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Standards in Genomic Sciences

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https://www.readbyqxmd.com/read/28932346/insights-from-the-draft-genome-into-the-pathogenicity-of-a-clinical-isolate-of-elizabethkingia-meningoseptica-em3
#1
Shicheng Chen, Marty Soehnlen, Frances P Downes, Edward D Walker
Elizabethkingia meningoseptica is an emerging, healthcare-associated pathogen causing a high mortality rate in immunocompromised patients. We report the draft genome sequence of E. meningoseptica Em3, isolated from sputum from a patient with multiple underlying diseases. The genome has a length of 4,037,922 bp, a GC-content 36.4%, and 3673 predicted protein-coding sequences. Average nucleotide identity analysis (>95%) assigned the bacterium to the species E. meningoseptica. Genome analysis showed presence of the curli formation and assembly operon and a gene encoding hemagglutinins, indicating ability to form biofilm...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28919942/genome-sequence-of-the-white-rot-fungus-irpex-lacteus-f17-a-type-strain-of-lignin-degrader-fungus
#2
Mengwei Yao, Wenman Li, Zihong Duan, Yinliang Zhang, Rong Jia
Irpex lacteus, a cosmopolitan white-rot fungus, degrades lignin and lignin-derived aromatic compounds. In this study, we report the high-quality draft genome sequence of I. lacteus F17, isolated from a decaying hardwood tree in the vicinity of Hefei, China. The genome is 44,362,654 bp, with a GC content of 49.64% and a total of 10,391 predicted protein-coding genes. In addition, a total of 18 snRNA, 842 tRNA, 15 rRNA operons and 11,710 repetitive sequences were also identified. The genomic data provides insights into the mechanisms of the efficient lignin decomposition of this strain...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28904743/complete-genome-sequence-of-the-sulfur-oxidizing-chemolithoautotrophic-sulfurovum-lithotrophicum-42bkt-t
#3
Wooyoung Jeon, Lia Priscilla, Gyuyeon Park, Heeseok Lee, Narae Lee, Dongyup Lee, Hyuksung Kwon, Iksung Ahn, Changha Lee, Hongweon Lee, Jungoh Ahn
A sulfur-oxidizing chemolithoautotrophic bacterium, Sulfurovum lithotrophicum 42BKT(T), isolated from hydrothermal sediments in Okinawa, Japan, has been used industrially for CO2 bio-mitigation owing to its ability to convert CO2 into C5H8NO4(-) at a high rate of specific mitigation (0.42 g CO2/cell/h). The genome of S. lithotrophicum 42BKT(T) comprised of a single chromosome of 2217,891 bp with 2217 genes, including 2146 protein-coding genes and 54 RNA genes. Here, we present its complete genome-sequence information, including information about the genes encoding enzymes involved in CO2 fixation and sulfur oxidation...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28904742/draft-genome-sequence-of-the-cellulolytic-endophyte-chitinophaga-costaii-a37t2-t
#4
Diogo N Proença, William B Whitman, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, Paula V Morais
Here we report the draft genome sequence of Chitinophaga costai A37T2(T) (=CIP 110584(T), =LMG 27458(T)), which was isolated from the endophytic community of Pinus pinaster tree. The total genome size of C. costaii A37T2(T) is 5.07 Mbp, containing 4204 coding sequences. Strain A37T2(T) encoded multiple genes likely involved in cellulolytic, chitinolytic and lipolytic activities. This genome showed 1145 unique genes assigned into 109 Cluster of Orthologous Groups in comparison with the complete genome of C. pinensis DSM 2588(T)...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28904741/complete-genome-of-arthrobacter-alpinus-strain-r3-8-bioremediation-potential-unraveled-with-genomic-analysis
#5
Wah-Seng See-Too, Robson Ee, Yan-Lue Lim, Peter Convey, David A Pearce, Taznim Begam Mohd Mohidin, Wai-Fong Yin, Kok Gan Chan
Arthrobacter alpinus R3.8 is a psychrotolerant bacterial strain isolated from a soil sample obtained at Rothera Point, Adelaide Island, close to the Antarctic Peninsula. Strain R3.8 was sequenced in order to help discover potential cold active enzymes with biotechnological applications. Genome analysis identified various cold adaptation genes including some coding for anti-freeze proteins and cold-shock proteins, genes involved in bioremediation of xenobiotic compounds including naphthalene, and genes with chitinolytic and N-acetylglucosamine utilization properties and also plant-growth-influencing properties...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28878862/permanent-draft-genome-sequence-of-frankia-sp-nrrl-b-16219-reveals-the-presence-of-canonical-nod-genes-which-are-highly-homologous-to-those-detected-in-candidatus-frankia-dg1-genome
#6
Amir Ktari, Imen Nouioui, Teal Furnholm, Erik Swanson, Faten Ghodhbane-Gtari, Louis S Tisa, Maher Gtari
Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219 is closely related to "Frankia discariae" with a 16S rRNA gene similarity of 99.78%. Because of the lack of genetic tools for Frankia, our understanding of the bacterial signals involved during the plant infection process and the development of actinorhizal root nodules is very limited...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28878861/genome-sequence-of-the-sulfur-oxidizing-bathymodiolus-thermophilus-gill-endosymbiont
