Dataset Information

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.

SUBMITTER: Wu D

PROVIDER: S-EPMC3073058 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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Publications

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Wu Dongying D Hugenholtz Philip P Mavromatis Konstantinos K Pukall Rüdiger R Dalin Eileen E Ivanova Natalia N NN Kunin Victor V Goodwin Lynne L Wu Martin M Tindall Brian J BJ Hooper Sean D SD Pati Amrita A Lykidis Athanasios A Spring Stefan S Anderson Iain J IJ D'haeseleer Patrik P Zemla Adam A Singer Mitchell M Lapidus Alla A Nolan Matt M Copeland Alex A Han Cliff C Chen Feng F Cheng Jan-Fang JF Lucas Susan S Kerfeld Cheryl C Lang Elke E Gronow Sabine S Chain Patrick P Bruce David D Rubin Edward M EM Kyrpides Nikos C NC Klenk Hans-Peter HP Eisen Jonathan A JA

Nature 20091201 7276

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 th ...[more]

PMID: 20033048

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Project description:With the astonishing rate that genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as "marker" genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities (e.g., construction of species trees, phylogenetic based assignment of metagenomic sequence reads to taxonomic groups, phylogeny-based assessment of alpha- and beta-diversity of microbial communities from metagenomic data). We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for "all bacteria and archaea", 114 for "all bacteria (greatly expanding on the ∼30 commonly used), and 100 s to 1000 s for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously.

Dataset Information

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Publications

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Similar Datasets

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