期刊界 All Journals 搜尽天下杂志传播学术成果专业期刊搜索期刊信息化学术搜索

1.

Genome sequences published outside of Standards in Genomic Sciences, March-April 2012

Oranmiyan W. Nelson George M. Garrity 《Standards in genomic sciences》2012,6(2):287-292

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Phylum Euryarchaeota

Halococcus hamelinensis, sequence accession PRJNA80845 [1]
“Methanocella conradii” HZ254, sequence accession CP003243 [2]
Thermococcus litoralis NS-C, sequence accession AHVB00000000 [3]

Phylum Crenarchaeota

Candidatus Nitrosopumilus salaria” BD31, sequence accession AEXL00000000 [4]
Candidatus Nitrosoarchaeum limnia, sequence accession AHJG00000000 [5]

Phylum Deinococcus-Thermus

Deinococcus gobiensis, sequence accession CP002536 [6]

Phylum Proteobacteria

Aggregatibacter actinomycetemcomitans strain ANH9381, sequence accession CP003099 [7]
Alishewanella jeotgali, sequence accession AHTH00000000 [8]
Enterobacter aerogenes KCTC 2190, sequence accession CP002824 [9]
Escherichia coli O104:H4, sequence accession AFOB02000092 [10]
Helicobacter pylori strains 17874, sequence accession PRJNA76569 [11]
Helicobacter pylori strains P79, sequence accession PRJNA76567 [11]
Janthinobacterium sp. Strain PAMC 25724, sequence accession AHHB00000000 [12]
Klebsiella oxytoca KCTC 1686, sequence accession CP003218 [13]
Klebsiella pneumoniae subsp. pneumoniae HS11286, sequence accession CP003200 (chromosome), CP003223 (plasmid pKPHS1), CP003224 (plasmid pKPHS2), CP003225 (plasmid pKPHS3), CP003226 (plasmid pKPHS4), CP003227 (plasmid pKPHS5), CP003228 (plasmid pKPHS6) [14]
Oceanimonas sp. GK1, sequence accession CP003171 [15]
“Pseudogulbenkiania ferrooxidans” Strain 2002, sequence accession NZ_ACIS01000000 [16]
Pseudomonas extremaustralis 14-3b, sequence accession AHIP00000000 [17]
Pseudomonas sp. Strain PAMC 25886, sequence accession AHHC00000000 [18]
Psychrobacter, sequence accession AHVZ00000000 [19]
Rahnella sp. Strain Y9602, sequence accession CP002505 [20]
Rhizobium sp. Strain PDO1-076, sequence accession AHZC00000000 [21]
Rhodospirillum photometricum DSM122, sequence accession HE663493 [22]
“Rickettsia sibirica sibirica”, sequence accession AHIZ00000000 [23]
Rickettsia sibirica subsp. mongolitimonae strain HA-91, sequence accession AHZB00000000 [24]
Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5, sequence accession [25]
Salmonella enterica subsp. enterica Serotype Senftenberg Strain SS209, sequence accession CAGQ00000000 [26]
Salmonella enterica subsp. enterica Serovar Typhi P-stx-12, sequence accession CP003278 (chromosome) and CP003279 (plasmid) [27]
Sphingomonas echinoides ATCC 14820, sequence accession AHIR00000000 [28]
Strain HIMB55, sequence accession AGIF00000000 [29]
Vibrio harveyi CAIM 1792, sequence accession AHHQ00000000 [30]
Wolbachia Strain wAlbB, sequence accession CAGB01000001 to CAGB01000165 [31]
Xanthomonas axonopodis pv. punicae Strain LMG 859, sequence accession CAGJ01000001 to CAGJ01000217 [32]

Phylum Tenericutes

Mycoplasma hyorhinis Strain GDL-1, sequence accession CP003231 [33]

