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Title: Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Here in this paper, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while they are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7] ;  [7] ;  [8] ;  [9] ;  [10] ;  [2]
  1. Univ. of Georgia, Athens, GA (United States). Dept. of Microbiology
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Newcastle Univ., Newcastle upon Tyne (United Kingdom). School of Biology
  4. Chinese Academy of Sciences (CAS), Beijing (China). China General Microbiological Culture Collection Center (CGMCC), Inst. of Microbiology
  5. American Type Culture Collection, Manassas, VA (United States); Novozymes North America Inc., Durham, NC (United States)
  6. American Type Culture Collection, Manassas, VA (United States); Microbiologics, St. Cloud, MN (United States)
  7. Ghent Univ., Ghent (Belgium). BCCM/LMG Bacteria Collection and Lab. of Microbiology
  8. Univ. of California, Davis, CA (United States)
  9. Michigan State Univ., East Lansing, MI (United States). Dept. of Microbiology and Molecular Genetics
  10. Univ. of Queensland, Brisbane (Australia). Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Genome sequencing; Type stains; Prokaryotes
OSTI Identifier:
1407293

Whitman, William B., Woyke, Tanja, Klenk, Hans-Peter, Zhou, Yuguang, Lilburn, Timothy G., Beck, Brian J., De Vos, Paul, Vandamme, Peter, Eisen, Jonathan A., Garrity, George, Hugenholtz, Philip, and Kyrpides, Nikos C.. Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. United States: N. p., Web. doi:10.1186/s40793-015-0017-x.
Whitman, William B., Woyke, Tanja, Klenk, Hans-Peter, Zhou, Yuguang, Lilburn, Timothy G., Beck, Brian J., De Vos, Paul, Vandamme, Peter, Eisen, Jonathan A., Garrity, George, Hugenholtz, Philip, & Kyrpides, Nikos C.. Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. United States. doi:10.1186/s40793-015-0017-x.
Whitman, William B., Woyke, Tanja, Klenk, Hans-Peter, Zhou, Yuguang, Lilburn, Timothy G., Beck, Brian J., De Vos, Paul, Vandamme, Peter, Eisen, Jonathan A., Garrity, George, Hugenholtz, Philip, and Kyrpides, Nikos C.. 2015. "Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains". United States. doi:10.1186/s40793-015-0017-x. https://www.osti.gov/servlets/purl/1407293.
@article{osti_1407293,
title = {Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains},
author = {Whitman, William B. and Woyke, Tanja and Klenk, Hans-Peter and Zhou, Yuguang and Lilburn, Timothy G. and Beck, Brian J. and De Vos, Paul and Vandamme, Peter and Eisen, Jonathan A. and Garrity, George and Hugenholtz, Philip and Kyrpides, Nikos C.},
abstractNote = {The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Here in this paper, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while they are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity},
doi = {10.1186/s40793-015-0017-x},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {2015},
month = {5}
}