Domain Archaea

PhylumCrenarchaeota

Thermogladius cellulolyticus” 1633, sequence accession CP003531 [1]

Phylum Euryarchaeota

Methanomassiliicoccus luminyensis, sequence accession CAJE01000001 through CAJE01000026 [2]

Pyrococcus sp. Strain ST04, sequence accession CP003534 [3]

Domain Bacteria

Phylum Nitrospirae

Leptospirillum ferrooxidans Strain C2-3, sequence accession AP012342 [4]

Phylum Cyanobacteria

Prochlorococcus marinus MED4, sequence accession BX548174 [5]

Phylum Proteobacteria

Acinetobacter sp. Strain HA, sequence accession AJXD00000000 [6]

Acinetobacter venetianus RAG-1T, sequence accession AKIQ00000000 [7]

Agrobacterium tumefaciens CCNWGS0286, sequence accession AGSM00000000 [8]

Alcaligenes faecalis subsp. faecalis NCIB 8687, sequence accession AKMR01000001 through AKMR01000186 [9]

Alishewanella agri BL06T, sequence accession AKKU00000000 [10]

Alishewanella aestuarii Strain B11T, sequence accession ALAB00000000 [11]

Bacillus methanolicus MGA3, sequence accession ADWW00000000 [12]

Bacillus methanolicus PB1, sequence accession AFEU00000000 [12]

Candidatus Sulfurovum sediminum”, sequence accession AJLE00000000 [13]

Bartonella birtlesii strain IBS 135T, sequence accession AKIP00000000 [14]

Brucella abortus A13334, sequence accession CP003176.1 (Chromosome I), CP003177.1 (Chromosome II) [15]

Brucella canis Strain HSK A52141, sequence accession CP003174.1 (chromosome I), and CP003175.1 (chromosome II) [16]

Brucella melitensis S66, sequence accession AHWB00000000 [17]

Brucella melitensis16M, sequence accession AHWC00000000 [18]

Brucella melitensis 16M1w, sequence accession AHWD00000000 [18]

Brucella melitensis 16M13w, sequence accession AHWE00000000 [18]

Burkholderia sp. Strain KJ006, sequence accession CP003514 (chromosome I), CP003515 (chromosome II), CP003516 (chromosome III), and CP003517 (plasmid pKJ006) [19].

Burkholderia terrae Strain BS001, sequence accession AKAU00000000 [20]

Burkholderia thailandensis MSMB43, sequence accession AJXB00000000 [21]

Catenovulum agarivorans YM01T, sequence accession AJWM00000000 [22]

Citrobacter sp. Strain A1, sequence accession AKTT00000000 [23]

Cronobacter sakazakii ES15, sequence accession CP003312 [24]

Dickeya zeae Strain ZJU1202, sequence accession AJVN00000000 [25]

Enterobacter cloacae GS1, sequence accession AJXP00000000 [26]

Enterococcus faecium Clinical Isolate LCT-EF128, sequence accession AJUP00000000 [27]

Enterobacter radicincitans DSM16656T, sequence accession AKYD00000000 [28]

Escherichia coli J53, sequnce accession AICK00000000 [29]

Escherichia coli LCT-EC106, sequence accession [30]

Escherichia coli NCCP15647, sequence accession AJMB00000000 [31]

Escherichia coli W26, sequence accession AGIA00000000 [32]

Gluconobacter oxydans WSH-003, sequence accession AHKI00000000 [33]

Halomonas stevensii S18214T, sequence accession AJTS00000000 [34]

Helicobacter cinaedi Strain PAGU611, sequence accession AP012344 (chromosome) and AP012345 (plasmid) [35]

Helicobacter pylori hpEurope Strain N6, sequence accession CAHX01000001 to CAHX01000054 [36]

Herbaspirillum lusitanum P6-12, sequence accession AJHH00000000 [37]

Herbaspirillum sp. Strain GW103, sequence accession AJVC00000000 [38]

Hydrocarboniphaga effusa strain AP103T, sequence accession AKGD00000000 [39]

