Whole-Genome Sequence and Biosynthetic Potential of Xenorhabdus szentirmaii PAM25, a Symbiont of Steinernema rarum

Xenorhabdus szentirmaii is a symbiotic bacterium of entomopathogenic Steinernema nematodes and a promising source of bioactive specialized metabolites. In this study, the genome of X. szentirmaii PAM25, isolated from Steinernema rarum PAM25, was sequenced to evaluate biosynthetic potential. Whole-genome sequencing generated a 4.68-Mb draft genome comprising 120 contigs, with 44% GC content, and 3992 predicted coding sequences. Biosynthetic mining with antiSMASH detected 18 biosynthetic gene clusters in X. szentirmaii PAM25, including NRPS, phenazine, siderophore, arylpolyene, RiPP, terpene, betalactone, and hybrid clusters, with high-similarity matches to fabclavine, iodinin, aerobactin, and aryl polyenes. GECCO and SanntiS supported the major biosynthetic predictions. BiG-SCAPE analysis showed that most clusters belonged to gene cluster families conserved across X. szentirmaii, whereas several NRPS-associated loci displayed accessory distributions. Notably, region 40.2, predicted as an NRPS–furan hybrid, formed an X. szentirmaii PAM25-specific singleton gene cluster family. Region 40.2 largely overlapped a predicted genomic island containing both biosynthetic cores and mobility-associated genes. These findings expand genomic knowledge of X. szentirmaii and reveal a largely conserved but partially strain-specific biosynthetic repertoire with potential for specialized-metabolite discovery.