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Alvarez-Costes, S.* ; Baker, C.S.* ; Constantine, R.* ; Carroll, E.L.* ; Guhlin, J.* ; Dutoit, L.* ; Ferreira, S.* ; Heimeier, D.* ; Gemmell, N.J.* ; Gillum, J.* ; Hamner, R.M.* ; Rayment, W.* ; Roe, W.* ; Te Aikā, B.* ; Urban, L. ; Alexander, A.*

Leveraging synteny to generate reference genomes for conservation: Assembling the genomes of Hector's and Māui dolphins.

Mol. Ecol. Notes:e14109 (2025)

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Escalating concern regarding the impacts of reduced genetic diversity on the conservation of endangered species has spurred efforts to obtain chromosome-level genomes through consortia such as the Vertebrate Genomes Project. However, assembling reference genomes for many threatened species remains challenging due to difficulties obtaining optimal input samples (e.g., fresh tissue, cell lines) that can characterise long-term conservation collections. Here, we present a pipeline that leverages genome synteny to construct high-quality genomes for species of conservation concern despite less-than-optimal samples and/or sequencing data, demonstrating its use on Hector's and Māui dolphins. These endemic New Zealand dolphins are threatened by human activities due to their coastal habitat and small population sizes. Hector's dolphins are classified as endangered by the IUCN, while the Māui dolphin is among the most critically endangered marine mammals. To assemble reference genomes for these dolphins, we created a pipeline combining de novo assembly tools with reference-guided techniques, utilising chromosome-level genomes of closely related species. The pipeline assembled highly contiguous chromosome-level genomes (scaffold N50: 110 MB, scaffold L50: 9, miniBUSCO completeness scores > 96.35%), despite non-optimal input tissue samples. We demonstrate that these genomes can provide insights relevant for conservation, including historical demography revealing long-term small population sizes, with subspecies divergence occurring ~20 kya, potentially linked to the Last Glacial Maximum. Māui dolphin heterozygosity was 40% lower than Hector's and comparable to other cetacean species noted for reduced genetic diversity. Through these exemplar genomes, we demonstrate that our pipeline can provide high-quality genomic resources to facilitate ongoing conservation genomics research.

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Publication type Article: Journal article

Document type Scientific Article

Corresponding Author

Keywords Cephalorhynchus Hectori ; Conservation Genomics ; Heterozygosity ; Historical Demography ; Reference Genomes ; Synteny; Population-size; New-zealand; Inbreeding Depression; Genetic Diversity; Climate-change; Cook Strait; Abundance; Genotype; Extinction; Evolution

ISSN (print) / ISBN 1471-8278

e-ISSN 1471-8286

Journal Molecular Ecology Notes

Quellenangaben Article Number: e14109

Publisher Wiley

Publishing Place 111 River St, Hoboken 07030-5774, Nj Usa

Non-patent literature Publications

Reviewing status Peer reviewed

Institute(s) Helmholtz Artifical Intelligence Cooperation Unit (HAICU)
Helmholtz Pioneer Campus (HPC)

Grants The University of Otago
Genomics Aotearoa
Rutherford Postdoctoral Fellowship
Rutherford Discovery Fellowship
ORG.one