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” A911T, sequence accession AGFR00000000 [13]

Edwardsiella ictaluri, sequence accession CP001600.1 [14]

Enterobacter cloacae subsp. dissolvens SDM, sequence accession AGSY00000000 [15]

Gluconobacter morbifer” G707T, 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 29570T, 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 3763T, sequence accession AGFX00000000 [64]

Pediococcus acidilactici MA18/5M, sequence accession AGKB00000000 [65]

Pediococcus claussenii ATCC BAA-344T, 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]