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Genome-based phylogenetic analysis of Streptomyces and its relatives

(2010) Alam, Mohammad Tauqeer; Merlo, Maria Elena; Takano, Eriko; Breitling, Rainer

Motivation: Streptomyces is one of the best-studied genera of the order Actinomycetales due to its great importance in medical science, ecology and the biotechnology industry. A comprehensive, detailed and robust phylogeny of Streptomyces and its relatives is needed for understanding how this group emerged and maintained such a vast diversity throughout evolution and how soil-living mycelial forms (e.g., Streptomyces s. str.) are related to parasitic, unicellular pathogens (e.g., Mycobacterium tuberculosis) or marine species (e.g., Salinispora tropica). The most important application area of such a phylogenetic analysis will be in the comparative re-annotation of genome sequences and the reconstruction of Streptomyces metabolic networks for biotechnology.
Methods: Classical 16S-rRNA-based phylogenetic reconstruction does not guarantee to produce well-resolved robust trees that reflect the overall relationship between bacterial species with widespread horizontal gene transfer. In our study we therefore combine three whole genome-based phylogenies with eight different, highly informative single-gene phylogenies to determine a new robust consensus tree of 45 Actinomycetales species with completely sequenced genomes.
Results: None of the individual methods achieved a resolved phylogeny of Streptomyces and its relatives. Single-gene approaches failed to yield a detailed phylogeny; even though the single trees are in good agreement among each other, they show very low resolution of inner branches. The three whole genome-based methods improve resolution considerably. Only by combining the phylogenies from single gene-based and genome-based approaches we finally obtained a consensus tree with well-resolved branches for the entire set of Actinomycetales species. This phylogenetic information is stable and informative enough for application to the system-wide comparative modeling of bacterial physiology.

Molecular Phylogenetics and Evolution, 54 (3)Check if we have the full text, and get it



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ID 13540
Mother ID 10558
Order Alam, M.T.
Name MolPhylgEvolTauqeerA
Publish yes
OAI name Article
Path root/2010/MolPhylgEvolTauqeerA/
Created on: 2010-02-24 09:06:08
Last modified: 2013-05-22 02:51:16
Digital ID 4b84ec0050e93
Journall Molecular Phylogenetics and Evolution
Volume number 54
Series number 3
Title Genome-based phylogenetic analysis of Streptomyces and its relatives
Title order Genome based phylogenetic analysis Streptomyces relatives
Exchangeable no
Printing on demand no
Number of pages 10
Year issued 2010
Year report 2010
Language en
Type Article / Letter to editor
Description Motivation: Streptomyces is one of the best-studied genera of the order Actinomycetales due to its great importance in medical science, ecology and the biotechnology industry. A comprehensive, detailed and robust phylogeny of Streptomyces and its relatives is needed for understanding how this group emerged and maintained such a vast diversity throughout evolution and how soil-living mycelial forms (e.g., Streptomyces s. str.) are related to parasitic, unicellular pathogens (e.g., Mycobacterium tuberculosis) or marine species (e.g., Salinispora tropica). The most important application area of such a phylogenetic analysis will be in the comparative re-annotation of genome sequences and the reconstruction of Streptomyces metabolic networks for biotechnology.
Methods: Classical 16S-rRNA-based phylogenetic reconstruction does not guarantee to produce well-resolved robust trees that reflect the overall relationship between bacterial species with widespread horizontal gene transfer. In our study we therefore combine three whole genome-based phylogenies with eight different, highly informative single-gene phylogenies to determine a new robust consensus tree of 45 Actinomycetales species with completely sequenced genomes.
Results: None of the individual methods achieved a resolved phylogeny of Streptomyces and its relatives. Single-gene approaches failed to yield a detailed phylogeny; even though the single trees are in good agreement among each other, they show very low resolution of inner branches. The three whole genome-based methods improve resolution considerably. Only by combining the phylogenies from single gene-based and genome-based approaches we finally obtained a consensus tree with well-resolved branches for the entire set of Actinomycetales species. This phylogenetic information is stable and informative enough for application to the system-wide comparative modeling of bacterial physiology.
Publisher University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute
Relation URI http://www.rug.nl/gbb/
Rights University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute
DOI 10.1016/j.ympev.2009.11.019
DOI flag 2
Keywords Phylogeny; Streptomyces; Actinomycetales; Rank order; rRNA
Author(s) Alam, Mohammad Tauqeer; Merlo, Maria Elena; Takano, Eriko; Breitling, Rainer


 
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