Genome Content and Phylogenomics Reveal both Ancestral and Lateral Evolutionary Pathways in Plant-Pathogenic Streptomyces Species

Appl Environ Microbiol. 2016 Jan 29;82(7):2146-2155. doi: 10.1128/AEM.03504-15.


Streptomyces spp. are highly differentiated actinomycetes with large, linear chromosomes that encode an arsenal of biologically active molecules and catabolic enzymes. Members of this genus are well equipped for life in nutrient-limited environments and are common soil saprophytes. Out of the hundreds of species in the genus Streptomyces, a small group has evolved the ability to infect plants. The recent availability of Streptomyces genome sequences, including four genomes of pathogenic species, provided an opportunity to characterize the gene content specific to these pathogens and to study phylogenetic relationships among them. Genome sequencing, comparative genomics, and phylogenetic analysis enabled us to discriminate pathogenic from saprophytic Streptomyces strains; moreover, we calculated that the pathogen-specific genome contains 4,662 orthologs. Phylogenetic reconstruction suggested that Streptomyces scabies and S. ipomoeae share an ancestor but that their biosynthetic clusters encoding the required virulence factor thaxtomin have diverged. In contrast, S. turgidiscabies and S. acidiscabies, two relatively unrelated pathogens, possess highly similar thaxtomin biosynthesis clusters, which suggests that the acquisition of these genes was through lateral gene transfer.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Evolution, Molecular*
  • Genome, Bacterial*
  • Phylogeny*
  • Plant Diseases / genetics*
  • Plant Diseases / microbiology*
  • Plants / microbiology
  • Streptomyces / classification
  • Streptomyces / genetics*
  • Streptomyces / metabolism


  • Bacterial Proteins

Grant support

The National Research Initiative of the U.S. Department of Agriculture (USDA) Cooperative State Research, Education, and Extension Service provided funding to Gregg S. Pettis under grant number 2007-35600-17813 and to Rosemary Loria under grant number 2010-65110-20416. The USDA National Institute of Food and Agriculture (NIFA) provided funding to Gregg S. Pettis under Hatch project number LAB94112.