Hydrogenophaga sp. Strain PBC, sequence accession AJWL00000000 [40]

Klebsiella oxytoca E718, sequence accession CP003683 [41]

Methylobacterium extorquens sp. strain 4-46, sequence accessions NC_010511, NC_010373, NC_010374 [42]

Methylobacterium extorquens strain BJ001, sequence accessions NC_010725, NC_010727, NC_010721 [42]

Methylobacterium extorquens strain CM4, sequence accessions NC_011757, NC_011758, NC_011760 [42]

Methylobacterium extorquens strain JCM 2831, sequence accessions NC_010510, NC_010509, NC_010514, NC_010517, NC_010518, NC_010502, NC_010504, NC_010507 [42]

Methylobacterium extorquens strain ORS 2060, sequence accessions NC_011894, NC_011892, NC_011887, NC_011893, NC_011895, NC_011888, NC_011889, NC_011890 [42]

Methylobacterium extorquens strain PA1, sequence accessions NC_010172 [42]

Methylobacterium sp. Strain GXF4, sequence accession AKFK00000000 [43]

Methylophaga sp. Strain JAM1, sequence accession CP003390 [44]

Methylophaga sp. Strain JAM7 sequence accession CP003380 (chromosome), CP003381 (plasmid) [44]

Modestobacter marinus Strain BC501, sequence accession FO203431 [45]

Mycobacterium massiliense M18, sequence accession AJSC00000000 [46]

Neisseria meningitidis Capsule Null Locus Strain, sequence accession CAJS01000001 through CAJS01000042 [47]

Novosphingobium sp. Strain Rr 2-17, sequence accession AKFJ00000000 [48]

Providencia stuartii Clinical Isolate MRSN 2154, sequence accession CP003488 [49]

Pseudaminobacter salicylatoxidans KCT001, sequence accession CAIU00000000 [50]

Pseudomonas aeruginosa Strain SJTD-1, sequence accession AKCM00000000 [51]

Pseudomonas aeruginosa Strain XMG, sequence accession AJXX00000000 [52]

Pseudomonas fuscovaginae CB98818, sequence accession ALAQ00000000 [53]

Pseudoalteromonas issachenkonii PAMC 22718, sequence accession AJTK00000000 [54]

Pseudomonas sp. Strain HYS, sequence accession AJJP00000000 [55]

Pseudomonas pseudoalcaligenes KF707, sequence accession AJMR00000000 [56]

Pseudomonas putida Strain ND6, sequence accession CP003588 [57]

Pseudomonas putida Strain SJTE-1, sequence accession AKCL00000000 [58]

Pseudomonas sp. Strain M47T1, sequence accession AJWX00000000 [59]

Pseudomonas stutzeri TS44, sequence accession AJXE00000000 [60]

Ralstonia sp. strain PBA, sequence accession AJWL00000000 [61]

Rhodanobacter strain DSM 23569, sequence accession AGIL00000000 [62]

Rhodanobacter strain 115, sequence accession AJXS00000000 [62]

Rhodanobacter DSM 17631, sequence accession AJXT00000000 [62]

Rhodanobacter DSM 18449, sequence accession AJXU00000000 [62]

Rhodanobacter DSM 18863, sequence accession AJXW00000000 [62]

Rhodanobacter DSM 24678, sequence accession AJXV00000000 [62]

Rickettsia conorii subsp. caspia, sequence accession AJUR00000000 [63]

Rickettsia australis strain PhillipsT, sequence accession AKVZ00000000 [64]

Rickettsia sp. Strain MEAM1, sequence accession AJWD00000000 [65]

Rickettsia conorii subsp. israelensis, sequence accession AJVP00000000 [66]

Serratia plymuthica Strain PRI-2C, sequence accession AJTB00000000 [67]

Serratia marcescens strain LCT-SM213, seqeunce accession AJUV00000000 [68]

Sinorhizobium fredii USDA257, sequence accession CP003563 through CP003582 [69]

Sphingobium indicum B90A, sequence accession AJXQ00000000 [70]

