A hawksbill sea turtle (Eretmochelys imbricata) glides over a coral reef. High-quality reference genomes now exist for all seven sea turtle species, enabling conservationists to develop genetic tools and management strategies for critically endangered species, such as the hawksbill.
Sea turtles have played a vital role in maintaining the health of marine ecosystems for over 100 million years. However, all seven species face significant threats, including habitat loss, climate change, pollution, bycatch in fishing gear, and illegal poaching. These pressures have led to drastic declines in their populations, with several species now classified as endangered or critically endangered.
Until recently, reference genomes existed for only two of the seven sea turtle species: the green and leatherback turtle. To address this gap, Revive & Restore funded a project as part of our Wild Genomes program to generate reference genomes for the remaining five species: the flatback (Natator depressus), hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), olive ridley (Lepidochelys olivacea), and Kemp’s ridley (Lepidochelys kempii). Led by Drs. Camila Mazzoni at the Leibniz Institute for Zoo and Wildlife Research in Berlin, Peter Dutton at NOAA’s Southwest Fisheries Science Center, and Lisa Komoroske at the University of Massachusetts Amherst. This project involved collaborations across multiple research groups and relied on a supportive network of sea turtle rehabilitation specialists to secure the necessary tissue samples from endangered populations.
Now, all five new genomes have been sequenced, assembled, and annotated, meeting Earth Biogenome Project standards with exceptional quality (BUSCO completeness scores exceeding 95%). The resulting publication in GigaScience marks a milestone for sea turtle conservation, as it completes the first comprehensive genomic catalog for an entire marine vertebrate family.
The research revealed a surprising finding: despite 70-80 million years of evolutionary divergence, sea turtle genomes show ultra-high levels of shared synteny, remarkably preserved chromosomal organization across all seven species. This extraordinary genomic stability means that genetic markers, diagnostic tools, and conservation approaches developed for one species can be potentially applied across others, dramatically reducing the time and resources required to develop management strategies. This cross-species compatibility is transformative for critically endangered species, such as the Kemp’s ridley and hawksbill, where obtaining samples is exceptionally challenging.
While the genomes share a remarkable overall structure, the team identified specific “hotspots” enriched with genes that control immune response, sensory perception, and environmental adaptation. These regions begin to elucidate how different sea turtle species thrive in vastly different habitats, from the cold-water depths favored by leatherbacks to the coral reef ecosystems of hawksbills. Understanding which genetic variants exist in these hotspots enables conservation managers to predict which populations may be more resilient to emerging threats, such as novel diseases, warming oceans, or changing food availability.
These high-quality reference genomes have the potential to transform sea turtle conservation in concrete ways. According to Dr. Dutton, they provide critical data for government regulatory agencies conducting conservation under the Endangered Species Act (ESA), helping to identify distinct population units, detect subspecies, and assess genetic diversity and gene flow between nesting beaches. In addition, demographic analyses enabled by these genomes have already begun to reveal that each species requires tailored conservation approaches. These insights directly inform management decisions such as defining conservation units and evaluating whether restored or relocated populations have sufficient genetic diversity to persist long-term.
The genomes also enable the development of non-invasive monitoring approaches using environmental DNA or shed scutes, improved forensic tools to combat illegal trade, and enhanced ability to track disease outbreaks across populations, all essential components of modern conservation in an era of rapid environmental change.
Revive & Restore is proud to have supported this project and is excited about the new conservation strategies these genomes will enable. By advancing our understanding of sea turtles at the genetic level, this work represents a significant step toward ensuring their survival in a rapidly changing world. The completion of this genomic catalog demonstrates how strategic investment in foundational biological resources can accelerate conservation innovation across an entire taxonomic group, providing tools that will benefit sea turtle populations for generations to come.
Read the complete publication: Arantes et al. (2025). “Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence.” GigaScience 14:1-17.
