Whole genome sequencing (WGS) and genome mining of Streptomyces sp. AFD10 for antibiotics and bioactive secondary metabolites biosynthetic gene clusters (BGCs)

Abstract

Genomic approaches are being frequently used as an advancement over the conventional drug screening strategies for exploring the medicinally useful microbial strains. This study reports the whole genome sequencing (WGS), and genome mining for antibiotics biosynthetic gene clusters (BGCs), of the desert originated Actinobacteria strain Streptomyces sp. AFD10. The genomic DNA was isolated and subjected to library preparation and sequencing on Illumina Hiseq 2500 platform. The raw sequence reads were analyzed for various quality parameters and assembled through SOAPdenovo (ver. 2). The assembled genome is composed of 467 scaffolds (N50 = 98,164) sizing around 7,891,201 bp with GC content of 72.6 %, and number of coding sequences 7246. The RAST (ver 2.0) annotation SEED Viewer subsystem overview of the genome showed the presence of 163 subsystems in the genome of Streptomyces sp. AFD10. The strain exhibited maximum ANI (average nucleotide identity) up to 97.79 % with Streptomyces violaceoruber. The AntiSMASH (version 4.2.0) analysis of assembled genome showed a total of 35 biosynthetic gene clusters (BGCs) related to the biosynthesis of antibiotics and secondary metabolites in the genome of Streptomyces sp. AFD10. The identified gene clusters were predicted to be involved in the biosynthesis of different structural classes of antibiotics such as, polyketides, tripeptides, terpenes, lantipeptides, lassopeptide and butyrolacton etc. Overall, the study revealed that the Actinobacteria strains originated from extreme environments such as deserts are a promising source of medicinally useful metabolites, and the genome mining approaches provide an alternative platform to explore these resources for the novel antibiotics discovery.