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Standards in Genomic Sciences

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https://www.readbyqxmd.com/read/27833718/two-draft-genome-sequences-of-pseudomonas-jessenii-strains-isolated-from-a-copper-contaminated-site-in-denmark
#1
Yanan Qin, Dan Wang, Kristian K Brandt, Christopher Rensing
Pseudomonas jessenii C2 and Pseudomonas jessenii H16 were isolated from low-Cu and high-Cu industrially contaminated soil, respectively. P. jessenii H16 displayed significant resistance to copper when compared to P. jessenii C2. Here we describe genome sequences and interesting features of these two strains. The genome of P. jessenii C2 comprised 6,420,113 bp, with 5814 protein-coding genes and 67 RNA genes. P. jessenii H16 comprised 6,807,788 bp, with 5995 protein-coding genes and 70 RNA genes. Of special interest was a specific adaptation to this harsh copper-contaminated environment as P...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27800124/draft-genome-sequence-of-streptomyces-sp-tp-a0867-an-alchivemycin-producer
#2
Hisayuki Komaki, Natsuko Ichikawa, Akio Oguchi, Moriyuki Hamada, Enjuro Harunari, Shinya Kodani, Nobuyuki Fujita, Yasuhiro Igarashi
Streptomyces sp. TP-A0867 (=NBRC 109436) produces structurally complex polyketides designated alchivemycins A and B. Here, we report the draft genome sequence of this strain together with features of the organism and assembly, annotation, and analysis of the genome sequence. The 9.9 Mb genome of Streptomyces sp. TP-A0867 encodes 8,385 putative ORFs, of which 7,232 were assigned with COG categories. We successfully identified a hybrid polyketide synthase (PKS)/ nonribosomal peptide synthetase (NRPS) gene cluster that could be responsible for alchivemycin biosynthesis, and propose the biosynthetic pathway...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27795808/draft-genome-sequence-of-micromonospora-sp-dsw705-and-distribution-of-biosynthetic-gene-clusters-for-depsipeptides-bearing-4-amino-2-4-pentadienoate-in-actinomycetes
#3
Hisayuki Komaki, Natsuko Ichikawa, Akira Hosoyama, Moriyuki Hamada, Enjuro Harunari, Arisa Ishikawa, Yasuhiro Igarashi
Here, we report the draft genome sequence of Micromonospora sp. DSW705 (=NBRC 110037), a producer of antitumor cyclic depsipeptides rakicidins A and B, together with the features of this strain and generation, annotation, and analysis of the genome sequence. The 6.8 Mb genome of Micromonospora sp. DSW705 encodes 6,219 putative ORFs, of which 4,846 are assigned with COG categories. The genome harbors at least three type I polyketide synthase (PKS) gene clusters, one nonribosomal peptide synthetase (NRPS) gene clusters, and three hybrid PKS/NRPS gene clusters...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27785333/draft-genome-sequence-of-streptomyces-sp-mww064-for-elucidating-the-rakicidin-biosynthetic-pathway
#4
Hisayuki Komaki, Arisa Ishikawa, Natsuko Ichikawa, Akira Hosoyama, Moriyuki Hamada, Enjuro Harunari, Takuya Nihira, Watanalai Panbangred, Yasuhiro Igarashi
Streptomyces sp. MWW064 (=NBRC 110611) produces an antitumor cyclic depsipeptide rakicidin D. Here, we report the draft genome sequence of this strain together with features of the organism and generation, annotation and analysis of the genome sequence. The 7.9 Mb genome of Streptomyces sp. MWW064 encoded 7,135 putative ORFs, of which 6,044 were assigned with COG categories. The genome harbored at least three type I polyketide synthase (PKS) gene clusters, seven nonribosomal peptide synthetase (NRPS) gene clusters, and four hybrid PKS/NRPS gene clusters, from which a hybrid PKS/NRPS gene cluster responsible for rakicidin synthesis was successfully identified...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777652/draft-genome-of-prochlorothrix-hollandica-ccap-1490-1-t-calu1027-the-chlorophyll-a-b-containing-filamentous-cyanobacterium
#5
Natalia Velichko, Mikhail Rayko, Ekaterina Chernyaeva, Alla Lapidus, Alexander Pinevich
Prochlorothrix hollandica is filamentous non-heterocystous cyanobacterium which possesses the chlorophyll a/b light-harvesting complexes. Despite the growing interest in unusual green-pigmented cyanobacteria (prochlorophytes) to date only a few sequenced genome from prochlorophytes genera have been reported. This study sequenced the genome of Prochlorothrix hollandica CCAP 1490/1(T) (CALU1027). The produced draft genome assembly (5.5 Mb) contains 3737 protein-coding genes and 114 RNA genes.
