title: A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.
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.
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Dongying
authors.initials: D
authors.lastname: Wu
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.forename: Rüdiger
authors.initials: R
authors.lastname: Pukall
authors.forename: Eileen
authors.initials: E
authors.lastname: Dalin
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.forename: Victor
authors.initials: V
authors.lastname: Kunin
authors.forename: Lynne
authors.initials: L
authors.lastname: Goodwin
authors.forename: Martin
authors.initials: M
authors.lastname: Wu
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Tindall
authors.forename: Sean D
authors.initials: SD
authors.lastname: Hooper
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.forename: Athanasios
authors.initials: A
authors.lastname: Lykidis
authors.forename: Stefan
authors.initials: S
authors.lastname: Spring
authors.forename: Iain J
authors.initials: IJ
authors.lastname: Anderson
authors.forename: Patrik
authors.initials: P
authors.lastname: D'haeseleer
authors.forename: Adam
authors.initials: A
authors.lastname: Zemla
authors.forename: Mitchell
authors.initials: M
authors.lastname: Singer
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Matt
authors.initials: M
authors.lastname: Nolan
authors.forename: Alex
authors.initials: A
authors.lastname: Copeland
authors.forename: Cliff
authors.initials: C
authors.lastname: Han
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
authors.forename: Jan-Fang
authors.initials: JF
authors.lastname: Cheng
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.forename: Cheryl
authors.initials: C
authors.lastname: Kerfeld
authors.forename: Elke
authors.initials: E
authors.lastname: Lang
authors.forename: Sabine
authors.initials: S
authors.lastname: Gronow
authors.forename: Patrick
authors.initials: P
authors.lastname: Chain
authors.forename: David
authors.initials: D
authors.lastname: Bruce
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Eisen
mesh_terms: D000199:Actins / Q000737:chemistry; D000595:Amino Acid Sequence; D001105:Archaea / Q000145:classification* / Q000235:genetics*; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D001426:Bacterial Proteins / Q000737:chemistry; D044822:Biodiversity; D030541:Databases, Genetic; D020459:Genes, rRNA / Q000235:genetics; D020745:Genome, Archaeal / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
chemical_list: D000199:Actins; D001426:Bacterial Proteins