Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds

ABSTRACT: Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in tu...

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Autores:
Caicedo Montoya, Carlos
Manzo Ruiz, Monserrat
Ríos Estepa, Rigoberto
Tipo de recurso:
Article of investigation
Fecha de publicación:
2021
Institución:
Universidad de Antioquia
Repositorio:
Repositorio UdeA
Idioma:
eng
OAI Identifier:
oai:bibliotecadigital.udea.edu.co:10495/23813
Acceso en línea:
http://hdl.handle.net/10495/23813
Palabra clave:
Streptomyces
Genoma
Genome
Compuestos bioactivos
Bioactive compounds
Pan-genome
Genome mining
Biosynthetic gene cluster
Pangenoma
http://aims.fao.org/aos/agrovoc/c_ec4deb8c
Rights
openAccess
License
https://creativecommons.org/licenses/by/2.5/co/
Description
Summary:ABSTRACT: Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.