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777651/draft-genome-sequence-of-the-marine-rhodobacteraceae-strain-o3-65-cultivated-from-oil-polluted-seawater-of-the-deepwater-horizon-oil-spill
#6
Helge-Ansgar Giebel, Franziska Klotz, Sonja Voget, Anja Poehlein, Katrin Grosser, Andreas Teske, Thorsten Brinkhoff
The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the Deepwater Horizon (DWH) oil spill and belongs to the ubiquitous, diverse and ecological relevant Roseobacter group within the Rhodobacteraceae. Here, we present a preliminary set of physiological features of strain O3.65 and a description and annotation of its draft genome sequence. Based on our data we suggest potential ecological roles of the isolate in the degradation of crude oil within the network of the oil-enriched microbial community...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777650/complete-genome-sequence-of-methanoculleus-bourgensis-strain-mab1-the-syntrophic-partner-of-mesophilic-acetate-oxidising-bacteria-saob
#7
Shahid Manzoor, Anna Schnürer, Erik Bongcam-Rudloff, Bettina Müller
Methanoculleus bourgensis strain MAB1 has been identified as the hydrogenotrophic partner of mesophilic acetate-oxidising bacteria, a syntrophic relationship operating close to the thermodynamic equilibrium and of considerable importance in ammonia-rich engineered biogas processes. Methanoculleus bourgensis strain MAB1 belongs to the order Methanomicrobiales, family Methanomicrobiaceae, within the phylum Euryarchaeota. The genome shows a total size of 2,859,299 bp encoding 3450 predicted protein-encoding genes, of which only 1472 (43 %) have been assigned tentative functions...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777649/genome-sequences-and-annotation-of-two-urinary-isolates-of-e-coli
#8
Travis K Price, Arya Mehrtash, Laurynas Kalesinskas, Kema Malki, Evann E Hilt, Catherine Putonti, Alan J Wolfe
The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition called asymptomatic bacteriuria results from colonization of the bladder with E. coli strains without symptoms. As part of an on-going attempt to identify and characterize the newly discovered female urinary microbiota, we report the genome sequences and annotation of two urinary isolates of E. coli: one (E78) was isolated from a female patient who self-reported cystitis; the other (E75) was isolated from a female patient who reported that she did not have symptoms of cystitis...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777648/mixs-hcr-a-mixs-extension-defining-a-minimal-information-standard-for-sequence-data-from-environments-pertaining-to-hydrocarbon-resources
#9
Nicolas Tsesmetzis, Pelin Yilmaz, Peter C Marks, Nikos C Kyrpides, Ian M Head, Bart P Lomans
Here we introduce a MIxS extension to facilitate the recording and cataloguing of metadata from samples related to hydrocarbon resources. The proposed MIxS-HCR package incorporates the core features of the MIxS standard for marker gene (MIMARKS) and metagenomic (MIMS) sequences along with a hydrocarbon resources customized environmental package. Adoption of the MIxS-HCR standard will enable the comparison and better contextualization of investigations related to hydrocarbon rich environments. The insights from such standardized way of reporting could be highly beneficial for the successful development and optimization of hydrocarbon recovery processes and management of microbiological issues in petroleum production systems...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777647/erratum-to-permanent-draft-genome-of-thermithiobacillus-tepidarius-dsm-3134-t-a-moderately-thermophilic-obligately-chemolithoautotrophic-member-of-the-acidithiobacillia
#10
Rich Boden, Lee P Hutt, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, Tatiparthi Reddy, Chew Yee Ngan, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Tanja Woyke, Nikos Kyrpides
[This corrects the article DOI: 10.1186/s40793-016-0188-0.].
