@ARTICLE{TreeBASE2Ref19285, author = {Dongying Wu and Philip Hugenholtz and Konstantinos Mavromatis and R?diger Pukall and Eileen Dalin and Natalia N Ivanova and Victor Kunin and Lynne Goodwin and Martin Wu and Brian J Tindall and Sean D Hooper and Amrita Pati and Athanasios Lykidis and Stefan Spring and Iain J Anderson and Patrik D?haeseleer and Adam Zemla and Mitchell Singer and Alla Lapidus and Matt Nolan and Alex Copeland and Feng Chen and Jan-Fang Cheng and Susan Lucas and Cheryl Kerfeld and Elke Lang and Sabine Gronow and Patrick Chain and David Bruce and Edward M Rubin and Nikos C Kyrpides and Hans-Peter Klenk and Jonathan A Eisen}, title = {A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.}, year = {2009}, keywords = {}, doi = {10.1038/nature08656}, url = {http://}, pmid = {}, journal = {Nature}, volume = {462}, number = {7276}, pages = {1056--1060}, 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.} }

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