Molecular Biodiversity in Fusarium subglutinans and F. temperatum: A Valuable Tool to Distinguish the Two Sister Species and Determine the Beauvericin Chemotype

<i>Fusarium subglutinans</i> and <i>F. temperatum</i> are widely distributed maize pathogens recognized as distinct species with a species-specific chemotype based on patterns of mycotoxins. Recent comparative genomic analysis revealed that genomes of both species carry a complete beauvericin (<i>Bea</i>) biosynthetic genes cluster, but the key gene <i>Bea1</i> in <i>F. subglutinans</i> is not functional likely due to a large insertion (NRPS22ins) and multiple mutations (SNP298 and SNP528). We used the recently published genome sequences for these species to develop PCR markers for investigating the distribution of three main mutations in the <i>Bea1</i> gene in a large collection of strains of both species from around the world. We also designed a PCR assay for a rapid and reliable discrimination of both species in the evaluation of crop exposure to mycotoxins. Overall, our results showed that SNP528 was the most common mutation, followed by NRPS22ins and SNP298. Moreover, phylogenetic analyses suggest that non-synonymous SNPs have occurred first, and that the resulting inactivation of BEA production has caused the accumulation of other polymorphisms, including the NRPS22ins, in the entire gene-coding region. The screening for genetic differences between these species could guide future crop management strategies.