ArticleGigaScience2025
Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Genetic recovery in an alpine climate-sensitive pika species during upward treeline shift.BMC genomics · 2026Article
- Divergence and conservation of satellite DNA in the loggerhead sea turtle (Caretta caretta): a comparative cytogenomic analysis.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles.GigaScience · 2025Article
- Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence.GigaScience · 2025Article
- DNA Methylation Carries Signatures of Sublethal Effects Under Thermal Stress in Loggerhead Sea Turtles.Evolutionary applications · 2024Article
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Authors and funding
10 authors.
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Abstract
backgroundCharacterizing genetic and epigenetic diversity is crucial for assessing the adaptive potential of threatened populations and species in the face of climate change. Sea turtles are particularly vulnerable due to their temperature-dependent sex determination (TSD) system, which heightens the risk of extreme sex ratio bias and extinction under future climate scenarios. High-quality genomic and epigenomic resources will therefore support conservation efforts for these endangered flagship species with such plastic traits.
findingsWe generated a chromosome-level genome assembly for the loggerhead sea turtle (Caretta caretta) from the globally important Cabo Verde rookery. Using Oxford Nanopore Technology (ONT) and Illumina reads followed by homology-guided scaffolding to the same species, we achieved a contiguous (N50: 129.7 Mbp) and complete (BUSCO: 97.1%) assembly, with 98.9% of the genome scaffolded into 28 chromosomes and 33,887 annotated genes. We also extracted the blood methylome profile from our ONT reads, which was confirmed to be representative of the reference population via whole-genome bisulfite sequencing of 10 additional loggerheads from the same population. Applying our novel resources, we revealed high conservation of synteny between sea turtle species, reconstructed population size fluctuations in line with major climatic events, and identified microchromosomes as key regions for monitoring genetic diversity and epigenetic flexibility. Isolating 199 TSD-linked genes, we further built a large network of functional protein associations and blood-based methylation patterns.
conclusionsWe present a high-quality loggerhead sea turtle genome and methylome from the globally significant East Atlantic population. By leveraging ONT sequencing, we generate genomic and epigenomic resources simultaneously and showcase the potential of this approach for driving molecular insights for conservation of endangered sea turtles.
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