A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

Dongying Wu, Philip Hugenholtz, Konstantinos Mavromatis, Rüdiger Pukall, Eileen Dalin, Natalia N. Ivanova, Victor Kunin, Lynne Goodwin, Martin Wu, Brian J. Tindall, Sean D. Hooper, Amrita Pati, Athanasios Lykidis, Stefan Spring, Iain J. Anderson, Patrik D’haeseleer, Adam Zemla, Mitchell Singer, Alla Lapidus, Matt Nolan, Alex Copeland, Cliff Han, Feng Chen, Jan-Fang Cheng, Susan Lucas, Cheryl Kerfeld, Elke Lang, Sabine Gronow, Patrick Chain, David Bruce, Edward M. Rubin, Nikos C. Kyrpides, Hans-Peter Klenk and Jonathan A. Eisen ()
Additional contact information
Dongying Wu: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Philip Hugenholtz: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Konstantinos Mavromatis: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Rüdiger Pukall: DSMZ, German Collection of Microorganisms and Cell Cultures
Eileen Dalin: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Natalia N. Ivanova: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Victor Kunin: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Lynne Goodwin: DOE Joint Genome Institute-Los Alamos National Laboratory, Los Alamos, California 87545, USA
Martin Wu: University of Virginia, Charlottesville, Virginia 22904, USA
Brian J. Tindall: DSMZ, German Collection of Microorganisms and Cell Cultures
Sean D. Hooper: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Amrita Pati: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Athanasios Lykidis: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Stefan Spring: DSMZ, German Collection of Microorganisms and Cell Cultures
Iain J. Anderson: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Patrik D’haeseleer: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Adam Zemla: Lawrence Livermore National Laboratory, Livermore, California 94550, USA
Mitchell Singer: University of California, Davis, Davis, California 95616, USA
Alla Lapidus: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Matt Nolan: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Alex Copeland: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Cliff Han: DOE Joint Genome Institute-Los Alamos National Laboratory, Los Alamos, California 87545, USA
Feng Chen: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Jan-Fang Cheng: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Susan Lucas: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Cheryl Kerfeld: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Elke Lang: DSMZ, German Collection of Microorganisms and Cell Cultures
Sabine Gronow: DSMZ, German Collection of Microorganisms and Cell Cultures
Patrick Chain: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
David Bruce: DOE Joint Genome Institute-Los Alamos National Laboratory, Los Alamos, California 87545, USA
Edward M. Rubin: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Nikos C. Kyrpides: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Hans-Peter Klenk: DSMZ, German Collection of Microorganisms and Cell Cultures
Jonathan A. Eisen: DOE Joint Genome Institute, Walnut Creek, California 94598, USA

Nature, 2009, vol. 462, issue 7276, 1056-1060

Abstract: Choice genomes sequenced The bacterial and archaeal genomes that have been sequenced to date were chosen for sequencing based mainly on their physiology, which is fine but has resulted in a distinct phylogenetic bias. An alternative approach has been taken in the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, which advocates choosing genomes based on the organism's phylogenetic position, with the aim filling in the gaps in sequencing along on bacterial and archaeal branches of the tree of life. The value of this approach has been demonstrated by a pilot study of the genome sequences of 56 culturable species selected to maximize phylogenetic coverage. Analysis of the sequences provides insights into phylogenetics, protein function and genome annotation.

Date: 2009
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DOI: 10.1038/nature08656

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