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1.

Complete Genome Sequence Analysis of a Duck Circovirus from Guangxi Pockmark Ducks

Liji Xie Zhixun Xie Guangyuan Zhao Jiabo Liu Yaoshan Pang Xianwen Deng Zhiqin Xie Qing Fan 《Journal of virology》2012,86(23):13136

We report here the complete genomic sequence of a novel duck circovirus (DuCV) strain, GX1104, isolated from Guangxi pockmark ducks in Guangxi, China. The whole nucleotide sequence had the highest homology (97.2%) with the sequence of strain TC/2002 (GenBank accession number AY394721.1) and had a low homology (76.8% to 78.6%) with the sequences of other strains isolated from China, Germany, and the United States. This report will help to understand the epidemiology and molecular characteristics of Guangxi pockmark duck circovirus in southern China. 相似文献

2.

Streptomyces antibioticalis, a Novel Species from a Sanitary Landfill Soil

Monisha Khanna Renu Solanki 《Indian journal of microbiology》2012,52(4):605-611

A novel isolate belonging to the genus Streptomyces, strain SL-4^T, was isolated from soil sample collected from a sanitary landfill, New Delhi, India. The taxonomic status of this isolate was studied by polyphasic approach including morphological, physiological and chemo-taxonomic characterization. Spore chains of SL-4^T were open loops, hooks or extended spirals of wide diameter (retinaculiperti). The cell wall peptidoglycan of the isolate SL-4^T contained L,L-diaminopimelic acid, suggesting that the strain has a cell wall of chemotype-I. The polar lipid profile of the isolate was of Type II, with phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The 16SrRNA gene sequence similarity between SL-4^T and its phylogenetic relatives Streptomyces atrovirens NRRLB 16357^T (DQ026672), S. albogriseolus NRRLB 1305^T (AJ494865), S viridodiastaticus NBRC 13106^T (AB184317), S. caelestis NRRL 2418^T (X80824), S. flavoviridis NBRC 12772^T (AB184842), S. pilosus NBRC 12807^T (AB184161) and S. longispororuber NBRC 13488^T (AB184440) was 99.65, 99.65, 99.64, 99.23, 99.15, 99.14 and 99.13 % respectively. Subsequent DNA–DNA hybridization experiments with the test strain and its clade members showed 55.27, 44.27, 36.86, and 15.65 % relatedness between SL-4^T and its relatives S. atrovirens,S. albogriseolus, S. viridodiastaticus and S. longispororuber respectively. The genotypic and phenotypic data was analyzed to verify possibility of the isolate SL-4^T representing novel member of the genus Streptomyces, for which the name S. antibioticalis is being proposed. The type strain is SL-4^T (=CCM 7434^T=MTCC 8588^T). 相似文献

3.

Genome sequences published outside of Standards in Genomic Sciences, October �C November 2011

Oranmiyan W. Nelson George M. Garrity 《Standards in genomic sciences》2011,5(2):254-261

