Skip to main content
Download PDF

Genome sequences published outside of Standards in Genomic Sciences, December 2011

Standards in Genomic Sciences volume 5, pages 416–419 (2011)Cite this article

Abstract

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

  1. Jiang X, Wang S, Cheng H, Huo Y, Zhang X, Zhu X, Han X, Ni P, Wu M. Genome sequence of Halobiforma lacisalsi AJ5, an extremely halophilic archaeon which harbors a bop Gene. J Bacteriol 2011; 193:7023–7024. PubMed http://dx.doi.org/10.1128/JB.06282-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06259-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  3. Valdes J, Ossandon F, Quatrini R, Dopson M, Holmes DS. Draft genome sequence of the extremely acidophilic biomining bacterium Aacidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus. J Bacteriol 2011; 193:7003–7004. PubMed http://dx.doi.org/10.1128/JB.06281-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Chen Y, Cui Y, Pu F, Jiang G, Zhao X, Yuan Y, Zhao W, Li D, Liu H, Li Y, et al. Draft genome sequence of an Acinetobacter genomic species 3 Strain harboring a blaNDM-1 Gene. J Bacteriol 2012; 194:204–205. PubMed http://dx.doi.org/10.1128/JB.06202-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS, Barbe V, et al. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet 2011; 7:e1002430. http://dx.doi.org/10.1371/journal.pgen.1002430

    Article  PubMed Central  PubMed  Google Scholar 

  6. Shepard SM, Danzeisen JL, Isaacson RE, Seemann T, Achtman M, Johnson TJ. Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli. J Bacteriol 2011. PubMed

  7. Lu S, Zhang X, Zhu Y, Kim KS, Yang J, Jin Q. Complete genome sequence of the neonatal-meningitis-associated Escherichia coli Strain CE10. J Bacteriol 2011; 193:7005. PubMed http://dx.doi.org/10.1128/JB.06284-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Ogino H, Azuma Y, Hosoyama A, Nakazawa H, Matsutani M, Hasegawa A, Otsuyama K, Matsushita K, Fujita N, Shirai M. Complete genome sequence of NBRC 3288, a unique cellulose-nonproducing strain of Gluconacetobacter xylinus isolated from vinegar. J Bacteriol 2011; 193:6997–6998. PubMed http://dx.doi.org/10.1128/JB.06158-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Lin Y, Fan H, Hao X, Johnstone L, Hu Y, Wei G, Alwathnani HA, Wang G, Rensing C. Draft genome sequence of Halomonas sp. Strain HAL1, a moderately halophilic arsenite-oxidizing bacterium isolated from gold-mine soil. J Bacteriol 2012; 194:199–200. PubMed http://dx.doi.org/10.1128/JB.06359-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Boden R, Cunliffe M, Scanlan J, Moussard H, Kits KD, Klotz MG, Jetten MSM, Vuilleumier S, Han J, Peters L, et al. Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J Bacteriol 2011; 193:7001–7002. PubMed http://dx.doi.org/10.1128/JB.06267-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Strabala TJ, Macdonald L, Liu V, Smit AM. Draft genome sequence of Novosphingobium nitrogenifigens Y88T. J Bacteriol 2012; 194:201. PubMed http://dx.doi.Org/10.1128/jB.06381-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06343-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Wei Q, Tarighi S, Dötsch A, Häussier 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. PubMed http://dx.doi.org/10.1371/journal.pone.0029276

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06200-11

    Article  PubMed Central  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06307-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06301-11

    Article  PubMed Central  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06285-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06233-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06208-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06293-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06388-11

