mb in size. The N50 contig length is 6145 bp, and its N50 scaffold length 178 362 kb. The genome of P. charcoti is predicted to contain 32 712 genes, 18 455 of which have been assigned preliminary functions. A total of 8951 orthologous groups common to 7 species of fish were identified, while 333 genes were identified in P. charcoti only; 2519 orthologous groups were also identified in both P. charcoti and N. coriiceps, another Antarctic fish. Four gene ontology terms were statistically overrepresented among the 333 genes unique to P. charcoti, according to gene ontology enrichment analysis. The draft P. charcoti genome will broaden our understanding of the evolution of Antarctic fish in their extreme environment. It will provide a basis for further investigating the unusual characteristics of Antarctic fishes. © The Author 2017. Published by Oxford University Press.

Whole genome sequencing of Mycobacterium tuberculosis SB24 isolated from Sabah, Malaysia

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Noraini Philip

2016-09-01

Full Text Available Mycobacterium tuberculosis (M. tuberculosis is the causative agent of tuberculosis (TB that causes millions of death every year. We have sequenced the genome of M. tuberculosis isolated from cerebrospinal fluid (CSF of a patient diagnosed with tuberculous meningitis (TBM. The isolated strain was referred as M. tuberculosis SB24. Genomic DNA of the M. tuberculosis SB24 was extracted and subjected to whole genome sequencing using PacBio platform. The draft genome size of M. tuberculosis SB24 was determined to be 4,452,489 bp with a G + C content of 65.6%. The whole genome shotgun project has been deposited in NCBI SRA under the accession number SRP076503.

Permanent Draft Genome of Strain ESFC-1: Ecological Genomics of a Newly Discovered Lineage of Filamentous Diazotrophic Cyanobacteria

Science.gov (United States)

Everroad, R. Craig; Stuart, Rhona K.; Bebout, Brad M.; Detweiler, Angela M.; Lee, Jackson Zan; Woebken, Dagmar; Bebout, Leslie E.; Pett-Ridge, Jennifer

2016-01-01

The nonheterocystous filamentous cyanobacterium, strain ESFC-1, is a recently described member of the order Oscillatoriales within the Cyanobacteria. ESFC-1 has been shown to be a major diazotroph in the intertidal microbial mat system at Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16S RNA gene, ESFC-1 appears to belong to a unique, genus-level divergence; the draft genome sequence of this strain has now been determined. Here we report features of this genome as they relate to the ecological functions and capabilities of strain ESFC-1. The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92 RNA genes. One striking feature of this cyanobacterium is the apparent lack of either uptake or bi-directional hydrogenases typically expected within a diazotroph. Additionally, a large genomic island is found that contains numerous low GC-content genes and genes related to extracellular polysaccharide production and cell wall synthesis and maintenance.

The sequence and de novo assembly of the giant panda genome

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Li, Ruiqiang; Fan, Wei; Tian, Geng; Zhu, Hongmei; He, Lin; Cai, Jing; Huang, Quanfei; Cai, Qingle; Li, Bo; Bai, Yinqi; Zhang, Zhihe; Zhang, Yaping; Wang, Wen; Li, Jun; Wei, Fuwen; Li, Heng; Jian, Min; Li, Jianwen; Zhang, Zhaolei; Nielsen, Rasmus; Li, Dawei; Gu, Wanjun; Yang, Zhentao; Xuan, Zhaoling; Ryder, Oliver A.; Leung, Frederick Chi-Ching; Zhou, Yan; Cao, Jianjun; Sun, Xiao; Fu, Yonggui; Fang, Xiaodong; Guo, Xiaosen; Wang, Bo; Hou, Rong; Shen, Fujun; Mu, Bo; Ni, Peixiang; Lin, Runmao; Qian, Wubin; Wang, Guodong; Yu, Chang; Nie, Wenhui; Wang, Jinhuan; Wu, Zhigang; Liang, Huiqing; Min, Jiumeng; Wu, Qi; Cheng, Shifeng; Ruan, Jue; Wang, Mingwei; Shi, Zhongbin; Wen, Ming; Liu, Binghang; Ren, Xiaoli; Zheng, Huisong; Dong, Dong; Cook, Kathleen; Shan, Gao; Zhang, Hao; Kosiol, Carolin; Xie, Xueying; Lu, Zuhong; Zheng, Hancheng; Li, Yingrui; Steiner, Cynthia C.; Lam, Tommy Tsan-Yuk; Lin, Siyuan; Zhang, Qinghui; Li, Guoqing; Tian, Jing; Gong, Timing; Liu, Hongde; Zhang, Dejin; Fang, Lin; Ye, Chen; Zhang, Juanbin; Hu, Wenbo; Xu, Anlong; Ren, Yuanyuan; Zhang, Guojie; Bruford, Michael W.; Li, Qibin; Ma, Lijia; Guo, Yiran; An, Na; Hu, Yujie; Zheng, Yang; Shi, Yongyong; Li, Zhiqiang; Liu, Qing; Chen, Yanling; Zhao, Jing; Qu, Ning; Zhao, Shancen; Tian, Feng; Wang, Xiaoling; Wang, Haiyin; Xu, Lizhi; Liu, Xiao; Vinar, Tomas; Wang, Yajun; Lam, Tak-Wah; Yiu, Siu-Ming; Liu, Shiping; Zhang, Hemin; Li, Desheng; Huang, Yan; Wang, Xia; Yang, Guohua; Jiang, Zhi; Wang, Junyi; Qin, Nan; Li, Li; Li, Jingxiang; Bolund, Lars; Kristiansen, Karsten; Wong, Gane Ka-Shu; Olson, Maynard; Zhang, Xiuqing; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun

