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 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; Carroll et al. 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.

Acknowledgments

We are grateful to the Kākāpō125+ Project led by the New Zealand Department of Conservation (DOC) in partnership with Te Rūnanga o Ngāi Tahu (TRONT).  The generation and availability of the short-read data used in this study is owed to the following additional parties: Genetic Rescue Foundation, University of Otago, New Zealand Genomics Limited, Rockefeller Institute, Duke University, Science Exchange and Experiment.com. We also thank  DOC and TRONT for providing the opportunity to explore structural variants in kākāpō using both short- and long-read data. JRW and TES are grateful to theShorebirds Trust, DOC, Genomics Aotearoa, and the University of Canterbury (UC) for their financial support and also extend their thanks to the UC Conservation, Systematics and Evolution Research Team (ConSERT), the UC Research Computational Cluster, especially Francois Bissey, and the New Zealand eScience Infrastructure for support in accessing the computational resources necessary for generating this manuscript.

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