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
Thermoproteus tenax, strain Kra1, DSM 2078^T sequence accession FN869859 [1]
Phylum Euryarchaeota
Haloarcula hispanica CGMCC 1.2049, sequence accession CP002921 (chromosome I), CP002922 (chromosome II), and CP002923 (plasmid pHH400) [2]
Methanococcus maripaludis, strain X1 (unculturable) sequence accession CP002913 [3]
Phylum Proteobacteria
Acinetobacter baumannii strain 1656-2, sequence accession CP001921 [4]
Arcobacter butzleri strain ED-1, sequence accession AP012047, AP012048, and AP012049 [5]
Brucella suis strain 1330, sequence accession CP002997 and CP002998 [6]
Campylobacter fetus subsp. venerealis NCTC 10354, sequence accession AFGH01000000 [7]
“Chromobacterium sp.” strain C-61, sequence accession CAEE01000001 to CAEE01001118 [8]
Cronobacter sakazakii strain E899, sequence accession AFMO00000000 [9]
“Desulfovibrio sp.” strain A2, sequence accession AGFG01000000 [10]
“Erythrobacter sp.” strain NAP1, sequence accession NZ_AAMW00000000 [11]
Escherichia coli strain XH140A, sequence accession AFVX01000000 [12]
Escherichia coli strain XH001, sequence accession AFYG01000000 [13]
Haemophilus haemolyticus strain M19107, sequence accession AFQN00000000 [14]
Haemophilus haemolyticus strain M19501, sequence accession AFQO00000000 [14]
Haemophilus haemolyticus strain M21127, sequence accession AFQP00000000 [14]
Haemophilus haemolyticus strain M21621, sequence accession AFQQ00000000 [14]
Haemophilus haemolyticus strain M21639, sequence accession AFQR00000000 [14]
Idiomarina sp.” strain A28L, sequence accession AFPO01000001 to AFPO01000028 [15]
Ketogulonicigenium vulgare” strain WSH-001, sequence accession CP002018 (chromosome), CP002019 (plasmid pKVU_100), and CP002020 (plasmid pKVU_200) [16]
Methylobacter tundripaludum strain SV96, sequence accession AEGW00000000 [17]
Pseudogulbenkiania sp.” strain NH8B, sequence accession AP012224 [18]
Pseudomonas aeruginosa NCGM1179, sequence accession DF126593 through DF126613 [19]
Pseudomonas putida strain B001, sequence accession CAED01000001 to CAEE01000262 [20]
Pseudomonas putida strain B6-2, sequence accession AGCS01000000 [21]
Pseudomonas stutzeri CGMCC 1.1803, sequence accession CP002881 [22]
Ralstonia solanacearum phylotype IB, strain Y45, sequence accession AFWL01000000 [23]
Rheinheimera sp.” strain A13L, sequence accession AFHI01000001 through AFHI01000072 [24]
Sphingobium yanoikuyae strain XLDN2-5, sequence accession AFXE01000000 [25]
Vibrio cholerae strain Amazonia, sequence accession AFSV01000000 [26]
Phylum Firmicutes
Bacillus coagulans strain XZL4, sequence accession AFWM01000000 [27]
Bacillus megaterium strain WSH-002, sequence accession CP003017 (chromosome), plasmids CP003018 (plasmid pBME_100), CP003019 (plasmid pBME_200), and CP003020 (plasmid pBME_300) [28]
Bacillus pumilus strain S-1, sequence accession AGBY00000000 [29]
“Desulfosporosinus sp.” strain OT, sequence accession AGAF01000000 [30]
Lentibacillus jeotgali strain Grbi, sequence accession AGAV01000000 [31]
Leuconostoc carnosum KCTC 3525, sequence accession BACM01000000 [32]
Listeria ivanovii subsp. ivanovii strain PAM 55, sequence accession FR687253 [33]
Paenibacillus riograndensis strain SBR5, sequence accession AGBD01000000 [34]
Sporolactobacillus inulinus strain CASD, sequence accession AFVQ00000000 [35]
Streptococcus pseudopneumoniae strain IS7493, sequence accession CP002925 and CP002926 [36]
Streptococcus salivarius strain 57.I, sequence accession CP002888 and CP002889 [37]
Streptococcus salivarius strain M18, sequence accession AGBV01000000 [38]
Streptococcus suis SS12, sequence accession CP002640 [39]
Streptococcus suis D9, sequence accession CP002641 [39]
Streptococcus suis D12, sequence accession CP002644 [39]
Streptococcus suis ST1, sequence accession CP002651 [39]
Weissella thailandensis strain fsh4-2, sequence accession HE575133 through HE575182 [40]
Phylum Tenericutes
Mycoplasma anatis strain 1340, sequence accession AFVJ00000000 [41]
Mycoplasma capricolum subsp. capripneumoniae strain M1601, sequence accession AENG01000000 [42]
Mycoplasma putrefaciens Type strain KS1, sequence accession CP003021 [43]
Corynebacterium pseudotuberculosis strain PAT10, sequence accession CP002924 [44]
Phylum Actinobacteria
Bifidobacterium animalis subsp. lactis strain BLC1, sequence accession CP003039 [45]
Bifidobacterium breve strain DPC 6330, sequence accession AFXX01000000 [46]
Brachybacterium squillarum strain M-6-3, sequence accession AGBX01000000 [47]
“Citricoccus sp.” strain CH26A, sequence accession AFXQ01000000 [48]
Corynebacterium glutamicum strain S9114, sequence accession AFYA01000000 [49]
Dietzia alimentaria strain 72, sequence accession AGFF01000000 [50]
Mycobacterium colombiense CECT 3035, sequence accession AFVW00000000 [51]
Mycobacterium tuberculosis NCGM2209, sequence accession DF126614 and DF126615 [52]
Rhodococcus erythropolis strain XP, sequence accession AGCF01000000 [53]
Serinicoccus profundi MCCC 1A05965^T, sequence accession AFYF00000000 [54]
Phylum Spirochaetes
Leptospira interrogans, sequence accession CP001221 (CI), CP001222 (CII) [55]
Phylum Bacteroidetes
Bacteroides faecis Type strain MAJ27^T, sequence accession AGDG01000000 [56]
Bizionia argentinensis, Type strain JUB59^T sequence accession AFXZ01000000 [57]
Flavobacterium branchiophilum strain FL-15, sequence accession FQ859183 [58]
“Flavobacteriaceae” strain S85, sequence accession AFPK00000000 [59]
Phylum Thermotogae
“Thermotoga sp.” strain RQ2, sequence accession CP000969 [60]

Non-Bacterial genomes

Aspergillus kawachii IFO 4308, sequence accession DF126447 through DF126592, BACL01000001 through BACL01001641, AP012272 [61]
Cajanus cajan pigeonpea, sequence accession PRJNA72815 [62]
Coxsackievirus A22, sequence accession JN542510 [63]
Gordonia phage GRU1, sequence accession JF923797 [64]
Gordonia phage GTE5, sequence accession JF923796 [64]
Heterocephalus glaber naked mole rat, sequence accession AFSB00000000, AFSB01000000 [65]
Human Adenovirus Prototype 17, sequence accession HQ910407 [66]
Macaca mulatta lasiota rhesus macaque, sequence accession AEHL00000000 [67]
Macaca mulatta mulatta rhesus macaque, sequence accession AEHK00000000 [67]
Porcine epidemic diarrhea virus, sequence accession JN547228 [68]

相似文献

4.

Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June �C September 2011

Oranmiyan W. Nelson George M. Garrity 《Standards in genomic sciences》2011,5(1):154-167

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 this subsequent versions of this list are invited to provide the bibliometric data for such references to the SIGS editorial office.

