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Standards in Genomic Sciences

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https://www.readbyqxmd.com/read/28593028/genomics-insights-into-production-of-2-methylisoborneol-and-a-putative-cyanobactin-by-planktothricoides-sp-sr001
#1
Shu Harn Te, Boon Fei Tan, Chek Yin Boo, Janelle Renee Thompson, Karina Yew-Hoong Gin
Planktothricoides is a free-living filamentous cyanobacterium belonging to the order Oscillatoriales and the family Phormidiaceae, capable of forming bloom in fresh and brackish waters. A unicyanobacterial non-axenic culture dominated by Planktothricoides sp. SR001 was obtained from a freshwater reservoir in Singapore. The draft genome presented here is the first tropical freshwater Planktothricoides sp. ever sequenced. The genome of 7.0Mbp contains 5,776 genes predicted using the JGI IMG pipeline. The whole genome sequence allows identification of genes encoding for nitrogen-fixation, accessory photosynthetic pigments and biosynthesis of an off-flavor compound, 2-methylisoborneol, which has been experimentally verified here based on metabolite detection...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28593027/draft-genome-sequence-of-desulfoplanes-formicivorans-pf12b-t-a-sulfate-reducing-bacterium-of-the-family-desulfomicrobiaceae
#2
Miho Watanabe, Hisaya Kojima, Manabu Fukui
Desulfoplanes formicivorans strain Pf12B(T) is the type strain of the type species in the genus Desulfoplanes, which is the one of the genera in the family Desulfomicrobiaceae within the order Desulfovibrionales. This deltaproteobacterium was isolated from a blackish meromictic lake sediment. D. formicivorans strain Pf12B(T) is a Gram-negative, motile and sulfate-reducing bacterium. Cells of strain Pf12B(T) are characterized by possession of vibroid morphology and red fluorescent pigment. Here we describe the features, draft genome sequence and annotation of this organism, the sole species of the genus Desulfoplanes...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28496941/chromosomal-features-of-escherichia-coli-serotype-o2-k2-an-avian-pathogenic-e-coli
#3
Steffen L Jørgensen, Egle Kudirkiene, Lili Li, Jens P Christensen, John E Olsen, Lisa Nolan, Rikke H Olsen
Escherichia coli causing infection outside the gastrointestinal system are referred to as extra-intestinal pathogenic E. coli. Avian pathogenic E. coli is a subgroup of extra-intestinal pathogenic E. coli and infections due to avian pathogenic E. coli have major impact on poultry production economy and welfare worldwide. An almost defining characteristic of avian pathogenic E. coli is the carriage of plasmids, which may encode virulence factors and antibiotic resistance determinates. For the same reason, plasmids of avian pathogenic E...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28496940/complete-genome-sequence-of-bacteriochlorophyll-synthesizing-bacterium-porphyrobacter-neustonensis-dsm-9434
#4
Qian Liu, Yue-Hong Wu, Hong Cheng, Lin Xu, Chun-Sheng Wang, Xue-Wei Xu
The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster. Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll a as well as grow under aerobic conditions. It is the type species of the genus Porphyrobacter. Here we describe the characteristics of the strain DSM 9434, including the genome sequence and annotation, synthesis of BChl a, and metabolic pathways of the organism. The genome of strain DSM 9434 comprises 3,090,363 bp and contains 2,902 protein-coding genes, 47 tRNA genes and 6 rRNA genes...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28491240/high-quality-permanent-draft-genome-sequence-of-chryseobacterium-bovis-dsm-19482-t-isolated-from-raw-cow-milk
#5
Sivan Laviad-Shitrit, Markus Göker, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T B K Reddy, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Tanja Woyke, Hans-Peter Klenk, Nikos C Kyrpides, Malka Halpern
Chryseobacterium bovis DSM 19482(T) (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28484582/genome-sequencing-and-description-of-oerskovia-enterophila-vjag-an-agar-and-cellulose-degrading-bacterium
