title: Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.
abstract: The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. Its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. To shed light on speciation, gene content evolution, and environmental adaptation in these unique actinobacteria, we sequenced draft genomes for 16 representative species of the genus and compared them with that of the type species N. dassonvillei subsp. dassonvillei DSM 43111(T). The core genome of 1,993 orthologous and paralogous gene clusters was identified, and the pan-genomic reservoir was found not only to accommodate more than 22,000 genes, but also to be open. The top ten paralogous genes in terms of copy number could be referred to three functional categories: transcription regulators, transporters, and synthases related to bioactive metabolites. Based on phylogenomic reconstruction, we inferred past evolutionary events, such as gene gains and losses, and identified a list of clade-specific genes implicated in environmental adaptation. These results provided insights into the genetic causes of environmental adaptability in this cosmopolitan actinobacterial group and the contributions made by its inherent features, including genome dynamics and the constituents of core and accessory proteins.
authors.affiliation: Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, People's Republic of China.
authors.forename: Hong-Wei
authors.initials: HW
authors.lastname: Li
authors.forename: Xiao-Yang
authors.initials: XY
authors.lastname: Zhi
authors.forename: Ji-Cheng
authors.initials: JC
authors.lastname: Yao
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhou
authors.forename: Shu-Kun
authors.initials: SK
authors.lastname: Tang
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
authors.forename: Jiao
authors.initials: J
authors.lastname: Zhao
authors.forename: Wen-Jun
authors.initials: WJ
authors.lastname: Li
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000235:genetics*; D000222:Adaptation, Physiological / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial; D055028:Comparative Genomic Hybridization; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D049810:Genetic Speciation; D016680:Genome, Bacterial; D023281:Genomics; D005810:Multigene Family; D010802:Phylogeny
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins