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).