Phylum Firmicutes

Bacillus subtilis, sequence accession BGSCID 3A27 through BGSCID 28A4 [34]
Clostridium difficile Strain CD37, sequence accession AHJJ00000000 [35]
Clostridium perfringens, sequence accession AFES00000000 [36]
Lactobacillus fructivorans KCTC 3543, sequence accession AEQY00000000 [37]
Lactococcus lactis IO-1, sequence accession AP012281 [38]
Lactobacillus plantarum strain NC8, sequence accession AGRI00000000 [39]
Paenibacillus dendritiformis C454, sequence accession AHKH00000000 [40]
Paenibacillus sp. Strain Aloe-11, sequence accession AGFI00000000 [41]
“Peptoniphilus rhinitidis” 1-13^T, sequence accession BAEW01000001 to BAEW01000056 [42]
Streptococcus macedonicus ACA-DC 198, sequence accession HE613569 and HE613570 [43]
Staphylococcus aureus VC40, sequence accession CP003033 [44]
Streptococcus infantarius subsp. infantarius Strain CJ18, sequence accession CP003295 (chromosome), CP003296 (plasmid) [45]
Streptococcus macedonicus ACA-DC 198, sequence accession HE613569 (chromosome), HE613570 (plasmid pSMA198) [46]

Phylum Actinobacteria

Actinoplanes sp. SE50/110, sequence accession CP003170 [47]
Amycolatopsis sp. Strain ATCC 39116, sequence accession [48]
Nocardia cyriacigeorgica GUH-2, sequence accession FO082843 [49]
Salinibacterium sp., sequence accession AHWA00000000 [50]
Streptomyces acidiscabies 84-104, sequence accession AHBF00000000 [51]

Non-Bacterial genomes

Bluetongue Virus Serotype 2, sequence accession AJ783905 (Seg-6) and JQ681257 (Seg-1), JQ681257 (Seg-1), JQ681258 (Seg-2), JQ681259 (Seg-3), JQ681260 (Seg-4), JQ681261 (Seg-5), JQ681262 (Seg-7), JQ6812563 (Seg-8), JQ6812564 (Seg-9), to JQ681265 (Seg-10) [52]
Virus Serotype 1, sequence accession AJ585111 (Seg-2), AJ586659 (Seg-6), JQ282770 (Seg-1), JQ282771 (Seg-3), JQ282772 (Seg-4), JQ282773 (Seg-5), JQ282774 (Seg-7), JQ282775 (Seg-8), JQ282776 (Seg-9), and JQ282777 (Seg-10) [52]
Chloroplast genome of Erycina pusilla, sequence accession JF_746994 [53]
Danio rerio, sequence accession JQ434101 [54]
Enterococcal Bacteriophage SAP6, sequence accession JF731128 [55]
Eubenangee virus, sequence accession JQ070376 through JQ070385 [56]
Fujian/411-like viruses, sequence accession CY087969 to CY088568 [57]
Hantavirus Variant of Rio Mamoré Virus, Maripa Virus, sequence accession JQ611712 (segment S), JQ611713 (segment M), and JQ611714 (segment L) [58]
Pata virus, sequence accession JQ070386 through JQ070395 [59]
Porcine Circovirus 2, sequence accession JQ413808 [60]
Porcine Reproductive and Respiratory Syndrome Virus, sequence accession JQ326271 [61]
Streptococcus mutans Phage M102AD, sequence accession DQ386162 [62]
Tilligery virus, sequence accession JQ070366 through JQ070375 [63]

相似文献

2.

Genome sequences published outside of Standards in Genomic Sciences, January-March 2012

Oranmiyan W. Nelson George M. Garrity 《Standards in genomic sciences》2012,6(1):126-135

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Phylum Crenarchaeota

Pyrobaculum strain 1860, sequence accession CP003098 [1]

Phylum Deinococcus-Thermus

“Thermus sp.” Strain CCB_US3_UF1, sequence accession CP003126 (chromosome), CP003127 (plasmid) [2]

