Stand. Genomic Sci. 2011 5:3
doi:10.1601/sigs.2495686
Genome sequences published outside of Standards in Genomic Sciences, December 2011

1 Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA

Electronic publication date: December 30, 2011.

OW Nelson and GM Garrity

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Oranmiyan W. Nelson1 and George M. Garrity1

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
  • Halobiforma lacisalsi AJ5, sequence accession AGFZ01000000 [1]
  • Thermococcus sp. strain AM4, sequence accession CP002952 [2]
  • Phylum Proteobacteria
  • Acidithiobacillus thiooxidans ATCC 19377, sequence accession AFOH01000000 [3]
  • Acinetobacter sp. strain D499, sequence accession AGFH01000000 [4]
  • Azospirillum brasilense Sp245, sequence accession HE577327 (chromosome), HE577328 (p1), HE577329 (p2), HE577330 (p3), HE577331 (p4), HE577332 (p5), HE577333 (p6) [5]
  • Azospirillum lipoferum strain 4B, sequence accession FQ311868 (chromosome), FQ311869 (p1), FQ311870 (p2), FQ311871 (p3), FQ311872 (p4), FQ311873 (p5), FQ311874 (p6) [5]
  • Escherichia coli F18, sequence accession AGTD01000000 [6]
  • Escherichia coli K88, sequence accession CP002729 (chromosome), CP002730 (pUMNK88_K88), CP002731 (pUMNK88_IncI1), CP002732 (pUMNK88_Ent), CP002733 (pUMNK88_Hly), and HQ023862 (pUMNK88) [6]
  • Escherichia coli Strain CE10, sequence accession CP003034 to CP003038 [7]
  • Gluconacetobacter xylinus, NBRC 3288, sequence accession AP012159 through AP012166 [8]
  • Halomonas sp. Strain HAL1, sequence accession AGIB00000000 [9]
  • Methylomonas methanica MC09, sequence accession CP002738 [10]
  • Novosphingobium nitrogenifigens Y88, sequence accession [11]
  • Pelagibacterium halotolerans B2, sequence accession CP003075 (chromosome), CP003076 (plasmid) [12]
  • Pseudomonas aeruginosa PAO1, sequence accession GSE34141 [13]
  • Pseudomonas putida Idaho, sequence accession AGFJ01000000 [14]
  • Sphingomonas elodea ATCC 31461, sequence accession AGFU01000000 [15]
  • Phylum Firmicutes
  • Acidaminococcus intestini RYC-MR95, sequence accession CP003058 [16]
  • Lactobacillus rhamnosus strain CASL, sequence accession AFYD00000000 [17]
  • Pseudomonas aeruginosa NCGM2.S1, sequence accession AP012280 [18]
  • Phylum Actinobacteria
  • Candidatus Frankia datiscae, sequence accession NC_015656 [19]
  • Corynebacterium pseudotuberculosis Strain CIP 52.97, sequence accession CP003061 [20]
  • Propionibacterium acnes Type II Strain ATCC 11828, sequence accession CP003084 [21]
  • Streptomyces chartreusis NRRL 12338, sequence accession AGDE00000000 [22]
  • Streptomyces chartreusis NRRL 3882, sequence accession AGDD00000000 [22]
  • Streptomyces lysosuperificus ATCC 31396, accession number AGDC00000000 [22]
  • Streptomyces sp. Strain Wigar10, sequence accession AGDF01000000 [23]
  • Phylum Spirochaetes
  • Borrelia afzelii PKo, sequence accession CP002933 (Chromosome), CP002942 (Ip17), CP002943 (Ip28-2), CP002944 (Ip28-3), CP002945 (Ip28-4), CP002946 (Ip28-7), CP002947 (IP28-8), CP002949 (Ip38), CP002950 (Ip54), CP002934 (cp26), CP002937 (cp32-1), CP002938 (cp32-3), CP002939 (cp32-5), CP002940 (cp32-7), CP002940 (cp32-9), CP002948 (cp32-10), CP002935 (cp32-11), CP002936 (cp32-12) [24]