#7
Ruby Ponnudurai, Lizbeth Sayavedra, Manuel Kleiner, Stefan E Heiden, Andrea Thürmer, Horst Felbeck, Rabea Schlüter, Stefan M Sievert, Rolf Daniel, Thomas Schweder, Stephanie Markert
Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the East Pacific Rise, lives in symbiosis with chemosynthetic Gammaproteobacteria within its gills. The intracellular symbiont population synthesizes nutrients for the bivalve host using the reduced sulfur compounds emanating from the vents as energy source. As the symbiont is uncultured, comprehensive and detailed insights into its metabolism and its interactions with the host can only be obtained from culture-independent approaches such as genomics and proteomics...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28878860/draft-genome-sequences-of-two-opportunistic-pathogenic-strains-of-staphylococcus-cohnii-isolated-from-human-patients
#8
Soraya Mendoza-Olazarán, José F Garcia-Mazcorro, Rayo Morfín-Otero, Licet Villarreal-Treviño, Adrián Camacho-Ortiz, Eduardo Rodríguez-Noriega, Paola Bocanegra-Ibarias, Héctor J Maldonado-Garza, Scot E Dowd, Elvira Garza-González
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...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28852435/complete-genome-sequence-of-the-nematicidal-bacillus-thuringiensis-mybt18246
#9
Jacqueline Hollensteiner, Anja Poehlein, Cathrin Spröer, Boyke Bunk, Anna E Sheppard, Philip Rosentstiel, Hinrich Schulenburg, Heiko Liesegang
10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of the genus 10.1601/nm.4857. The defining feature of the species is the ability to produce parasporal crystal inclusion bodies, consisting of δ-endotoxins, encoded by cry-genes. Here we present the complete annotated genome sequence of the nematicidal 10.1601/nm.5000 strain MYBT18246. The genome comprises one 5,867,749 bp chromosome and 11 plasmids which vary in size from 6330 bp to 150,790 bp. The chromosome contains 6092 protein-coding and 150 RNA genes, including 36 rRNA genes...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28814988/the-draft-genome-of-the-hyperthermophilic-archaeon-pyrodictium-delaneyi-strain-hulk-an-iron-and-nitrate-reducer-reveals-the-capacity-for-sulfate-reduction
#10
Lucas M Demey, Caitlin R Miller, Michael P Manzella, Rachel R Spurbeck, Sukhinder K Sandhu, Gemma Reguera, Kazem Kashefi
Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (47.9501 latitude, -129.0970 longitude, depth 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared 99.77% similarity with the complete genome of the type strain Su06(T), which shares with strain Hulk the ability to reduce iron and nitrate for respiration. The annotation of the genome of strain Hulk identified genes for the reduction of several sulfur-containing electron acceptors, an unsuspected respiratory capability in this species that was experimentally confirmed for strain Hulk...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28770030/the-complete-genome-sequence-of-the-cold-adapted-crude-oil-degrader-pedobacter-steynii-dx4
#11
Sijing Chang, Gaosen Zhang, Ximing Chen, Haozhi Long, Yilin Wang, Tuo Chen, Guangxiu Liu
Pedobacter steynii DX4 was isolated from the soil of Tibetan Plateau and it can use crude oil as sole carbon and energy source at 15 °C. The genome of Pedobacter steynii DX4 has been sequenced and served as basis for analysis its metabolic mechanism. It is the first genome of crude oil degrading strain in Pedobacter genus. The 6.58 Mb genome has an average G + C content of 41.31% and encodes 5464 genes. In addition, annotation revealed that Pedobacter steynii DX4 has cold shock proteins, abundant response regulators for cell motility, and enzymes involved in energy conversion and fatty acid metabolism...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28770029/complete-genome-sequence-of-the-sand-sediment-actinobacterium-nocardioides-dokdonensis-fr1436-t
#12
Min-Jung Kwak, Soon-Kyeong Kwon, Jihyun F Kim
Nocardioides dokdonensis, belonging to the class Actinobacteria, was first isolated from sand sediment of a beach in Dokdo, Korea, in 2005. In this study, we determined the genome sequence of FR1436, the type strain of N. dokdonensis, and analyzed its gene contents. The genome sequence is the second complete one in the genus Nocardioides after that of Nocardioides sp. JS614. It is composed of a 4,376,707-bp chromosome with a G + C content of 72.26%. From the genome sequence, 4,104 CDSs, three rRNA operons, 51 tRNAs, and one tmRNA were predicted, and 71...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28770028/first-draft-genome-sequence-of-a-strain-from-the-genus-fusibacter-isolated-from-salar-de-ascot%C3%A3-n-in-northern-chile
#13
Antonio E Serrano, Lorena V Escudero, Cinthya Tebes-Cayo, Mauricio Acosta, Olga Encalada, Sebastián Fernández-Moroso, Cecilia Demergasso