Phylum Crenarchaeota
Phylum Euryarchaeota
Pyrococcus yayanosii CH1, sequence accession CP002779 [1]
Methanocella paludicola, sequence accession AP011532 [2]
Halorhabdus tiamatea, sequence accession AFNT00000000 [3]
Thermococcus sp. Strain 4557, sequence accession CP002920 [4]
Phylum Chloroflexi
Phylum Proteobacteria
Ralstonia solanacearum strain Po82, sequence accession CP002819 (chromosome) and CP002820 (megaplasmid) [5
Desulfovibrio alaskensis G20, sequence accession CP000112 [6]
Methylophaga aminisulfidivorans MP^T, sequence accession AFIG00000000 [7]
Acinetobacter sp. P8-3-8, sequence accession AFIE00000000 [8]
Sphingomonas strain KC8, sequence accession AFMP01000000 [9]
Brucella pinnipedialis B2/94, sequence accession CP002078 and CP002079 [10]
Salmonella enterica Serovar Typhimurium UK-1, sequence accession CP002614 (chromosome), CP002615 (plasmid) [11]
Bordetella pertussis CS, sequence accession CP002695 [12]
Alteromonas sp. Strain SN2, sequence accession CP002339 [13]
Escherichia coli O104:H4, sequence accession AFOB00000000 (LB226692) and AFPS00000000 (01-09591) [14]
Acidithiobacillus caldus, sequence accession CP002573 (Chromosome), CP002574 (pLAtcm), CP002575 (pLAtc1), CP002576 (pLAtc2), CP002577 (pLAtc3) [15]
Cupriavidus necator N-1, sequence accession CP002877 (chromosome 1), CP002878 (chromosome 2), CP002879 (pBB1), and CP002880 (pBB2) [16]
Oligotropha carboxidovorans OM4, sequence accession CP002821 (OM4 chromosome), CP002822 (pHCG3b), CP002823 (pOC167B) [17]
Oligotropha carboxidovorans OM5, sequence accession CP002826 (OM5 chromosome), CP002827 (pHCG3), and CP002828 (pOC167) [17]
Pantoea ananatis LMG20103, sequence accession CP001875 [18]
Helicobacter bizzozeronii strain CIII-1, sequence accession FR871757 (chromosome) and FR871758 (HBZ-1) [19]
Vibrio anguillarum 775, sequence accession CP002284 to CP002285 [20]
Zymomonas mobilis subsp. pomaceae, sequence accession CP002865 (chromosome), CP002866 (p29192_1), CP002867 (p29192_2) [21]
Agrobacterium sp. strain ATCC 31749, sequence accession AECL01000000 [22]
Xanthomonas spp. strain Xrc, sequence accesssion CP002789 [23]
Xanthomonas spp. strain Xoc, sequence accesssion AAQN00000000 [23]
Glaciecola sp. Strain 4H-3-7+YE-5, sequence accession CP002526 (chromosome) and CP002527 (plasmid) [24]
Escherichia coli Strain HM605, sequence accession CADZ01000001 through CADZ01000154 [25]
Salinisphaera shabanensis, sequence accession AFNV00000000 [26]
Methyloversatilis universalis FAM5^T, sequence accession AFHG00000000 [27]
Alicycliphilus denitrificans Strain BC, sequence accession CP002449 (chromosome), CP002450 (megaplasmid), CP002451 (plasmid) [28].
Alicycliphilus denitrificans K601^T, sequence accession CP002657 (chromosome) and CP002658 (plasmid) [28]
Oligotropha carboxidovorans Strain OM4, sequence accession CP002821 (chromosome), CP002822 (pHCG3b), CP002823 (pOC167B) [29]
Oligotropha carboxidovorans Strain OM5, sequence accession CP002826 (chromosome), CP002827 (pHCG3), and CP002828 (pOC167) [29]
Bradyrhizobiaceae strain SG-6C, sequence accession AFOF01000000 [30]
Hyphomicrobium sp. Strain MC1, sequence accession FQ859181 [31]
Shewanella sp. Strain HN-41, sequence accession AFOZ01000000 [32]
Myxococcus fulvus HW-1, sequence accession CP002830 [33]
Nitrosomonas sp. Strain AL212, sequence accession NC_015222 (chromosome), NC_015223 pNAL21201), NC_015221 (pNAL21202) [34]
Ruegeria sp. Strain KLH11, sequence accession ACCW00000000 [35]
Acidovorax avenae subsp. avenae RS-1, sequence accession AFPT01000000 [36]
Escherichia coli (ExPEC), sequence accession AFAT00000000 [37]
Vibrio mimicus SX-4, sequence accession ADOO01000000 [38]
Agrobacterium tumefaciens Strain F2, sequence accession AFSD00000000 [39]
Pasteurella multocida subsp. gallicida AFRR01000001 to AFRR01000489 [40]
Pseudomonas aeruginosa 138244, sequence accession AEVV00000000 [41]
Pseudomonas aeruginosa 152504, sequence accession AEVW00000000 [41]
Campylobacter jejuni strain 305, sequence accession ADHL00000000 [42]
Campylobacter jejuni strain DFVF1099, sequence accession ADHK00000000 [42]
Xanthomonas campestris pv. raphani strain 756C, sequence accession CP002789 [43]
Xanthomonas campestris pv. raphani strain BLS256, sequence accession AAQN01000001 [43]
Rickettsia heilongjiangensis, sequence accession CP002912 [44]
Acidiphilium sp. Strain PM (DSM 24941), sequence accession AFPR00000000 [45]
Pseudomonas putida Strain S16, sequence accession CP002870 [46]
Acinetobacter lwoffii, sequence accession AFQY01000000 [47]
Phylum Firmicutes
Caldalkalibacillus thermarum strain TA2.A1, sequence accession AFCE00000000 [48]
Listeria monocytogenes Scott A, sequence accession AFGI00000000 [49]
Lactococcus garvieae 8831, sequence accession AFCD00000000 [50]
Natranaerobius thermophilus JW/NM-WN-LF, sequence accession CP001034 (chromosome), CP001035 (plasmid) [51]
Melissococcus plutonius ATCC 35311, sequence accession AP012200 (chromosome) and AP012201 (plasmid) [52]
Lactobacillus buchneri NRRL B-30929, sequence accession CP002652 (chromosome), CP002653 (plasmid pLBU01), CP002654 (plasmid pLBU02), and CP002655 (plasmid pLBU03) [53]
Lactobacillus kefiranofaciens ZW3 , sequence accession CP002764 (chromosome), CP002765 (plasmid), and CP002766 (plasmid) [54]
Bacillus megaterium strain QM B1551, sequence accession CP001983 (chromosome), CP001984 to CP001990 (plasmids pBM100 through pBM700) [55]
