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.

Identifying and conserving sympatric diversity in trout of the genus Salmo, with particular reference to Lough Melvin, Ireland

“…Also, reproductive isolation may rely more on regulatory gene changes, producing epigenetic differences, rather than protein coding ones (Hamilton & Miller, 2018). Reproductive isolation and local adaptation can also be produced by chromosomal structural changes and other changes in genomic architecture even in the presence of substantial gene flow that results in uniformity at genetic markers (Cayuela et al, 2020; Hale et al, 2021; Wellenreuther et al, 2019; Wold et al, 2021). Phenotypic plasticity may be responsible for some of the spawning phenotypes of Eurasian trout in Lake Ohrid (Section 4.7) and Lake Sevan (Section 4.8).…”

The relevance of pedigrees in the conservation genomics era

“…To further characterise variants across the genome, including structural variants (SVs), pedigrees may be used to inform the curation of a pangenome, which is the assembly of multiple individuals with the aim to capture all standing genomic diversity in a population or species of interest (Brockhurst et al, 2019 ; Tettelin et al, 2005 ). In this instance, a pedigree can be leveraged to identify distantly related individuals to ensure the pangenome is representative (Wold et al, 2021 ). Finally, pedigree‐based linkage maps have been a valuable resource for scaffolded genome assemblies by enabling higher assembly accuracy, order, and contiguity (Catchen et al, 2020 ).…”

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

“…Pangenomes offer a straightforward solution to address the challenges associated with SV discovery and genotyping with shortread sequence data. Although originally developed to characterize variation in bacteria (Tettelin et al, 2005), they are commonly used in studies of complex trait diversity in humans (Pang et al, 2010) and agriculturally significant species (e.g., cattle, goats, soybean and maize; Bickhart et al, 2020;Golicz, Batley, & Edwards, 2016;H. Li, Feng, & Chu, 2020;Low et al, 2020;McHale et al, 2012;Yang et al, 2019).…”