Phylum Proteobacteria

“Achromobacter arsenitoxydans” SY8, sequence accession AGUF00000000 [3]
Acidovorax sp. Strain NO1, sequence accession AGTS00000000 [4]
Acinetobacter baumannii AB4857, sequence accession AHAG00000000 [5]
Acinetobacter baumannii AB5075, sequence accession AHAH00000000 [5]
Acinetobacter baumannii AB5256, sequence accession AHAI00000000 [5]
Acinetobacter baumannii AB5711, sequence accession AHAJ00000000 [5]
Aeromonas salmonicida, sequence accession AGVO00000000 [6]
Aggregatibacter actinomycetemcomitans RHAA1, sequence accession AHGR00000000 [7]
Agrobacterium tumefaciens 5A, sequence accession AGVZ00000000 [8]
Azoarcus sp. Strain KH32C, sequence accession AP012304, AP012305 [9]
Burkholderia sp. Strain YI23, sequence accession CP003087 (Chromosome 1), CP003088 (Chromosome 2), CP003089 (Chromosome 3), CP003090 (plasmid BYI23_D), CP003091 (plasmid BYI23_E) CP003092 (plasmid BYI23_F) [10]
Brucella suis VBI22, sequence accession CP003128, CP003129 [11]
Comamonas testosteroni ATCC 11996, sequence accession AHIL00000000 [12]
“Commensalibacter intestini” A911^T, sequence accession AGFR00000000 [13]
Edwardsiella ictaluri, sequence accession CP001600.1 [14]
Enterobacter cloacae subsp. dissolvens SDM, sequence accession AGSY00000000 [15]
“Gluconobacter morbifer” G707^T, sequence accession AGQV00000000 [16]
Legionella dumoffii TEX-KL, sequence accession AGVT00000000 [17]
Legionella dumoffii NY-23, sequence accession AGVU00000000 [17]
Legionella pneumophila serogroup 12 Strain 570-CO-H, sequence accession CP003192 [18]
Marinobacterium stanieri S30, sequence accession AFPL00000000 [19]
“Marinobacter manganoxydans” MnI7-9, sequence accession CP001978 to CP001980 [20]
Mesorhizobium alhagi CCNWXJ12-2T, sequence accession AHAM00000000 [21]
Mesorhizobium amorphae, sequence accession AGSN00000000 [22]
Methylomicrobium alcaliphilum 20Z, sequence accession FO082060 and FO082061 [23]
Mitsuaria sp. Strain H24L5A, sequence accession CAFG01000001 to CAFG01000607 [24]
Novosphingobium pentaromativorans US6-1, sequence accession AGFM00000000 [25]
Pantoea ananatis B1-9, sequence accession CAEI01000001 to CAEI01000169 [26]
Pantoea ananatis LMG 5342, sequence accession HE617160 (chromosome), HE617161 (pPANA10) [27]
Pantoea ananatis Strain PA13, sequence accession CP003085 and CP003086 [28]
Pseudomonas aeruginosa, sequence accession AFXI00000000 [29]
Pseudomonas aeruginosa, sequence accession AFXJ00000000 [29]
Pseudomonas aeruginosa, sequence accession AFXK00000000 [29]
Pseudomonas chlororaphis GP72, sequence accession AHAY01000000 [30]
Pseudomonas fluorescens F113, sequence accession CP003150 [31]
Pseudomonas fluorescens Wayne 1R, sequence accession CADX01000001 to CADX01000090 [32]
Pseudomonas fluorescens Wood1R, sequence accession CAFF01000001 to CAFF01001437 [32]
Pseudomonas psychrotolerans L19, sequence accession AHBD00000000 [33]
Pseudoalteromonas rubra ATCC 29570^T, sequence accession AHCD00000000 [34]
Pseudomonas stutzeri SDM-LAC, sequence accession AGSX00000000 [35]
Pseudoxanthomonas spadix BD-a59, sequence accession CP003093 [36]
Rickettsia slovaca, sequence accession CP002428 [37]
Salmonella enterica serovar Pullorum RKS5078, sequence accession CP003047 [38]
Sinorhizobium meliloti CCNWSX0020, sequence accession AGVV00000000 [39]
Sphingobium sp. Strain SYK-6, sequence accession AP012222 and AP012223 [40]
Sphingomonas sp. Strain PAMC 26605, sequence accession AHIS00000000 [41]
Stenotrophomonas maltophilia RR-10, sequence accession AGRB00000000 [42]
Strain HIMB30, sequence accession AGIG00000000 [43]
Taylorella equigenitalis, sequence accession CP003059 [44]
Vibrio campbellii DS40M4, sequence accession AGIE00000000 [45]
Vibrio fischeri SR5, sequence accession AHIH00000000 [46]
Yersinia enterocolitica, sequence accession AGQO00000000 [47]

