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The promise and challenges of characterising genome-wide structural variants: A case study in a critically endangered parrot
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  • Jana Wold,
  • Joseph Guhlin,
  • Peter Dearden,
  • Anna Santure,
  • Tammy Steeves
Jana Wold
University of Canterbury

Corresponding Author:[email protected]

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Joseph Guhlin
University of Otago
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Peter Dearden
University of Otago
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Anna Santure
University of Auckland
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Tammy Steeves
University of Canterbury
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There is growing interest in the role of structural variants (SVs) as drivers of local adaptation and speciation. From a biodiversity genomics perspective, the characterisation 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 characterisation of genome-wide SV diversity within and among populations. Here, we explore a near whole-species resequence dataset, 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 characterised 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 characterisation of SVs remains challenging at the population-scale. We are optimistic that increased accessibility to long-read sequencing and advancements in bioinformatic approaches including multi-reference 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.
28 Nov 2022Submitted to Molecular Ecology Resources
20 Dec 2022Submission Checks Completed
20 Dec 2022Assigned to Editor
20 Dec 2022Review(s) Completed, Editorial Evaluation Pending
03 Jan 2023Reviewer(s) Assigned
26 Jan 2023Editorial Decision: Revise Minor
24 Feb 20231st Revision Received
25 Feb 2023Submission Checks Completed
25 Feb 2023Assigned to Editor
25 Feb 2023Review(s) Completed, Editorial Evaluation Pending
09 Mar 2023Editorial Decision: Accept