A high-quality reference genome is an invaluable investment

Increased accessibility to high-quality reference genomes through partnerships with global genome consortia are providing high-quality, contiguous, well annotated genome assemblies that include both short and long read data and scaffolding approaches (e.g., VGP, Bat1K, Bird10K; Rhie et al., 2021; Teeling et al., 2018; Zhang, 2015), both for intensively managed threatened species and their close relatives (Whibley, Kelley, & Narum, 2020). As costs of generating and analyzing WGS data continue to drop, a growing number of conservation genomicists working on species beyond global genome consortia are investing in the assembly and annotation of high-quality reference genomes. We readily recognize that not all conservation programs are able to access the resources or sample quality to generate a high-quality, contiguous, well annotated reference genome, nor do we recommend this action for all threatened species. However, as described below, this investment is a near necessity for the accurate characterization of de novo SVs, particularly if the goal is to characterize a broad range of SV types. Further, as described below, if the goal is to characterize SVs–including complex SVs–across the genome, a pangenome is invaluable (Figure 2).