Genome-based phylogenetic analysis of Streptomyces and its relativesCitation formats

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Genome-based phylogenetic analysis of Streptomyces and its relatives. / Alam, Mohammad Tauqeer; Merlo, Maria Elena; Takano, Eriko; Breitling, Rainer.

In: Molecular phylogenetics and evolution, Vol. 54, No. 3, 03.2010, p. 763-772.

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Alam, MT, Merlo, ME, Takano, E & Breitling, R 2010, 'Genome-based phylogenetic analysis of Streptomyces and its relatives', Molecular phylogenetics and evolution, vol. 54, no. 3, pp. 763-772. https://doi.org/10.1016/j.ympev.2009.11.019

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Alam, Mohammad Tauqeer ; Merlo, Maria Elena ; Takano, Eriko ; Breitling, Rainer. / Genome-based phylogenetic analysis of Streptomyces and its relatives. In: Molecular phylogenetics and evolution. 2010 ; Vol. 54, No. 3. pp. 763-772.

Bibtex

@article{87734cc2481341d5b1deb2c243cc53af,
title = "Genome-based phylogenetic analysis of Streptomyces and its relatives",
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. {\textcopyright} 2009 Elsevier Inc. All rights reserved.",
keywords = "Actinomycetales, Phylogeny, Rank order, rRNA, Streptomyces",
author = "Alam, {Mohammad Tauqeer} and Merlo, {Maria Elena} and Eriko Takano and Rainer Breitling",
year = "2010",
month = mar,
doi = "10.1016/j.ympev.2009.11.019",
language = "English",
volume = "54",
pages = "763--772",
journal = "Molecular phylogenetics and evolution",
issn = "1055-7903",
publisher = "Elsevier BV",
number = "3",

}

RIS

TY - JOUR

T1 - Genome-based phylogenetic analysis of Streptomyces and its relatives

AU - Alam, Mohammad Tauqeer

AU - Merlo, Maria Elena

AU - Takano, Eriko

AU - Breitling, Rainer

PY - 2010/3

Y1 - 2010/3

N2 - 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. © 2009 Elsevier Inc. All rights reserved.

AB - 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. © 2009 Elsevier Inc. All rights reserved.

KW - Actinomycetales

KW - Phylogeny

KW - Rank order

KW - rRNA

KW - Streptomyces

U2 - 10.1016/j.ympev.2009.11.019

DO - 10.1016/j.ympev.2009.11.019

M3 - Article

VL - 54

SP - 763

EP - 772

JO - Molecular phylogenetics and evolution

JF - Molecular phylogenetics and evolution

SN - 1055-7903

IS - 3

ER -