SRA

Background: Characterising 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 increases feminisation and extinction risk under future climate scenarios. High-quality genomic and epigenomic resources will therefore support conservation efforts for these endangered flagship species with such plastic traits. Findings: We 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, 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 29,883 annotated genes. We then extracted the ONT-derived methylome and validated it via whole genome bisulfite sequencing of ten loggerheads from the same population. Applying our novel resources, we reconstructed population size fluctuations and matched them with major climatic events and niche availability. We identified microchromosomes as key regions for monitoring genetic diversity and epigenetic flexibility. Isolating 191 TSD-linked genes, we further built the largest network of functional associations and methylation patterns for sea turtles to date. Conclusions: We 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.