#6
Vanessa Jag, Anja Poehlein, Frank R Bengelsdorf, Rolf Daniel, Peter Dürre
A nonmotile, Gram-positive bacterium that shows an elongated and branching cell shape was isolated from soil samples from the botanical garden of Ulm University, Ulm, Germany. Here, the isolation procedure, identification, genome sequencing and metabolic features of the strain are described. Phylogenetic analysis allowed to identify the isolated strain as Oerskovia enterophila. The genus Oerskovia belongs to the family Cellulomonadaceae within the order Actinomycetales. The length of cells of O. enterophila ranges from 1 μm to 15 μm, depending on the growth phase...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28428834/genome-sequencing-and-analysis-of-ralstonia-solanacearum-phylotype-i-strains-fjat-91-fjat-452-and-fjat-462-isolated-from-tomato-eggplant-and-chili-pepper-in-china
#7
Yidan Sun, Keke Wang, Carlos Caceres-Moreno, Wei Jia, Aojun Chen, Heng Zhang, Renyi Liu, Alberto P Macho
Ralstonia solanacearum is an extremely destructive pathogen able to cause disease in a wide range of host plants. Here we report the draft genome sequences of the strains FJAT-91, FJAT-452 and FJAT-462, isolated from tomato, eggplant, and chili pepper, respectively, in China. In addition to the genome annotation, we performed a search for type-III secreted effectors in these strains, providing a detailed annotation of their presence and distinctive features compared to the effector repertoire of the reference phylotype I strain (GMI1000)...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28428833/complete-genome-sequence-of-kosakonia-oryzae-type-strain-ola-51-t
#8
Yuanyuan Li, Shuying Li, Mingyue Chen, Guixiang Peng, Zhiyuan Tan, Qianli An
Strain Ola 51(T) (=LMG 24251(T) = CGMCC 1.7012(T)) is the type strain of the species Kosakonia oryzae and was isolated from surface-sterilized roots of the wild rice species Oryza latifolia grown in Guangdong, China. Here we summarize the features of the strain Ola 51(T) and describe its complete genome sequence. The genome contains one circular chromosome of 5,303,342 nucleotides with 54.01% GC content, 4773 protein-coding genes, 16 rRNA genes, 76 tRNA genes, 13 ncRNA genes, 48 pseudo genes, and 1 CRISPR array...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28344744/automation-of-pacbio-smrtbell-ngs-library-preparation-for-bacterial-genome-sequencing
#9
Nguyet Kong, Whitney Ng, Kao Thao, Regina Agulto, Allison Weis, Kristi Spittle Kim, Jonas Korlach, Luke Hickey, Lenore Kelly, Stephen Lappin, Bart C Weimer
BACKGROUND: The PacBio RS II provides for single molecule, real-time DNA technology to sequence genomes and detect DNA modifications. The starting point for high-quality sequence production is high molecular weight genomic DNA. To automate the library preparation process, there must be high-throughput methods in place to assess the genomic DNA, to ensure the size and amounts of the sheared DNA fragments and final library. FINDINGS: The library construction automation was accomplished using the Agilent NGS workstation with Bravo accessories for heating, shaking, cooling, and magnetic bead manipulations for template purification...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28270909/high-quality-permanent-draft-genome-sequence-of-the-bradyrhizobium-elkanii-type-strain-usda-76-t-isolated-from-glycine-max-l-merr
#10
Wayne Reeve, Peter van Berkum, Julie Ardley, Rui Tian, Margaret Gollagher, Dora Marinova, Patrick Elia, T B K Reddy, Manoj Pillay, Neha Varghese, Rekha Seshadri, Natalia Ivanova, Tanja Woyke, Mohamed N Baeshen, Nabih A Baeshen, Nikos Kyrpides
Bradyrhizobium elkanii USDA 76(T) (INSCD = ARAG00000000), the type strain for Bradyrhizobium elkanii, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Glycine max (L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume, B. elkanii USDA 76(T) was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria sequencing project...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28265340/high-quality-draft-genome-sequence-of-an-extremely-halophilic-archaeon-natrinema-altunense-strain-aj2-t
