List of sequenced archaeal genomes

Last updated

This list of sequenced archaeal genomes contains all the archaea known to have publicly available complete genome sequences that have been assembled, annotated and deposited in public databases. Methanococcus jannaschii was the first archaeon whose genome was sequenced, in 1996. [1]

Contents

Currently in this list there are 39 genomes belonging to Crenarchaeota species, 105 belonging to the Euryarchaeota, 1 genome belonging to Korarchaeota and to the Nanoarchaeota, 3 belonging to the Thaumarchaeota and 1 genome belonging to an unclassified Archaea, totalling 150 Archaeal genomes.

Crenarchaeota

Acidilobales

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Acidilobus saccharovorans 345-151,496,0001,547 [2] CP001742 2010

Desulforococcales

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Aeropyrum pernix K11,669,6952,694 [3] NC_000854 (NCBI Reference Sequence)1999
Desulfurococcus kamchatkensis 1221n1,365,0001,521 [4] CP001140 2009
Hyperthermus butylicus DSM 54561,667,0001,669 [5] CP000493 2007
Ignicoccus hospitalis KIN4/I, DSM 183861,297,0001,496 [6] CP000816 2008
Ignisphaera aggregans AQ1.S1, DSM 172301,875,0002,042 [7] CP002098 2010
Pyrolobus fumarii 1A, DSM 112041,843,0002,038 [8] CP002838 2011
Staphylothermus hellenicus P8, DSM 127101,580,0001,716 [9] CP002051 2011
Staphylothermus marinus F1, DSM 36391,570,0001,659 [10] CP000575 2011
Thermosphaera aggregans M11TL, DSM 114861,316,0001,457 [11] CP001939 2010

Sulfolobales

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Acidianus hospitalis W12,137,0002,424 [12] CP002535 2011
Metallosphaera cuprina Ar-41,840,0002,077 [13] CP002656 2011
Metallosphaera sedula DSM 53482,191,0002,347 [14] CP000682 2008
Sulfolobus acidocaldarius DSM 6392,225,9592,223 [15] CP000077 2005
Sulfolobus islandicus HVE10/42,655,000 [16] CP002426 2011
Sulfolobus islandicus L.D.8.52,722,0002,996 [17] Chromosome CP001731

Plasmid pLD8501 CP001732

2009
Sulfolobus islandicus L.S.2.152,736,0003,068 [17] CP001399 2009
Sulfolobus islandicus M.14.252,608,0002,900 [17] CP001400 2009
Sulfolobus islandicus M.16.272,692,0002,956 [17] CP001401 2009
Sulfolobus islandicus M.16.42,586,0002,869 [17] CP001402 2009
Sulfolobus islandicus REY15A2,522,000 [16] CP002425 2011
Sulfolobus islandicus Y.G.57.142,702,0003,079 [17] CP001403 2009
Sulfolobus islandicus Y.N.15.512,812,0003,318 [17] Chromosome CP001404

Plasmid pYN01 CP001405

2009
Sulfolobus islandicus LAL14/12,465,1772,601 [18] CP003928 2013
Sulfolobus solfataricus P22,992,2452,995 [19] AE006641 2001
Sulfolobus solfataricus 98/22,668,0002,728DOE Joint Genome Institute CP001800 2009
Sulfolobus tokodaii 72,694,7652,826 [20] BA000023 2001

Thermoproteales

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Caldivirga maquilingensis IC-1672,077,0002,011DOE Joint Genome Institute CP000852 2007
Pyrobaculum aerophilum IM22,222,4302,605 [21] AE009441 2002
Pyrobaculum arsenaticum PZ6, DSM 135142,121,0002,410DOE Joint Genome Institute CP000660 2007
Pyrobaculum calidifontis JCM 115482,009,0002,213DOE Joint Genome Institute CP000561 2007
Pyrobaculum islandicum DSM 41841,826,0002,063DOE Joint Genome Institute CP000504 2006
Pyrobaculum sp. 1860Unpublished [22] CP003098 2011
Thermofilum pendens Hrk 51,781,0001,930 [23] Chromosome CP000505