Phylum Tenericutes

Candidatus Mycoplasma haemominutum, sequence accession HE613254 [48]
Mycoplasma haemocanis strain Illinois, sequence accession CP003199 [49]
Mycoplasma iowae, sequence accession AGFP00000000 [50]
Mycoplasma pneumoniae Type 2a Strain 309, sequence accession AP012303 [51]

Phylum Firmicutes

Bacillus cereus F837/76, sequence accession CP003187 (chromosome) CP003188 (pF837_55kb), CP003189 (pF837_10kb) [52]
Brevibacillus laterosporus Strain GI-9, sequence accession CAGD01000001 to CAGD01000061 [53]
Clostridium sporogenes PA 3679, sequence accession AGAH00000000 [54]
Enterococcus mundtii CRL1656, sequence accession AFWZ00000000.1 [55]
Geobacillus thermoleovorans CCB_US3_UF5, sequence accession CP003125 [56]
Lactobacillus curvatus Strain CRL705, sequence accession AGBU01000000 [57]
Lactobacillus rhamnosus ATCC 8530, sequence accession CP003094 [58]
Lactobacillus rhamnosus R0011, sequence accession AGKC00000000 [59]
Lactococcus garvieae TB25, sequence accession AGQX01000000 [60]
Lactococcus garvieae LG9, sequence accession AGQY01000000 [60]
Lactococcus lactis subsp. cremoris A76, sequence accession CP003132 (chromosome), CP003136 (pQA505), CP003135 (PQA518), CP003134 (pQA549), CP003133 (pQA554) [61]
Leuconostoc citreum LBAE C10, sequence accession CAGE00000000 [62]
Leuconostoc citreum LBAE C11, sequence accession CAGF00000000 [62]
Leuconostoc citreum LBAE E16, sequence accession CAGG00000000 [62]
Leuconostoc mesenteroides subsp. mesenteroides Strain J18, sequence accession CP003101 [63]
Paenibacillus peoriae Strain KCTC 3763^T, sequence accession AGFX00000000 [64]
Pediococcus acidilactici MA18/5M, sequence accession AGKB00000000 [65]
Pediococcus claussenii ATCC BAA-344^T, sequence accession CP003137 (chromosome), CP003138 (pPECL-1), CP003139 (pPECL-2), CP003140 (pPECL-3), CP003141 (pPECL-4), CP003142 (pPECL-5), CP003143 (pPECL-6), CP003144 (pPECL-7), CP003145 (pPECL-8) [66]
Staphylococcus aureus M013, sequence accession CP003166 [67]
Staphylococcus aureus subsp. aureus TW20, sequence accession FN433596 [68]
Weissella confusa LBAE C39-2, sequence accession CAGH00000000 [69]

Phylum Actinobacteria

Corynebacterium casei, sequence accession CAFW01000001 to CAFW01000106 [70]
Corynebacterium glutamicum, sequence accession AGQQ00000000 [71]
Leucobacter chromiiresistens, sequence accession AGCW00000000 [72]
Mycobacterium abscessus, sequence accession AGQU00000000 [73]
Propionibacterium acnes ST9, sequence accession CP003195 [74]
Propionibacterium acnes ST22, sequence accession CP003196 [74]
Propionibacterium acnes ST27, sequence accession CP003197 [74]
Saccharomonospora azurea SZMC 14600, sequence accession AHBX00000000 [75]
Streptomyces sp. Strain TOR3209, sequence accession AGNH00000000 [76]
Streptomyces sp. Strain W007, sequence accession AGSW00000000 [77]