2013-01-01

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes. PMID:20010809

Metagenome-Assembled Genome Sequences of Acetobacterium sp. Strain MES1 and Desulfovibrio sp. Strain MES5 from a Cathode-Associated Acetogenic Microbial Community.

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Ross, Daniel E; Marshall, Christopher W; May, Harold D; Norman, R Sean

2017-09-07

Draft genome sequences of Acetobacterium sp. strain MES1 and Desulfovibrio sp. strain MES5 were obtained from the metagenome of a cathode-associated community enriched within a microbial electrosynthesis system (MES). The draft genome sequences provide insight into the functional potential of these microorganisms within an MES and a foundation for future comparative analyses. Copyright © 2017 Ross et al.

High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes.

Science.gov (United States)

Huang, Jing; Qiao, Zi Xu; Tang, Jing Wei; Wang, Gejiao

2015-01-01

Pontibacillus yanchengensis Y32(T) is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the features of P. yanchengensis strain Y32(T) together with a comparison with other four Pontibacillus genomes. The 4,281,464 bp high-quality-draft genome of strain Y32(T) is arranged into 153 contigs containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of strain Y32(T) possesses many genes related to its halophilic character, flagellar assembly and chemotaxis to support its survival in a salt-rich environment.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

Science.gov (United States)

Kisand, Veljo; Lettieri, Teresa

2013-04-01

De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize

High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain hu-01

OpenAIRE

Hu, XinJun; Li, Ang; Lv, LongXian; Yuan, Chunhui; Guo, Lihua; Jiang, Xiawei; Jiang, Haiyin; Qian, GuiRong; Zheng, BeiWen; Guo, Jing; Li, LanJuan

2014-01-01

Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order Bacillales , class Bacilli and phylum Firmicutes . The increasing relevance of S. cohnii to human health prompted us to determine the genomic sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a multidrug-resistant isolate from a hospital in China. Here we describe the features of S. cohnii subsp. cohnii strain hu-01, together with the genome sequence and its annotation. This is the first genom...

Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm.

Science.gov (United States)

Jin, Jingjing; Lee, May; Bai, Bin; Sun, Yanwei; Qu, Jing; Rahmadsyah; Alfiko, Yuzer; Lim, Chin Huat; Suwanto, Antonius; Sugiharti, Maria; Wong, Limsoon; Ye, Jian; Chua, Nam-Hai; Yue, Gen Hua

2016-12-01

Oil palm is the world's leading source of vegetable oil and fat. Dura, Pisifera and Tenera are three forms of oil palm. The genome sequence of Pisifera is available whereas the Dura form has not been sequenced yet. We sequenced the genome of one elite Dura palm, and re-sequenced 17 palm genomes. The assemble genome sequence of the elite Dura tree contained 10,971 scaffolds and was 1.701 Gb in length, covering 94.49% of the oil palm genome. 36,105 genes were predicted. Re-sequencing of 17 additional palm trees identified 18.1 million SNPs. We found high genetic variation among palms from different geographical regions, but lower variation among Southeast Asian Dura and Pisifera palms. We mapped 10,000 SNPs on the linkage map of oil palm. In addition, high linkage disequilibrium (LD) was detected in the oil palms used in breeding populations of Southeast Asia, suggesting that LD mapping is likely to be practical in this important oil crop. Our data provide a valuable resource for accelerating genetic improvement and studying the mechanism underlying phenotypic variations of important oil palm traits. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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

Science.gov (United States)

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

2018-03-07

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

Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence.

