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

Abstract

The forces that maintain stable boundaries between closely related groups are poorly characterized in theFungi. In other organisms prezygotic barriers, such as assortative mating, are sufficient to reinforce local adaptation and prevent hybridization, yet assortative mating and other prezygotic barriers are largely absent in most fungi. Postzygotic barriers, such as large structural changes across the genome, can also maintain lineage segregation through hybrid incompatibility. The role of structural variation in speciation has been well characterized in a wide array of animals and plants, but not in theFungi, where it may be relatively uncommon. Here, we use a pan-genomic approach in the globally distributed ectomycorrhizal fungusBoletus edulisBull. with 310 whole genome sequences and 22 newly generated reference genomes to identify whether large genomic changes are necessary to maintain lineage segregation in the presence of ongoing gene flow. In addition, we evaluate the extent to which different lineages possess unique repertories of saprotrophic and effector gene families to determine whether lineages exhibit distinct ecological capacities that contribute toward lineage segregation. We show thatB. edulispossesses one of the most diverse pan-genomes of eukaryotes, with the lowest proportion of core proteins identified in theFungi. Pan-genomic clustering correlates more with geography than with gene flow or phylogenetic relatedness. We also show that structural variation is abundant withinB. edulis, but is rarely fixed within a lineage or even shared between two individuals. Moreover, we find that a similar degree of genomic synteny exists between genomes of different lineages as between genomes of the same lineage. Functional protein analysis shows that a new lineage ofB. edulisfrom tropical Guatemala has significant contractions in most saprotrophic gene families and possesses a distinct saprotrophic enzyme repertoire. This lineage also a carries a clear signal of a demographic bottleneck, has very low genome-wide heterozygosity, and an inflated genome size, consistent with a substantial shift in ecological niche. In addition, we reveal preliminary evidence for subtle differences in host preference among EuropeanB. edulis. Altogether, our results provide clear evidence that large changes in genome structure or proteome content are not necessary or perhaps even sufficient to maintain long-term lineage fidelity in the presence of ongoing gene flow. Instead, it appears that subtle differences in ecological tendencies can maintain stable boundaries through time.

Runs of homozygosity reveal contrasting histories of inbreeding across global lineages of the edible porcini mushroom, Boletus edulis

“…This is to be expected given the high genetic divergence of the lineages, but could lead to issues calling ROHs based on the common reference, as missing sites might result in fewer ROHs being detected with our conservative approach (Thorburn et al, 2023). We therefore mapped the reads from each sample to the lineage-specific reference genomes described by Tremble, Brejon Lamartinière et al (2023): YSU-09856 (N50 = 184 kbp) for the AK lineage, WTU-68809 (N50 = 130 kbp) for the BC lineage, BD-953 (N50 = 329 kbp) for the CO lineage, C-F-109468 (N50 = 170 kbp) for the EU lineage, DUKE-0193972 (N50 = 161 kbp) for the EC lineage, KST39 (N50 = 238 kbp) for the GU lineage, and the pseudochromosomal reference BD747 for the WC lineage. We retained all sites with a depth of coverage ≥9, missing data <10% and mapping quality ≥30, and we removed indels using the following command in Vcftools: '--remove-indels --minDP 10 --minQ 30 --max-missing 0.9'.…”

“…is arguably the most important commercially harvested wild mushroom. It has a broad geographical distribution across Eurasia and North America, where it forms obligate mycorrhizal associations with the dominant northern hemisphere forest tree species (Tremble, Brejon Lamartinière et al, 2023). However, the population dynamics of this species remain poorly understood.…”

“…Globally, seven distinct and largely non-overlapping lineages have been described, five restricted to North America, one spanning both North America and boreal Asia, and one in Europe (Tremble, Brejon Lamartinière et al, 2023;.…”

“…These lineages split 1.2-2.6 million years ago and show high levels of genomic divergence, despite some of them being sympatric in parts of North America and the presence of occasional gene flow (Tremble, Brejon Lamartinière et al, 2023). On a large geographical scale, within-lineage structure is limited , while on a fine geographical scale, genetic diversity varies in relation to woodland age, with multiple close relatives being found in younger forest patches, indicating restricted dispersal and a high potential for inbreeding (Hoffman et al, 2020).…”

Tracking signatures of selection in natural populations of ectomycorrhizal fungi – progress, challenges, and prospects

“…Recent studies have shown large intraspecific genomic variation in ECM fungi (e.g. Tremble et al, 2023a), raising questions about how natural selection affects ECM fungal populations. What are the signatures of adaptation in ECM fungal genomes?…”