Whole genome sequencing and comparative genomic analysis of Streptomyces sp. YH02 isolated from the soil sediment in Yuncheng Salt Lake

Abstract:

Objective To elucidate the phylogenetic position and mine the gene resources for synthesis of secondary metabolites from Streptomyces sp. YH02, a Gram-positive actinomycete strain isolated from the soil sediment of Yuncheng Salt Lake in Shanxi.Methods Illumina and PacBio platforms were used for whole genome sequencing of YH02, which was followed by gene prediction, functional annotation, prediction of secondary metabolite synthetic gene clusters (BGCs), comparative genomic analysis, and morphological, physiological, and biochemical characterization.Results The YH02 genome was a linear chromosome spanning 8 285 116 bp, with the G+C content of 71.77% and 7 237 open reading frames. Gene annotations in the GO, COG, KEGG, and CAZy identified 2 829, 5 478, 4 805, and 279 genes, respectively. The subcellular localization analysis predicted various secretion system-related proteins and 1 030 transporters. Additionally, 32 secondary metabolite BGCs were predicted in strain YH02, involving the synthesis of various natural products such as terpenoids, non-ribosomal peptides, polyketides, and ribosomally synthesized and post-translationally modified peptides. The comparative genomic analysis revealed 15 739 pan-genome orthologous gene clusters and 4 267 core genome orthologous gene clusters. The phylogenetic analysis based on the 16S rRNA gene sequence revealed a proximate phylogenetic affiliation between strain YH02 and Streptomyces venezuelae ATCC 10712 as well as Streptomyces zaomyceticus NBC 00278. However, the average nucleotide identity (ANI) value was below the threshold of 95.00%, and the digital DNA-DNA hybridization (dDDH) value was less than 70.00%. YH02 exhibited light pink aerial mycelia on the ISP 2 medium. It showed significant differences in tolerance to pH, sodium chloride, and growth temperature compared with its closely related strains. Additionally, this strain demonstrated weak starch hydrolysis activity, positive gelatin liquefaction, positive nitrate reduction, and slow milk coagulation.Conclusion Based on the findings from genomic, physiological, and biochemical analyses, strain YH02 is confirmed as a potential new species of Streptomyces. This study not only enriches the microbial resource pool but also provides a theoretical basis and potential genetic resources for mining the natural products with unique mechanisms of action.

Key words:Streptomyces;whole genome sequencing;secondary metabolite synthetic gene clusters;comparative genomics