Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

Dongying Wu; Martin Wu; Aaron Halpern; Douglas B. Rusch; Shibu Yooseph; Marvin Frazier; J. Craig Venter; Jonathan A. Eisen

doi:10.1371/journal.pone.0018011

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Open Access

Peer-reviewed

Research Article

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

Dongying Wu,

Affiliation Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California Davis Genome Center, University of California Davis, Davis, California, United States of America
⨯
Martin Wu,

Affiliations Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California Davis Genome Center, University of California Davis, Davis, California, United States of America, University of Virginia, Charlottesville, Virginia, United States of America
⨯
Aaron Halpern,

Affiliations The J. Craig Venter Institute, Rockville, Maryland, United States of America, The J. Craig Venter Institute, La Jolla, California, United States of America
⨯
Douglas B. Rusch,

Affiliations The J. Craig Venter Institute, Rockville, Maryland, United States of America, The J. Craig Venter Institute, La Jolla, California, United States of America
⨯
Shibu Yooseph,

Affiliations The J. Craig Venter Institute, Rockville, Maryland, United States of America, The J. Craig Venter Institute, La Jolla, California, United States of America
⨯
Marvin Frazier,

Affiliations The J. Craig Venter Institute, Rockville, Maryland, United States of America, The J. Craig Venter Institute, La Jolla, California, United States of America
⨯
J. Craig Venter,

Affiliations The J. Craig Venter Institute, Rockville, Maryland, United States of America, The J. Craig Venter Institute, La Jolla, California, United States of America
⨯
Jonathan A. Eisen

* E-mail: jaeisen@ucdavis.edu

Affiliation Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California Davis Genome Center, University of California Davis, Davis, California, United States of America
⨯

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

Dongying Wu,
Martin Wu,
Aaron Halpern,
Douglas B. Rusch,
Shibu Yooseph,
Marvin Frazier,
J. Craig Venter,
Jonathan A. Eisen

Published: March 18, 2011
https://doi.org/10.1371/journal.pone.0018011

Reader Comments (28)

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28 Aug 2011
19:26 GMT
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Blog post discussing the paper at "Cyme and Cystidium": Raiders Of The Lost Domain Posted by jeisen on 28 Aug 2011 at 19:26 GMT
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25 Aug 2011
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Additional Media Coverage of This Article Posted by PLOS_ONE_Group on 25 Aug 2011 at 13:05 GMT
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11 Aug 2011
21:15 GMT
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Nature Podcast discussing "Fourth domain" search Posted by jeisen on 11 Aug 2011 at 21:15 GMT
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11 Aug 2011
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Blog post by Carl Zimmer about new "no fourth domain" paper Posted by jeisen on 11 Aug 2011 at 21:11 GMT
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11 Aug 2011
16:34 GMT
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More information on GOS Posted by jeisen on 11 Aug 2011 at 16:34 GMT
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11 Aug 2011
16:34 GMT
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More information on GOS Posted by jeisen on 11 Aug 2011 at 16:34 GMT
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11 Aug 2011
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More information on GOS Posted by jeisen on 11 Aug 2011 at 16:34 GMT
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21 Apr 2011
11:41 GMT
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Echoing Watson and Crick Posted by conrad_halling on 19 Mar 2011 at 23:52 GMT
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11 Apr 2011
14:53 GMT
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de INFO online (from Brazil) news story Posted by jeisen on 11 Apr 2011 at 14:53 GMT
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04 Apr 2011
23:52 GMT
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DNA matches to novel Rec genes? Posted by KForslund on 04 Apr 2011 at 23:37 GMT
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31 Mar 2011
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PHYSORG article Posted by jeisen on 31 Mar 2011 at 16:57 GMT
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25 Mar 2011
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Slashdot article discussing this paper Posted by jeisen on 25 Mar 2011 at 23:31 GMT
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25 Mar 2011
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Article in The Economist about this paper Posted by jeisen on 25 Mar 2011 at 23:29 GMT
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21 Mar 2011
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Video news story about the paper Posted by jeisen on 21 Mar 2011 at 15:08 GMT
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20 Mar 2011
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early-diverging bacteria? Posted by sbkroken on 20 Mar 2011 at 19:09 GMT
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19 Mar 2011
23:40 GMT
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Great article and great use of science2.0 tools with it. Posted by BoraZivkovic on 19 Mar 2011 at 23:40 GMT
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19 Mar 2011
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PZ Myers Blog Post Posted by jeisen on 19 Mar 2011 at 16:07 GMT
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19 Mar 2011
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Blog post w/ more background information Posted by jeisen on 19 Mar 2011 at 15:54 GMT
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19 Mar 2011
09:25 GMT
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Follow up analysis of RpoB homologs Posted by jeisen on 19 Mar 2011 at 09:25 GMT
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19 Mar 2011
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Carl Zimmer blog post Posted by jeisen on 19 Mar 2011 at 08:45 GMT
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19 Mar 2011
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New Scientist article Posted by jeisen on 19 Mar 2011 at 08:44 GMT
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19 Mar 2011
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Blog post with more detail about this paper Posted by jeisen on 19 Mar 2011 at 08:38 GMT
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19 Mar 2011
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Fascinating! Posted by skoch3 on 19 Mar 2011 at 05:40 GMT

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Phylogenetic analysis
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Ribosomal RNA
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Metagenomics
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