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A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. / Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos; Pukall, Rüdiger; Dalin, Eileen; Ivanova, Natalia N.; Kunin, Victor; Goodwin, Lynne; Wu, Martin; Tindall, Brian J.; Hooper, Sean D.; Pati, Amrita; Lykidis, Athanasios; Spring, Stefan; Anderson, Iain J.; Dhaeseleer, Patrik; Zemla, Adam; Singer, Mitchell; Lapidus, Alla; Nolan, Matt; Copeland, Alex; Han, Cliff; Chen, Feng; Cheng, Jan Fang; Lucas, Susan; Kerfeld, Cheryl; Lang, Elke; Gronow, Sabine; Chain, Patrick; Bruce, David; Rubin, Edward M.; Kyrpides, Nikos C.; Klenk, Hans Peter; Eisen, Jonathan A.

In: Nature, Vol. 462, No. 7276, 24.12.2009, p. 1056-1060.

Research output: Contribution to journal › Article › peer-review

Harvard

Wu, D, Hugenholtz, P, Mavromatis, K, Pukall, R, Dalin, E, Ivanova, NN, Kunin, V, Goodwin, L, Wu, M, Tindall, BJ, Hooper, SD, Pati, A, Lykidis, A, Spring, S, Anderson, IJ, Dhaeseleer, P, Zemla, A, Singer, M, Lapidus, A, Nolan, M, Copeland, A, Han, C, Chen, F, Cheng, JF, Lucas, S, Kerfeld, C, Lang, E, Gronow, S, Chain, P, Bruce, D, Rubin, EM, Kyrpides, NC, Klenk, HP & Eisen, JA 2009, 'A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea', Nature, vol. 462, no. 7276, pp. 1056-1060. https://doi.org/10.1038/nature08656

APA

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

Vancouver

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009 Dec 24;462(7276):1056-1060. https://doi.org/10.1038/nature08656

Author

Wu, Dongying ; Hugenholtz, Philip ; Mavromatis, Konstantinos ; Pukall, Rüdiger ; Dalin, Eileen ; Ivanova, Natalia N. ; Kunin, Victor ; Goodwin, Lynne ; Wu, Martin ; Tindall, Brian J. ; Hooper, Sean D. ; Pati, Amrita ; Lykidis, Athanasios ; Spring, Stefan ; Anderson, Iain J. ; Dhaeseleer, Patrik ; Zemla, Adam ; Singer, Mitchell ; Lapidus, Alla ; Nolan, Matt ; Copeland, Alex ; Han, Cliff ; Chen, Feng ; Cheng, Jan Fang ; Lucas, Susan ; Kerfeld, Cheryl ; Lang, Elke ; Gronow, Sabine ; Chain, Patrick ; Bruce, David ; Rubin, Edward M. ; Kyrpides, Nikos C. ; Klenk, Hans Peter ; Eisen, Jonathan A. / A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. In: Nature. 2009 ; Vol. 462, No. 7276. pp. 1056-1060.

