Concluding remarks
As SV-based studies become more ubiquitous over time, we anticipate many of the caveats and trade-offs discussed above will be better resolved and we are excited to see the wide application of SVs in the biodiversity genomic literature. In particular, multi-reference approaches, like genome graphs, promise to alleviate many of the challenges associated with genome-wide SV characterisation (Bayer et al., 2020; Ebler et al., 2020 preprint; Eizenga et al., 2020; Hurgobin & Edwards, 2017). For example, for SV studies in species with robust pedigrees like kākāpō, it may be more economical to target a subset of highly represented individuals for long-read sequencing and the construction of genome graphs. Similar approaches for SV discovery are underway to better inform breeding and selection in agriculturally significant species such as cattle, soybean and tomato (Alonge et al., 2020; Cappetta et al., 2020; Liu et al., 2020; Talenti et al., 2022). Individual- and population-scale genotyping may then be possible with short-read data and assessments of genome-wide SV diversity.
Data accessibility and benefits sharing
This research was undertaken as part of the Kākāpō125+ Project that includes research partnerships between the University of Canterbury’s Conservation, Systematics and Evolutionary Research Team (ConSERT, including JRW, TES), Genomics Aotearoa (including AWS, JGG, PKD, TES), New Zealand Department of Conservation (DOC) and Te Rūnanga o Ngāi Tahu (TRONT). The goal of the Kākāpō125+ Project is to facilitate the development and implementation of conservation management strategies to enhance the recovery of this critically endangered taonga, or treasured, species. Approval to access the Kākāpō125+ short-read data used in this study was granted to TES and her research team by DOC and TRONT. The Kākāpō125+ Project short-read data is stored in the Aotearoa Genomic Data Repository (AGDR):
https://data.agdr.org.nz/ and is subject to the Kākāpō125+ Genomics Data Sharing Terms and Conditions described here:
https://www.doc.govt.nz/our-work/kakapo-recovery/what-we-do/research-for-the-future/kakapo125-gene-sequencing/request-kakapo125-data/. The generation of the long-read data was conducted under DOC authorisation (authorisation number: 97814-FAU) and enabled by High Quality Genomes and Population Genomics at Genomics Aotearoa. In accordance with FAIR and CARE data principles (Carroll et al., 2020, 2021; Mc Cartney et al., 2022), the long-read data is also stored in the AGDR and data sharing subject to approval by DOC and TRONT.