Bacillus megaterium strain DSM319, sequence accession CP001982 (chromosome) [55]
Listeria monocytogenes serovar 4a strain M7, sequence accession CP002816 [56]
Bacillus coagulans 2-6, sequence accession CP002472 [57]
Streptococcus salivarius strain CCHSS3, sequence accession FR873481 [58]
Paenibacillus elgii B69, sequence accession AFHW01000000 [59]
Lactobacillus pentosus MP-10, sequence accession FR871759 through FR871848 [60]
Leuconostoc pseudomesenteroides KCTC 3652, sequence accession AEOQ00000001 through AEOQ00001160 [61]
Lactobacillus mali KCTC 3596, sequence accession BACP01000001 through BACP01000122 [62]
Paenibacillus polymyxa Type Strain ATCC 842^T, sequence accession AFOX01000000 [63]
Streptococcus salivarius strain JIM8777, sequence accssion FR873482 [64]
Lactobacillus cypricasei KCTC 13900, sequence accession BACS01000001 to BACS01000487 [65]
Lactobacillus zeae KCTC 3804, sequence accession BACQ01000001 to BACQ101000113 [66]
Listeria monocytogenes Serovar 4a Strain M7, sequence accession CP002816 [67]
Lactobacillus salivarius GJ-24, sequence accession AFOI00000000 [68]
Lactobacillus johnsonii PF01, sequence accession AFQJ01000000 [69]
Clostridium acetobutylicum DSM 1731, sequence accession CP002660 through CP002662 [70]
Lactobacillus suebicus KCTC 3549, sequence accession BACO01000000 [71]
Brevibacillus laterosporus LMG 15441, sequence accession AFRV00000000 [72]
Lactobacillus salivarius NIAS840, sequence accession AFMN00000000 [73]
Bifidobacterium animalis subsp. lactis CNCM I-2494, sequence accession CP002915 [74]
Megasphaera elsdenii, sequence accession HE576794 [75]
Lactobacillus versmoldensis KCTC 3814, sequence accession BACR01000001 to BACR01000102 [76]
Lactobacillus pentosus IG1, sequence accession FR874848 to FR874860 [77]
Alicyclobacillus acidocaldarius Strain Tc-4-1, sequence accession CP002902 [78]
Streptococcus thermophilus Strain JIM8232, sequence accession FR875178 [79]
Streptococcus equi subsp. zooepidemicus Strain ATCC 35246, sequence accession CP002904 [80]
Bacillus amyloliquefaciens XH7, sequence accession CP002927 [81]
Leuconostoc kimchii Strain C2, sequence accession CP002898 [82]
Lactobacillus malefermentans KCTC 3548, sequence accession BACN01000001 to BACN01000172 [83]
Weissella koreensis KACC 15510, sequence accession CP002900 [84]
Phylum Tenericutes
Mycoplasma bovis Strain Hubei-1, sequence accession CP002513 [85]
Mycoplasma fermentans Strain M64, sequence accession NC_014921 [86]
Haloplasma contractile, sequence accession AFNU00000000 [87]
Mycoplasma ovipneumoniae Strain SC01, sequence accession AFHO01000000 [88]
Phylum Actinobacteria
Kocuria rhizophila P7-4, sequence accession AFID00000000 [89]
Streptomyces S4, sequence accession CADY01000000 [90]
Corynebacterium nuruki S6-4^T, sequence accession AFIZ00000000 [91]
Propionibacterium humerusii, sequence accession AFAM00000000.1 [92]
Strain JDM601, sequence accession CP002329 [93]
Streptomyces sp. strain Tü6071, sequence accession AFHJ01000000 [94]
Bifidobacterium breve UCC2003, sequence accession CP000303 [95]
Propionibacterium acnes, sequence accession CP002815 [96]
Amycolicicoccus subflavus DQS3-9A1^T, sequence accession CP002786 (chromosome), CP002787 (plasmid pAS9A-1), and CP002788 (plasmid pAS9A-2). [97]
Gordonia neofelifaecis NRRL B-59395, sequence accession AEUD01000000 [98]
Pseudonocardia dioxanivorans strain CB1190, sequence accession NC_015312-4 and CP002595-7 [99]
Bifidobacterium longum subsp. longum KACC 91563, sequence accession CP002794 to CP002796 [100]
Streptomyces cattleya NRRL 8057, sequence accession FQ859185 (chromosome) and FQ859184 (megaplasmid) [101]
Rhodococcus sp. Strain R04, sequence accession AFAQ01000000 [102]
Mycobacterium bovis BCG Moreau, sequence accession [103]
Saccharopolyspora spinosa NRRL 18395, sequence accession [104]
Mycobacterium tuberculosis CCDC5079, sequence accession [105]
Mycobacterium tuberculosis CCDC5180, sequence accession [105]
Amycolatopsis mediterranei S699, sequence accession CP002896 [106]
Nesterenkonia sp. Strain F, sequence accession AFRW01000000 [107]
Streptomyces xinghaiensis NRRL B24674^T, sequence accession AFRP01000000 [108]
Phylum Chlamydiae
Chlamydophila abortus variant strain LLG, sequence accession AFHM01000000 [109]
Chlamydia psittaci 6BC, sequence accession CP002586 (chromosome), CP002587 (plasmid) [110]
Chlamydia psittaci Cal10, sequence accession AEZD00000000 (draft chromosome and plasmid) [110]
Chlamydia trachomatis, sequence accession CP002024 [111]
Phylum Spirochaetes
Spirochaeta thermophila DSM 6192, sequence accession CP001698 [112]
Brachyspira intermedia, sequence accession CP002874 (chromosome) and CP002875 (plasmid) [113]
Phylum Fibrobacteres
Phylum Bacteroidetes
Porphyromonas gingivalis TDC60, sequence accession AP012203 [114]
Krokinobacter sp. strain 4H-3-7-5, sequence accession CP002528 [115]
Lacinutrix sp. strain 5H-3-7-4, sequence accession CP002825 [115]
Bacterium HQM9, sequence accession AFPB00000000 [116]
Anaerophaga sp. Strain HS1, sequence accession AFSL00000000 [117]
Capnocytophaga canimorsus Strain 5, sequence accession CP002113 [118]
Mesoflavibacter zeaxanthinifaciens strain S86, sequence accession AFOE00000000 [119]
Phylum Verrucomicrobia
Phylum Lentisphaerae
Phylum Thermotogae
Kosmotoga olearia Strain TBF 19.5.1, sequence accession CP001634 [120]
Domain Archaea
"Candidatus Nitrosoarchaeum koreensis" MY1, sequence accession AFPU00000000 [121]