Science.gov (United States)

Iquebal, M A; Tomar, Rukam S; Parakhia, M V; Singla, Deepak; Jaiswal, Sarika; Rathod, V M; Padhiyar, S M; Kumar, Neeraj; Rai, Anil; Kumar, Dinesh

2017-07-13

Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25-80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73 Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes. Secretome analysis revealed CAZY genes representing 1085 enzymatic genes, glycoside hydrolases, carbohydrate esterases, carbohydrate-binding modules, auxillary activities, glycosyl transferases and polysaccharide lyases. Repeat analysis revealed 11171 SSRs, LTR, GYPSY and COPIA elements. Comparative analysis with other existing ascomycotina genome predicted conserved domain family of WD40, CYP450, Pkinase and ABC transporter revealing insight of evolution of pathogenicity and virulence. This study would help in understanding pathogenicity and virulence at molecular level and development of new combating strategies. Such approach is imperative in endeavour of genome based solution in stem rot disease management leading to better productivity of groundnut crop in tropical region of world.

Genome sequence of the pathogenic Herbaspirillum seropedicae strain Os34, isolated from rice roots.

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Ye, Weijun; Ye, Shuting; Liu, Jian; Chang, Siping; Chen, Mingyue; Zhu, Bo; Guo, Longbiao; An, Qianli

2012-12-01

Most Herbaspirillum seropedicae strains are beneficial endophytes to plants. In contrast, H. seropedicae strain Os34, isolated from rice roots, is pathogenic. The draft genome sequence of strain Os34 presented here allows in-depth comparative genome analyses to understand the specific mechanisms of beneficial and pathogenic Herbaspirillum-plant interactions.

Genome sequence of the pathogenic Herbaspirillum seropedicae strain Os45, isolated from rice roots.

Science.gov (United States)

Zhu, Bo; Ye, Shuting; Chang, Siping; Chen, Mingyue; Sun, Li; An, Qianli

2012-12-01

Most Herbaspirillum seropedicae strains are beneficial to plants. In contrast, H. seropedicae strain Os45, isolated from rice roots, is pathogenic. The draft genome sequence of strain Os45 presented here allows an in-depth comparative genome analysis to understand the subtle mechanisms of beneficial and pathogenic Herbaspirillum-plant interactions.

Genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia

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Anastasiia Kovaliova

2017-03-01

Full Text Available Here we report the draft genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia. The draft genome has a size of 4.9 Mb and encodes multiple K+-transporters and proton-consuming decarboxylases. The phylogenetic analysis based on concatenated ribosomal proteins revealed that strain DV clusters together with the acid-tolerant Desulfovibrio sp. TomC and Desulfovibrio magneticus. The draft genome sequence and annotation have been deposited at GenBank under the accession number MLBG00000000.

Genome sequence of the agar-degrading marine bacterium Alteromonadaceae sp. strain G7.

Science.gov (United States)

Kwak, Min-Jung; Song, Ju Yeon; Kim, Byung Kwon; Chi, Won-Jae; Kwon, Soon-Kyeong; Choi, Soobeom; Chang, Yong-Keun; Hong, Soon-Kwang; Kim, Jihyun F

2012-12-01

Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases.

Genome Sequence of the Agar-Degrading Marine Bacterium Alteromonadaceae sp. Strain G7

OpenAIRE

Kwak, Min-Jung; Song, Ju Yeon; Kim, Byung Kwon; Chi, Won-Jae; Kwon, Soon-Kyeong; Choi, Soobeom; Chang, Yong-Keun; Hong, Soon-Kwang; Kim, Jihyun F.

2012-01-01

Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases.

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.

Science.gov (United States)

Peng, Xinxia; Alföldi, Jessica; Gori, Kevin; Eisfeld, Amie J; Tyler, Scott R; Tisoncik-Go, Jennifer; Brawand, David; Law, G Lynn; Skunca, Nives; Hatta, Masato; Gasper, David J; Kelly, Sara M; Chang, Jean; Thomas, Matthew J; Johnson, Jeremy; Berlin, Aaron M; Lara, Marcia; Russell, Pamela; Swofford, Ross; Turner-Maier, Jason; Young, Sarah; Hourlier, Thibaut; Aken, Bronwen; Searle, Steve; Sun, Xingshen; Yi, Yaling; Suresh, M; Tumpey, Terrence M; Siepel, Adam; Wisely, Samantha M; Dessimoz, Christophe; Kawaoka, Yoshihiro; Birren, Bruce W; Lindblad-Toh, Kerstin; Di Palma, Federica; Engelhardt, John F; Palermo, Robert E; Katze, Michael G

2014-12-01

The domestic ferret (Mustela putorius furo) is an important animal model for multiple human respiratory diseases. It is considered the 'gold standard' for modeling human influenza virus infection and transmission. Here we describe the 2.41 Gb draft genome assembly of the domestic ferret, constituting 2.28 Gb of sequence plus gaps. We annotated 19,910 protein-coding genes on this assembly using RNA-seq data from 21 ferret tissues. We characterized the ferret host response to two influenza virus infections by RNA-seq analysis of 42 ferret samples from influenza time-course data and showed distinct signatures in ferret trachea and lung tissues specific to 1918 or 2009 human pandemic influenza virus infections. Using microarray data from 16 ferret samples reflecting cystic fibrosis disease progression, we showed that transcriptional changes in the CFTR-knockout ferret lung reflect pathways of early disease that cannot be readily studied in human infants with cystic fibrosis disease.

