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Citation for Study 10965

Citation title: "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.".

Study name: "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.".

This study is part of submission 10955 (Status: Published).

Citation

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., D?haeseleer P., Zemla A., Singer M., Lapidus A., Nolan M., Copeland A., Chen F., Cheng J., Lucas S., Kerfeld C., Lang E., Gronow S., Chain P., Bruce D., Rubin E.M., Kyrpides N.C., Klenk H., & Eisen J.A. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276): 1056-1060.

Authors

• Wu D.
• Hugenholtz P.
• Mavromatis K.
• Pukall R.
• Dalin E.
• Ivanova N.N.
• Kunin V.
• Goodwin L.
• Wu M. (submitter)
• Tindall B.J.
• Hooper S.D.
• Pati A.
• Lykidis A.
• Spring S.
• Anderson I.J.
• D?haeseleer P.
• Zemla A.
• Singer M.
• Lapidus A.
• Nolan M.
• Copeland A.
• Chen F.
• Cheng J.
• Lucas S.
• Kerfeld C.
• Lang E.
• Gronow S.
• Chain P.
• Bruce D.
• Rubin E.M.
• Kyrpides N.C.
• Klenk H.
• Eisen J.A.

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.

External links

• DOI: 10.1038/nature08656

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10965
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@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.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 19285
  AU  - Wu,Dongying 
  AU  - Hugenholtz,Philip 
  AU  - Mavromatis,Konstantinos 
  AU  - Pukall,R?diger 
  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  - D?haeseleer,Patrik 
  AU  - Zemla,Adam 
  AU  - Singer,Mitchell 
  AU  - Lapidus,Alla 
  AU  - Nolan,Matt 
  AU  - Copeland,Alex 
  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
  T1  - A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.
  PY  - 2009
  KW  - 
  UR  - http://dx.doi.org/10.1038/nature08656
  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.
  L3  - 10.1038/nature08656
  JF  - Nature
  VL  - 462
  IS  - 7276
  SP  - 1056
  EP  - 1060
  ER  -