Fusibacter sp. 3D3 (ATCC BAA-2418) is an arsenate-reducing halotolerant strain within the Firmicutes phylum, isolated from the Salar de Ascotán, a hypersaline salt flat in Northern Chile. This high-Andean closed basin is an athalassohaline environment located at the bottom of a tectonic basin surrounded by mountain range, including some active volcanoes. This landscape can be an advantageous system to explore the effect of salinity on microorganisms that mediate biogeochemical reactions. Since 2000, microbial reduction of arsenic has been evidenced in the system, and the phylogenetic analysis of the original community plus the culture enrichments has revealed the predominance of Firmicutes phylum...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28770027/the-genome-of-the-cotton-bacterial-blight-pathogen-xanthomonas-citri-pv-malvacearum-strain-msct1
#14
Kurt C Showmaker, Mark A Arick, Chuan-Yu Hsu, Brigitte E Martin, Xiaoqiang Wang, Jiayuan Jia, Martin J Wubben, Robert L Nichols, Tom W Allen, Daniel G Peterson, Shi-En Lu
Xanthomonas citri pv. malvacearum is a major pathogen of cotton, Gossypium hirsutum L.. In this study we report the complete genome of the X. citri pv. malvacearum strain MSCT1 assembled from long read DNA sequencing technology. The MSCT1 genome is the first X. citri pv. malvacearum genome with complete coding regions for X. citri pv. malvacearum transcriptional activator-like effectors. In addition functional and structural annotations are presented in this study that will provide a foundation for future pathogenesis studies with MSCT1...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28770026/neisseria-lactamica-y92-1009-complete-genome-sequence
#15
Anish K Pandey, David W Cleary, Jay R Laver, Martin C J Maiden, Xavier Didelot, Andrew Gorringe, Robert C Read
We present the high quality, complete genome assembly of Neisseria lactamica Y92-1009 used to manufacture an outer membrane vesicle (OMV)-based vaccine, and a member of the Neisseria genus. The strain is available on request from the Public Health England Meningococcal Reference Unit. This Gram negative, dipplococcoid bacterium is an organism of worldwide clinical interest because human nasopharyngeal carriage is related inversely to the incidence of meningococcal disease, caused by Neisseria meningitidis. The organism sequenced was isolated during a school carriage survey in Northern Ireland in 1992 and has been the subject of a variety of laboratory and clinical studies...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28748024/insights-into-cedecea-neteri-strain-m006-through-complete-genome-sequence-a-rare-bacterium-from-aquatic-environment
#16
Kok-Gan Chan, Wen-Si Tan
Cedecea neteri M006 is a rare bacterium typically found as an environmental isolate from the tropical rainforest Sungai Tua waterfall (Gombak, Selangor, Malaysia). It is a Gram-reaction-negative, facultative anaerobic, bacillus. Here, we explore the features of Cedecea neteri M006, together with its genome sequence and annotation. The genome comprised 4,965,436 bp with 4447 protein-coding genes and 103 RNA genes.
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28729898/draft-genome-sequences-of-strains-salinicola-socius-smb35-t-salinicola-sp-mh3r3-1-and-chromohalobacter-sp-smb17-from-the-verkhnekamsk-potash-mining-region-of-russia
#17
Björn E Olsson, Ekaterina S Korsakova, Lyudmila N Anan'ina, Anna A Pyankova, Olga V Mavrodi, Elena G Plotnikova, Dmitri V Mavrodi
Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of Salinicola socius SMB35(T), Salinicola sp. MH3R3-1 and Chromohalobacter sp...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28725337/complete-genome-sequence-of-leuconostoc-suionicum-dsm-20241-t-provides-insights-into-its-functional-and-metabolic-features
#18
Byung Hee Chun, Se Hee Lee, Hye Hee Jeon, Dong-Woon Kim, Che Ok Jeon
The genome of Leuconostoc suionicum DSM 20241(T) (=ATCC 9135(T) = LMG 8159(T) = NCIMB 6992(T)) was completely sequenced and its fermentative metabolic pathways were reconstructed to investigate the fermentative properties and metabolites of strain DSM 20241(T) during fermentation. The genome of L. suionicum DSM 20241(T) consists of a circular chromosome (2026.8 Kb) and a circular plasmid (21.9 Kb) with 37.58% G + C content, encoding 997 proteins, 12 rRNAs, and 72 tRNAs. Analysis of the metabolic pathways of L...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28725336/high-quality-draft-genome-sequence-of-a-biofilm-forming-lignocellulolytic-aspergillus-niger-strain-atcc-10864
#19
Sujay Paul, Yvette Ludeña, Gretty K Villena, Fengan Yu, David H Sherman, Marcel Gutiérrez-Correa
Filamentous fungus Aspergillus niger has high industrial value due to their lignocellulolytic enzyme activities and ATCC 10864 is one of the few type strains of A. niger which has a unique biofilm forming capability. Here we report the first draft genome sequence of A. niger ATCC 10864 strain. The genome of A. niger ATCC 10864 is 36,172,237 bp long and comprise of 310 scaffolds with 49.5% average GC content. A total of 10,804 protein-coding genes were predicted among which 10,761 genes were with putative functions...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28593028/genomics-insights-into-production-of-2-methylisoborneol-and-a-putative-cyanobactin-by-planktothricoides-sp-sr001
#20
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
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