Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution.
Identifieur interne : 001F80 ( PubMed/Corpus ); précédent : 001F79; suivant : 001F81Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution.
Auteurs : Se-Ran Jun ; Gregory E. Sims ; Guohong A. Wu ; Sung-Hou KimSource :
- Proceedings of the National Academy of Sciences of the United States of America [ 1091-6490 ] ; 2010.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Proteome.
- classification : Prokaryotic Cells.
- methods : Proteomics, Sequence Alignment, Sequence Analysis, Protein.
- physiology : Prokaryotic Cells.
- Genome, Phylogeny.
Abstract
We present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (FFPs) of whole proteomes. Features are l-mers of amino acids, and each organism is represented by a profile of frequencies of all features. The selection of feature length is critical in the FFP method, and we have developed a procedure for identifying the optimal feature lengths for inferring the phylogeny of prokaryotes, strictly speaking, a proteome phylogeny. Our FFP trees are constructed with whole proteomes of 884 prokaryotes, 16 unicellular eukaryotes, and 2 random sequences. To highlight the branching order of major groups, we present a simplified proteome FFP tree of monophyletic class or phylum with branch support. In our whole-proteome FFP trees (i) Archaea, Bacteria, Eukaryota, and a random sequence outgroup are clearly separated; (ii) Archaea and Bacteria form a sister group when rooted with random sequences; (iii) Planctomycetes, which possesses an intracellular membrane compartment, is placed at the basal position of the Bacteria domain; (iv) almost all groups are monophyletic in prokaryotes at most taxonomic levels, but many differences in the branching order of major groups are observed between our proteome FFP tree and trees built with other methods; and (v) previously "unclassified" genomes may be assigned to the most likely taxa. We describe notable similarities and differences between our FFP trees and those based on other methods in grouping and phylogeny of prokaryotes.
DOI: 10.1073/pnas.0913033107
PubMed: 20018669
Links to Exploration step
pubmed:20018669Le document en format XML
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Wu</name></author><author><name sortKey="Kim, Sung Hou" sort="Kim, Sung Hou" uniqKey="Kim S" first="Sung-Hou" last="Kim">Sung-Hou Kim</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2010">2010</date><idno type="RBID">pubmed:20018669</idno><idno type="pmid">20018669</idno><idno type="doi">10.1073/pnas.0913033107</idno><idno type="wicri:Area/PubMed/Corpus">001F80</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001F80</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution.</title><author><name sortKey="Jun, Se Ran" sort="Jun, Se Ran" uniqKey="Jun S" first="Se-Ran" last="Jun">Se-Ran Jun</name><affiliation><nlm:affiliation>Department of Chemistry, University of California, Berkeley, CA 94720, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sims, Gregory E" sort="Sims, Gregory E" uniqKey="Sims G" first="Gregory E" last="Sims">Gregory E. Sims</name></author><author><name sortKey="Wu, Guohong A" sort="Wu, Guohong A" uniqKey="Wu G" first="Guohong A" last="Wu">Guohong A. Wu</name></author><author><name sortKey="Kim, Sung Hou" sort="Kim, Sung Hou" uniqKey="Kim S" first="Sung-Hou" last="Kim">Sung-Hou Kim</name></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="eISSN">1091-6490</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genome</term><term>Phylogeny</term><term>Prokaryotic Cells (classification)</term><term>Prokaryotic Cells (physiology)</term><term>Proteome (genetics)</term><term>Proteomics (methods)</term><term>Sequence Alignment (methods)</term><term>Sequence Analysis, Protein (methods)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Proteome</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Prokaryotic Cells</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Proteomics</term><term>Sequence Alignment</term><term>Sequence Analysis, Protein</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Prokaryotic Cells</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome</term><term>Phylogeny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (FFPs) of whole proteomes. Features are l-mers of amino acids, and each organism is represented by a profile of frequencies of all features. The selection of feature length is critical in the FFP method, and we have developed a procedure for identifying the optimal feature lengths for inferring the phylogeny of prokaryotes, strictly speaking, a proteome phylogeny. Our FFP trees are constructed with whole proteomes of 884 prokaryotes, 16 unicellular eukaryotes, and 2 random sequences. To highlight the branching order of major groups, we present a simplified proteome FFP tree of monophyletic class or phylum with branch support. In our whole-proteome FFP trees (i) Archaea, Bacteria, Eukaryota, and a random sequence outgroup are clearly separated; (ii) Archaea and Bacteria form a sister group when rooted with random sequences; (iii) Planctomycetes, which possesses an intracellular membrane compartment, is placed at the basal position of the Bacteria domain; (iv) almost all groups are monophyletic in prokaryotes at most taxonomic levels, but many differences in the branching order of major groups are observed between our proteome FFP tree and trees built with other methods; and (v) previously "unclassified" genomes may be assigned to the most likely taxa. We describe notable similarities and differences between our FFP trees and those based on other methods in grouping and phylogeny of prokaryotes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20018669</PMID><DateCompleted><Year>2010</Year><Month>03</Month><Day>09</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1091-6490</ISSN><JournalIssue CitedMedium="Internet"><Volume>107</Volume><Issue>1</Issue><PubDate><Year>2010</Year><Month>Jan</Month><Day>05</Day></PubDate></JournalIssue><Title>Proceedings of the National Academy of Sciences of the United States of America</Title><ISOAbbreviation>Proc. Natl. Acad. Sci. 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To highlight the branching order of major groups, we present a simplified proteome FFP tree of monophyletic class or phylum with branch support. In our whole-proteome FFP trees (i) Archaea, Bacteria, Eukaryota, and a random sequence outgroup are clearly separated; (ii) Archaea and Bacteria form a sister group when rooted with random sequences; (iii) Planctomycetes, which possesses an intracellular membrane compartment, is placed at the basal position of the Bacteria domain; (iv) almost all groups are monophyletic in prokaryotes at most taxonomic levels, but many differences in the branching order of major groups are observed between our proteome FFP tree and trees built with other methods; and (v) previously "unclassified" genomes may be assigned to the most likely taxa. We describe notable similarities and differences between our FFP trees and those based on other methods in grouping and phylogeny of prokaryotes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jun</LastName><ForeName>Se-Ran</ForeName><Initials>SR</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of California, Berkeley, CA 94720, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sims</LastName><ForeName>Gregory E</ForeName><Initials>GE</Initials></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Guohong A</ForeName><Initials>GA</Initials></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Sung-Hou</ForeName><Initials>SH</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>P50 GM062412</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United 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