Genomic analyses and mating tests among sympatric isolates of Beauveria bassiana provide evidence for a diverse cryptic species complex

We investigated the extent of recombination among isolates of Beauveria bassiana s.l. to assess whether gene flow occurs among them in nature and infer whether non-outcrossing populations may represent cryptic species. We sequenced and assembled genomes of 14 isolates collected from soil in Queensland, Australia, and each was genotyped at their mating type locus. We reconstructed a phylogeny from sequences of B. bassiana available on the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) database and those generated in this study. The isolates from Queensland sequenced in this study form a distinct clade relative to the isolates from other countries on NCBI, and they separated into four genetic groups with high pairwise FST values between them. One of these groups had both MAT1-1 and MAT1-2 mating types, but the other three each had only a single mating type. We crossed isolates from the different genetic groups on Sabouraud dextrose agar yeast extract (SDAY) solid medium and used vegetative compatibility and the production of sexual structures as measures of whether sexual or parasexual recombination is likely to occur in nature. Vegetative compatibility was found within genetic groups when opposite mating types were crossed, with the production of synnemata and perithecia-like structures. However, sexual structures (perithecia, asci, or ascospores) did not develop. Isolates from the different genetic groups were not vegetatively compatible when crossed. We used analyses of linkage disequilibrium to test for evidence of past recombination among the Queensland genetic groups. Two of them had low indices of association and were reticulate in network analyses, which supports recombination (and therefore sexual or parasexual reproduction) within these two genetic groups, but we found no evidence for recombination among the four genetic groups. Our results indicate that B. bassiana is a diverse complex of multiple cryptic species.