Stenotrophomonas maltophilia PML168, sequence accession CAJH01000001 through CAJH01000097 [71]

Salmonella enterica serotype Newport CVM35185, sequence accession AHTJ00000000 [72]

Salmonella enterica serotype Newport CVM33953, sequence accession AHTM00000000 [72]

Salmonella enterica serotype Newport CVM21550, sequence accession AHTT00000000 [72]

Salmonella enterica serotype Newport CVM21538, sequence accession AHTV00000000 [72]

Salmonella enterica serotype Newport CVM37978, sequence accession AHUC00000000 [72]

Salmonella enterica serotype Newport CVM19593, sequence accession AHUD00000000 [72]

Salmonella enterica serotype Newport CVM19443, sequence accession AHUB00000000 [72]

Salmonella enterica serotype Newport CVM19470, sequence accession AHUE00000000 [72]

Salmonella enterica serovar Typhi UJ308A, sequence accession AJTD00000000 [73]

Salmonella enterica Serovar Typhi UJ816A, sequence accession AJTE00000000 [73]

Serratia sp. Strain M24T3, sequence accession [74]

Sulfuricella denitrificans skB26, sequence accession BAFJ01000001 through BAFJ01000023 [75]

Xanthomonas campestris JX, sequence accession AJVO00000000 [76]

Yersinia pestis Strain 2501, sequence accession AKVQ00000000 [77]

Phylum Firmicutes

Aeromonas aquariorum, sequence accession BAFL01000001 through BAFL01000036, and AP012343 [78]

Aerococcus viridans LL1, sequence accession AJTG00000000 [79]

Bacillus anthracis H9401, sequence accession CP002091.1 (chromosome), CP002092.1.1 (plasmid pXO1), and CP002093.1 (plasmid pXO2) [80]

Bacillus atrophaeus C89, sequence accession AJRJ00000000 [81]

Bacillus cereus NC7401, sequence accession AP007209 (chromosome), AP007210 (plasmid pNCcld), AP007211 (plasmid pNC1, 48 kb), AP007212 (plasmid pNC2, 5 kb), AP007213 (plasmid pNC3, 4 kb), and AP007214 (plasmid pNC4, 3 kb) [82]

Bacillus siamensis KCTC 13613T, sequence accession AJVF00000000 [83]

Bacillus sp. Strain 5B6, sequence accession AJST00000000 [84]

Bacillus sp. Strain 916, sequence accession AFSU00000000 [85]

Citreicella aestuarii Strain 357, sequence accession AJKJ00000000 [86]

Clostridium beijerinckii Strain G117, sequence acceession AKWA00000000 [87]

Corynebacterium pseudotuberculosis Strain 1/06-A, sequence accession CP003082 [88]

Enterobacter sp. Isolate Ag1, sequence accession AKXM00000000 [89]

Enterococcus faecalis D32, sequence accession CP003726 through CP003728 [90]

Enterococcus faecalis strain NP-10011, sequence accession AB712291 [91]

Enterococcus hirae (Streptococcus faecalis) ATCC 9790, sequence accession CP003504 (chromosome), NC_015845 (plasmid pTG9790) [92]

Geobacillus thermoglucosidans” TNO-09.020, sequence accession AJJN00000000 [93]

Lactococcus garvieae IPLA 31405, sequence accession AKFO00000000 [94]

Lactobacillus mucosae LM1, sequence accession AHIT00000000 [95]

Lactobacillus rossiae DSM 15814, sequence accession AKZK00000000 [96]

Paenibacillus polymyxa OSY-DF, sequence accession AIPP00000000 [97]

Pediococcus pentosaceus strain IE-3, sequence accession CAHU01000001 through CAHU01000091 [98]

Pelosinus fermentans A11, sequence accession AKVM00000000 [99]

Pelosinus fermentans B4, sequence accession AKVJ00000000 [99]

Pelosinus fermentans JBW45, sequence accession AKVO00000000 [100]