  • Borrelia afzelii ACA-1, sequence accession ABCU02000001-2 (Chromosome), CP001239 (Ip17), CP001238 (Ip28-1), CP001244 (Ip28-2), CP001241 (Ip28-3), CP001249 (Ip28-4), CP001242 (Ip-7), CP001246 (Ip38), CP001247 (Ip54), CP001250 (cp26), CP001243 (cp32-1), CP001237 (cp32-3), CP001240 (cp32-4), CP001248 (cp32-5), CP001245 (cp32-10) [24]
  • Borrelia garinii PBr, sequence accession ABJV02000001-5 (Chromosome), CP001309 (Ip17), CP001301 (Ip25), CP001310 (Ip28-1), CP001307 (Ip28-3), CP001304 (Ip28-4), CP001311 (Ip28-7), CP001302 (Ip36), CP001308 (Ip54), CP001305 (Ip26), CP001303 (Ip32-5), CP001306 (Ip32-10) [24]
  • Borrelia garinii Far 04, sequence accession ABPZ02000001-33 (Chromosome), CP001315 (Ip17), CP001317 (Ip25), CP001316 (Ip28-1), CP001314 (Ip36), CP001318 (Ip54), CP001319 (Ip26), CP001320 (Ip32-10) [24]
  • Non-Bacterial genomes
  • B1 Human Adenovirus HAdV-16 strain E26, sequence accession JN860680 [25]
  • B1 Human Adenovirus HAdV-3/16, sequence accession JN860678 [25]
  • B1 Human Adenovirus HAdV-3+7, sequence accession JN860679 [25]
  • B1 Human Adenovirus HAdV-7d2, sequence accession JN860677 [25]
  • B1 Human Adenovirus HAdV-7h, sequence accession JN860676 [25]
  • Bacillus cereus bacteriophage BCP78, sequence accession JN797797 [26]
  • Circoviridae member (not yet validated), sequence accession JF803741 [27]
  • Coccolithovirus Emiliania huxleyi Virus 203, sequence accession JF974291 [28]
  • Cryptococcus gattii BC, sequence accession SRP006436 [29]
  • Erwinia amylovora plasmid pEI70, sequence accession CP002951 [30]
  • Mortierella alpina, sequence accession ADAG00000000 [31]
  • Parvovirus Aj-BtPV-1, sequence accession JN860679 [32]
  • Parvovirus Eh-BtPV-1, sequence accession JN860679 [32]
  • Penicillium marneffei PM1, sequence accession AGCC00000000 [33]
  • Pseudomonas fluorescens phage OBP, sequence accession JN627160 [34]
  • Salmonella bacteriophage SPN3US, sequence accession JN641803 [35]
  • Tailam virus, sequence accession JN689227 [36]
References
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2. Oger P, Sokolova TG, Kozhevnikova DA, Chernyh NA, Bartlett DH, Bonch-Osmolovskaya EA, Lebedinsky AV. Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. strain AM4, capable of organotrophic growth and growth at the expense of hydrogenogenic or sulfidogenic oxidation of carbon monoxide. J Bacteriol 2011; 193:7019-7020. [doi:10.1128/JB.06259-11] [pmid:22123768]
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11. Strabala TJ, Macdonald L, Liu V, Smit AM. Draft genome sequence of Novosphingobium nitrogenifigens Y88T. J Bacteriol 2012; 194:201. [doi:10.1128/JB.06381-11] [pmid:22156397]
12. Huo YY, Cheng H, Han XF, Jiang XW, Sun C, Zhang XQ, Zhu XF, Liu YF, Li PF, Ni PX, et al. Complete genome sequence of Pelagibacterium halotolerans B2T. J Bacteriol 2012; 194:197-198. [doi:10.1128/JB.06343-11] [pmid:22156395]
