From populations to pan-genomes: investigating the role of ecology and genomic architecture in maintaining species boundaries in the porcini mushroom, Boletus edulis

Hybridization among diverged species is common across all domains of eukaryotic life, but appears to be particularly common in fungi. However, some fungi exhibit a greater tendency for hybridization than others and it is unclear what mechanisms facilitate or prevent hybridization. Here, we generated 253 whole genome sequences and 22 reference genomes within the globally distributed ectomycorrhizal species complex Boletus edulis Bull. and use a multi-faceted genomic approach to identify patterns of ongoing hybridization and determine whether hybridization is mediated by changes in genome structure, ecology, or both. We found that hybridization is common among species of B. edulis despite 2.1 million years of divergence. However, not all lineages that hybridize today exhibit patterns of introgression, indicating the presence of strong reproductive boundaries among some species. Using a pan-genomic approach we find that genome structural variation is abundant within B. edulis, but that the presence of ongoing introgression does not correlate with genome structural similarity or overall gene content. Instead, we find that the composition of ecologically relevant gene families more accurately predicts the presence of introgression among lineages and B. edulis as a group may specialize on chitin decomposition. Altogether, we show that ecological preferences are likely the primary driver of reproductive barriers in B. edulis.