Non-Bacterial genomes

North-European Cucumber Cucumis sativus L., sequence accession FI132140-FI136208, GS765762-GS766880, GS815969-GS874855 [122]
Castor bean Ricinus communis organelle genome, sequence accession JF937588(chloroplast), HQ874649 (mitochondria) [123]
Stretch Lagoon Orbivirus Umatilla, sequence accession HQ842619 through HQ842628 [124]
Atlantic cod Gadus morhua, sequence accession CAEA01000001 through CAEA01554869 [125]
Potato Solanum tuberosum L., sequence accession GS025503 through GS026177 [126]
ΦCA82, sequence accession HQ264138 [127]
Paramecium caudatumreveals mitochondria, sequence accession NC001324 [128]
bacteriophage IME08, sequence accession NC_014260 [129]
virus (ILTV), sequence accession HQ_630064 [130]
Australian kangaroo Macropus eugenii, sequence accession ABQO000000000 [131]
Aichi virus, sequence accession FJ890523 [132]
"Candidatus Tremblaya princeps" Strain PCVAL, sequence accession CP002918 [133]

相似文献

5.

Genomic Basis of a Polyagglutinating Isolate of Neisseria meningitidis

Lavanya Rishishwar Lee S. Katz Nitya V. Sharma Lori Rowe Michael Frace Jennifer Dolan Thomas Brian H. Harcourt Leonard W. Mayer I. King Jordan 《Journal of bacteriology》2012,194(20):5649-5656

Containment strategies for outbreaks of invasive Neisseria meningitidis disease are informed by serogroup assays that characterize the polysaccharide capsule. We sought to uncover the genomic basis of conflicting serogroup assay results for an isolate (M16917) from a patient with acute meningococcal disease. To this end, we characterized the complete genome sequence of the M16917 isolate and performed a variety of comparative sequence analyses against N. meningitidis reference genome sequences of known serogroups. Multilocus sequence typing and whole-genome sequence comparison revealed that M16917 is a member of the ST-11 sequence group, which is most often associated with serogroup C. However, sequence similarity comparisons and phylogenetic analysis showed that the serogroup diagnostic capsule polymerase gene (synD) of M16917 belongs to serogroup B. These results suggest that a capsule-switching event occurred based on homologous recombination at or around the capsule locus of M16917. Detailed analysis of this locus uncovered the locations of recombination breakpoints in the M16917 genome sequence, which led to the introduction of an ∼2-kb serogroup B sequence cassette into the serogroup C genomic background. Since there is no currently available vaccine for serogroup B strains of N. meningitidis, this kind capsule-switching event could have public health relevance as a vaccine escape mutant. 相似文献

6.

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

7.

Characterization of the Invasive,Multidrug Resistant Non-typhoidal Salmonella Strain D23580 in a Murine Model of Infection

Jiseon Yang Jennifer Barrila Kenneth L. Roland Jacquelyn Kilbourne C. Mark Ott Rebecca J. Forsyth Cheryl A. Nickerson 《PLoS neglected tropical diseases》2015,9(6)

A distinct pathovar of Salmonella enterica serovar Typhimurium, ST313, has emerged in sub-Saharan Africa as a major cause of fatal bacteremia in young children and HIV-infected adults. D23580, a multidrug resistant clinical isolate of ST313, was previously shown to have undergone genome reduction in a manner that resembles that of the more human-restricted pathogen, Salmonella enterica serovar Typhi. It has since been shown through tissue distribution studies that D23580 is able to establish an invasive infection in chickens. However, it remains unclear whether ST313 can cause lethal disease in a non-human host following a natural course of infection. Herein we report that D23580 causes lethal and invasive disease in a murine model of infection following peroral challenge. The LD₅₀ of D23580 in female BALB/c mice was 4.7 x 10⁵ CFU. Tissue distribution studies performed 3 and 5 days post-infection confirmed that D23580 was able to more rapidly colonize the spleen, mesenteric lymph nodes and gall bladder in mice when compared to the well-characterized S. Typhimurium strain SL1344. D23580 exhibited enhanced resistance to acid stress relative to SL1344, which may lend towards increased capability to survive passage through the gastrointestinal tract as well as during its intracellular lifecycle. Interestingly, D23580 also displayed higher swimming motility relative to SL1344, S. Typhi strain Ty2, and the ST313 strain A130. Biochemical tests revealed that D23580 shares many similar metabolic features with SL1344, with several notable differences in the Voges-Proskauer and catalase tests, as well alterations in melibiose, and inositol utilization. These results represent the first full duration infection study using an ST313 strain following the entire natural course of disease progression, and serve as a benchmark for ongoing and future studies into the pathogenesis of D23580. 相似文献

8.

