Genetic sequencing of sea turtles can help understand disease that threatens species

The most comprehensive sequencing to date of the genomes of the Leatherback and Green sea turtles shows they are mostly identical. An article in PNAS helps scientists understand how the group has evolved and provides ideas for conservation strategies.

By André Julião  |  Agência FAPESP – As if pollution, fishery bycatch (incidental capture of non-targeted species hooked or entangled in fishing gear) and poaching were not enough, sea turtles suffer from a type of cancer that limits their survival. In recent decades, some of the damage done by human activity has been mitigated by conservation actions. New perspectives in understanding the disease and possibly finding treatment are now opening up, thanks to the work done by an international consortium of scientists in achieving the most comprehensive sequencing to date of the genomes of two of the seven species of sea turtle: the Leatherback turtle (Dermochelys coriacea) and the Green turtle (Chelonia mydas). This research extends knowledge of their immune system and evolution.

Preliminary results are published in the journal PNAS. The authors of the article include Brazilian researchers supported by FAPESP.

“Sea turtles are vulnerable to this form of cancer, which is called fibropapillomatosis, caused by a herpes virus specific to these animals. Most research has focused on cases in C. mydas, but it’s also been found in other species,” said one of the authors, Elisa Karen da Silva Ramos, a PhD candidate at the State University of Campinas’s Institute of Biology (IB-UNICAMP) in São Paulo state, Brazil. 

Her doctoral research was supported by FAPESP. She conducted some of the analysis while on a research internship in Germany at the Leibniz Institute for Zoo and Wildlife Research (IZW) in Berlin, also with support from FAPESP. 

“C. mydas appears to have more genes associated with the immune system in specific chromosomes, and this may offer clues as to how it combats the virus,” she said.

More detailed analysis of this region of the genome is in progress, and the researchers expect confirmation soon of what exactly is happening to these genes in this species.

The research is part of the Vertebrate Genomes Project, which aims to generate high-quality, complete reference genomes of all 66,000 known vertebrate species.

The genomes of the other five species of sea turtle are currently being mapped. The new data will enable scientists to advance their understanding of these reptiles’ defenses against disease, as well as other aspects of their evolution.

“Our analysis of D. coriacea and C. mydas identified differences between the two species in the number of genes associated with immunity. It also enabled us to locate the main histocompatibility complex [MHC], which contains crucial genes for the response to pathogens,” said Blair Bentley, first author of the article and a postdoctoral fellow at the University of Massachusetts (UMass Amherst) in the United States.

The genomic data can be used to investigate this and other diseases, he added, as well as furnishing directions for future treatment and conservation actions.

Second thoughts

“Sea turtles evolve very slowly and are vulnerable to extinction, so it’s important to understand which genes enable them to succeed in the marine environment. This is reflected in mutations and the number of gene copies,” said Mariana Freitas Nery, a professor at IB-UNICAMP and also one of the co-authors of the article.

Nery is principal investigator for a project supported by FAPESP to investigate the genomes of species whose ancestors abandoned the aquatic environment and adapted to life on land, only to return to a watery existence. “We imagine them having second thoughts,” she quipped (read more at: agencia.fapesp.br/35827).

Sea turtles diverged from terrestrial ancestors that returned to the sea some 100 million years ago. D. coriacea and C. mydas separated about 60 million years ago, but their genomes are still mostly identical owing to the group’s slow evolution. 

Among the differences detected are genes associated with olfactory sensors. Although they live in the oceans, marine turtles breathe air and have a terrestrial ancestor. They therefore have sensors that detect molecules in the air and sensors that perceive molecules dissolved in water. Such perceptions are essential for migration and reproduction, as well as for identifying prey, predators, and other members of the same species.

“C. mydas lives nearer the coast and has more contact with pollution and other adverse conditions than D. coriacea, which spends most of its life in deep water. Furthermore, C. mydas has a varied diet whereas D. coriacea migrates great distances to feed on jellyfish,” Ramos said.

The researchers fear slow evolution makes sea turtles unfit for adaptation to rapid environmental changes, including those caused by the climate crisis. “In the case of D. coriacea, for example, we show that diversity is low in the functional regions of the genome, suggesting these populations may not be able to adapt to the rapid rise in temperature due to human activity,” Bentley said.

The article “Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories” is at: www.pnas.org/doi/abs/10.1073/pnas.2201076120.