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 Dhaeseleer, Adam Zemla, Mitchell Singer, Alla Lapidus, Matt NolanAlex 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, Jonathan A Eisen

Research output: Contribution to journalArticle

716 Scopus citations

Abstract

Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic phylogenomic efforts to compile a phylogeny-driven Genomic Encyclopedia of Bacteria and Archaea in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.

Original languageEnglish (US)
Pages (from-to)1056-1060
Number of pages5
JournalNature
Volume462
Issue number7276
DOIs
StatePublished - Dec 24 2009

ASJC Scopus subject areas

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    Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N. N., Kunin, V., Goodwin, L., Wu, M., Tindall, B. J., Hooper, S. D., Pati, A., Lykidis, A., Spring, S., Anderson, I. J., Dhaeseleer, P., Zemla, A., Singer, M., Lapidus, A., ... Eisen, J. A. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. https://doi.org/10.1038/nature08656