#11
Hong Cheng, Ying-Yi Huo, Jing Hu, Xue-Wei Xu, Min Wu
Natrinema altunense strain AJ2(T), a halophilic archaeal strain, was isolated from a high-altitude (3884 m) salt lake in Xinjiang, China. This strain requires at least 1.7 M NaCl to grow and can grow anaerobically in the presence of nitrate. To understand the genetics underlying its extreme phenotype, we de novo assembled the entire genome sequence of AJ2(T) (=CGMCC 1.3731(T)=JCM 12890(T)). We assembled 3,774,135 bp of a total of 4.4 Mb genome in only 20 contigs and noted its high GC content (64.6%). Subsequently we predicted the gene content and generated genome annotation to identify the relationship between the epigenetic characteristics and genomic features...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28250895/high-quality-draft-genome-sequence-of-the-fermenting-bacterium-anaerobium-acetethylicum-type-strain-glubs11-t-dsm-29698
#12
Yogita Patil, Nicolai Müller, Bernhard Schink, William B Whitman, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T B K Reddy, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, Madan Junghare
Anaerobium acetethylicum strain GluBS11(T) belongs to the family Lachnospiraceae within the order Clostridiales. It is a Gram-positive, non-motile and strictly anaerobic bacterium isolated from biogas slurry that was originally enriched with gluconate as carbon source (Patil, et al., Int J Syst Evol Microbiol 65:3289-3296, 2015). Here we describe the draft genome sequence of strain GluBS11(T) and provide a detailed insight into its physiological and metabolic features. The draft genome sequence generated 4,609,043 bp, distributed among 105 scaffolds assembled using the SPAdes genome assembler method...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28194258/complete-genome-sequence-of-pseudomonas-stutzeri-strain-rch2-isolated-from-a-hexavalent-chromium-cr-vi-contaminated-site
#13
Romy Chakraborty, Hannah Woo, Paramvir Dehal, Robert Walker, Marcin Zemla, Manfred Auer, Lynne A Goodwin, Alexey Kazakov, Pavel Novichkov, Adam P Arkin, Terry C Hazen
Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28174620/complete-genome-sequence-of-thermus-brockianus-ge-1-reveals-key-enzymes-of-xylan-xylose-metabolism
#14
Christian Schäfers, Saskia Blank, Sigrid Wiebusch, Skander Elleuche, Garabed Antranikian
Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile bacterium that was isolated from the Geysir geothermal area, Iceland. Like other thermophiles, Thermus species are often used as model organisms to understand the mechanism of action of extremozymes, especially focusing on their heat-activity and thermostability. Genome-specific features of T. brockianus GE-1 and their properties further help to explain processes of the adaption of extremophiles at elevated temperatures...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28174619/complete-genome-sequence-of-jiangella-gansuensis-strain-yim-002-t-dsm-44835-t-the-type-species-of-the-genus-jiangella-and-source-of-new-antibiotic-compounds
#15
Jian-Yu Jiao, Lorena Carro, Lan Liu, Xiao-Yang Gao, Xiao-Tong Zhang, Wael N Hozzein, Alla Lapidus, Marcel Huntemann, T B K Reddy, Neha Varghese, Michalis Hadjithomas, Natalia N Ivanova, Markus Göker, Manoj Pillay, Jonathan A Eisen, Tanja Woyke, Hans-Peter Klenk, Nikos C Kyrpides, Wen-Jun Li
Jiangella gansuensis strain YIM 002(T) is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the GenomicEncyclopedia ofBacteria andArchaea project, and here we describe the complete genome sequence and annotation of this taxon...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28168014/complete-genome-sequence-of-pseudoalteromonas-phage-vb_psps-h40-1-formerly-h40-1-that-infects-pseudoalteromonas-sp-strain-h40-and-is-used-as-biological-tracer-in-hydrological-transport-studies
#16
René Kallies, Bärbel Kiesel, Matthias Schmidt, Johannes Kacza, Nawras Ghanem, Anja Narr, Jakob Zopfi, Lukas Y Wick, Jörg Hackermüller, Hauke Harms, Antonis Chatzinotas
