Abstract
<title>Abstract</title> <p> Endophytic fungi are emerging as prolific so urces of bioactive secondary metabolites, yet the relationship between their genetic diversity and biosynthetic capacity remains poorly understood. In this study, we combined genetic diversity analysis (using ISSR markers) with genome mining (using antiSMASH) to characterize endophytic <italic>Alternaria alternata</italic> isolates recovered from six medicinal plant species ( <italic>Salvia nemorosa</italic> , <italic>Gundelia tournefortii</italic> , <italic>Tamarix ramosissima</italic> , <italic>Alhagi maurorum</italic> , <italic>Alcea rosea</italic> , and <italic>Zygophyllum fabago</italic> ) collected in East Azerbaijan Province, Iran. Molecular identification using ITS1 sequencing confirmed that all isolates belonged to <italic>A. alternata</italic> , forming a well- supported clade in phylogenetic analysis. Genome mining of the <italic>A. alternata</italic> reference genome revealed an exceptionally high number of biosynthetic gene clusters (BGCs) - a total of 42 clusters - including 10 T1PKS, 8 NRPS, 6 terpenes, 4 hybrid T1PKS-NRPS, 3 siderophores, 2 indoles, 2 beta-lactones, and 7 other types. Predicted metabolites include alternariol, tenuazonic acid, ferrichrome-like siderophores, and various terpenes, suggesting potential ecological roles in host defense, iron acquisition, and chemical communication. Despite the high genetic diversity previously detected among isolates, the core BGC repertoire appears conserved, indicating that <italic>A. alternata</italic> maintains a stable biosynthetic potential across different host plants. This study provides the first integrated analysis of genetic diversity and biosynthetic capacity in endophytic <italic>A. alternata</italic> and positions this fungus as a promising candidate for bioprospecting novel bioactive compounds. </p>