13. Wei Q, Tarighi S, Dötsch A, Häussler S, Müsken M, Wright VJ, Cámara M, Williams P, Haenen S, Boerjan B, et al. Phenotypic and genome-wide analysis of an antibiotic-resistant small colony variant (SCV) of Pseudomonas aeruginosa. PLoS ONE 2011; 6:e29276. [doi:10.1371/journal.pone.0029276] [pmid:22195037]
14. Tao F, Tang H, Gai Z, Su F, Wang X, He X, Xu P. Genome sequence of Pseudomonas putida Idaho, a unique organic solvent-tolerant bacterium. J Bacteriol 2011; 193:7011-7012. [doi:10.1128/JB.06200-11] [pmid:22123764]
15. Gai Z, Wang X, Zhang X, Su F, Wang X, Tang H, Tai C, Tao F, Ma C, Xu P. Genome sequence of Sphingomonas elodea ATCC 31461, a highly productive industrial strain of gellan gum. J Bacteriol 2011; 193:7015-7016. [doi:10.1128/JB.06307-11] [pmid:22123766]
16. D’Auria G, Galán JC, Rodríguez-Alcayna M, Moya A, Baquero F, Latorre A. Complete genome sequence of Acidaminococcus intestini RYC-MR95, a Gram-negative bacterium from the phylum Firmicutes. J Bacteriol 2011; 193:7008-7009. [doi:10.1128/JB.06301-11] [pmid:22123762]
17. Yu B, Su F, Wang L, Zhao B, Qin J, Ma C, Xu P, Ma Y. Genome sequence of Lactobacillus rhamnosus strain CASL, an efficient l-lactic acid producer from cheap substrate cassava. J Bacteriol 2011; 193:7013-7014. [doi:10.1128/JB.06285-11] [pmid:22123765]
18. Miyoshi-Akiyama T, Matsumura K, Kobayashi N, Maeda S, Kirikae T. Genome sequence of clinical isolate Mycobacterium tuberculosis NCGM2209. J Bacteriol 2011; 193:6792. [doi:10.1128/JB.06233-11] [pmid:22072647]
19. Persson T, Benson DR, Normand P, Vanden Heuvel B, Pujic P, Chertkov O, Teshima H, Bruce DC, Detter C, Tapia R, et al. Genome sequence of “Candidatus Frankia datiscae” Dg1, the uncultured microsymbiont from nitrogen-fixing root nodules of the dicot Datisca glomerata. J Bacteriol 2011; 193:7017-7018. [doi:10.1128/JB.06208-11] [pmid:22123767]
20. Cerdeira LT, Schneider MPC, Pinto AC, de Almeida SS, dos Santos AR, Barbosa EGV, Ali A, Aburjaile FF, de Abreu VAC, Guimarães LC, et al. Complete genome sequence of Corynebacterium pseudotuberculosis strain CIP 52.97, isolated from a horse in Kenya. J Bacteriol 2011; 193:7025-7026. [doi:10.1128/JB.06293-11] [pmid:22123771]
21. Horváth B, Hunyadkürti J, Vörös A, Fekete C, Urbán E, Kemény L, Nagy I. Genome Sequence of Propionibacterium acnes Type II Strain ATCC 11828. J Bacteriol 2012; 194:202-203. [doi:10.1128/JB.06388-11] [pmid:22156398]
22. Doroghazi JR, Ju KS, Brown DW, Labeda DP, Deng Z, Metcalf WW, Chen W, Price NPJ. Genome sequences of three tunicamycin-producing Streptomyces strains, S. chartreusis NRRL 12338, S. chartreusis NRRL 3882, and S. lysosuperificus ATCC 31396. J Bacteriol 2011; 193:7021-7022. [doi:10.1128/JB.06262-11] [pmid:22123769]
23. Klassen JL, Adams SM, Bramhacharya S, Giles SS, Goodwin LA, Woyke T, Currie CR. Draft genome sequence of Streptomyces sp. strain Wigar10, isolated from a surface-sterilized garlic bulb. J Bacteriol 2011; 193:6999-7000. [doi:10.1128/JB.06257-11] [pmid:22123757]
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Acknowledgements

We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.

Funding for SIGS is provided by a grant from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707.

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