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Antonie van Leeuwenhoek

, Volume 110, Issue 4, pp 563–583 | Cite as

Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis

  • David P. LabedaEmail author
  • Christopher A. Dunlap
  • Xiaoying Rong
  • Ying Huang
  • James R. Doroghazi
  • Kou-San Ju
  • William W. Metcalf
Original Paper

Abstract

The family Streptomycetaceae, notably species in the genus Streptomyces, have long been the subject of investigation due to their well-known ability to produce secondary metabolites. The emergence of drug resistant pathogens and the relative ease of producing genome sequences has renewed the importance of Streptomyces as producers of new natural products and resulted in revived efforts in isolating and describing strains from novel environments. A previous large study of the phylogeny in the Streptomycetaceae based on 16S rRNA gene sequences provided a useful framework for the relationships among species, but did not always have sufficient resolution to provide definitive identification. Multi-locus sequence analysis of 5 house-keeping genes has been shown to provide improved taxonomic resolution of Streptomyces species in a number of previous reports so a comprehensive study was undertaken to evaluate evolutionary relationships among species within the family Streptomycetaceae where type strains are available in the ARS Culture Collection or genome sequences are available in GenBank. The results of the analysis supported the distinctiveness of Kitasatospora and Streptacidiphilus as validly named genera since they cluster outside of the phylogenetic radiation of the genus Streptomyces. There is also support for the transfer of a number of Streptomyces species to the genus Kitasatospora as well for reducing at least 31 species clusters to a single taxon. The multi-locus sequence database resulting from the study is a useful tool for identification of new isolates and the phylogenetic analysis presented also provides a road map for planning future genome sequencing efforts in the Streptomycetaceae.

Keywords

MLSA Streptomyces Kitasatospora Streptacidiphilus Systematics 

Abbreviation

DDH

DNA–DNA hybridization

Notes

Acknowledgements

The able technical assistance of E. Basehoar in determining the house keeping gene sequences and A. McGovern and H. Walker in determining draft genome sequences is gratefully acknowledged. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer. DPL and the ARS Culture Collection CRIS project was supported by ARS National Program 301. CAD was supported by ARS National Program 206. XR and YH were supported partially by the Specialized Research Fund for State Key Laboratories of China. WWM was supported by the National Institutes of Health (GM PO1 GM077596). JRD was funded by an Institute for Genomic Biology Postdoctoral Fellowship. KSJ was funded by an NIH NRSA Postdoctoral Fellowship (GM100658).

Supplementary material

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Copyright information

© Springer International Publishing Switzerland (outside the USA) 2016

Authors and Affiliations

  • David P. Labeda
    • 1
    Email author
  • Christopher A. Dunlap
    • 2
  • Xiaoying Rong
    • 3
  • Ying Huang
    • 3
  • James R. Doroghazi
    • 4
  • Kou-San Ju
    • 4
  • William W. Metcalf
    • 4
  1. 1.Mycotoxin Prevention and Applied Microbiology Research UnitNational Center for Agricultural Utilization ResearchPeoriaUSA
  2. 2.Crop Bioprotection Research UnitUSDA, Agricultural Research Service, National Center for Agricultural Utilization ResearchPeoriaUSA
  3. 3.State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingPeople’s Republic of China
  4. 4.Department of Microbiology and Institute for Genomic BiologyUniversity of Illinois at Champaign-UrbanaUrbanaUSA

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