The Plot Thickens: Haploid and Triploid-Like Thalli, Hybridization, and Biased Mating Type Ratios in .

The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in . Here, we infer the genome organization and reproduction in by analyzing genomic data from a pure culture and from thalli, and performing a PCR survey of the MAT locus in natural populations. We found that the read count variation in the four specimens, including the pure culture derived from a single sexual spore of , is consistent with haploidy. By contrast, the read counts from a thallus' metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for and , suggesting widespread sexual reproduction, but highly skewed in Europe for , consistent with predominant asexuality. Taken together, we propose that fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are hybrids between and an unknown lineage, reconciling classic systematic and genetic studies with recent genomic observations.