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Genome-based phylogenetic analysis of Streptomyces and its relatives

Alam, M. T., Merlo, M. E., Takano, E. & Breitling, R. Mar-2010 In : Molecular Phylogenetics and Evolution. 54, 3, p. 763-772 10 p.

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  • Mohammad Tauqeer Alam
  • Maria Elena Merlo
  • Eriko Takano
  • Rainer Breitling

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 tropical). 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. Ill 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. (C) 2009 Elsevier Inc. All rights reserved.

Original languageEnglish
Pages763-772
Number of pages10
JournalMolecular Phylogenetics and Evolution
Journal publication dateMar-2010
Volume54
Issue3
DOIs
StatePublished
Peer-reviewedYes
Total WOS citations15

Keywords

  • Phylogeny, Streptomyces, Actinomycetales, Rank order, rRNA, RIBOSOMAL-RNA, GENE CONTENT, PHYLUM ACTINOBACTERIA, COELICOLOR A3(2), SEQUENCE DATA, TREES, EVOLUTION, TAXONOMY, PROPOSAL, BIOLOGY

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