BibTeX

@article{fdf2a1a9e89c492e97b8c646faf7b8a4,
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.",
author = "Dongying Wu and Philip Hugenholtz and Konstantinos Mavromatis and R{\"u}diger Pukall and Eileen Dalin and Ivanova, {Natalia N.} and Victor Kunin and Lynne Goodwin and Martin Wu and Tindall, {Brian J.} and Hooper, {Sean D.} and Amrita Pati and Athanasios Lykidis and Stefan Spring and Anderson, {Iain J.} and Patrik Dhaeseleer and Adam Zemla and Mitchell Singer and Alla Lapidus and Matt Nolan and Alex Copeland and Cliff Han and Feng Chen and Cheng, {Jan Fang} and Susan Lucas and Cheryl Kerfeld and Elke Lang and Sabine Gronow and Patrick Chain and David Bruce and Rubin, {Edward M.} and Kyrpides, {Nikos C.} and Klenk, {Hans Peter} and Eisen, {Jonathan A.}",
note = "Funding Information: Acknowledgements . We thank the following people for assistance in aspects of the project including planning and discussions (R. Stevens, G. Olsen, R. Edwards, J. Bristow, N. Ward, S. Baker, T. Lowe, J. Tiedje, G. Garrity, A. Darling, S. Giovannoni), analysis of genomes whose work could not be included in this report (B. Henrissat, G. Xie, J. Kinney, I. Paulsen, N. Rawlings, M. Huntemann), project management (M. Miller, M. Fenner, M. McGowen, A. Greiner), sequencing and finishing (K. Ikeda, M. Chovatia, P. Richardson, T. Glavinadelrio, C. Detter), culture growth, DNA extraction, and metadata (D. Gleim, E. Brambilla, S. Schneider, M. Schr{\"o}der, M. Jando, G. Gehrich-Schr{\"o}ter, C. Wahrenburg, K. Steenblock, S. Welnitz, M. Kopitz, R. F{\"a}hnrich, H. Pomrenke, A. Sch{\"u}tze, M. Rohde, M. G{\"o}ker), and manuscript editing (M. Youle). This work was performed under the auspices of the US Department of Energy{\textquoteright}s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract no. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contract no. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract no. DE-AC02-06NA25396. Support for J.A.E., D.W. and M.W. was provided by the Gordon and Betty Moore Foundation Grant no. 1660 to J.A.E. Support for work at DSMZ was provided under DFG INST 599/1-1.",
year = "2009",
month = dec,
day = "24",
doi = "10.1038/nature08656",
language = "English",
volume = "462",
pages = "1056--1060",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7276",

}

RIS

TY - JOUR

T1 - A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

AU - Wu, Dongying

AU - Hugenholtz, Philip

AU - Mavromatis, Konstantinos

AU - Pukall, Rüdiger

AU - Dalin, Eileen

AU - Ivanova, Natalia N.

AU - Kunin, Victor

AU - Goodwin, Lynne

AU - Wu, Martin

AU - Tindall, Brian J.

AU - Hooper, Sean D.

AU - Pati, Amrita

AU - Lykidis, Athanasios

AU - Spring, Stefan

AU - Anderson, Iain J.

AU - Dhaeseleer, Patrik

AU - Zemla, Adam

AU - Singer, Mitchell

AU - Lapidus, Alla

AU - Nolan, Matt

AU - Copeland, Alex

AU - Han, Cliff

AU - Chen, Feng

AU - Cheng, Jan Fang

AU - Lucas, Susan

AU - Kerfeld, Cheryl

AU - Lang, Elke

AU - Gronow, Sabine

AU - Chain, Patrick

AU - Bruce, David

AU - Rubin, Edward M.

AU - Kyrpides, Nikos C.

AU - Klenk, Hans Peter

AU - Eisen, Jonathan A.

N1 - Funding Information: Acknowledgements . We thank the following people for assistance in aspects of the project including planning and discussions (R. Stevens, G. Olsen, R. Edwards, J. Bristow, N. Ward, S. Baker, T. Lowe, J. Tiedje, G. Garrity, A. Darling, S. Giovannoni), analysis of genomes whose work could not be included in this report (B. Henrissat, G. Xie, J. Kinney, I. Paulsen, N. Rawlings, M. Huntemann), project management (M. Miller, M. Fenner, M. McGowen, A. Greiner), sequencing and finishing (K. Ikeda, M. Chovatia, P. Richardson, T. Glavinadelrio, C. Detter), culture growth, DNA extraction, and metadata (D. Gleim, E. Brambilla, S. Schneider, M. Schröder, M. Jando, G. Gehrich-Schröter, C. Wahrenburg, K. Steenblock, S. Welnitz, M. Kopitz, R. Fähnrich, H. Pomrenke, A. Schütze, M. Rohde, M. Göker), and manuscript editing (M. Youle). This work was performed under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract no. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contract no. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract no. DE-AC02-06NA25396. Support for J.A.E., D.W. and M.W. was provided by the Gordon and Betty Moore Foundation Grant no. 1660 to J.A.E. Support for work at DSMZ was provided under DFG INST 599/1-1.

PY - 2009/12/24

Y1 - 2009/12/24

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=72949101201&partnerID=8YFLogxK

U2 - 10.1038/nature08656

DO - 10.1038/nature08656

M3 - Article

C2 - 20033048

AN - SCOPUS:72949101201

VL - 462

SP - 1056

EP - 1060

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7276

ER -

ID: 99520255