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777646/a-draft-genome-sequence-of-pseudomonas-veronii-r4-a-grapevine-vitis-vinifera-l-root-associated-strain-with-high-biocontrol-potential
#11
Christian Montes, Fabiola Altimira, Hayron Canchignia, Álvaro Castro, Evelyn Sánchez, María Miccono, Eduardo Tapia, Álvaro Sequeida, Jorge Valdés, Paz Tapia, Carolina González, Humberto Prieto
A new plant commensal Pseudomonas veronii isolate (strain R4) was identified from a Xiphinema index biocontrol screen. Isolated from grapevine roots from vineyards in central Chile, the strain R4 exhibited a slower yet equivalently effective nematicide activity as the well-characterized P. protegens CHA0. Whole genome sequencing of strain R4 and comparative analysis among the available Pseudomonas spp. genomes allowed for the identification of gene clusters that encode putative extracellular proteases and lipase synthesis and secretion systems, which are proposed to mediate-at least in part-the observed nematicidal activity...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27721915/high-quality-draft-genome-sequence-of-sedimenticola-selenatireducens-strain-ak4oh1-t-a-gammaproteobacterium-isolated-from-estuarine-sediment
#12
Tiffany S Louie, Donato Giovannelli, Nathan Yee, Priya Narasingarao, Valentin Starovoytov, Markus Göker, Hans-Peter Klenk, Elke Lang, Nikos C Kyrpides, Tanja Woyke, Elisabetta Bini, Max M Häggblom
Sedimenticola selenatireducens strain AK4OH1(T) (= DSM 17993(T) = ATCC BAA-1233(T)) is a microaerophilic bacterium isolated from sediment from the Arthur Kill intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1(T) was the first representative of its genus to be isolated for its unique coupling of the oxidation of aromatic acids to the respiration of selenate. It is a versatile heterotroph and can use a variety of carbon compounds, but can also grow lithoautotrophically under hypoxic and anaerobic conditions...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27708749/permanent-draft-genome-of-thermithiobaclillus-tepidarius-dsm-3134-t-a-moderately-thermophilic-obligately-chemolithoautotrophic-member-of-the-acidithiobacillia
#13
Rich Boden, Lee P Hutt, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, Tatiparthi Reddy, Chew Yee Ngan, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Tanja Woyke, Nikos Kyrpides
Thermithiobacillus tepidarius DSM 3134(T) was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27688836/whole-genome-shotgun-sequence-of-bacillus-amyloliquefaciens-tf28-a-biocontrol-entophytic-bacterium
#14
Shumei Zhang, Wei Jiang, Jing Li, Liqiang Meng, Xu Cao, Jihua Hu, Yushuai Liu, Jingyu Chen, Changqing Sha
Bacillus amyloliquefaciens TF28 is a biocontrol endophytic bacterium that is capable of inhibition of a broad range of plant pathogenic fungi. The strain has the potential to be developed into a biocontrol agent for use in agriculture. Here we report the whole-genome shotgun sequence of the strain. The genome size of B. amyloliquefaciens TF28 is 3,987,635 bp which consists of 3754 protein-coding genes, 65 tandem repeat sequences, 47 minisatellite DNA, 2 microsatellite DNA, 63 tRNA, 7rRNA, 6 sRNA, 3 prophage and CRISPR domains...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27660670/genome-sequence-of-candidatus-arsenophonus-lipopteni-the-exclusive-symbiont-of-a-blood-sucking-fly-lipoptena-cervi-diptera-hippoboscidae
#15
Eva Nováková, Václav Hypša, Petr Nguyen, Filip Husník, Alistair C Darby
Candidatus Arsenophonus lipopteni (Enterobacteriaceae, Gammaproteobacteria) is an obligate intracellular symbiont of the blood feeding deer ked, Lipoptena cervi (Diptera: Hippoboscidae). The bacteria reside in specialized cells derived from host gut epithelia (bacteriocytes) forming a compact symbiotic organ (bacteriome). Compared to the closely related complex symbiotic system in the sheep ked, involving four bacterial species, Lipoptena cervi appears to maintain its symbiosis exclusively with Ca. Arsenophonus lipopteni...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27651857/the-complete-genome-sequences-of-sulfur-oxidizing-gammaproteobacteria-sulfurifustis-variabilis-skn76-t-and-sulfuricaulis-limicola-ha5-t
