Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

Larissa S Arantes; Tom Brown; Diego De Panis; Scott D Whiting; Erina J Young; Erin L LaCasella; Gabriella A Carvajal; Adam Kennedy; Deana Edmunds; Blair P Bentley; Jennifer Balacco; Conor Whelan; Nivesh Jain; Tatiana Tilley; Brian O'Toole; Patrick Traore; Erich D Jarvis; Oliver Berry; Peter H Dutton; Lisa M Komoroske; Camila J Mazzoni

doi:10.1093/gigascience/giaf105

Back

Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

Journal article

Open access

Peer reviewed

Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

Larissa S Arantes, Tom Brown, Diego De Panis, Scott D Whiting, Erina J Young, Erin L LaCasella, Gabriella A Carvajal, Adam Kennedy, Deana Edmunds, Blair P Bentley, …

Gigascience, Vol.14, giaf105

2025

DOI: https://doi.org/10.1093/gigascience/giaf105

PMID: 40971593

Files and links (1)

pdf

Published3.76 MBDownload View

CC BY V4.0, Open Access

Abstract

Animals

Evolution, Molecular

Genetic Variation

Genome

Genomics - methods

Haplotypes

Phylogeny

Synteny

Turtles - classification

Turtles - genetics

Background Reference genomes for the entire sea turtle clade have the potential to reveal the genetic basis of traits driving the ecological and phenotypic diversity in these ancient and iconic marine species. Furthermore, these genomic resources can support conservation efforts and deepen our understanding of their unique evolution. Results We present haplotype-resolved, chromosome-level reference genomes and high-quality gene annotations for 5 sea turtle species. This completes the catalog of reference genomes of the entire sea turtle clade when combined with our previously published reference genomes. Our analysis reveals remarkable genome synteny and collinearity across all species, despite the clade’s origin dating back more than 60 million years. Regions of high interspecific genetic distance and intraspecific genetic diversity are consistently clustered in genomic hotspots, which are enriched with genes coding for immune response proteins, olfactory receptors, zinc fingers, and G-protein-coupled receptors. These hotspot regions may offer insights into the genetic mechanisms driving phenotypic divergence among species and represent areas of significant adaptive potential. Ancient demographic analysis revealed a synchronous population expansion among sea turtle species during the Pleistocene, with varying magnitudes of demographic change, likely shaped by their diverse ecological adaptations and biogeographic contexts. Conclusions Our work provides genomic resources for exploring genetic diversity, evolutionary adaptations, and demographic histories of sea turtles. We outline genomic regions with increased diversity, linked to immune response, sensory evolution, and adaptation to varying environments that have historically been subject to strong diversifying selection and likely will underpin sea turtles’ responses to future environmental change. These reference genomes can assist conservation by providing insights into the demographic and evolutionary processes that sustain and threaten these iconic species.

Details

Title: Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence
Authors/Creators: Larissa S Arantes - Leibniz Institute for Zoo and Wildlife Research
Tom Brown - Leibniz Institute for Zoo and Wildlife Research
Diego De Panis - Leibniz Institute for Zoo and Wildlife Research
Scott D Whiting - Department of Biodiversity, Conservation and Attractions
Erina J Young - Murdoch University
Erin L LaCasella - NOAA National Marine Fisheries Service Southwest Fisheries Science Center
Gabriella A Carvajal - Florida Atlantic University
Adam Kennedy - New England Aquarium
Deana Edmunds - New England Aquarium
Blair P Bentley - Smith College
Jennifer Balacco - Rockefeller University
Conor Whelan - Rockefeller University
Nivesh Jain - Rockefeller University
Tatiana Tilley - Rockefeller University
Brian O'Toole - Rockefeller University
Patrick Traore - Rockefeller University
Erich D Jarvis - Rockefeller University
Oliver Berry - Commonwealth Scientific and Industrial Research Organisation
Peter H Dutton - NOAA National Marine Fisheries Service Southwest Fisheries Science Center
Lisa M Komoroske - University of Massachusetts Amherst
Camila J Mazzoni - Leibniz Institute for Zoo and Wildlife Research
Publication Details: Gigascience, Vol.14, giaf105
Publisher: Oxford University Press on behalf of GigaScience.
Number of pages: 17
Grant note: CSIRO's Environomics Future Science Platform WGM_2021-026 / Revive & Restore via a Catalyst Science Fund #1904439 / NSF-IOS NOAA Fisheries University of Massachusetts Amherst
Identifiers: 991005815048807891
Murdoch Affiliation: School of Veterinary Medicine
Language: English
Resource Type: Journal article

UN Sustainable Development Goals (SDGs)

This output has contributed to the advancement of the following goals:

Metrics

5 File views/ downloads

13 Record Views

1 Times Cited - Web of Science

InCites Highlights

These are selected metrics from InCites Benchmarking & Analytics tool, related to this output

Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.35 Zoology & Animal Ecology; 3.35.683 Reptile Ecology
Web Of Science research areas: Biology
ESI research areas: Biology & Biochemistry