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Front Microbiol. 2016 Jun 27;7:998. doi: 10.3389/fmicb.2016.00998. eCollection 2016.

Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level.

Author information

1
Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology - Chinese Academy of Sciences Guangzhou, China.
2
Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics - Chinese Academy of Sciences Beijing, China.
3
Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics - Chinese Academy of SciencesBeijing, China; University of Chinese Academy of SciencesBeijing, China.
4
Core Genomic Facility, Beijing Institute of Genomics - Chinese Academy of Sciences Beijing, China.

Abstract

Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea's genetic data sources.

KEYWORDS:

comparative genomics; genome dynamics; marine environment adaptation; pan-genomics; streptomycete

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