Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection

Abstract

Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, MATA and MATB. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus Trichaptum (Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of three Trichaptum species. We characterized the chromosomal location of MATA and MATB, the molecular structure of MAT regions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multiple MAT alleles segregating before the speciation event of Trichaptum species. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes. In vitro crosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci in Trichaptum is due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.

Introgression between highly divergent fungal sister species

“…The two species are broadly sympatric and can grow on the same host, and sometimes they are found together on the same substrate. They are in general phylogenetically well separated species (Kauserud and Schumacher 2003; Seierstad et al 2020; Peris et al 2022), but some individuals clustered incongruently for different loci in a previous study including only a few molecular markers (Seierstad et al 2020). Here, the authors suggested introgression or incomplete lineage sorting as possible explanations for the conflicting phylogenetic signals (Seierstad et al 2020).…”

“…Mycelia from fresh cultures, grown on 3% MEA with a nylon sheet between the MEA and the mycelia, were scraped off the plate and DNA was extracted using the E.Z.N.A. ® Fungal HP DNA Kit (Omega Bio-Tek, Norcross, GA, USA) according to the DNA extraction procedure explained in Peris et al (2022). Illumina libraries were prepared by the Norwegian Sequencing Center (NSC) as explained in Peris et al (2022).…”

“…® Fungal HP DNA Kit (Omega Bio-Tek, Norcross, GA, USA) according to the DNA extraction procedure explained in Peris et al (2022). Illumina libraries were prepared by the Norwegian Sequencing Center (NSC) as explained in Peris et al (2022). Samples were sequenced at NSC on either the Illumina Hiseq 4000 or the Illumina Novaseq I.…”

“…Population structure has been found within T. abietinum (Seierstad et al 2020; Peris et al 2022). In North America, two populations referred to as the North American A and the North American B population occur in sympatry and are reproductively isolated (i.e., form intersterile groups; Macrae 1967; Magasi 1976; Peris et al 2022).…”

“…Further, we assessed the possibility of current gene flow by testing compatibility across species through in vitro crossing experiments. We hypothesised that T. fuscoviolaceum and T. abietinum populations do not hybridize frequently due to a well resolved phylogeny and earlier crossing experiments revealing the species to be intersterile (Macrae 1967; Seierstad et al 2020; Peris et al 2022). However, due to their overlapping habitat, ecology, and morphology, we hypothesised that the sister species might have a shared history that involves introgression, possibly having occurred among ancient populations.…”