Plasmid pTPEN01 CP000506

2008
Thermoproteus neutrophilus V24Sta1,769,0002,053DOE Joint Genome Institute CP001014 2008
Thermoproteus tenax Kra11,841,0002,100 [24] FN869859 2011
Thermoproteus uzoniensis 768-201,936,0002,229 [25] CP002590 2011
Vulcanisaeta distributa DSM 144292,374,0002,592 [26] CP002100 2010
Vulcanisaeta moutnovskia 768-282,298,0002,393 [27] CP002529 2011

Euryarchaeota

Archaeoglobi

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Archaeoglobus fulgidus DSM43042,178,4002,407 [28] AE000782 1997
Archaeoglobus veneficus SNP6, DSM 111951,901,0002,194DOE Joint Genome Institute CP002588 2011
Archaeoglobus profundus Av18, DSM 56311,563,0001,911 [29] Chromosome CP001857

Plasmid pArcpr01 CP001858

2010
Ferroglobus placidus AEDII12DO, DSM 106422,196,0002,622 [30] CP001899 2011

Halobacteria

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Halalkalicoccus jeotgali B3, DSM 187963,690,0003925 [31] Chromosome I CP002062

Plasmid 1 CP002063
Plasmid 2 CP002064
Plasmid 3 CP002065
Plasmid 4 CP002066
Plasmid 5 CP002067
Plasmid 6 CP002068

2010
Haloarcula hispanica CGMCC 1.20493,484,0003,561 [32] Chromosome I CP002921

Chromosome II CP002922
Plasmid pHH400 CP002923

2011
Haloarcula marismortui ATCC 430493,131,7243,131 [33] Chromosome I AY596297

Chromosome II AY596298
Plasmid pNG100 AY596290
Plasmid pNG200 AY596291
Plasmid pNG300 AY596292
Plasmid pNG400 AY596293
Plasmid pNG500 AY596294
Plasmid pNG600 AY596295
Plasmid pNG700 AY596296

2004
Halobacterium salinarum R1, DSM 6712,000,0002,801 [34] Chromosome NC_010364

Plasmid PHS1 NC_010366
Plasmid PHS2 NC_010369
Plasmid PHS3 NC_010368
Plasmid PHS4 NC_010367

2008
Halobacterium speciesNRC-12,014,2392,058 [35] Chromosome NC_002607

Plasmid pNRC100 NC_002607
Plasmid pNRC200 NC_002608

2000
Halobiforma lacisalsi AJ5, JCM 129834,320,0004,682 [36] AGFZ00000000 2011
Haloferax volcanii DS2 [37] Chromosome CP001956

Plasmid pHV1 CP001957
Plasmid pHV2 CP001954
Plasmid pHV3 CP001953
Plasmid pHV4 CP001955

2010
Halogeometricum borinquense PR3, DSM 115513,920,0004,059 [38] Chromosome CP001690

Plasmid pHBOR01 CP001691
Plasmid pHBOR02 CP001692
Plasmid pHBOR03 CP001693
Plasmid pHBOR04 CP001694
Plasmid pHBOR05 CP001695

2009
Halomicrobium mukohataei arg-2, DSM 122863,332,0003,475 [39] Chromosome CP001688

Plasmid pHmuk01 CP001689

2009
Halopiger xanaduensis SH-63,668,0003,685DOE Joint Genome InstituteChromosome CP002839

Plasmid pHALXA01 CP002840
Plasmid pHALXA02 CP002841
Plasmid pHALXA03 CP002842

2011 (Chromosome)
Haloquadratum walsbyi C23, DSM 168543,148,000 [40] Chromosome FR746099

Plasmid PL6A FR746101
Plasmid PL6B FR746102
Plasmid PL100 FR746100

2011
Haloquadratum walsbyi HBSQ001, DSM 167903,132,0002,914 [41] Chromosome AM180088

Plasmid PL47 AM180089

2006
Halorhabdus tiamatea SARL4B3,840,0004,034 [42] AFNT00000000 2011
Halorhabdus utahensis AX-2, DSM 129403116 Kb3076 [43] CP001687 2009
Halorubrum lacusprofundi ATCC 492394,300,0003,725DOE Joint Genome InstituteChromosome 1 CP001365

