Yen Eugenie C, Gilbert James D, Balard Alice, Taxonera Albert, Fairweather Kirsten, Ford Heather L, Thorburn Doko-Miles J, Rossiter Stephen J, Martín-Durán José M, Eizaguirre Christophe
School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4DQ, UK.
Project Biodiversity, Mercado Municipal, Local 22, Santa Maria, Ilha do Sal, 4111, Cabo Verde.
Gigascience. 2025 Jan 6;14. doi: 10.1093/gigascience/giaf054.
Characterizing 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.
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 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.
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.
表征遗传和表观遗传多样性对于评估受威胁种群和物种在气候变化面前的适应潜力至关重要。海龟因其温度依赖型性别决定（TSD）系统而特别脆弱，这增加了未来气候情景下极端性别比例偏差和灭绝的风险。因此，高质量的基因组和表观基因组资源将支持对具有这种可塑性特征的濒危旗舰物种的保护工作。
我们从具有全球重要意义的佛得角繁殖地为蠵龟（Caretta caretta）生成了一个染色体水平的基因组组装。使用牛津纳米孔技术（ONT）和Illumina读数，随后通过同源性引导的支架构建到同一物种，我们实现了一个连续的（N50：129.7 Mbp）和完整的（BUSCO：97.1%）组装，98.9%的基因组被支架构建到28条染色体上，并有33,887个注释基因。我们还从ONT读数中提取了血液甲基化组图谱，通过对来自同一群体的另外10只蠵龟进行全基因组亚硫酸氢盐测序，证实该图谱代表了参考群体。应用我们的新资源，我们揭示了海龟物种之间的高度共线性保守性，重建了与主要气候事件一致的种群大小波动，并确定微染色体是监测遗传多样性和表观遗传灵活性的关键区域。分离出199个与TSD相关的基因，我们进一步构建了一个大型的功能蛋白关联和基于血液的甲基化模式网络。
我们展示了来自具有全球重要意义的东大西洋种群的高质量蠵龟基因组和甲基化组。通过利用ONT测序，我们同时生成了基因组和表观基因组资源，并展示了这种方法在推动濒危海龟保护的分子见解方面的潜力。
