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991.
Pati A Sikorski J Gronow S Munk C Lapidus A Copeland A Glavina Del Tio T Nolan M Lucas S Chen F Tice H Cheng JF Han C Detter JC Bruce D Tapia R Goodwin L Pitluck S Liolios K Ivanova N Mavromatis K Mikhailova N Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Spring S Rohde M Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,2(3):260-269
Brachyspira murdochii Stanton et al. 1992 is a non-pathogenic, host-associated spirochete of the family Brachyspiraceae. Initially isolated from the intestinal content of a healthy swine, the 'group B spirochaetes' were first described as Serpulina murdochii. Members of the family Brachyspiraceae are of great phylogenetic interest because of the extremely isolated location of this family within the phylum 'Spirochaetes'. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a type strain of a member of the family Brachyspiraceae and only the second genome sequence from a member of the genus Brachyspira. The 3,241,804 bp long genome with its 2,893 protein-coding and 40 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
992.
Sikorski J Munk C Lapidus A Ngatchou Djao OD Lucas S Glavina Del Rio T Nolan M Tice H Han C Cheng JF Tapia R Goodwin L Pitluck S Liolios K Ivanova N Mavromatis K Mikhailova N Pati A Sims D Meincke L Brettin T Detter JC Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Rohde M Lang E Spring S Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,2(2):194-202
Thermocrinis albus Eder and Huber 2002 is one of three species in the genus Thermocrinis in the family Aquificaceae. Members of this family have become of significant interest because of their involvement in global biogeochemical cycles in high-temperature ecosystems. This interest had already spurred several genome sequencing projects for members of the family. We here report the first completed genome sequence a member of the genus Thermocrinis and the first type strain genome from a member of the family Aquificaceae. The 1,500,577 bp long genome with its 1,603 protein-coding and 47 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
993.
Spring S Rachel R Lapidus A Davenport K Tice H Copeland A Cheng JF Lucas S Chen F Nolan M Bruce D Goodwin L Pitluck S Ivanova N Mavromatis K Ovchinnikova G Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CC Brettin T Detter JC Tapia R Han C Heimerl T Weikl F Brambilla E Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,2(3):245-259
Thermosphaera aggregans Huber et al. 1998 is the type species of the genus Thermosphaera, which comprises at the time of writing only one species. This species represents archaea with a hyperthermophilic, heterotrophic, strictly anaerobic and fermentative phenotype. The type strain M11TL(T) was isolated from a water-sediment sample of a hot terrestrial spring (Obsidian Pool, Yellowstone National Park, Wyoming). Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,316,595 bp long single replicon genome with its 1,410 protein-coding and 47 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
994.
Lail K Sikorski J Saunders E Lapidus A Glavina Del Rio T Copeland A Tice H Cheng JF Lucas S Nolan M Bruce D Goodwin L Pitluck S Ivanova N Mavromatis K Ovchinnikova G Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Chain P Brettin T Detter JC Schütze A Rohde M Tindall BJ Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Chen F 《Standards in genomic sciences》2010,2(2):176-185
Spirosoma linguale Migula 1894 is the type species of the genus. S. linguale is a free-living and non-pathogenic organism, known for its peculiar ringlike and horseshoe-shaped cell morphology. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is only the third completed genome sequence of a member of the family Cytophagaceae. The 8,491,258 bp long genome with its eight plasmids, 7,069 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
995.
Kiss H Cleland D Lapidus A Lucas S Del Rio TG Nolan M Tice H Han C Goodwin L Pitluck S Liolios K Ivanova N Mavromatis K Ovchinnikova G Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Lu M Brettin T Detter JC Göker M Tindall BJ Beck B McDermott TR Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Cheng JF 《Standards in genomic sciences》2010,3(2):153-162
'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus 'Thermobaculum'. Strain YNP1(T) is the only cultivated member of an acid tolerant, extremely thermophilic species belonging to a phylogenetically isolated environmental clone group within the phylum Chloroflexi. At present, the name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is likely to be the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
996.
Tanja Woyke Damon Tighe Konstantinos Mavromatis Alicia Clum Alex Copeland Wendy Schackwitz Alla Lapidus Dongying Wu John P. McCutcheon Bradon R. McDonald Nancy A. Moran James Bristow Jan-Fang Cheng 《PloS one》2010,5(4)
While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200–900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes. 相似文献
997.
Pitluck S Yasawong M Munk C Nolan M Lapidus A Lucas S Glavina Del Rio T Tice H Cheng JF Bruce D Detter C Tapia R Han C Goodwin L Liolios K Ivanova N Mavromatis K Mikhailova N Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Rohde M Spring S Sikorski J Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,3(2):108-116
Thermosediminibacter oceani (Lee et al. 2006) is the type species of the genus Thermosediminibacter in the family Thermoanaerobacteraceae. The anaerobic, barophilic, chemoorganotrophic thermophile is characterized by straight to curved Gram-negative rods. The strain described in this study was isolated from a core sample of deep sea sediments of the Peruvian high productivity upwelling system. This is the first completed genome sequence of a member of the genus Thermosediminibacter and the seventh genome sequence in the family Thermoanaerobacteraceae. The 2,280,035 bp long genome with its 2,285 protein-coding and 63 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
998.
Mavromatis K Yasawong M Chertkov O Lapidus A Lucas S Nolan M Del Rio TG Tice H Cheng JF Pitluck S Liolios K Ivanova N Tapia R Han C Bruce D Goodwin L Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Detter JC Rohde M Brambilla E Spring S Göker M Sikorski J Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Klenk HP Kyrpides NC 《Standards in genomic sciences》2010,3(2):136-144
Spirochaeta smaragdinae Magot et al. 1998 belongs to the family Spirochaetaceae. The species is Gram-negative, motile, obligately halophilic and strictly anaerobic and is of interest because it is able to ferment numerous polysaccharides. S. smaragdinae is the only species of the family Spirochaetaceae known to reduce thiosulfate or element sulfur to sulfide. This is the first complete genome sequence in the family Spirochaetaceae. The 4,653,970 bp long genome with its 4,363 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
999.
Masahiro Nakajima Atsushi Takahashi Ikuyo Kou Cristina Rodriguez-Fontenla Juan J. Gomez-Reino Tatsuya Furuichi Jin Dai Akihiro Sudo Atsumasa Uchida Naoshi Fukui Michiaki Kubo Naoyuki Kamatani Tatsuhiko Tsunoda Konstantinos N. Malizos Aspasia Tsezou Antonio Gonzalez Yusuke Nakamura Shiro Ikegawa 《PloS one》2010,5(3)
Osteoarthritis (OA) is a common disease that has a definite genetic component. Only a few OA susceptibility genes that have definite functional evidence and replication of association have been reported, however. Through a genome-wide association study and a replication using a total of ∼4,800 Japanese subjects, we identified two single nucleotide polymorphisms (SNPs) (rs7775228 and rs10947262) associated with susceptibility to knee OA. The two SNPs were in a region containing HLA class II/III genes and their association reached genome-wide significance (combined P = 2.43×10−8 for rs7775228 and 6.73×10−8 for rs10947262). Our results suggest that immunologic mechanism is implicated in the etiology of OA. 相似文献
1000.
Athanasios Lykidis Danilo Pérez-Pantoja Thomas Ledger Kostantinos Mavromatis Iain J. Anderson Natalia N. Ivanova Sean D. Hooper Alla Lapidus Susan Lucas Bernardo González Nikos C. Kyrpides 《PloS one》2010,5(3)