Phylum Spirochaetes

Borrelia valaisiana VS116, sequence accession ABCY02000001 (chromosome), CP001439 (plasmid Ip17), CP001437 (Ip25), CP001440 (plasmid Ip 28-3), CP001442 (plasmid Ip28-8), CP001436 (Ip 36), CP001433 (plasmid Ip 54), CP001438 (plasmid cp9), CP001432 (plasmid cp26), CP001441 (plasmid cp32-5), CP001434 (plasmid cp32-7), CP001435 (plasmid cp32-10) [78]
“Borrelia bissettii” DN127, sequence accession CP002746 (chromosome), CP002756 (plasmid Ip12), CP002757 (plasmid Ip25), CP002758 (plasmid 28-3), CP002759 (plasmid Ip 28-4), CP002760 (Ip28-7), CP002761 (plasmid Ip54), CP002762 (plasmid Ip56), CP002755 (plasmid cp9), CP002747 (plasmid cp26), CP002749 (plasmid cp32-3), CP002750 (plasmid cp32-4), CP002751 (plasmid 32-5), CP002752 (plasmid cp32-6), CP002753 (plasmid cp32-7), CP0027554 (plasmid cp32-9), CP002748 (plasmid cp32-11) [78]
Borrelia spielmanii A14S, sequence accession ABKB02000001 (chromosome), CP001468 (plasmid Ip17), CP001471 (Ip28-3), CP001470 (plasmid Ip28-4), CP001465 (plasmid Ip28-2), CP001466 (plasmid Ip36), CP001464 (plasmid Ip38), CP001469 (plasmid Ip54), ABKB02000016, ABKB02000020 (plasmid cp9), CP001467 (plasmid cp26), ABKB02000026 (plasmid cp32-3), ABKB02000031 (plasmid 32-5), ABKB02000021 (plasmid cp32-12), ABKB02000014 (unidentified) [78]

Non-Bacterial genomes

Aspergillus flavus, sequence accession GSE32177 [79]
Bacteriophage SPN3UB, sequence accession JQ288021 [80]
Bamboo mitochondria, sequence accession JQ235166 to JQ235179 [81]
Boea hygrometrica chloroplast, sequence accession JN107811 [82]
Boea hygrometrica mitochondrial, sequence accession JN107812 [82]
Canine Picornavirus, sequence accession JN831356 [83]
Chandipura virus (CHPV) CIN0327, sequence accession GU212856.1 [84]
Chandipura virus (CHPV) CIN0451, sequence accession GU212857.1 [84]
Chandipura virus (CHPV) CIN0751, sequence accession GU212858.1 [84]
Chandipura virus (CHPV) CIN0755, sequence accession GU190711.1 [84]
Chinese Porcine Parvovirus Strain PPV2010, sequence accession JN872448 [85]
Common midwife toad megavirus, sequence accession JQ231222 [86]
Dengue Virus Serotype 4, sequence accession JN983813 [87]
Duck Tembusu Virus, sequence accession JF270480 [88]
Duck Tembusu Virus, sequence accession JQ314464 [88]
Duck Tembusu Virus, sequence accession JQ314465 [88]
Emiliania huxleyi Virus 202, sequence accession HQ634145 [89]
Emiliania huxleyi Virus EhV-88, sequence accession JF974310 [89]
Emiliania huxleyi EhV-201, sequence accession JF974311 [89]
Emiliania huxleyi EhV-207, sequence accession JF974317 [89]
Emiliania huxleyi EhV-208, sequence accession JF974318 [89]
Glarea lozoyensis, sequence accession GUE00000000 [90]
Nannochloropis gaditana, sequence accession AGNI00000000 [91]
Oryza sativa cv., sequence accession DRA000499 [92]
Partetravirus, sequence accession JN990269 [93]
Porcine Bocavirus PBoV5, sequence accession JN831651 [94]
Porcine epidemic diarrhea virus, sequence accession JQ282909 [95]
Pseudomonas aeruginosa lytic bacteriophage PA1Ø, sequence accession HM624080 [96]
Pseudomonas fluorescens phage OBP, sequence accesssion JN627160 [97]
RNA Virus from Avocado, sequence accession JN880414 [98]
Salmonella enterica Serovar Typhimurium Bacteriophage SPN1S, sequence accession JN391180 [99]
Schistosoma haematobium, sequence accession PRJNA78265 [100]
Schistosoma mansoni, sequence accession ERP00038 [101]
Stenopirates sp., sequence accession JN100019 [102]
T7-Like Virus, sequence accession JN651747 [103]
Vibrio harveyi siphophage VHS1, sequence accession JF713456 [104]
Tyrolean ice man, sequence accession ERP001144 [105]

相似文献

3.

Genome sequences published outside of Standards in Genomic Sciences,October - November 2012

Oranmiyan W. Nelson George M. Garrity 《Standards in genomic sciences》2012,7(2):331-350

相似文献

4.

