Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution.
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| Title: | Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution. |
|---|---|
| Authors: | Se-Ran Jun1, Sims, Gregory E.1, Wu, Guohong A.1, Sung-Hou Kim1,2 SHKim@cchem.berkeley.edu |
| Source: | Proceedings of the National Academy of Sciences of the United States of America. 1/5/2010, Vol. 107 Issue 1, p133-138. 6p. |
| Subjects: | Phylogeny, Prokaryotes, Eukaryotic cells, Intracellular pathogens, Amino acids |
| Abstract: | We present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (FFPs) of whole proteomes. Features are /-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. [ABSTRACT FROM AUTHOR] |
| Copyright of Proceedings of the National Academy of Sciences of the United States of America is the property of National Academy of Sciences and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Se-Ran+Jun%22">Se-Ran Jun</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Sims%2C+Gregory+E%2E%22">Sims, Gregory E.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Wu%2C+Guohong+A%2E%22">Wu, Guohong A.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Sung-Hou+Kim%22">Sung-Hou Kim</searchLink><relatesTo>1,2</relatesTo><i> SHKim@cchem.berkeley.edu</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Proceedings+of+the+National+Academy+of+Sciences+of+the+United+States+of+America%22">Proceedings of the National Academy of Sciences of the United States of America</searchLink>. 1/5/2010, Vol. 107 Issue 1, p133-138. 6p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Phylogeny%22">Phylogeny</searchLink><br /><searchLink fieldCode="DE" term="%22Prokaryotes%22">Prokaryotes</searchLink><br /><searchLink fieldCode="DE" term="%22Eukaryotic+cells%22">Eukaryotic cells</searchLink><br /><searchLink fieldCode="DE" term="%22Intracellular+pathogens%22">Intracellular pathogens</searchLink><br /><searchLink fieldCode="DE" term="%22Amino+acids%22">Amino acids</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: We present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (FFPs) of whole proteomes. Features are /-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. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Proceedings of the National Academy of Sciences of the United States of America is the property of National Academy of Sciences and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1073/pnas.0913033107 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 6 StartPage: 133 Subjects: – SubjectFull: Phylogeny Type: general – SubjectFull: Prokaryotes Type: general – SubjectFull: Eukaryotic cells Type: general – SubjectFull: Intracellular pathogens Type: general – SubjectFull: Amino acids Type: general Titles: – TitleFull: Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Se-Ran Jun – PersonEntity: Name: NameFull: Sims, Gregory E. – PersonEntity: Name: NameFull: Wu, Guohong A. – PersonEntity: Name: NameFull: Sung-Hou Kim IsPartOfRelationships: – BibEntity: Dates: – D: 05 M: 01 Text: 1/5/2010 Type: published Y: 2010 Identifiers: – Type: issn-print Value: 00278424 Numbering: – Type: volume Value: 107 – Type: issue Value: 1 Titles: – TitleFull: Proceedings of the National Academy of Sciences of the United States of America Type: main |
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