Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Gregory C Kettler; Adam C Martiny; Katherine Huang; Jeremy Zucker; Maureen L Coleman; Sebastien Rodrigue; Feng Chen; Alla Lapidus; Steven Ferriera; Justin Johnson; Claudia Steglich; George M Church; Paul Richardson; Sallie W Chisholm

doi:10.1371/journal.pgen.0030231

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Research Article

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Gregory C Kettler ,

Contributed equally to this work with: Gregory C Kettler, Adam C Martiny

Affiliations Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America , Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
⨯
Adam C Martiny ,

Contributed equally to this work with: Gregory C Kettler, Adam C Martiny

¤ Current address: Department of Earth System Science and Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America

Affiliation Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
⨯
Katherine Huang,

Affiliation Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Jeremy Zucker,

Affiliation Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
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Maureen L Coleman,

Affiliation Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Sebastien Rodrigue,

Affiliation Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Feng Chen,

Affiliation Joint Genome Institute, United States Department of Energy, Walnut Creek, California, United States of America
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Alla Lapidus,

Affiliation Joint Genome Institute, United States Department of Energy, Walnut Creek, California, United States of America
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Steven Ferriera,

Affiliation J. Craig Venter Institute, Rockville, Maryland, United States of America
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Justin Johnson,

Affiliation J. Craig Venter Institute, Rockville, Maryland, United States of America
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Claudia Steglich,

Affiliation Department of Biology II/Experimental Bioinformatics, University Freiburg, Freiburg, Germany
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George M Church,

Affiliation Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
⨯
Paul Richardson,

Affiliation Joint Genome Institute, United States Department of Energy, Walnut Creek, California, United States of America
⨯
Sallie W Chisholm

*To whom correspondence should be addressed. E-mail: chisholm@mit.edu

Affiliations Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America , Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
⨯

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Gregory C Kettler,
Adam C Martiny,
Katherine Huang,
Jeremy Zucker,
Maureen L Coleman,
Sebastien Rodrigue,
Feng Chen,
Alla Lapidus,
Steven Ferriera,
Justin Johnson

Published: December 21, 2007
https://doi.org/10.1371/journal.pgen.0030231

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Re-annotation of the Prochlorococcus and Synechococcus genomes

Posted by PLOS_Genetics on 18 Mar 2008 at 16:55 GMT

We re-annotated 12 sequenced Prochlorococcus and four finished marine Synechococcus genomes by a uniform method for the purpose of this study.
http://plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030231#article1.body1.sec3.sec2.p1

As described in the methods, the authors re-annotated the Prochlorococcus and Synechococcus genomes so that their comparisons would be based on a consistent annotation pipeline. They assigned new locus tags and added them to the Genbank records for the Prochlorococcus genomes for which they are responsible.

The authors do not refer to any particular Synechococcus loci in the main text. However, in the supporting information tables they use Synechoccocus locus tags that were generated by their own pipeline, rather than those used in Genbank. To avoid confusion and for the benefit of future readers, the authors would now like to indicate which new names correspond to which previous ones for both the Synechococcus loci and the Prochlorococcus genomes that had been previously published:

SynCC9902:
http://www.plosgenetics.org/attachments/SynCC9902_altnames.txt

MIT9313:
http://www.plosgenetics.org/attachments/MIT9313_altnames.txt

SynCC9605:
http://www.plosgenetics.org/attachments/SynCC9605_altnames.txt

SynWH8102:
http://www.plosgenetics.org/attachments/SynWH8102_altnames.txt

MIT9312:
http://www.plosgenetics.org/attachments/MIT9312_altnames.txt

SS120:
http://www.plosgenetics.org/attachments/SS120_altnames.txt

MED4:
http://www.plosgenetics.org/attachments/MED4_altnames.txt

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Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

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Re-annotation of the Prochlorococcus and Synechococcus genomes

Posted by PLOS_Genetics on 18 Mar 2008 at 16:55 GMT