Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

Standards in Genomic Sciences

Volumn 9, Issue 3, 2013, Pages 1278-1284

  Kyrpides, Nikos C ^a   Woyke, Tanja ^a   Eisen, Jonathan A ^b   Garrity, George ^c,d   Lilburn, Timothy G ^e   Beck, Brian J ^e   Whitman, William B ^f   Hugenholtz, Phil ^g   Klenk, Hans Peter ^h  

^a DOE JOINT GENOME INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Michigan State University ^*  (United States)

^d NamesforLife   (United States)

^e AMERICAN TYPE CULTURE COLLECTION   (United States)

^f UNIVERSITY OF GEORGIA   (United States)

^g UNIVERSITY OF QUEENSLAND   (Australia)

^h LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARCHAEAL GENOME; ARTICLE; BACTERIAL GENOME; BOOK; COMMUNITY; CYANOBACTERIUM; GENE SEQUENCE; GENOMICS; MICROBIAL GENOME; MICROBIAL GROWTH; NONHUMAN; PHYLOGENY; PUBLICATION; RNA ISOLATION; SEQUENCE DATABASE;

EID: 84893384297     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.5068949     Document Type: Article

References (20)

1. Lapage SP, Sneath PHA, Lessel EF, Skerman VDB, Seeliger HPR, Clark WA, eds. (International Code of Nomenclature (1990 Revision). Bacteriological Code. American Society for Microbiology, Washington, D. C.,1992
2. Trüper HG, Euzéby JP. International Code of Nomenclature of Prokaryotes. Appendix 9: Orthography. Int J Syst Evol Microbiol 2009; 59:2107-2113. [doi:10.1099/ijs.0.016741-0] [pmid:19567558]
3. Tindall BJ, Kämpfer P, Euzéby JP, Oren A. Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice. Int J Syst Evol Microbiol 2006; 56:2715-2720. [doi:10.1099/ijs.0.64780-0] [pmid:17082418]
4. Tindall BJ, Garrity GM. Proposals to clarify how type strains are deposited and made available to the scientific community for the purpose of systematic. Int J Syst Evol Microbiol 2008; 58:1987-1990. [doi:10.1099/ijs.0.2008/006155-0] [pmid:18676495]
5. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopedia of Bacteria and Archaea. Nature 2009; 462:1056-1060. [doi:10.1038/nature08656] [pmid:20033048]
6. Liolios K, Chen IM, Mavromatis K, Tavernarakis H, Hugenholtz P, Markovitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346. [doi:10.1093/nar/gkp848] [pmid:19914934]
7. Kyrpides NC. Fifteen Years of Microbial Genomics: Meeting the Challenges and Fulfilling the Dream. Nat Biotechnol 2009; 27:627. [doi:10.1038/nbt.1552] [pmid:19587669]
8. P Hugenholtz. Exploring prokaryotic diversity in the genomic era. Genome Biology 2002; 3:reviews0003.1-0003.8.
9. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. Stand Genomic Sci 2009; 1:63-67. [doi:10.4056/sigs.632] [pmid:21304638]
10. Göker M, Klenk HP. Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects. Stand Genomic Sci 2013; 8:360-374. [doi:10.4056/sigs.3446951] [pmid:23991265]
11. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. Nat Methods 2010; 7:455-457. [doi:10.1038/nmeth.1457] [pmid:20436475]
12. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278. [doi:10.1093/bioinformatics/btp393] [pmid:19561336]
13. Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Anquiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalshuk G, et al. Toward a standards-compliant genomic and metagenomic publication record. OMICS 2008; 12:157-160. [doi:10.1089/omi.2008.A2B2] [pmid:18564916]
14. Garrity GM. The state of standards in genomic sciences. Stand Genomic Sci 2011; 5:262-268. [doi:10.4056/sigs.2515706] [pmid:22675577]
15. Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, et al. A Catalog of Reference Genomes from the Human Microbiome. Science 2010; 328:994-999. [doi:10.1126/science.1183605] [pmid:20489017]
16. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol 2011; 29:415-420. [doi:10.1038/nbt.1823] [pmid:21552244]
17. Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mzrachi I, et al. The GenomicStandards Consortium. PLoS Biol 2011; 9:e1001088. [doi:10.1371/journal.pbio.1001088] [pmid:21713030]
18. Anderson I, Scheuner C, Göker M, Mavromatis K, Hooper SD, Porat I, Klenk HP, Ivanova N, Kyrpides NC. Novel Insights into the Diversity of Catabolic Metabolism from Ten Haloarchaeal Genomes. PLoS ONE 2011; 6:e20237. [doi:10.1371/journal.pone.0020237] [pmid:21633497]
19. Zhang T, Datta S, Eichler J, Ivanova N, Axen SD, Kerfeld CA, Chen F, Kyrpides NC, Hugenholtz P, Cheng JF, et al. Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance. Green Chem (In press).
20. Anderson I, Abt B, Lykidis A, Klenk HP, Kyrpides NC, Ivanova N. Genomics of aerobic cellulose utilization systems in actinobacteria. PLoS ONE 2012; 7:e39331. [doi:10.1371/journal.pone.0039331] [pmid:22723998]