Genome Sequence of Legionella massiliensis, Isolated from a Cooling Tower Water Sample.

Science.gov (United States)

Pagnier, Isabelle; Croce, Olivier; Robert, Catherine; Raoult, Didier; La Scola, Bernard

2014-10-16

We present the draft genome sequence of Legionella massiliensis strain LegA(T), recovered from a cooling tower water sample, using an amoebal coculture procedure. The strain described here is composed of 4,387,007 bp, with a G+C content of 41.19%, and its genome has 3,767 protein-coding genes and 60 predicted RNA genes. Copyright © 2014 Pagnier et al.

Genome Sequence of the Enterobacter mori Type Strain, LMG 25706, a Pathogenic Bacterium of Morus alba L. ▿

Science.gov (United States)

Zhu, Bo; Zhang, Guo-Qing; Lou, Miao-Miao; Tian, Wen-Xiao; Li, Bin; Zhou, Xue-Ping; Wang, Guo-Feng; Liu, He; Xie, Guan-Lin; Jin, Gu-Lei

2011-01-01

Enterobacter mori is a plant-pathogenic enterobacterium responsible for the bacterial wilt of Morus alba L. Here we present the draft genome sequence of the type strain, LMG 25706. To the best of our knowledge, this is the first genome sequence of a plant-pathogenic bacterium in the genus Enterobacter. PMID:21602328

Genome Sequence of the Necrotrophic Plant Pathogen Alternaria brassicicola Abra43

Science.gov (United States)

Belmas, Elodie; Briand, Martial; Kwasiborski, Anthony; Colou, Justine; N’Guyen, Guillaume; Iacomi, Béatrice; Grappin, Philippe; Campion, Claire; Simoneau, Philippe; Barret, Matthieu

2018-01-01

ABSTRACT Alternaria brassicicola causes dark spot (or black spot) disease, which is one of the most common and destructive fungal diseases of Brassicaceae spp. worldwide. Here, we report the draft genome sequence of strain Abra43. The assembly comprises 29 scaffolds, with an N50 value of 2.1 Mb. The assembled genome was 31,036,461 bp in length, with a G+C content of 50.85%. PMID:29439047

Draft genome sequence of Lactococcus garvieae str. PAQ102015-99, an outbreak strain isolated from a commercial trout farm in the Northwestern United States.

Science.gov (United States)

We announce the draft genome assembly of Lactococcus garvieae str. PAQ102015-99, a recently isolated strain from an outbreak of lactococcosis at a commercial trout farm in the Northwestern US. The draft genome comprises 14 contigs totaling 2,068,357 bp with an N50 of 496,618 bp and average G+C conte...

Draft Genome Sequence of a Kale (Brassica oleracea L.) Root Endophyte, Pseudomonas sp. Strain C9.

Science.gov (United States)

Laugraud, Aurelie; Young, Sandra; Gerard, Emily; O'Callaghan, Maureen; Wakelin, Steven

2017-04-13

Pseudomonas sp. strain C9 is a plant growth-promoting bacterium isolated from the root tissue of Brassica oleracea L. grown in soil from Marlborough, New Zealand. Its draft genome of 6,350,161 bp contains genes associated with plant growth promotion and biological control. Copyright © 2017 Laugraud et al.

Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

Energy Technology Data Exchange (ETDEWEB)

Lamour, Kurt H [ORNL; McDonald, W Hayes [ORNL; Savidor, Alon [ORNL

2006-01-01

Genome sequences of the soybean pathogen, Phytophthora sojae, and the sudden oak death pathogen, Phytophthora ramorum, suggest a photosynthetic past and reveal recent massive expansion and diversification of potential pathogenicity gene families. Abstract: Draft genome sequences of the soybean pathogen, Phytophthora sojae, and the sudden oak death pathogen, Phytophthora ramorum, have been determined. O mycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms and the presence of many Phytophthora genes of probable phototroph origin support a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors and, in particular, a superfamily of 700 proteins with similarity to known o mycete avirulence genes.

Whole-genome sequence of Starmerella bacillaris PAS13, a nonconventional enological yeast with antifungal activity

DEFF Research Database (Denmark)

Lemos Junior, Wilson Jose Fernandes; Treu, Laura; Duarte, Vinicius da Silva

2017-01-01

Starmerella bacillaris is a fermentative yeast commonly found in vineyards. Here, we present the draft genome sequence of S. bacillaris PAS13, a nonconventional enological yeast with a potential role as a biocontrol agent. This gene sequence will provide insights into the genetic basis of yeast...

Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics.

Science.gov (United States)

Hosokawa, Masahito; Nishikawa, Yohei; Kogawa, Masato; Takeyama, Haruko

2017-07-12

Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels. Because single cells are isolated in compartments, their genomes are amplified to saturation without contamination. This enables the high-throughput acquisition of contamination-free and cell specific sequence reads from single cells (21,000 single-cells/h), resulting in enhancement of the sequence data quality compared to conventional methods. This method allowed WGA of both single bacterial cells and human cancer cells. The obtained sequencing coverage rivals those of conventional techniques with superior sequence quality. In addition, we also demonstrate de novo assembly of uncultured soil bacteria and obtain draft genomes from single cell sequencing. This sd-MDA is promising for flexible and scalable use in single-cell sequencing.

Genome sequences of two Leuconostoc pseudomesenteroides strains isolated from Danish dairy starter cultures

DEFF Research Database (Denmark)

Pedersen, Thomas Bæk; Kot, Witold Piotr; Hansen, L.H.

2014-01-01

The lactic acid bacterium Leuconostoc pseudomesenteroides can be found in mesophilic cheese starters, where it produces aromatic compounds from, e.g., citrate. Here, we present the draft genome sequences of two L. pseudomesenteroides strains isolated from traditional Danish cheese starters....

Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828.

Science.gov (United States)

Read, Timothy D; Petit, Robert A; Joseph, Sandeep J; Alam, Md Tauqeer; Weil, M Ryan; Ahmad, Maida; Bhimani, Ravila; Vuong, Jocelyn S; Haase, Chad P; Webb, D Harry; Tan, Milton; Dove, Alistair D M

2017-07-14

The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to as fishes. As both a phenotypic extreme and a member of the group Chondrichthyes - the sister group to the remaining gnathostomes, which includes all tetrapods and therefore also humans - its genome is of substantial comparative interest. Whale sharks are also listed as an endangered species on the International Union for Conservation of Nature's Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem. A genome map for this species would aid in defining effective conservation units and understanding global population structure. We characterised the nuclear genome of the whale shark using next generation sequencing (454, Illumina) and de novo assembly and annotation methods, based on material collected from the Georgia Aquarium. The data set consisted of 878,654,233 reads, which yielded a draft assembly of 1,213,200 contigs and 997,976 scaffolds. The estimated genome size was 3.44Gb. As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the holocephalan elephant shark. The whale shark contained a novel Toll-like-receptor (TLR) protein with sequence similarity to both the TLR4 and TLR13 proteins of mammals and TLR21 of teleosts. The data are publicly available on GenBank, FigShare, and from the NCBI Short Read Archive under accession number SRP044374. This represents the first shotgun elasmobranch genome and will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this and other shark species, as well as providing comparative data for studies of evolutionary biology and immunology across the jawed vertebrate lineages.

Draft Genome Sequences of Sanguibacteroides justesenii, gen. nov., sp. nov., Strains OUH 308042T (= ATCC BAA-2681T) and OUH 334697 (= ATCC BAA-2682), Isolated from Blood Cultures from Two Different Patients

DEFF Research Database (Denmark)

Sydenham, Thomas Vognbjerg; Hasman, Henrik; Justesen, Ulrik Stenz

2015-01-01

We announce here the draft genome sequences of Sanguibacteroides justesenii, gen. nov., sp. nov., strains OUH 308042T (= DSM 28342T = ATCC BAA-2681T) and OUH 334697 (= DSM 28341 = ATCC BAA-2682), isolated from blood cultures from two different patients and composed of 51 and 39 contigs for totals...

Genome sequence of a Proteus mirabilis strain isolated from the salivary glands of larval Lucilia sericata

Science.gov (United States)

We announced a draft genome sequence of a Proteus mirabilis strain derived from Lucilia sericata salivary glands. This strain is demonstrated to attract and induce oviposition by L. sericata, a common blow fly important to medicine, agriculture, and forensics. The genome will help to dissect inter...

