Expanding the conservation genomics toolbox: incorporating structural
variants to enhance genomic studies for species of conservation concern
Abstract
Structural variants (SVs) are large rearrangements (> 50
bp) within the genome that impact the form and structure of chromosomes.
As a result, SVs are a significant source of functional genomic
diversity, i.e. variation at genomic regions underpinning phenotype
differences, that can have large effects on individual and population
fitness. While there are increasing opportunities to investigate
functional genomic diversity in threatened species via single nucleotide
polymorphism (SNP) datasets, SVs remain understudied despite their
potential influence on complex traits of conservation interest. In this
future-focused Opinion, we contend that characterizing SVs offers the
conservation genomics community an exciting opportunity to complement
SNP-based approaches to enhance species recovery. We identify three
critical resources to characterize SVs de novo: 1) High-quality,
contiguous, annotated reference genome(s); 2) Whole genome resequence
data from representative individuals of the target species/populations;
and 3) Well-curated metadata including pedigrees. We also leverage the
existing literature–predominantly in human health, agriculture and
eco-evol biology–to identify pangenomic approaches for readily
characterizing SVs and consider how integrating these into the
conservation genomics toolbox may transform the way we intensively
manage some of the world’s most threatened species.