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

9.

Novel Variant Serotype of Streptococcus suis Isolated from Piglets with Meningitis

Zihao Pan Jiale Ma Wenyang Dong Wenchao Song Kaicheng Wang Chengping Lu Huochun Yao 《Applied and environmental microbiology》2015,81(3):976-985

Streptococcus suis is an emerging zoonotic pathogen causing severe infections in pigs and humans. In previous studies, 33 serotypes of S. suis have been identified using serum agglutination. Here, we describe a novel S. suis strain, CZ130302, isolated from an outbreak of acute piglet meningitis in eastern China. Strong pathogenicity of meningitis caused by strain CZ130302 was reproduced in the BALB/c mouse model. The strain showed a high fatality rate (8/10), higher than those for known virulent serotype 2 strains P1/7 (1/10) and 9801 (2/10). Cell adhesion assay results with bEnd.3 and HEp2 cells showed that CZ130302 was significantly close to P1/7 and 9801. Both the agglutination test and its complementary test showed that strain CZ130302 had no strong cross-reaction with the other 33 S. suis serotypes. The multiplex PCR assays revealed no specified bands for all four sets used to detect the other 33 serotypes. In addition, genetic analysis of the whole cps gene clusters of all serotypes was performed in this study. The results of comparative genomics showed that the cps gene cluster of CZ130302, which was not previously reported, showed no homology to the gene sequences of the other strains. Especially, the wzy, wzx, and acetyltransferase genes of strain CZ130302 are phylogenetically distinct from strains of the other 33 serotypes. Therefore, this study suggested that strain CZ130302 represents a novel variant serotype of S. suis (designated serotype Chz) which has a high potential to be virulent and associated with meningitis in animals. 相似文献

10.

Surveillance and Genome Analysis of Human Bocavirus in Patients with Respiratory Infection in Guangzhou, China

Lin Xu Xia He Ding-mei Zhang Fa-shen Feng Zhu Wang Lin-lin Guan Jue-heng Wu Rong Zhou Bo-jian Zheng Kwok-yung Yuen Meng-feng Li Kai-yuan Cao 《PloS one》2012,7(9)

Human bocavirus (HBoV) is a novel parvovirus associated with respiratory tract diseases and gastrointestinal illness in adult and pediatric patients throughout the world. To investigate the epidemiological and genetic variation of HBoV in Guangzhou, South China, we screened 3460 throat swab samples from 1686 children and 1774 adults with acute respiratory infection symptoms for HBoV between March 2010 and February 2011, and analyzed the complete genome sequence of 2 HBoV strains. Specimens were screened for HBoV by real-time PCR and other 6 common respiratory viruses by RT-PCR or PCR. HBoV was detected in 58 (1.68%) out of 3460 samples, mostly from pediatric patients (52/58) and inpatient children (47/58). Six adult patients were detected as HBoV positive and 5 were emergency cases. Of these HBoV positive cases, 19 (32.76%) had co-pathogens including influenza virus (n = 5), RSV (n = 5), parainfluenza (n = 4), adenovirus (n = 1), coronavirus (n = 7). The complete genome sequences of 2 HBoVs strains (Genbank no. JN794565 and JN794566) were analyzed. Phylogenetic analysis showed that the 2 HBoV strains were HBoV1, and were most genetically close to ST2 (GenBank accession number DQ0000496). Recombination analysis confirmed that HBoV strain GZ9081 was an intra–genotype recombinant strain among HBoV1 variants. 相似文献

11.

Complete Genome of a Porcine Calicivirus Strain in Anhui Province,China, Is Significantly Shorter than That of the Other Chinese Strain

Kezhang Fan Rong Wang 《Journal of virology》2012,86(24):13823

Caliciviruses that cause diarrhea have been reported in both industrial and developing countries, including China, in recent years. Here, we report the complete genome of a porcine calicivirus strain, Ah-1, which is prevalent in swine groups in Anhui Province. This viral genome is 7,342 nucleotides (nt) long, excluding the poly(A) of the 3′ end, which is 202 nt shorter in the 3′ untranslated region (UTR) than that of the other Chinese porcine calicivirus strain (Ch-sw-sav1; GenBank accession number FJ387164), previously isolated in the Shanghai area, China, though they shared 98.8% sequence identity over the whole genome excluding the 202-nt-shorter region. 相似文献

12.

Extensive homologous recombination in classical swine fever virus: A re-evaluation of homologous recombination events in the strain AF407339

Youhua Chen You-Fang Chen 《Saudi Journal of Biological Sciences》2014,21(4):311-316

In this short report, the genome-wide homologous recombination events were re-evaluated for classical swine fever virus (CSFV) strain AF407339. We challenged a previous study which suggested only one recombination event in AF407339 based on 25 CSFV genomes. Through our re-analysis on the 25 genomes in the previous study and the 41 genomes used in the present study, we argued that there should be possibly at least two clear recombination events happening in AF407339 through genome-wide scanning. The reasons for identifying only one recombination event in the previous study might be due to the limited number of available CSFV genome sequences at that time and the limited usage of detection methods. In contrast, as identified by most detection methods using all available CSFV genome sequences, two major recombination events were found at the starting and ending zones of the genome AF407339, respectively. The first one has two parents AF333000 (minor) and AY554397 (major) with beginning and ending breakpoints located at 19 and 607 nt of the genome respectively. The second one has two parents AF531433 (minor) and GQ902941 (major) with beginning and ending breakpoints at 8397 and 11,078 nt of the genome respectively. Phylogenetic incongruence analysis using neighbor-joining algorithm with 1000 bootstrapping replicates further supported the existence of these two recombination events. In addition, we also identified additional 18 recombination events on the available CSFV strains. Some of them may be trivial and can be ignored. In conclusion, CSFV might have relatively high frequency of homologous recombination events. Genome-wide scanning of identifying recombination events should utilize multiple detection methods so as to reduce the risk of misidentification. 相似文献

13.