Draft Genome Sequencing and Comparative Analysis of Aspergillus sojae NBRC4239

Science.gov (United States)

Sato, Atsushi; Oshima, Kenshiro; Noguchi, Hideki; Ogawa, Masahiro; Takahashi, Tadashi; Oguma, Tetsuya; Koyama, Yasuji; Itoh, Takehiko; Hattori, Masahira; Hanya, Yoshiki

2011-01-01

We conducted genome sequencing of the filamentous fungus Aspergillus sojae NBRC4239 isolated from the koji used to prepare Japanese soy sauce. We used the 454 pyrosequencing technology and investigated the genome with respect to enzymes and secondary metabolites in comparison with other Aspergilli sequenced. Assembly of 454 reads generated a non-redundant sequence of 39.5-Mb possessing 13 033 putative genes and 65 scaffolds composed of 557 contigs. Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae. Comparative analysis identified serine carboxypeptidase and aspartic protease genes unique to A. sojae NBRC4239. While A. oryzae possessed three copies of α-amyalse gene, A. sojae NBRC4239 possessed only a single copy. Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae. The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries. PMID:21659486

Draft genome sequence of the white-rot fungus Obba rivulosa 3A-2

Science.gov (United States)

Otto Miettinen; Robert Riley; Kerrie Barry; Daniel Cullen; Ronald P. de Vries; Matthieu Hainaut; Annele Hatakka; Bernard Henrissat; Kristiina Hilden; Rita Kuo; Kurt LaButti; Anna Lipzen; Miia R. Makela; Laura Sandor; Joseph W. Spatafora; Igor V. Grigoriev; David S. Hibbett

2016-01-01

We report here the first genome sequence of the white-rot fungus Obba rivulsa (Polyporales, Basidiomycota), a polypore known for its lignin-decomposing ability. The genome is based on the homokaryon 3A-2 originating in Finland. The genome is typical in size and carbohydrate active enzyme (CAZy) content for wood-decomposing basidiomycetes.

Culture-independent genome sequencing of Coxiella burnetii from a native heart valve of a Tunisian patient with severe infective endocarditis

Directory of Open Access Journals (Sweden)

J. Delaloye

2018-01-01

Full Text Available We report draft genome of a Coxiella burnetii strain sequenced from the native valve of a patient presenting with severe endocarditis in Tunisia. The genome could be sequenced without a cellular or axenic culture step. The MST5 strain was demonstrated to be closely related to the published reference genome of C. burnetii CbuK_Q154.

A draft genome of the honey bee trypanosomatid parasite Crithidia mellificae.

Directory of Open Access Journals (Sweden)

Charles Runckel

Full Text Available Since 2006, honey bee colonies in North America and Europe have experienced increased annual mortality. These losses correlate with increased pathogen incidence and abundance, though no single etiologic agent has been identified. Crithidia mellificae is a unicellular eukaryotic honey bee parasite that has been associated with colony losses in the USA and Belgium. C. mellificae is a member of the family Trypanosomatidae, which primarily includes other insect-infecting species (e.g., the bumble bee pathogen Crithidia bombi, as well as species that infect both invertebrate and vertebrate hosts including human pathogens (e.g.,Trypanosoma cruzi, T. brucei, and Leishmania spp.. To better characterize C. mellificae, we sequenced the genome and transcriptome of strain SF, which was isolated and cultured in 2010. The 32 megabase draft genome, presented herein, shares a high degree of conservation with the related species Leishmania major. We estimate that C. mellificae encodes over 8,300 genes, the majority of which are orthologs of genes encoded by L. major and other Leishmania or Trypanosoma species. Genes unique to C. mellificae, including those of possible bacterial origin, were annotated based on function and include genes putatively involved in carbohydrate metabolism. This draft genome will facilitate additional investigations of the impact of C. mellificae infection on honey bee health and provide insight into the evolution of this unique family.

Genomic Sequence of Saccharomyces cerevisiae BAW-6, a Yeast Strain Optimal for Brewing Barley Shochu.

Science.gov (United States)

Kajiwara, Yasuhiro; Mori, Kazuki; Tashiro, Kosuke; Higuchi, Yujiro; Takegawa, Kaoru; Takashita, Hideharu

2018-04-05

Here, we report the draft genome sequence of Saccharomyces cerevisiae strain BAW-6, which is used for the production of barley shochu, a traditional Japanese spirit. This genomic information can be used to elucidate the genetic basis underlying the high alcohol production capacity and citric acid tolerance of shochu yeast. Copyright © 2018 Kajiwara et al.

Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen.

Science.gov (United States)

Nielsen, Maja; Schreiber, Lars; Finster, Kai; Schramm, Andreas

2015-01-01

Bacillus azotoformans MEV2011, isolated from soil, is a microaerotolerant obligate denitrifier, which can also produce N2 by co-denitrification. Oxygen is consumed but not growth-supportive. The draft genome has a size of 4.7 Mb and contains key genes for both denitrification and dissimilatory nitrate reduction to ammonium.

