Genome-based phylogenetic analysis of Streptomyces and its relatives

Alam, M.T., Merlo, M.E., Takano, E. and Breitling, R. (2010) Genome-based phylogenetic analysis of Streptomyces and its relatives. Molecular Phylogenetics and Evolution, 54(3), pp. 763-772. (doi:10.1016/j.ympev.2009.11.019)

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Abstract

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

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Breitling, Professor Rainer
Authors: Alam, M.T., Merlo, M.E., Takano, E., and Breitling, R.
Subjects:Q Science > QH Natural history
College/School:College of Medical Veterinary and Life Sciences > Institute of Molecular Cell and Systems Biology
Journal Name:Molecular Phylogenetics and Evolution
ISSN:1055-7903

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