Genome compartmentalization in a fungal insect pathogen reveals a second mating-type locus on an accessory chromosome

The genomes of many fungal pathogens include rapidly evolving regions with high transposable element densities. Such regions often contain genes important for pathogenicity and may be non-core genomic elements carried on accessory chromosomes that are variably present among isolates considered to be members of the same species. Here we present a pangenomic analysis of a fungal insect pathogen, Metarhizium acridum, using six chromosomal assemblies that include isolates from four different continents. We show that the pangenome of M. acridum exhibits a continuum of compartmentalization, with a core genome that contains most of the carbohydrate-active enzymes, while accessory genes are primarily located in gene-sparse regions which encode many small secreted proteins, termed effectors, that are active during host interaction. Furthermore, we identified the first accessory chromosome in M. acridum. In contrast to the accessory chromosomes of many other fungal species, this chromosome does not encode any known effectors or secondary metabolite proteins related to pathogen-host interactions. Instead, the accessory chromosome is enriched in functions related to sexual reproduction and carries genes from both the MAT1-1 and MAT1-2 mating-type idiomorphs, in addition to the canonical MAT locus found on the core chromosomes. Notable as, within the genus Metarhizium, M. acridum is one of few species considered to regularly reproduce sexually. Our findings suggest that the presence of this accessory chromosome further facilitates sexual reproduction, possibly even primary homothallism, in the otherwise heterothallic M. acridum. Overall, our study suggests a novel mechanism in which an accessory chromosome may enhance the capacity for a fungal pathogen to undergo recombination.