Genome sequence of Bradyrhizobium sp. LMTR 3, a diazotrophic symbiont of Lima bean (Phaseolus lunatus

Directory of Open Access Journals (Sweden)

Ernesto Ormeño-Orrillo

2017-09-01

Full Text Available Bradyrhizobium sp. LMTR 3 is a representative strain of one of the geno(species of diazotrophic symbionts associated with Lima bean (Phaseolus lunatus in Peru. Its 7.83 Mb genome was sequenced using the Illumina technology and found to encode a complete set of genes required for nodulation and nitrogen fixation, and additional genes putatively involved in root colonization. Its draft genome sequence and annotation have been deposited at GenBank under the accession number MAXC00000000.

A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar.

Science.gov (United States)

Perry, George H; Reeves, Darryl; Melsted, Páll; Ratan, Aakrosh; Miller, Webb; Michelini, Katelyn; Louis, Edward E; Pritchard, Jonathan K; Mason, Christopher E; Gilad, Yoav

2012-01-01

We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ~3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of ~2.6 million scaffolds (N50 scaffold size = 13,597 bp) based on short paired-end sequencing reads. We compared the aye-aye genome sequence data with four other published primate genomes (human, chimpanzee, orangutan, and rhesus macaque) as well as with the mouse and dog genomes as nonprimate outgroups. Unexpectedly, we observed strong evidence for a relatively slow substitution rate in the aye-aye lineage compared with these and other primates. In fact, the aye-aye branch length is estimated to be ~10% shorter than that of the human lineage, which is known for its low substitution rate. This finding may be explained, in part, by the protracted aye-aye life-history pattern, including late weaning and age of first reproduction relative to other lemurs. Additionally, the availability of this draft lemur genome sequence allowed us to polarize nucleotide and protein sequence changes to the ancestral primate lineage-a critical period in primate evolution, for which the relevant fossil record is sparse. Finally, we identified 293,800 high-confidence single nucleotide polymorphisms in the donor individual for our aye-aye genome sequence, a captive-born individual from two wild-born parents. The resulting heterozygosity estimate of 0.051% is the lowest of any primate studied to date, which is understandable considering the aye-aye's extensive home-range size and relatively low population densities. Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar's forests.

Whole genome sequences of the raspberry and strawberry pathogens Phytophthora rubi and P. fragariae

Science.gov (United States)

Phytophthora rubi and P. fragariae are two closely related oomycete plant pathogens that exhibit strong morphological and physiological similarities, but are specialized to infect different hosts of economic importance, namely raspberry and strawberry. Here, we report the draft genome sequences of t...

Draft Genome Sequence of Two Sphingopyxis sp. Strains, Dominant Members of the Bacterial Community Associated with a Drinking Water Distribution System Simulator

Science.gov (United States)

We report the draft genome of two Sphingopyxis spp. strains isolated from a chloraminated drinking water distribution system simulator. Both strains are ubiquitous residents and early colonizers of water distribution systems. Genomic annotation identified a class 1 integron (in...

Genome Sequence of an Endophytic Fungus, Fusarium solani JS-169, Which Has Antifungal Activity.

Science.gov (United States)

Kim, Jung A; Jeon, Jongbum; Park, Sook-Young; Kim, Ki-Tae; Choi, Gobong; Lee, Hyun-Jung; Kim, Yangsun; Yang, Hee-Sun; Yeo, Joo-Hong; Lee, Yong-Hwan; Kim, Soonok

2017-10-19

An endophytic fungus, Fusarium solani strain JS-169, isolated from a mulberry twig, showed considerable antifungal activity. Here, we report the draft genome sequence of this strain. The assembly comprises 17 scaffolds, with an N 50 value of 4.93 Mb. The assembled genome was 45,813,297 bp in length, with a G+C content of 49.91%. Copyright © 2017 Kim et al.

Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5

NARCIS (Netherlands)

Urshev, Z.; Hajo, K.; Lenoci, L.; Bron, P.A.; Dijkstra, A.; Alkema, W.; Wels, M.; Siezen, R.J.; Minkova, S.; Hijum, S.A. van

2016-01-01

Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 originates from homemade Bulgarian yogurt and was selected for its ability to form a strong association with Streptococcus thermophilus The genome sequence will facilitate elucidating the genetic background behind the contribution of LBB.B5 to the

The genome draft of coconut (Cocos nucifera).