#16
Kazuhiro Umezawa, Tomohiro Watanabe, Aya Miura, Hisaya Kojima, Manabu Fukui
Sulfurifustis variabilis and Sulfuricaulis limicola are autotrophic sulfur-oxidizing bacteria belonging to the family Acidiferrobacteraceae in the order Acidiferrobacterales. The type strains of these species, strain skN76(T) and strain HA5(T), were isolated from lakes in Japan. Here we describe the complete genome sequences of Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T). The genome of Sulfurifustis variabilis skN76(T) consists of one circular chromosome with size of 4.0 Mbp including 3864 protein-coding sequences...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27617060/complete-genome-sequence-of-the-antarctic-halorubrum-lacusprofundi-type-strain-acam-34
#17
Iain J Anderson, Priya DasSarma, Susan Lucas, Alex Copeland, Alla Lapidus, Tijana Glavina Del Rio, Hope Tice, Eileen Dalin, David C Bruce, Lynne Goodwin, Sam Pitluck, David Sims, Thomas S Brettin, John C Detter, Cliff S Han, Frank Larimer, Loren Hauser, Miriam Land, Natalia Ivanova, Paul Richardson, Ricardo Cavicchioli, Shiladitya DasSarma, Carl R Woese, Nikos C Kyrpides
Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. We report here the complete genome sequence of H. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27617059/advances-in-biodiversity-metagenomics-and-the-unveiling-of-biological-dark-matter
#18
Robert J Robbins, Leonard Krishtalka, John C Wooley
BACKGROUND: Efforts to harmonize genomic data standards used by the biodiversity and metagenomic research communities have shown that prokaryotic data cannot be understood or represented in a traditional, classical biological context for conceptual reasons, not technical ones. RESULTS: Biology, like physics, has a fundamental duality-the classical macroscale eukaryotic realm vs. the quantum microscale microbial realm-with the two realms differing profoundly, and counter-intuitively, from one another...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27617058/draft-genome-sequence-of-thermoactinomyces-sp-strain-as95-isolated-from-a-sebkha-in-thamelaht-algeria
#19
Oliver K I Bezuidt, Mohamed A Gomri, Rian Pierneef, Marc W Van Goethem, Karima Kharroub, Don A Cowan, Thulani P Makhalanyane
The members of the genus Thermoactinomyces are known for their protein degradative capacities. Thermoactinomyces sp. strain AS95 is a Gram-positive filamentous bacterium, isolated from moderately saline water in the Thamelaht region of Algeria. This isolate is a thermophilic aerobic bacterium with the capacity to produce extracellular proteolytic enzymes. This strain exhibits up to 99 % similarity with members of the genus Thermoactinomyces, based on 16S rRNA gene sequence similarity. Here we report on the phenotypic features of Thermoactinomyces sp...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27617057/complete-genome-sequence-of-desulfurivibrio-alkaliphilus-strain-aht2-t-a-haloalkaliphilic-sulfidogen-from-egyptian-hypersaline-alkaline-lakes
#20
Emily Denise Melton, Dimitry Y Sorokin, Lex Overmars, Olga Chertkov, Alicia Clum, Manoj Pillay, Natalia Ivanova, Nicole Shapiro, Nikos C Kyrpides, Tanja Woyke, Alla L Lapidus, Gerard Muyzer
Desulfurivibrio alkaliphilus strain AHT2(T) is a strictly anaerobic sulfidogenic haloalkaliphile isolated from a composite sediment sample of eight hypersaline alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D. alkaliphilus AHT2(T) is Gram-negative and belongs to the family Desulfobulbaceae within the Deltaproteobacteria. Here we report its genome sequence, which contains a 3.10 Mbp chromosome. D. alkaliphilus AHT2(T) is adapted to survive under highly alkaline and moderately saline conditions and therefore, is relevant to the biotechnology industry and life under extreme conditions...
2016: Standards in Genomic Sciences
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