Identification and Genome Characterization of the First Sicinivirus Isolate from Chickens in Mainland China by Using Viral Metagenomics

Hongzhuan Zhou Shanshan Zhu Rong Quan Jing Wang Li Wei Bing Yang Fuzhou Xu Jinluo Wang Fuyong Chen Jue Liu 《PloS one》2015,10(10)

Unlike traditional virus isolation and sequencing approaches, sequence-independent amplification based viral metagenomics technique allows one to discover unexpected or novel viruses efficiently while bypassing culturing step. Here we report the discovery of the first Sicinivirus isolate (designated as strain JSY) of picornaviruses from commercial layer chickens in mainland China by using a viral metagenomics technique. This Sicinivirus isolate, which contains a whole genome of 9,797 nucleotides (nt) excluding the poly(A) tail, possesses one of the largest picornavirus genome so far reported, but only shares 88.83% and 82.78% of amino acid sequence identity to that of ChPV1 100C (KF979332) and Sicinivirus 1 strain UCC001 (NC_023861), respectively. The complete 939 nt 5′UTR of the isolate strain contains at least twelve stem-loop domains (A–L), representing the highest set of loops reported within Sicinivirus genus. The conserved ''barbell-like'' structure was also present in the 272 nt 3′UTR of the isolate as that in the 3′ UTR of Sicinivirus 1 strain UCC001. The 8,586 nt large open reading frame encodes a 2,862 amino acids polyprotein precursor. Moreover, Sicinivirus infection might be widely present in commercial chicken farms in Yancheng region of the Jiangsu Province as evidenced by all the tested stool samples from three different farms being positive (17/17) for Sicinivirus detection. This is the first report on identification of Sicinivirus in commercial layer chickens with a severe clinical disease in mainland China, however, further studies are needed to evaluate the pathogenic potential of this picornavirus in chickens. 相似文献

14.

Are Differences in Genomic Data Sets due to True Biological Variants or Errors in Genome Assembly: An Example from Two Chloroplast Genomes

Zhiqiang Wu Luke R. Tembrock Song Ge 《PloS one》2015,10(2)

DNA sequencing has been revolutionized by the development of high-throughput sequencing technologies. Plummeting costs and the massive throughput capacities of second and third generation sequencing platforms have transformed many fields of biological research. Concurrently, new data processing pipelines made rapid de novo genome assemblies possible. However, high quality data are critically important for all investigations in the genomic era. We used chloroplast genomes of one Oryza species (O. australiensis) to compare differences in sequence quality: one genome (GU592209) was obtained through Illumina sequencing and reference-guided assembly and the other genome (KJ830774) was obtained via target enrichment libraries and shotgun sequencing. Based on the whole genome alignment, GU592209 was more similar to the reference genome (O. sativa: AY522330) with 99.2% sequence identity (SI value) compared with the 98.8% SI values in the KJ830774 genome; whereas the opposite result was obtained when the SI values in coding and noncoding regions of GU592209 and KJ830774 were compared. Additionally, the junctions of two single copies and repeat copies in the chloroplast genome exhibited differences. Phylogenetic analyses were conducted using these sequences, and the different data sets yielded dissimilar topologies: phylogenetic replacements of the two individuals were remarkably different based on whole genome sequencing or SNP data and insertions and deletions (indels) data. Thus, we concluded that the genomic composition of GU592209 was heterogeneous in coding and non-coding regions. These findings should impel biologists to carefully consider the quality of sequencing and assembly when working with next-generation data. 相似文献

15.

Invasive Non-Typhoidal Salmonella Typhimurium ST313 Are Not Host-Restricted and Have an Invasive Phenotype in Experimentally Infected Chickens

Bryony N. Parsons Suzanne Humphrey Anne Marie Salisbury Julia Mikoleit Jay C. D. Hinton Melita A. Gordon Paul Wigley 《PLoS neglected tropical diseases》2013,7(10)

Salmonella enterica serovar Typhimurium Sequence Type (ST) 313 is a major cause of invasive non-Typhoidal salmonellosis in sub-Saharan Africa. No animal reservoir has been identified, and it has been suggested that ST313 is adapted to humans and transmission may occur via person-to-person spread. Here, we show that ST313 cause severe invasive infection in chickens as well as humans. Oral infection of chickens with ST313 isolates D23580 and Q456 resulted in rapid infection of spleen and liver with all birds infected at these sites by 3 days post-infection. In contrast, the well-defined ST19 S. Typhimurium isolates F98 and 4/74 were slower to cause invasive disease. Both ST19 and ST313 caused hepatosplenomegaly, and this was most pronounced in the ST313-infected animals. At 3 and 7 days post-infection, colonization of the gastrointestinal tract was lower in birds infected with the ST313 isolates compared with ST19. Histological examination and expression of CXCL chemokines in the ileum showed that both D23580 (ST313) and 4/74 (ST19) strains caused increased CXCL expression at 3 days post-infection, and this was significantly higher in the ileum of D23580 vs 4/74 infected birds. At 7 days post-infection, reduced chemokine expression occurred in the ileum of the D23580 but not 4/74-infected birds. Histological analysis showed that D23580 infection resulted in rapid inflammation and pathology including villous flattening and fusion at 3 days post-infection, and subsequent resolution by 7 days. In contrast, 4/74 induced less inflammation and pathology at 3 days post-infection. The data presented demonstrate that ST313 is capable of causing invasive disease in a non-human host. The rapid invasive nature of infection in the chicken, coupled with lower gastrointestinal colonization, supports the hypothesis that ST313 is a distinct pathovariant of S. Typhimurium that has evolved to become a systemic pathogen that can cause disease in several hosts. 相似文献

16.

