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Leveraging synteny to generate reference genomes for conservation: Assembling the genomes of Hector’s and Māui dolphins
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  • Sebastian Alvarez Costes,
  • Charles Baker,
  • Rochelle Constantine,
  • Emma Carroll,
  • Joseph Guhlin,
  • Ludovic Dutoit,
  • Sara Ferreira,
  • Dorothea Heimeier,
  • Neil Gemmell,
  • Joanne Gillum,
  • Rebecca Hamner,
  • Will Rayment,
  • Wendi Roe,
  • Ben Te Aika,
  • Lara Urban,
  • Alana Alexander
Sebastian Alvarez Costes
University of Otago
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Charles Baker
Oregon State University
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Rochelle Constantine
University of Auckland
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Emma Carroll
The University of Auckland
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Joseph Guhlin
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Ludovic Dutoit
University of Otago Department of Zoology
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Sara Ferreira
University of Otago
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Dorothea Heimeier
The University of Auckland - City Campus
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Neil Gemmell
University of Otago
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Joanne Gillum
University of Otago
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Rebecca Hamner
Oregon State University
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Will Rayment
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Wendi Roe
Massey University School of Veterinary Science
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Ben Te Aika
University of Otago
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Lara Urban
University of Otago
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Alana Alexander
University of Otago

Corresponding Author:[email protected]

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Abstract

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 characterize 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, utilizing 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.
19 Sep 2024Submitted to Molecular Ecology Resources
20 Sep 2024Submission Checks Completed
20 Sep 2024Assigned to Editor
20 Sep 2024Review(s) Completed, Editorial Evaluation Pending
26 Sep 2024Reviewer(s) Assigned