Whole-genome sequencing of Streptomyces sp. MUM 161J from mangrove soil in East Malaysia

Abstract

Whole-genome sequencing provides an essential foundation for investigating the genetic diversity and biosynthetic potential of Streptomyces, a genus widely recognised for its production of structurally diverse secondary metabolites. Here, we report the genome sequence of Streptomyces sp. MUM 161J using PacBio Revio high-fidelity whole-genome sequencing. A total of 117,499 reads comprising 1,656,239,452 bases, with a read N50 of 14,515 bp, were assembled using Hifiasm version 0.25.0-r726. The resulting assembly comprised two contigs totaling 11,071,069 bp, with a contig N50 of 10,651,607 bp and a G+C content of 71.03%. The length-weighted mean mapped depth was 149.2×, and 99.99% of primary reads mapped to the assembly. BUSCO recovered 98.9% complete lineage markers, while CheckM2 estimated 100.0% completeness and 0.56% contamination. Genome annotation using Bakta identified 8,894 standard coding-sequence predictions, including 24 pseudogene calls, plus three separately reported short open reading frames. The annotation also included 70 tRNA features, 18 rRNA genes and two transfer-messenger RNA features. Genome-based comparisons revealed close relatedness to Streptomyces malaysiensis JCM 10672^T, with an average nucleotide identity of 98.84% and digital DNA–DNA hybridisation of 87.5%. AntiSMASH analysis predicted 46 biosynthetic regions, highlighting the potential for diverse specialised metabolite biosynthesis. The genome sequence provides a valuable resource for subsequent taxonomic, comparative and functional investigations, while further analysis of the contig relationships and chromosomal termini will be needed to resolve its physical genome organisation.