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

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),more » 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.« less

Authors:
 [1];  [1];  [2];  [3];  [4];  [4];  [5];  [6];  [7]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Univ. of California, Davis, CA (United States)
  3. Michigan State Univ., East Lansing, MI (United States). Dept. of Microbiology and Molecular Genetics; NamesforLife, LLC, East Lansing, MI (United States)
  4. American Type Culture Collection, Manassas, VA (United States)
  5. Univ. of Georgia, Athens, GA (United States). Dept. of Microbiology
  6. Univ. of Queensland, Brisbane, QLD (Australia). Australian Centre for Ecogenomics
  7. Leibniz Inst. DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
Publication Date:
Research Org.:
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1407208
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 9; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

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. Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. United States: N. p., 2014. Web. doi:10.4056/sigs.5068949.
Kyrpides, Nikos C., Woyke, Tanja, Eisen, Jonathan A., Garrity, George, Lilburn, Timothy G., Beck, Brian J., Whitman, William B., Hugenholtz, Phil, & Klenk, Hans-Peter. Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. United States. doi:10.4056/sigs.5068949.
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. Sun . "Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project". United States. doi:10.4056/sigs.5068949. https://www.osti.gov/servlets/purl/1407208.
@article{osti_1407208,
title = {Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project},
author = {Kyrpides, Nikos C. and Woyke, Tanja and Eisen, Jonathan A. and Garrity, George and Lilburn, Timothy G. and Beck, Brian J. and Whitman, William B. and Hugenholtz, Phil and Klenk, Hans-Peter},
abstractNote = {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.},
doi = {10.4056/sigs.5068949},
journal = {Standards in Genomic Sciences},
issn = {1944-3277},
number = ,
volume = 9,
place = {United States},
year = {2014},
month = {6}
}

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