Abstract
Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 MYA, yet the genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remain largely unknown. Additionally, many populations have declined drastically due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for green (Chelonia mydas) and leatherback (Dermochelys coriacea) turtles, representing the two extant sea turtle families (MRCA ∼60 MYA). These genomes are highly syntenic and homologous, but localized non-collinearity was associated with higher copy numbers of immune, zinc-finger, or olfactory receptor (OR) genes in green turtles, and ORs related to waterborne odorants were greatly expanded in green turtles. These findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size and extremely low diversity compared to other reptiles, and a higher proportion of deleterious variants, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.
Statement of significance Sea turtles represent a clade whose populations have undergone recent global declines. We analyzed de novo genomes for both extant sea turtle families through the Vertebrate Genomes Project to inform their conservation and evolutionary biology. The highly conserved genomes were largely differentiated by localized gene-rich regions of divergence, particularly in microchromosomes, suggesting that these overlooked genomic elements may play key functional roles in sea turtle evolution. We further demonstrate that dissimilar evolutionary histories impact standing genomic diversity and genetic load, and are critical to consider when using these metrics to assess adaptive potential and extinction risk. Examination of these relationships may be important to reveal drivers of adaptation and diversity in sea turtles and other vertebrates with conserved genome synteny.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Updated manuscript and supplementary information uploaded after the identification of some errors.
Abbreviations
- TE
- transposable element
- RE
- repetitive element
- RRC
- region of reduced collinearity
- FP
- Fibropapillomatosis
- ROH
- runs of homozygosity
