title: Comparative Genomics Reveals the Core and Accessory Genomes of Streptomyces Species.
abstract: The development of rapid and efficient genome sequencing methods has enabled us to study the evolutionary background of bacterial genetic information. Here, we present comparative genomic analysis of 17 Streptomyces species, for which the genome has been completely sequenced, using the pan-genome approach. The analysis revealed that 34,592 ortholog clusters constituted the pan-genome of these Streptomyces species, including 2,018 in the core genome, 11,743 in the dispensable genome, and 20,831 in the unique genome. The core genome was converged to a smaller number of genes than reported previously, with 3,096 gene families. Functional enrichment analysis showed that genes involved in transcription were most abundant in the Streptomyces pan-genome. Finally, we investigated core genes for the sigma factors, mycothiol biosynthesis pathway, and secondary metabolism pathways; our data showed that many genes involved in stress response and morphological differentiation were commonly expressed in Streptomyces species. Elucidation of the core genome offers a basis for understanding the functional evolution of Streptomyces species and provides insights into target selection for the construction of industrial strains.
authors.affiliation: School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Ji-Nu
authors.initials: JN
authors.lastname: Kim
authors.affiliation: Laboratory of Molecular Microbiology, School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Yeonbum
authors.initials: Y
authors.lastname: Kim
authors.affiliation: Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.
authors.forename: Yujin
authors.initials: Y
authors.lastname: Jeong
authors.affiliation: Laboratory of Molecular Microbiology, School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Jung-Hye
authors.initials: JH
authors.lastname: Roe
authors.affiliation: School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Byung-Gee
authors.initials: BG
authors.lastname: Kim
authors.affiliation: Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.
authors.forename: Byung-Kwan
authors.initials: BK
authors.lastname: Cho
mesh_terms: D019295:Computational Biology; D005798:Genes, Bacterial; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D013302:Streptomyces / Q000145:classification* / Q000235:genetics*
keywords: Streptomyces; comparative genomics; core genome; pan-genome