Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.

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 c...

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Autores principales:	Hong-Wei Li, Xiao-Yang Zhi, Ji-Cheng Yao, Yu Zhou, Shu-Kun Tang, Hans-Peter Klenk, Jiao Zhao, Wen-Jun Li
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/485134f423794d02a54550ebf51351c8
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spelling	oai:doaj.org-article:485134f423794d02a54550ebf51351c82021-11-18T07:48:27ZComparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.1932-620310.1371/journal.pone.0061528https://doaj.org/article/485134f423794d02a54550ebf51351c82013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23626695/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The 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.Hong-Wei LiXiao-Yang ZhiJi-Cheng YaoYu ZhouShu-Kun TangHans-Peter KlenkJiao ZhaoWen-Jun LiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 4, p e61528 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hong-Wei Li Xiao-Yang Zhi Ji-Cheng Yao Yu Zhou Shu-Kun Tang Hans-Peter Klenk Jiao Zhao Wen-Jun Li Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.
description	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.
format	article
author	Hong-Wei Li Xiao-Yang Zhi Ji-Cheng Yao Yu Zhou Shu-Kun Tang Hans-Peter Klenk Jiao Zhao Wen-Jun Li
author_facet	Hong-Wei Li Xiao-Yang Zhi Ji-Cheng Yao Yu Zhou Shu-Kun Tang Hans-Peter Klenk Jiao Zhao Wen-Jun Li
author_sort	Hong-Wei Li
title	Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.
title_short	Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.
title_full	Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.
title_fullStr	Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.
title_full_unstemmed	Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.
title_sort	comparative genomic analysis of the genus nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/485134f423794d02a54550ebf51351c8
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Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.

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