Comparative Whole-Genome Sequence Analysis of Alternaria alternata KACC 411286 That Produces Alternariol-Derived Toxins and Its Secondary Metabolite Biosynthetic Potential

Alternaria alternata can produce alternariol (AOH), alternariol monomethyl ether (AME), altenusin (ALN), and altenuene (ALT) on fruits and vegetables. Much is unknown about the biosynthetic gene clusters (BGCs) of secondary metabolites (SMs) including ALT in A. alternata isolated from strawberries. In the current study, we sequenced the whole genome of AOH- and AME-producing A. alternata KACC 411286 isolated from strawberry jam and carried out comparative analyses of the ALT BGC in its genome with those of other fungal strains after verification of its production of ALN and ALT. Our data showed that the assembled genome of A. alternata KACC 411286 is 34.2 Mb in size with 10 chromosomes. Gene Ontology analysis showed that genes involved in RNA transcription and protein synthesis and turnover are enriched in the genome of A. alternata KACC 411286. We identified a total of 40 SM BGCs, including the ALT BGC, in A. alternata KACC 411286. The comparative analysis showed that ALT BGCs are highly conserved between two A. alternata (KACC 411286 and ATCC 66981) and A. arborescens EGS 39–128. The functional conservation analyses of all six ALT biosynthetic genes also revealed that each gene in A. alternata KACC 411286 shares high amino acid and DNA sequence identity (above 78% identity) with its corresponding gene in four other Alternaria spp. except pksI in A. arborescens EGS 39–128 (55% identity at both the protein and DNA levels) and pksI in A. tenuissima BMP 0304 (53% at the DNA level). Our findings could provide a molecular basis for understanding the biosynthetic mechanisms of SMs, including ALT, in A. alternata KACC 411286 to reduce the contamination of fruits with multiple mycotoxins.