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Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species

Adamek, Martina, Alanjary, Mohammad, Sales-Ortells, Helena, Goodfellow, Michael, Bull, Alan T., Winkler, Anika, Wibberg, Daniel, Kalinowski, Jörn, Ziemert, Nadine (2018) Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species. BMC Genomics, 19 (426). ISSN 1471-2164. E-ISSN 1471-2164. (doi:10.1186/s12864-018-4809-4) (KAR id:67198)

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https://doi.org/10.1186/s12864-018-4809-4

Abstract

Background

Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis’ strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes.

Conclusions

Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.

Item Type: Article
DOI/Identification number: 10.1186/s12864-018-4809-4
Subjects: Q Science
Divisions: Divisions > Division of Natural Sciences > School of Biosciences
Depositing User: Susan Davies
Date Deposited: 04 Jun 2018 13:47 UTC
Last Modified: 01 Aug 2019 10:43 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/67198 (The current URI for this page, for reference purposes)
Bull, Alan T.: https://orcid.org/0000-0001-6223-7722
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