Whole-Genome Sequencing Identifies a New Aspergillus tubingensis Strain from Eremostachys isochila with Intraspecific Variation in Pharmaceutically Relevant Biosynthetic Gene Clusters

Fungal endophytes are promising sources of pharmaceutically relevant secondary metabolites, yet the genomic basis of their biosynthetic potential remains poorly characterized. We sequenced the genome of endophyte S23, isolated from healthy Eremostachys isochila, and compared it with 13 reference genomes. ITS, multilocus, and genome-scale phylogenies identified S23 as Aspergillus tubingensis. CAZyme, secretome, effector, and virulence-factor analyses showed limited plant-pathogenic potential, with secreted LysM-domain proteins, chitinases, and β-1,3-glucanases as candidate determinants of endophytic adaptation. Biosynthetic gene cluster (BGC) mining identified 95 clusters, mostly conserved across A. tubingensis, including one S23-specific type I polyketide synthase cluster. S23 was identified as the only A. tubingensis genome carrying the complete ten-gene yanuthone D cluster, while the other five strains retained only three cluster genes and lacked the core polyketide synthase gene. This locus conflicts with the species phylogeny, arguing against simple vertical inheritance. The burnettiene A cluster showed a patchy intraspecific distribution, being complete in S23 but absent from three A. tubingensis strains. Nidulanin A and TAN-1612 BGCs were conserved, and the core kojic acid gene, kojA, was absent from all A. tubingensis genomes, including S23. These findings highlight distinctive biosynthetic features of S23 and provide targets for experimental validation of its metabolite production.