Chromosome 2 CP001366
Plasmid pHLAC01 CP001367

2009 (Chromosomes 1 and 2)
Haloterrigena turkmenica VKM B-1734, DSM 55115,440,0005,351 [44] Chromosome CP001860

Plasmid pHTUR01 CP001861
Plasmid pHTUR02 CP001862
Plasmid pHTUR03 CP001863
Plasmid pHTUR04 CP001864
Plasmid pHTUR05 CP001865
Plasmid pHTUR06 CP001866

2010
Natrialba asiatica ATCC 700177 [45] Survey 2004
Natrialba magadii ATCC 430993,751,0004,364DOE Joint Genome Institute CP001932 2010
Natronomonas pharaonis DSM21602,595,2212,675 [46] Chromosome CR936257

Plasmid PL131 CR936258
Plasmid PL23 CR936259

2005

Methanobacteria

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Methanobacterium sp. AL-212,583,000DOE Joint Genome Institute,
Univ of Illinois at Urbana-Champaign		 CP002551 2011
Methanobacterium sp. SWAN-12,546,0002,500DOE Joint Genome Institute,
Univ Illinois at Urbana-Champaign		 CP002772 2011
Methanobacterium thermoautotrophicum delta-H1,751,3771,869 [47] AE000666 1997
Methanobrevibacter ruminantium M12,937,0002,283 [48] CP001719 2010
Methanobrevibacter smithii DSM 23751,704,0001,748Washington University ABYW00000000 2008
Methanobrevibacter smithii F1, DSM 23741,707,0001,749Washington University ABYV00000000 2010
Methanobrevibacter smithii PS, ATCC 350611,853,0001,841 [49] CP000678 2007
Methanobrevibacter smithii TS94A1,889,0001,808 [50] AELU00000000 2011
Methanobrevibacter smithii TS94B1,886,0001,856 [50] AELV00000000 2011
Methanobrevibacter smithii TS94C1,910,0001,812 [50] AELW00000000 2011
Methanobrevibacter smithii TS95A1,992,0001,961 [50] AELX00000000 2011
Methanobrevibacter smithii TS95B1,972,0001,895 [50] AELY00000000 2011
Methanobrevibacter smithii TS95C1,978,0001,874 [50] AELZ00000000 2011
Methanobrevibacter smithii TS95D2,011,0001,860 [50] AEMA00000000 2011
Methanobrevibacter smithii TS96A1,975,0001,852 [50] AEMB00000000 2011
Methanobrevibacter smithii TS96B1,869,0001,742 [50] AEMC00000000 2011
Methanobrevibacter smithii TS96C1,818,0001,764 [50] AEMD00000000 2011
Methanobrevibacter smithii TS145A1,782,0001,786 [50] AEKU00000000 2011
Methanobrevibacter smithii TS145B1,797,0001,880 [50] AELL00000000 2011
Methanobrevibacter smithii TS146A1,792,0001,823 [50] AELM00000000 2011
Methanobrevibacter smithii TS146B1,794,0001,814 [50] AELN00000000 2011
Methanobrevibacter smithii TS146C1,947,0002,355 [50] AELO00000000 2011
Methanobrevibacter smithii TS146D1,713,0001,693 [50] AELP00000000 2011
Methanobrevibacter smithii TS146E1,952,0001,887 [50] AELQ00000000 2011
Methanobrevibacter smithii TS147A2,008,0001,969 [50] AELR00000000 2011
Methanobrevibacter smithii TS147B1,965,0001,911 [50] AELS00000000 2011
Methanobrevibacter smithii TS147C1,973,0002,014 [50] AELT00000000 2011
Methanosphaera stadtmanae DSM 30911,767,4031,534 [51] CP000102 2005
Methanothermobacter marburgensis Marburg DSM 21331,634,0001,806 [52] CP001710 2010
Methanothermus fervidus V24S, DSM 20881,243,0001,361 [53] CP002278 2010