Science.gov (United States)

Xiao, Yong; Xu, Pengwei; Fan, Haikuo; Baudouin, Luc; Xia, Wei; Bocs, Stéphanie; Xu, Junyang; Li, Qiong; Guo, Anping; Zhou, Lixia; Li, Jing; Wu, Yi; Ma, Zilong; Armero, Alix; Issali, Auguste Emmanuel; Liu, Na; Peng, Ming; Yang, Yaodong

2017-11-01

Coconut palm (Cocos nucifera,2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with a total growth area of more than 12 million hectares [1]. Coconut palm is generally classified into 2 main categories: "Tall" (flowering 8-10 years after planting) and "Dwarf" (flowering 4-6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years, which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of the Cocos nucifera genome: a major genomic resource that could be used to facilitate molecular breeding in Cocos nucifera and accelerate the breeding process in this important crop. A total of 419.67 gigabases (Gb) of raw reads were generated by the Illumina HiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42 Gb, variety "Hainan Tall") to an estimated ×173.32 read depth. A total scaffold length of 2.20 Gb was generated (N50 = 418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28 039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30: 28 889), Phoenix dactylifera (DPV01: 41 660), and Elaeis guineensis (EG5: 34 802). BUSCO evaluation demonstrated that the obtained scaffold sequences covered 90.8% of the coconut genome and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome consisted of transposable elements, of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the

New Genome Sequence of an Echinaceapurpurea Endophyte, Arthrobacter sp. Strain EpSL27, Able To Inhibit Human-Opportunistic Pathogens.

Science.gov (United States)

Miceli, Elisangela; Presta, Luana; Maggini, Valentina; Fondi, Marco; Bosi, Emanuele; Chiellini, Carolina; Fagorzi, Camilla; Bogani, Patrizia; Di Pilato, Vincenzo; Rossolini, Gian Maria; Mengoni, Alessio; Firenzuoli, Fabio; Perrin, Elena; Fani, Renato

2017-06-22

We announce here the draft genome sequence of Arthrobacter sp. strain EpSL27, isolated from the stem and leaves of the medicinal plant Echinacea purpurea and able to inhibit human-pathogenic bacterial strains. The genome sequencing of this strain may lead to the identification of genes involved in the production of antimicrobial molecules. Copyright © 2017 Miceli et al.

Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales.

Science.gov (United States)

Prakash, Hariprasath; Rudramurthy, Shivaprakash Mandya; Gandham, Prasad S; Ghosh, Anup Kumar; Kumar, Milner M; Badapanda, Chandan; Chakrabarti, Arunaloke

2017-09-18

Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome sequences of A. elegans and A. trapeziformis are available in public database, but not A. variabilis. We, therefore, performed the whole genome sequence of A. variabilis to explore its genomic structure and possible genes determining the virulence of the organism. The whole genome of A. variabilis NCCPF 102052 was sequenced and the genomic structure of A. variabilis was compared with already available genome structures of A. elegans, A. trapeziformis and other medically important Mucorales. The total size of genome assembly of A. variabilis was 39.38 Mb with 12,764 protein-coding genes. The transposable elements (TEs) were low in Apophysomyces genome and the retrotransposon Ty3-gypsy was the common TE. Phylogenetically, Apophysomyces species were grouped closely with Phycomyces blakesleeanus. OrthoMCL analysis revealed 3025 orthologues proteins, which were common in those three pathogenic Apophysomyces species. Expansion of multiple gene families/duplication was observed in Apophysomyces genomes. Approximately 6% of Apophysomyces genes were predicted to be associated with virulence on PHIbase analysis. The virulence determinants included the protein families of CotH proteins (invasins), proteases, iron utilisation pathways, siderophores and signal transduction pathways. Serine proteases were the major group of proteases found in all Apophysomyces genomes. The carbohydrate active enzymes (CAZymes) constitute the majority of the secretory proteins. The present study is the maiden attempt to sequence and analyze the genomic structure of A. variabilis. Together with available genome sequence of A. elegans and A. trapeziformis, the study helped to indicate the possible virulence determinants of

An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.).

Science.gov (United States)

Parween, Sabiha; Nawaz, Kashif; Roy, Riti; Pole, Anil K; Venkata Suresh, B; Misra, Gopal; Jain, Mukesh; Yadav, Gitanjali; Parida, Swarup K; Tyagi, Akhilesh K; Bhatia, Sabhyata; Chattopadhyay, Debasis

2015-08-11

Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes.

Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei

KAUST Repository

Vega, Fernando E.

2015-07-31

The coffee berry borer, Hypothenemus hampei, is the most economically important insect pest of coffee worldwide. We present an analysis of the draft genome of the coffee berry borer, the third genome for a Coleopteran species. The genome size is ca. 163 Mb with 19,222 predicted protein-coding genes. Analysis was focused on genes involved in primary digestion as well as gene families involved in detoxification of plant defense molecules and insecticides, such as carboxylesterases, cytochrome P450, gluthathione S-transferases, ATP-binding cassette transporters, and a gene that confers resistance to the insecticide dieldrin. A broad range of enzymes capable of degrading complex polysaccharides were identified. We also evaluated the pathogen defense system and found homologs to antimicrobial genes reported in the Drosophila genome. Ten cases of horizontal gene transfer were identified with evidence for expression, integration into the H. hampei genome, and phylogenetic evidence that the sequences are more closely related to bacterial rather than eukaryotic genes. The draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.