Genome sequences published outside of Standards in Genomic Sciences, December 2011

《Standards in genomic sciences》2011,5(3):416-419

相似文献

5.

The first special issue of Standards in Genomic Sciences from the Genomic Standards Consortium

Field D Kottmann R Sterk P 《Standards in genomic sciences》2010,3(3):214-215

相似文献

6.

A second special issue of Standards In Genomic Sciences from the Genomic Standards Consortium

Field D Kottmann R Morrison N Sterk P 《Standards in genomic sciences》2011,5(2):194

相似文献

7.

Meeting report for SIGS1: First Conference of the Standards in Genomic Sciences eJournal

Nelson OW Harrison SH Garrity GM 《Standards in genomic sciences》2009,1(1):72-76

相似文献

8.

Report of the 14th Genomic Standards Consortium Meeting,Oxford, UK,September 17-21, 2012.

Neil Davies Dawn Field Linda Amaral-Zettler Katharine Barker Mesude Bicak Sarah Bourlat Jonathan Coddington John Deck Alexei Drummond Jack A. Gilbert Frank Oliver Gl?ckner Renzo Kottmann Chris Meyer Norman Morrison Matthias Obst Robert Robbins Lynn Schriml Peter Sterk Steven Stones-Havas 《Standards in genomic sciences》2014,9(3):1236-1250

This report summarizes the proceedings of the 14^th workshop of the Genomic Standards Consortium (GSC) held at the University of Oxford in September 2012. The primary goal of the workshop was to work towards the launch of the Genomic Observatories (GOs) Network under the GSC. For the first time, it brought together potential GOs sites, GSC members, and a range of interested partner organizations. It thus represented the first meeting of the GOs Network (GOs1). Key outcomes include the formation of a core group of “champions” ready to take the GOs Network forward, as well as the formation of working groups. The workshop also served as the first meeting of a wide range of participants in the Ocean Sampling Day (OSD) initiative, a first GOs action. Three projects with complementary interests – COST Action ES1103, MG4U and Micro B3 – organized joint sessions at the workshop. A two-day GSC Hackathon followed the main three days of meetings. 相似文献

9.

Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012

JA Gilbert Y Bao H Wang SA Sansone SC Edmunds N Morrison F Meyer LM Schriml N Davies P Sterk J Wilkening GM Garrity D Field R Robbins DP Smith I Mizrachi C Moreau 《Standards in genomic sciences》2012,6(2):276-286

This report details the outcome of the 13(th) Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation. 相似文献

10.

Collection of published tRNA sequences 总被引：13，自引：11，他引：2

下载免费PDF全文

M. Sprinzl F. Grüter D.H. Gauss 《Nucleic acids research》1978,5(5):r15-r27

相似文献

11.

Genomic Islands in the Corynebacterium efficiens Genome

下载免费PDF全文

Ren Zhang Chun-Ting Zhang 《Applied microbiology》2005,71(6):3126-3130

Corynebacterium efficiens is a gram-positive nonpathogenic bacterium which can grow and produce glutamate at 40°C or above. By using the cumulative GC profile method, we have identified four genomic islands which have many unifying genomic island-specific features in the C. efficiens genome. The presence of the gene encoding an aspartate kinase in a genomic island helps explain the unexpected low thermal stability of this enzyme; i.e., the adaptive mutations have not occurred extensively due to the recent horizontal gene transfer. 相似文献

12.

Genome sequences of Halobacterium species 总被引：1，自引：1，他引：0

Ng WV Berquist BR Coker JA Capes M Wu TH DasSarma P DasSarma S 《Genomics》2008,91(6):548-552

相似文献

13.

Compilation of published signal sequences. 总被引：195，自引：16，他引：195

下载免费PDF全文

M E Watson 《Nucleic acids research》1984,12(13):5145-5164

相似文献

14.