Pelosinus fermentans R7, sequence accession AKVN00000000 [101]

Planococcus antarcticus DSM 14505, sequence accession AJYB00000000 [102]

Pseudomonas stutzeri Strain JM300, sequence accession CP003725 [103]

Rhodococcus sp. strain DK17, sequence accession AJLQ00000000 [104]

Staphylococcus aureus Strain LCT-SA112, sequence accession AJLP00000000 [105]

Staphylococcus capitis QN1, sequence accession AJTG00000000 [106]

Staphylococcus equorum subsp. equorum Mu2, sequence accession CAJL01000001 to CAJL01000030 [107]

Staphylococcus hominis ZBW5, sequence accession AKGC00000000 [108]

Staphylococcus saprophyticus subsp. saprophyticus M1-1, sequence accession AHKB00000000 [109]

Streptococcus mutans GS-5, sequence accession CP003686 [110]

Streptococcus pyogenes M1 476, sequence accession AP012491 [111]

Streptococcus salivarius PS4, sequence accession AJFW00000000 [112]

Streptococcus thermophilus Strain MN-ZLW-002, sequence accession CP003499 [113]

Ureibacillus thermosphaericus Strain Thermo-BF, sequence accession AJIK00000000 [114]

Phylum Tenericutes

Mycoplasma leachii Strain PG50T, sequence accession CP002108.1 [115]

Mycoplasma mycoides subsp. mycoides, sequence accession CP002107.1 [115]

Mycoplasma wenyonii Strain Massachusetts, sequence accession CP003703 [116]

Phylum Actinobacteria

Actinomyces massiliensis Strain 4401292T, sequence accession AKIO00000000 [117]

Bifidobacterium animalis subsp. lactis B420, sequence accesion CP003497 [118]

Bifidobacterium animalis subsp. lactis

Bi-07, sequence accesion CP003498 [118]

Bifidobacterium bifidum strain BGN4, sequence accession CP001361 [119]

Brevibacterium massiliense Strain 541308T, sequence accession CAJD00000000 [120]

Corynebacterium bovis DSM 20582, sequence accession AENJ00000000 [121]

Corynebacterium diphtheriae Biovar Intermedius NCTC 5011, sequence accession AJVH00000000 [122]

Corynebacterium pseudotuberculosis strain 1/06-A, sequence accession CP003082 [123]

Corynebacterium pseudotuberculosis strain 3/99-5 sequence accession CP003152.1 [124]

Corynebacterium pseudotuberculosis strain 42/02-A, sequence accession CP003062 [124]

Microbacterium yannicii, sequence accession CAJF01000001 through CAJF01000067 [125]

Micromonospora lupini Lupac 08, sequence accession CAIE01000001 [126]

Mycobacterium bolletii Strain M24, sequence accession AJLY00000000 [127]

Mycobacterium intracellulare Clinical Strain MOTT-36Y, sequence accession CP003491 [128]

Mycobacterium massiliense M18, sequence accession AJSC00000000 [129]

Mycobacterium massiliense strain GO 06, sequence accession CP003699 [130]

Mycobacterium massiliense strain M154, sequence accession AJMA00000000 [131]

Mycobacterium tuberculosis RGTB327, sequence accession CP003233 [132]

Mycobacterium tuberculosis MTB423, sequence accession CP003234 [132]

Parascardovia denticolens IPLA 20019, sequence accession AKII00000000 [133]

Saccharothrix espanaensis DSM 44229T, sequence accession HE804045 [134]

Streptomyces auratus Strain AGR0001, sequence accession AJGV00000000 [135]

Streptomyces cattleya” DSM46488T, sequence accession FQ859185 and FQ859184 [136]

Streptomyces globisporus C-1027, sequence accession AJUO00000000 [137]

Streptococcus mutans GS-5, sequence accession CP003686 [138]

Streptomyces sp. Strain AA1529, sequence accession ALAP00000000 [139]

Streptomyces sulphureus L180, sequence accession AJTQ0000000 [140]

