Expanding the conservation genomics toolbox: incorporating structural variants to enhance functional studies for species of conservation concern

Abstract

Increased capability in the conservation genomics community, combined with decreased sequencing costs, is providing new opportunities for the application of whole-genome sequence data to enhance species recovery. Indeed, assessments of genome-wide diversity based on SNP data are already informing the conservation management of threatened species around the world. However, SNP data alone may not sufficiently capture all of the information necessary for the effective conservation management of critically endangered species that suffer from severe inbreeding depression. For threatened species that require significant intervention, it is critical that we as conservation genomicists expand our repertoire to include assessments of functional diversity. Structural variants are a likely source of functional diversity, as their frequency and genomic context affect the dosage and regulation of gene expression through mechanisms that alter genome organization and impact fitness. In this future-focused Opinion, we leverage the existing literature - predominantly focused on model and agricultural species - to identify pan-genomic and chromosomic approaches for readily characterizing structural variants and to consider how integrating these into the conservation genomics toolbox will transform the way we manage some of the world’s most threatened species.