Widespread recombination in published animal mtDNA sequences 总被引：14，自引：0，他引：14

Tsaousis AD Martin DP Ladoukakis ED Posada D Zouros E 《Molecular biology and evolution》2005,22(4):925-933

Mitochondrial DNA (mtDNA) recombination has been observed in several animal species, but there are doubts as to whether it is common or only occurs under special circumstances. Animal mtDNA sequences retrieved from public databases were unambiguously aligned and rigorously tested for evidence of recombination. At least 30 recombination events were detected among 186 alignments examined. Recombinant sequences were found in invertebrates and vertebrates, including primates. It appears that mtDNA recombination may occur regularly in the animal cell but rarely produces new haplotypes because of homoplasmy. Common animal mtDNA recombination would necessitate a reexamination of phylogenetic and biohistorical inference based on the assumption of clonal mtDNA transmission. Recombination may also have an important role in producing and purging mtDNA mutations and thus in mtDNA-based diseases and senescence. 相似文献

15.

Examination of Genome Homogeneity in Prokaryotes Using Genomic Signatures

Jon Bohlin Eystein Skjerve 《PloS one》2009,4(12)

Background

DNA word frequencies, normalized for genomic AT content, are remarkably stable within prokaryotic genomes and are therefore said to reflect a “genomic signature.” The genomic signatures can be used to phylogenetically classify organisms from arbitrary sampled DNA. Genomic signatures can also be used to search for horizontally transferred DNA or DNA regions subjected to special selection forces. Thus, the stability of the genomic signature can be used as a measure of genomic homogeneity. The factors associated with the stability of the genomic signatures are not known, and this motivated us to investigate further. We analyzed the intra-genomic variance of genomic signatures based on AT content normalization (0^th order Markov model) as well as genomic signatures normalized by smaller DNA words (1^st and 2^nd order Markov models) for 636 sequenced prokaryotic genomes. Regression models were fitted, with intra-genomic signature variance as the response variable, to a set of factors representing genomic properties such as genomic AT content, genome size, habitat, phylum, oxygen requirement, optimal growth temperature and oligonucleotide usage variance (OUV, a measure of oligonucleotide usage bias), measured as the variance between genomic tetranucleotide frequencies and Markov chain approximated tetranucleotide frequencies, as predictors.

Principal Findings

Regression analysis revealed that OUV was the most important factor (p<0.001) determining intra-genomic homogeneity as measured using genomic signatures. This means that the less random the oligonucleotide usage is in the sense of higher OUV, the more homogeneous the genome is in terms of the genomic signature. The other factors influencing variance in the genomic signature (p<0.001) were genomic AT content, phylum and oxygen requirement.

Conclusions

Genomic homogeneity in prokaryotes is intimately linked to genomic GC content, oligonucleotide usage bias (OUV) and aerobiosis, while oligonucleotide usage bias (OUV) is associated with genomic GC content, aerobiosis and habitat. 相似文献

16.

Genome sequences and evolutionary biology, a two-way interaction

Charlesworth D Charlesworth B McVean GA 《Trends in ecology & evolution》2001,16(5):235-242

Complete genome sequences are accumulating rapidly, culminating with the announcement of the human genome sequence in February 2001. In addition to cataloguing the diversity of genes and other sequences, genome sequences will provide the first detailed and complete data on gene families and genome organization, including data on evolutionary changes. Reciprocally, evolutionary biology will make important contributions to the efforts to understand functions of genes and other sequences in genomes. Large-scale, detailed and unbiased comparisons between species will illuminate the evolution of genes and genomes, and population genetics methods will enable detection of functionally important genes or sequences, including sequences that have been involved in adaptive changes. 相似文献

17.

On the unreliability of published DNA sequences 总被引：4，自引：1，他引：3

Paul D. Bridge Peter J. Roberts Brian M. Spooner Gita Panchal 《The New phytologist》2003,160(1):43-48

相似文献

18.

Genome Surfing As Driver of Microbial Genomic Diversity

Mallory J. Choudoir Kevin Panke-Buisse Cheryl P. Andam Daniel H. Buckley 《Trends in microbiology》2017,25(8):624-636

Download video (10MB)Help with mp4 files 相似文献

19.

Genome organization in three dimensions: thinking outside the line

Haeusler RA Engelke DR 《Cell cycle (Georgetown, Tex.)》2004,3(3):273-275

相似文献

20.

Genome sequences of eight morphologically diverse Alphaproteobacteria

Brown PJ Kysela DT Buechlein A Hemmerich C Brun YV 《Journal of bacteriology》2011,193(17):4567-4568

The Alphaproteobacteria comprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium. 相似文献