A directed approach for the identification of transcripts harbouring the spliced leader sequence and the effect of trans-splicing knockdown in Schistosoma mansoni

Marina de Moraes Mour?o Mainá Bitar Francisco Pereira Lobo Ana Paula Peconick Priscila Grynberg Francisco Prosdocimi Michael Waisberg Gustavo Coutinho Cerqueira Andréa Mara Macedo Carlos Renato Machado Timothy Yoshino Glória Regina Franco 《Memórias do Instituto Oswaldo Cruz》2013,108(6):707-717

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17.

Draft Genome Sequence of Xylaria grammica EL000614, a Strain Producing Grammicin,a Potent Nematicidal Compound

Sook-Young Park Jongbum Jeon Jung A Kim Mi Jin Jeon Nan Hee Yu Seulbi Kim Ae Ran Park Jin-Cheol Kim Yerim Lee Youngmin Kim Eu Ddeum Choi Min-Hye Jeong Yong-Hwan Lee Soonok Kim 《Mycobiology》2021,49(3):294

An endolichenic fungus, Xylaria grammica strain EL000614, showed strong nematicidal effects against plant pathogenic nematode, Meloidogyne incognita by producing grammicin. We report genome assembly of X. grammica EL000614 comprised of 25 scaffolds with a total length of 54.73 Mb, N50 of 4.60 Mb, and 99.8% of BUSCO completeness. GC contents of this genome were 44.02%. Gene families associated with biosynthesis of secondary metabolites or regulatory proteins were identified out of 13,730 gene models predicted. 相似文献

18.

Comparative Screening of Digestion Tract Toxic Genes in Proteus mirabilis

Xiaolu Shi Yiman Lin Yaqun Qiu Yinghui Li Min Jiang Qiongcheng Chen Yixiang Jiang Jianhui Yuan Hong Cao Qinghua Hu Shenghe Huang 《PloS one》2016,11(3)

Proteus mirabilis is a common urinary tract pathogen, and may induce various inflammation symptoms. Its notorious ability to resist multiple antibiotics and to form urinary tract stones makes its treatment a long and painful process, which is further challenged by the frequent horizontal gene transferring events in P. mirabilis genomes. Three strains of P. mirabilis C02011/C04010/C04013 were isolated from a local outbreak of a food poisoning event in Shenzhen, China. Our hypothesis is that new genes may have been acquired horizontally to exert the digestion tract infection and toxicity. The functional characterization of these three genomes shows that each of them independently acquired dozens of virulent genes horizontally from the other microbial genomes. The representative strain C02011 induces the symptoms of both vomit and diarrhea, and has recently acquired a complete type IV secretion system and digestion tract toxic genes from the other bacteria. 相似文献

19.

Alleles of a Polymorphic ETV6 Binding Site in DCDC2 Confer Risk of Reading and Language Impairment

Natalie?R. Powers John?D. Eicher Falk Butter Yong Kong Laura?L. Miller Susan?M. Ring Matthias Mann Jeffrey?R. Gruen 《American journal of human genetics》2013,93(1):19-28

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20.

Small molecule sensitization to TRAIL is mediated via nuclear localization,phosphorylation and inhibition of chaperone activity of Hsp27

G Mellier D Liu G Bellot A Lisa Holme S Pervaiz 《Cell death & disease》2013,4(10):e890

The small chaperone protein Hsp27 confers resistance to apoptosis, and therefore is an attractive anticancer drug target. We report here a novel mechanism underlying the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) sensitizing activity of the small molecule LY303511, an inactive analog of the phosphoinositide 3-kinase inhibitor inhibitor LY294002, in HeLa cells that are refractory to TRAIL-induced apoptosis. On the basis of the fact that LY303511 is derived from LY294002, itself derived from quercetin, and earlier findings indicating that quercetin and LY294002 affected Hsp27 expression, we investigated whether LY303511 sensitized cancer cells to TRAIL via a conserved inhibitory effect on Hsp27. We provide evidence that upon treatment with LY303511, Hsp27 is progressively sequestered in the nucleus, thus reducing its protective effect in the cytosol during the apoptotic process. LY303511-induced nuclear translocation of Hsp27 is linked to its sustained phosphorylation via activation of p38 kinase and MAPKAP kinase 2 and the inhibition of PP2A. Furthermore, Hsp27 phosphorylation leads to the subsequent dissociation of its large oligomers and a decrease in its chaperone activity, thereby further compromising the death inhibitory activity of Hsp27. Furthermore, genetic manipulation of Hsp27 expression significantly affected the TRAIL sensitizing activity of LY303511, which corroborated the Hsp27 targeting activity of LY303511. Taken together, these data indicate a novel mechanism of small molecule sensitization to TRAIL through targeting of Hsp27 functions, rather than its overall expression, leading to decreased cellular protection, which could have therapeutic implications for overcoming chemotherapy resistance in tumor cells. 相似文献