Plant conservation hologenomics: integrating population genomics with mycobiome assessments for protected orchid species

Growing evidence of the microbiome’s importance for plant ecology highlights the need for conservation strategies that consider both plants and their microbial partners, the holobiont. Population genomics are valuable tools for designing conservation strategies but rarely accounts for host- or site-specific microbial interactions. Orchids, with their dependence on specific mycorrhizal fungi, exemplify the need to include the microbiome in conservation planning. We here combine population genomics with exploration of root mycobiomes for three closely related orchid taxa ( Platanthera chlorantha , P. bifolia var. bifolia and P. bifolia var. latissima ) across 22 populations in Denmark to identify ecologically and evolutionary significant units. Our data revealed that Platanthera chlorantha and P. bifolia s.l. hosted different mycobiomes, suggesting a strong host effect on the fungal symbionts. Population genomic analyses identified three different clusters, one matching P. bifolia var. bifolia and two clusters dividing P. chlorantha into two geographically separate units. The genomic profile of P. bifolia var. latissima was similar to that of P. bifolia var. bifolia but indicated some introgression from P. chlorantha . By combining the mycobiome and population genomic data we reveal that the three detected clusters were associated with different mycobiomes, resulting in a significant correlation between host genomics and mycobiome. Root mycobiomes were correlated with variation in soil nutrients, suggesting a role of the orchids’ fungal partners in adaptation to local edaphic conditions. We propose to identify evolutionary significant units in Platanthera in Denmark based on the novel combination of host genomic and mycobiome profiles, in a conservation hologenomics approach.