Phylum Spirochaetes

Borrelia crocidurae, sequence accession CP003426 (chromosome), CP003427 to CP003465 (plasmids) [141]

Treponema sp. Strain JC4, sequence accession JQ783348 [142]

Phylum Bacteroidetes

Flavobacterium sp. Strain F52, sequence accession AKZQ00000000 [143]

Fusobacterium nucleatum subsp. fusiforme ATCC 51190T, sequence accession AKXI00000000 [144]

Imtechella halotolerans” K1T, sequence accession AJJU00000000 [145]

Virus genomes

Bacteriophage

Actinophage PIS136, sequence accession JX006077 [146]

Aeromonas hydrophila Phage CC2, sequence accession JX123262 [147]

Bacteriophage BC-611, sequence accession AB712291 [148]

Bacteriophage SSU5, sequence accession JQ965645 [149]

Blattabacterium sp. strain BGIGA, sequence accession [150]

Caulobacter crescentus Bacteriophage φCbK, sequence accession JX163858 [151]

Celeribacter Bacteriophage P12053L, sequence accession JQ809650 [152]

Croceibacter Bacteriophage P2559S, sequence accession JQ867099 [153]

Cronobacter sakazakii Temperate Bacteriophage phiES15 JQ780327 [154]

Marinomonas Bacteriophage P12026, sequence accession JQ867100 [155]

Pectobacterium carotovorum subsp. carotovorum Bacteriophage PP1, sequence accession JQ837901 [156]

Persicivirga bacteriophages P12024L, sequence accession JQ823123 [157]

Persicivirga bacteriophages P12024S, sequence accession JQ823122 [157]

phage clP1, sequence accession JN051154 [158]

Pseudomonas aeruginosa Siphophage MP1412, sequence accession JX131330 [159]

Pseudomonas aeruginosa Temperate Phage MP29, sequence accession EU272036 [160]

Pseudomonas aeruginosa Temperate Phage MP42, sequence accession JQ762257 [160]

Pseudomonas Phage Φ-S1, sequence accession JX173487 [161]

Siphophage MP1412, sequence accession JX131330 [162]

Staphylococcus aureus Bacteriophage GH15, sequence accession JQ686190 [163]

Vibrio vulnificus Bacteriophage SSP002, sequence accession JQ692107 [164]

Eukaryotic viruses

African bovine rotaviruses RVA/Cow-wt/ZAF/1603/2007/G6P, sequence accession S9(VP7) JN831209, S4(VP4) JN831210, S6(VP6) JN831211, S1(VP1) JN831212, S2(VP2) JN831213, S3(VP3) JN831214, S5(NSP1) JN831204, S8(NSP2) JN831205, S7(NSP3) JN831206, S10(NSP4) JN831207, S11(NSP5) JN831208 [165]

African bovine rotaviruses RVA/Cow-wt/ZAF/1604/2007/G8P, sequence accession S9(VP7) JN831220, S4(VP4) JN831221, S6(VP6) JN831222, S1(VP1) JN831223, S2(VP2) JN831224, S3(VP3) JN831225, S5(NSP1) JN831215, S8(NSP2) JN831216, S7(NSP3) JN831217, S10(NSP4) JN831218, S11(NSP5) JN831219 [165]

African bovine rotaviruses RVA/Cow-wt/ZAF/1605/2007/G6P, sequence accession S9(VP7) JN831231, S4(VP4) JN831232, S6(VP6) JN831233, S1(VP1) JN831234, S2(VP2) JN831235, S3(VP3) JN831236, S5(NSP1) JN831226, S8(NSP2) JN831227, S7(NSP3) JN831228, S10(NSP4) JN831229, S11(NSP5) JN831230 [165]

Avian Leukosis Virus, sequence accession JX254901 [166]

Avian Influenza Virus H3N2, sequence accession JX175250 through JX175257 [167]

Avian Influenza Virus H5N2, sequence accession JQ990145 through JQ990152 [168]

Avian-Like H4N8 Swine Influenza, sequence accession JX151007 through JX151014 [169]