Methanococci

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Methanocaldococcus fervens AG861,485,0001,663DOE Joint Genome InstituteChromosome CP001696

Plasmid pMEFER01 CP001697

2009 (Chromosome)
Methanocaldococcus infernus ME1,328,0001,513DOE Joint Genome Institute CP002009 2010
Methanocaldococcus jannaschii DSM 26611,664,9701,715 [54] Chromosome: L77117

Large plasmid: L77118
Small plasmid: L77119

1996
Methanocaldococcus vulcanius M7, DSM 120941,746,0001,808DOE Joint Genome InstituteChromosome CP001787

Plasmid pMETVU01 CP001788
Plasmid pMETVU02 CP001789

2009
Methanocaldococcus sp. FS406-221,760,0001,893DOE Joint Genome InstituteChromosome CP001901

Plasmid pFS01 CP001902

2010 (Chromosome)
Methanococcus aeolicus Nankai-31,569,0001,554DOE Joint Genome Institute CP000743 2007
Methanococcus maripaludis C51,780,0001,896DOE Joint Genome Institute CP000609 2007
Methanococcus maripaludis C61,744,0001,874DOE Joint Genome Institute CP000867 2007
Methanococcus maripaludis C71,772,0001,858DOE Joint Genome Institute CP000745 2007
Methanococcus maripaludis S21,661,1371,722 [55] NC_005791 (NCBI Reference Sequence)2004
Methanococcus maripaludis X11,746,0001,892 [56] CP002913 2011
Methanococcus vannielii SB1,720,0001,755DOE Joint Genome Institute CP000742 2007
Methanococcus voltae A31,936,0001,768DOE Joint Genome Institute CP002057 2010
Methanothermococcus okinawensis IH11,662,0001,662DOE Joint Genome InstituteChromosome CP002792

Plasmid pMETOK01 CP002793

2011 (Chromosome)
Methanotorris igneus Kol5, DSM 56661,854,0001,843DOE Joint Genome Institute CP002737 2011

Methanomicrobia

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Candidatus Methanoregula boonei 6A82,542,0002,518DOE Joint Genome Institute [57] CP000780 2007
Methanocella sp. Rice Cluster I (RC-I)MRE503,179,9163103Genome sequence, [58] then taxonomic placement [59] AM114193 2005
Methanocella paludicola SANAE2,957,6353004 [60] AP011532 2011
Methanocella conradii HZ2541,316,3802512 [61] CP003243 2012
Methanococcoides burtonii DSM62422,575,0322,273 [62] CP000300 2009
Methanocorpusculum labreanum Z1,804,0001,830 [63] CP000559 2009
Methanoculleus marisnigri JR1, DSM 14982,478,0002,560 [64] CP000562 2009
Methanohalobium evestigatum Z-73032,406,2322,254DOE Joint Genome Institute [65] Chromosome: CP002069

Plasmid pMETEV01: CP002070

2010 (Chromosome)
Methanohalophilus mahii SLP, DSM 52192,012,0002,095 [66] CP001994 2010
Methanoplanus petrolearius SEBR 4847, DSM 115712,843,0002,881 [67] CP002117 2011
Methanosalsum zhilinae WeN5, DSM 40172,138,0002,086 CP002101 2010
Methanosaeta concilii GP-63,008,000 [68] CP002565 2010
Methanosaeta harundinacea 6Ac2,559,000 [22] CP003117 2011
Methanosaeta thermophila PT1,879,0001,785DOE Joint Genome Institute CP000477 2006
Methanosarcina acetivorans C2A5,751,4924,540 [69] AE010299 2002
Methanosarcina barkeri Fusaro, DSM 8044,837,4083,607 [70] Chromosome CP000099

