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The promise and challenges of characterizing genome‐wide structural variants: A case study in a critically endangered parrot
Author(s) -
Wold Jana R.,
Guhlin Joseph G.,
Dearden Peter K.,
Santure Anna W.,
Steeves Tammy E.
Publication year - 2025
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.13783
Subject(s) - biology , genome , genotyping , genomics , population genomics , evolutionary biology , computational biology , genetics , reference genome , personal genomics , whole genome sequencing , genotype , gene
Abstract There is growing interest in the role of structural variants (SVs) as drivers of local adaptation and speciation. From a biodiversity genomics perspective, the characterization of genome‐wide SVs provides an exciting opportunity to complement single nucleotide polymorphisms (SNPs). However, little is known about the impacts of SV discovery and genotyping strategies on the characterization of genome‐wide SV diversity within and among populations. Here, we explore a near whole‐species resequence data set, and long‐read sequence data for a subset of highly represented individuals in the critically endangered kākāpō ( Strigops habroptilus ). We demonstrate that even when using a highly contiguous reference genome, different discovery and genotyping strategies can significantly impact the type, size and location of SVs characterized genome‐wide. Further, we found that the mean number of SVs in each of two kākāpō lineages differed both within and across generations. These combined results suggest that genome‐wide characterization of SVs remains challenging at the population‐scale. We are optimistic that increased accessibility to long‐read sequencing and advancements in bioinformatic approaches including multireference approaches like genome graphs will alleviate at least some of the challenges associated with resolving SV characteristics below the species level. In the meantime, we address caveats, highlight considerations, and provide recommendations for the characterization of genome‐wide SVs in biodiversity genomic research.