Pseudoalteromonas phage vB_PspS-H40/1 is a lytic phage that infects Pseudoalteromonas sp. strain H40. Both, the phage and its host were isolated in the 1970s from seawater samples collected from the North Sea near the island of Helgoland, Germany. The phage particle has an icosahedral capsid with a diameter of ~43 to 45 nm and a long non-contractile tail of ~68 nm in length, a typical morphology for members of the Siphoviridae family. The linear dsDNA genome of Pseudoalteromonas phage vB_PspS-H40/1 has a sequence length of 45,306 bp and a GC content of 40...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28163828/potential-probiotic-associated-traits-revealed-from-completed-high-quality-genome-sequence-of-lactobacillus-fermentum-3872
#17
Burhan Lehri, Alan M Seddon, Andrey V Karlyshev
The article provides an overview of the genomic features of Lactobacillus fermentum strain 3872. The genomic sequence reported here is one of three L. fermentum genome sequences completed to date. Comparative genomic analysis allowed the identification of genes that may be contributing to enhanced probiotic properties of this strain. In particular, the genes encoding putative mucus binding proteins, collagen-binding proteins, class III bacteriocin, as well as exopolysaccharide and prophage-related genes were identified...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28163827/the-complete-genome-sequence-of-the-yogurt-isolate-streptococcus-thermophilus-aca-dc-2
#18
Voula Alexandraki, Maria Kazou, Jochen Blom, Bruno Pot, Effie Tsakalidou, Konstantinos Papadimitriou
Streptococcus thermophilus ACA-DC 2 is a newly sequenced strain isolated from traditional Greek yogurt. Among the 14 fully sequenced strains of S. thermophilus currently deposited in the NCBI database, the ACA-DC 2 strain has the smallest chromosome, containing 1,731,838 bp. The annotation of its genome revealed the presence of 1,850 genes, including 1,556 protein-coding genes, 70 RNA genes and 224 potential pseudogenes. A large number of pseudogenes were identified. This was also accompanied by the absence of pathogenic features suggesting evolution of strain ACA-DC 2 through genome decay processes, most probably due to adaptation to the milk ecosystem...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28163826/draft-genome-sequences-of-eight-bacteria-isolated-from-the-indoor-environment-staphylococcus-capitis-strain-h36-s-capitis-strain-h65-s-cohnii-strain-h62-s-hominis-strain-h69-microbacterium-sp-strain-h83-mycobacterium-iranicum-strain-h39-plantibacter-sp-strain
#19
Despoina S Lymperopoulou, David A Coil, Denise Schichnes, Steven E Lindow, Guillaume Jospin, Jonathan A Eisen, Rachel I Adams
We report here the draft genome sequences of eight bacterial strains of the genera Staphylococcus, Microbacterium, Mycobacterium, Plantibacter, and Pseudomonas. These isolates were obtained from aerosol sampling of bathrooms of five residences in the San Francisco Bay area. Taxonomic classifications as well as the genome sequence and gene annotation of the isolates are described. As part of the "Built Environment Reference Genome" project, these isolates and associated genome data provide valuable resources for studying the microbiology of the built environment...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28163825/genomic-analysis-of-four-strains-of-corynebacterium-pseudotuberculosis-bv-equi-isolated-from-horses-showing-distinct-signs-of-infection
#20
Rafael A Baraúna, Rommel T J Ramos, Adonney A O Veras, Pablo H C G de Sá, Luís C Guimarães, Diego A das Graças, Adriana R Carneiro, Judy M Edman, Sharon J Spier, Vasco Azevedo, Artur Silva
The genomes of four strains (MB11, MB14, MB30, and MB66) of the species Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, completely assembled, and their gene content and structure were analyzed. The strains were isolated from horses with distinct signs of infection, including ulcerative lymphangitis, external abscesses on the chest, or internal abscesses on the liver, kidneys, and lungs. The average size of the genomes was 2.3 Mbp, with 2169 (Strain MB11) to 2235 (Strain MB14) predicted coding sequences (CDSs)...
2017: Standards in Genomic Sciences
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