Plasmid 1 CP000098

2006 (Chromosome)
Methanosarcina mazei Go14,096,3453,371 [71] AE008384 2002
Methanosphaerula palustris E1-9c, DSM 199582,922,0002,859DOE Joint Genome Institute CP001338 2008
Methanospirillum hungatei JF-13,544,7383,139DOE Joint Genome Institute CP000254 2006

Methanopyri

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Methanopyrus kandleri AV191,694,9691,691 [72] AE009439 2002

Thermococci

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Pyrococcus abyssi GE51,765,1181,784 [73] NC_000868 (NCBI Reference Sequence)2000
Pyrococcus furiosus DSM 36381,908,2562,065 [74] AE009950 1999
Pyrococcus horikoshii OT31,738,5052,061 [75] NC_000961 (NCBI Reference Sequence)1998
Pyrococcus sp. NA21,861,0001,984 [22] CP002670 2011
Pyrococcus yayanosii CH11,716,0001,952 [76] CP002779 2011
Thermococcus barophilus MP, DSM 118362,010,0002,196 [77] CP002372 2011
Thermococcus gammatolerans EJ32,045,0002,206 [78] CP001398 2009
Thermococcus kodakaraensis KOD12,088,7372,306 [79] AP006878 2005
Thermococcus onnurineus NA11,847,0002,027 [80] NC_011529 (NCBI Reference Sequence)2008
Thermococcus sibiricus MM 7391,845,0002,085 [81] CP001463 2009
Thermococcus sp. 45572,011,0002,181 [82] CP002920 2011
Thermococcus sp. AM42,086,0002,279 [83] CP002952 2011

Thermoplasmata

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Ferroplasma acidarmanus Fer11,865,0001,742 [84] AABC00000000 2007
Picrophilus torridus DSM 97901,545,8951,535 [85] AE017261 2004
Thermoplasma acidophilum DSM 17281,564,9061,478 [86] NC_002578 (NCBI Reference Sequence)2000
Thermoplasma volcanium GSS11,584,8041,526 [87] NC_002689 (NCBI Reference Sequence)2000

Unclassified Euryarchaeota

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Aciduliprofundum boonei T4691,486,0001,587DOE Joint Genome Institute CP001941 2010

Korarchaeota

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Candidatus Korarchaeum cryptofilum OPF81,590,0001,661 [88] CP000968 2008

Nanoarchaeota

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Nanoarchaeum equitans Kin4-M490,885536 [89] AE017199 2003

Thaumarchaeota

Cenarchaeales

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Cenarchaeum symbiosum A2,045,0002,066 [90] DP000238 2006

Nitrosopumilales

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
Candidatus Nitrosoarchaeum limnia SFB11,769,0002,171 [91] AEGP00000000 2011
Nitrosopumilus maritimus SCM11,645,0001,842 [92] CP000866 2010

Unclassified Archaea

Species Strain Base Pairs Genes Reference GenBank identifierPublication year
halophilic archaeon sp. DL31Unpublished [22] CP002988 2011

See also

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References

  1. ↑ Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, et al. (August 1996). "Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii". Science. 273 (5278): 1058–73. Bibcode:1996Sci...273.1058B. doi:10.1126/science.273.5278.1058. PMID   8688087. S2CID   41481616.
  2. ↑ Mardanov AV, Svetlitchnyi VA, Beletsky AV, Prokofeva MI, Bonch-Osmolovskaya EA, Ravin NV, Skryabin KG (August 2010). "The genome sequence of the crenarchaeon Acidilobus saccharovorans supports a new order, Acidilobales, and suggests an important ecological role in terrestrial acidic hot springs". Applied and Environmental Microbiology. 76 (16): 5652–7. Bibcode:2010ApEnM..76.5652M. doi:10.1128/AEM.00599-10. PMC   2918975 . PMID   20581186.
  3. ↑ Kawarabayasi Y, Hino Y, Horikawa H, Yamazaki S, Haikawa Y, Jin-no K, et al. (April 1999). "Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1". DNA Research. 6 (2): 83–101, 145–52. doi: 10.1093/dnares/6.2.83 . PMID   10382966.
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