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

Kyrpides, Nikos C., Woyke, Tanja, Eisen, Jonathan A., Garrity, George, Lilburn, Timothy G., Beck, Brian J., Whitman, William B., Hugenholtz, Phil and Klenk, Hans-Peter (2013) Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Standards in Genomic Sciences, 9 3: 628-634. doi:10.4056/sigs.5068949

Author Kyrpides, Nikos C.
Woyke, Tanja
Eisen, Jonathan A.
Garrity, George
Lilburn, Timothy G.
Beck, Brian J.
Whitman, William B.
Hugenholtz, Phil
Klenk, Hans-Peter
Title Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
Journal name Standards in Genomic Sciences   Check publisher's open access policy
ISSN 1944-3277
Publication date 2013-01-01
Year available 2014
Sub-type Article (original research)
DOI 10.4056/sigs.5068949
Open Access Status DOI
Volume 9
Issue 3
Start page 628
End page 634
Total pages 7
Place of publication Michigan State University, East lansing, MI United States
Publisher Michigan State University * Genomic Standards Consortium
Language eng
Subject 1311 Genetics
Abstract The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project with the objective of sequencing 250 bacterial and archaeal genomes. The two major goals of that project were (a) to test the hypothesis that there are many benefits to the use the phylogenetic diversity of organisms in the tree of life as a primary criterion for generating their genome sequence and (b) to develop the necessary framework, technology and organization for large-scale sequencing of microbial isolate genomes. While the GEBA pilot project has not yet been entirely completed, both of the original goals have already been successfully accomplished, leading the way for the next phase of the project. Here we propose taking the GEBA project to the next level, by generating high quality draft genomes for 1,000 bacterial and archaeal strains. This represents a combined 16-fold increase in both scale and speed as compared to the GEBA pilot project (250 isolate genomes in 4+ years). We will follow a similar approach for organism selection and sequencing prioritization as was done for the GEBA pilot project (i.e. phylogenetic novelty, availability and growth of cultures of type strains and DNA extraction capability), focusing on type strains as this ensures reproducibility of our results and provides the strongest linkage between genome sequences and other knowledge about each strain. In turn, this project will constitute a pilot phase of a larger effort that will target the genome sequences of all available type strains of the Bacteria and Archaea.
Keyword Nomenclature
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID DE-AC02-05CH11231
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
School of Chemistry and Molecular Biosciences
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