    Article  PubMed Central  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06262-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  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. PubMed http://dx.doi.org/10.1128/JB.06257-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. Casjens SR, Mongodin EF, Qiu WG, Dunn JJ, Luft BJ, Fraser-Liggett CM, Schutzer SE. Whole-Genome Sequences of two Borrelia afzelii and two Borrelia garinii lyme disease agent isolates. J Bacteriol 2011; 193:6995–6996. PubMed http://dx.doi.org/10.1128/JB.05951-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Dehghan S, Liu EB, Seto J, Torres SF, Hudson NR, Kajon AE, Metzgar D, Dyer DW, Chodosh J, Jones MS, et al. Five genome sequences of subspecies B1 human adenoviruses associated with acute respiratory disease. J Virol 2012; 86:635–636. PubMed http://dx.doi.org/10.1128/JVI.06593-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Lee JH, Shin H, Son B, Ryu S. Complete genome sequence of Bacillus cereus bacteriophage BCP78. J Virol 2012; 86:637–638. PubMed http://dx.doi.org/10.1128/JVI.06520-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Wen L, He K, Yu Z, Mao A, Ni Y, Zhang X, Guo R, Li B, Wang X, Zhou J, et al. Complete Genome sequence of a novel porcine Circovirus-like agent. J Virol 2012; 86:639. PubMed http://dx.doi.org/10.1128/JVI.06469-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ. Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203. J Virol 2011; 85:13468–13469. PubMed http://dx.doi.org/10.1128/JVI.06440-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  29. Gillece JD, Schupp JM, Balajee SA, Harris J, Pearson T, Yan Y, Keim P, DeBess E, Marsden-Haug N, Wohrle R, et al. Whole genome sequence analysis of Cryptococcus gattii from the pacific northwest reveals unexpected diversity. PLoS ONE 2011; 6:e28550. PubMed http://dx.doi.org/10.1371/journal.pone.0028550

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. Llop P, Cabrefiga J, Smits THM, Dreo T, Barbé S, Pulawska J, Bultreys A, Blom J, Duffy B, Montesinos E, et al. Erwinia amylovora novel plasmid pEI70: Complete sequence, biogeography, and role in aggressiveness in the fire blight phytopathogen. PLoS ONE 2011; 6:e28651. PubMed http://dx.doi.org/10.1371/journal.pone.0028651

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  31. Wang L, Chen W, Feng Y, Ren Y, Gu Z, Chen H, Wang H, Thomas MJ, Zhang B, Berquin IM, et al. Genome characterization of the oleaginous fungus Mortierella alpina. PLoS ONE 2011; 6:e28319. PubMed http://dx.doi.org/10.1371/journal.pone.0028319

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  32. Canuti M, Eis-Huebinger AM, Deijs M, de Vries M, Drexler JF, Oppong SK, Müller MA, Klose SM, Wellinghausen N, Cottontail VM, et al. Two novel parvoviruses in frugivorous new and old world bats. PLoS ONE 2011; 6:e29140. http://dx.doi.org/10.1371/journal.pone.0029140

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  33. Woo PCY, Lau SKP, Liu B, Cai JJ, Chong KTK, Tse H, Kao RYT, Chan CM, Chow WN, Yuen KY. Draft genome sequence of Penicillium marneffei strain PM1. Eukaryot Cell 2011; 10:1740–1741. PubMed http://dx.doi.org/10.1128/EC.05255-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  34. Cornelissen A, Hardies SC, Shaburova OV, Krylov VN, Mattheus W, Kropinski AM, Lavigne R. Complete genome sequence of the giant virus OBP and comparitive genome analysis of the diverse φpKZ-related phages. J Virol 2011. PubMed http://dx.doi.org/10.1128/JVI.06330-11

  35. Lee JH, Shin H, Kim H, Ryu S. Complete genome sequence of Salmonella bacteriophage SPN3US. J Virol 2011; 85:13470–13471. PubMed http://dx.doi.org/10.1128/JVI.06344-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  36. Woo PCY, Lau SKP, Wong BHL, Wong AYP, Poon RWS, Yuen KY. Complete genome sequence of a novel Paramyxovirus, Tailam virus, discovered in Sikkim rats. J Virol 2011; 85:13473–13474. PubMed http://dx.doi.org/10.1128/JVI.06356-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

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

    Oranmiyan W. Nelson & George M. Garrity

Authors
  1. Oranmiyan W. Nelson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. George M. Garrity
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Reprints and permissions

About this article

Cite this article

Nelson, O.W., Garrity, G.M. Genome sequences published outside of Standards in Genomic Sciences, December 2011. Stand in Genomic Sci 5, 416–419 (2011). https://doi.org/10.4056/sigs.2495686

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.4056/sigs.2495686

Environmental Microbiome

ISSN: 2524-6372