Received: Jun 13, 2026 / Accepted: Oct 20, 2026 / Published: Oct 31, 2026
Streptomyces species are renowned for their capacity to produce diverse bioactive secondary metabolites and remain an important source of novel natural products. We performed an integrated genome-based characterization of Streptomyces sp. YIM 121038 using whole-genome phylogeny, genome similarity analyses, functional annotation, and biosynthetic gene cluster (BGC) prediction. Genome-scale analysis showed that YIM 121038 possesses a typical high-GC (72.86%) and gene-rich genome (10.13 Mbp, 9,312 coding sequences), together with a large 967.9-kb linear plasmid representing the largest accessory replicon among the analyzed strains. Whole-genome phylogenomic reconstruction using TYGS clustered YIM 121038 within the S. spectabilis lineage, a finding consistently supported by OrthoANI and digital DNA–DNA hybridization (dDDH) analyses. YIM 121038 exhibited the highest genomic similarity to S. spectabilis NRRL 2792 (92.25% OrthoANI; 67.8% dDDH) and S. spectabilis ATCC 27465 (92.16% OrthoANI; 65.8% dDDH), while remaining below the accepted species delineation thresholds. Genome mining with antiSMASH identified 45 putative biosynthetic gene clusters on the chromosome and nine on the linear plasmid, including numerous NRPS-, type I PKS-, terpene-, RiPP-, and hybrid-associated clusters, indicating substantial biosynthetic diversity. Consistently, KEGG functional annotation revealed a broad representation of genes involved in secondary metabolism and core metabolic pathways. The agreement among phylogenomic, genome similarity, and functional analyses demonstrates that YIM 121038 possesses a characteristic Streptomyces genome architecture together with extensive potential for specialized metabolite biosynthesis. These findings provide a comprehensive genomic framework for understanding the evolutionary position and biosynthetic potential of YIM 121038 and support future experimental investigation of its specialized metabolites.
