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A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

Author

Listed:
  • Dongying Wu

    (DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    University of California, Davis, Davis, California 95616, 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
    Lawrence Livermore National Laboratory, Livermore, California 94550, 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
    DOE Joint Genome Institute-Los Alamos National Laboratory, Los Alamos, California 87545, 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
    University of California, Davis, Davis, California 95616, USA)

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.

Suggested Citation

  • 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 P, 2009. "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea," Nature, Nature, vol. 462(7276), pages 1056-1060, December.
    • Handle: RePEc:nat:nature:v:462:y:2009:i:7276:d:10.1038_nature08656
    DOI: 10.1038/nature08656
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    Cited by:

    1. Natasha K. Dudek & Jesus G. Galaz-Montoya & Handuo Shi & Megan Mayer & Cristina Danita & Arianna I. Celis & Tobias Viehboeck & Gong-Her Wu & Barry Behr & Silvia Bulgheresi & Kerwyn Casey Huang & Wah C, 2023. "Previously uncharacterized rectangular bacterial structures in the dolphin mouth," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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