Avian Paramyxovirus, sequence accession JQ886184 [170]

Avian Tembusu-Related Virus Strain WR, sequence accession JX196334 [171]

Bluetongue Virus Serotype 9, sequence accession JX003687 to JX003696 [172]

Bluetongue Virus Serotype 16, sequence accession [173]

Bombyx mori Nucleopolyhedrovirus, sequence accession JQ991009 [174]

Bovine Viral Diarrhea Virus 2, sequence accession JF714967 [175]

Bovine Foamy Viruses, sequence accession JX307861 [176]

Canine Noroviruses, sequence accession FJ692500 and FJ692501 [177]

Chicken Anemia Virus, sequence accession JX260426 [178]

Chikungunya Virus, sequence accession JX088705 [179]

Chinese Virulent Avian Coronavirus GX-YL5, sequence accession HQ848267 [180]

Chinese Virulent Avian Coronavirus GX-YL9, sequence accession HQ850618 [180]

Coxsackievirus B4, sequence accession JX308222 [181]

Enterovirus C (HEV-C117), sequence accession JX262382 [182]

Genotype 4 Hepatitis E Virus Strain, sequence accession JQ993308 [183]

H10N8 Avian Influenza Virus, sequence accession JQ924786 to JQ924793 [184]

H9N2 Subtype Influenza Virus FJG9, sequence accession JF715008.1, JN869514.1 through JN869520.1 [185].

Herpes Simplex Virus 1 Strain McKrae, sequence accession JX142173 [186]

Human Coronavirus NL63, sequence accession JX104161 [187]

Human G10P Rotavirus, sequence accession AB714258 through AB714268 [188]

Ikoma Lyssavirus, sequence accession JX193798 [189]

Korean sacbrood viruses AmSBV-Kor19, sequence accession JQ390592 [190]

Korean sacbrood viruses AmSBV-Kor21, sequence accession JQ390591 [190]

Mitochondrion of Frankliniella occidentalis, sequence accession JN835456 [191]

New Circular DNA Virus from Grapevine, sequence accession JQ901105 [192]

Novel Porcine Epidemic Diarrhea Virus, sequence accession JX112709 [193]

Pararetrovirus, sequence accession JQ926983 [194]

Parechovirus, sequence accession JX050181 [195]

Peste des Petits Ruminants Virus, sequence accession JX217850 [196]

Polyomavirus, sequence accession JQ412134 [197]

Porcine Circovirus 2b Strain CC1, sequence accession JQ955679 [198]

Porcine circovirus type 2 (PCV2), sequence accession JX294717 [199]

Porcine Epidemic Diarrhea Virus Strain AJ1102, sequence accession JX188454 [200]

Porcine Sapelovirus Strain YC2011, sequence accession JX286666 [201]

Respiratory Syndrome Virus Strain QY2010, sequence accession JQ743666 [202]

SAT 2 Foot-and-Mouth Disease Virus, sequence accession JX014255 [203]

SAT 2 Foot-and-Mouth Disease Virus PAT, sequence accession JX014256 [203]

Street Rabies Virus, sequence accession HQ450386 [204]

Waterfowl aviadenovirus goose adenovirus 4, sequence accession JF510462 [205]

Plant genomes

Plants

cpDNA of Smilax china, sequence accession NC_015104 [206]

Elodea canadensis, sequence accession JQ310743 [207]

Ogura-type mitochondrial genome, sequence accession AB694743 [208]

Fungus

Aspergillus oryzae Strain 3.042, sequence accession AKHY00000000 [209]

Rhodosporidium toruloides MTCC 457, sequence accession AJMJ00000000 [210]

Animal genomes

Helicoverpa armigera, sequence accession HQ613271 [211]

Plasmids

plasmidIncN plasmid pRSB201, sequence accession JN102341 [212]

plasmidIncN plasmid pRSB203, sequence accession JN102342 [212]

plasmidIncN plasmid pRSB205, sequence accession JN102343 [212]

plasmidIncN plasmid pRSB206, sequence accession JN102344 [212]