Scientists unveil the highest quality map of sea turtles’ genomes

Collaborative, international research effort unveils that the key to sea turtles’ future may lie in their evolutionary history.

Green Sea Turtle. Photo: RobertoCostaPinto/ Wikimedia Commons. This file is licensed under the Creative Commons Attribution-Share Alike 4.0 International license.

Around 100 million years ago, a group of land-dwelling turtles took to the oceans, eventually evolving into the sea turtles that we know today. However, the genetic foundations that have enabled them to thrive in oceans throughout the world have remained largely unknown. In a study, recently published in the Proceedings of the National Academy of Sciences, an international team of researchers led by the University of Massachusetts Amherst (UMass), USA, in collaboration with the Leibniz Institute for Zoo and Wildlife Research in Berlin, Germany, and the Vertebrate Genome Project (VGP), which includes the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, Germany, and the Rockefeller University Vertebrate Genome Lab in New York, USA, revealed an incredibly detailed genetic map of two species—green and leatherback turtles—that is packed with surprises that might hold the key to their survival in a rapidly changing world. Knowing the genetic background of this remarkable adaptation may prove crucial for its conservation in current times of rapid environmental change.

Think of a single species’ genome, the genetic set of instructions used to build the species, as a library. Each chromosome is a book, and the individual genes themselves are sentences.
Sequencing any species’ genome is an enormous amount of work, akin to translating that entire library into a language that scientists can read, and has only been possible in the last two decades. For green sea turtles, a “draft” genome, including approximately 100,000 pieces of genetic information, has been available since 2013, “but” says Blair Bentley, a postdoctoral researcher in environmental conservation at UMass Amherst and the lead author of the new research, “these pieces of genetic information weren’t precisely mapped out. It was as if you walked into a library and found 100,000 pages of one book lying on the floor.” Errors, omissions, gaps, misassemblies, and fragmentation in draft genomes can lead to incorrect conclusions.

To more precisely catalogue the genomes of the green sea turtle (Chelonia mydas) and the leatherback sea turtle (Dermochelys coriacea), the international team turned to new technologies including Pacbio long read sequencing – an innovation recently named 2022 Method of the Year. This has made it possible to sequence genomes from virtually any living species, and to do so with far more accuracy than was previously possible. The sequencing of the turtles’ genomes was performed by two Vertebrate Genome Project sequencing hubs: the leatherback sea turtle genome was sequenced at Rockefeller University in the Vertebrate Genome Laboratory (VGL), led by Erich Jarvis, who chairs the VGP, and Olivier Fedrigo, who is Director of the VGL, while the green sea turtle genome was sequenced at the MPI-CBG, led by Eugene Myers, in collaboration with Sylke Winkler from the MPI-CBG and the DRESDEN-concept Genome Center. All are coauthors on the new study. The researchers used a combination of different "long-read" sequencing technologies to achieve complete and contiguous genomes. Longer pieces of sequence are important because they can resolve and span complex and repetitive parts of the genome, allowing clear assignments. These genomes are among the highest quality genomes assembled for reptiles (birds not included) to date in terms of both contiguity and completeness. "I am very excited that our high-quality reference genome enabled the results of this study. I expect that these high-quality reference genomes will revolutionize genomics," says Gene Myers. “These advances allowed us to do the equivalent of shelving everything according to the Dewey Decimal System so that we can begin to understand how everything fits together,” says Bentley.

Once the authors had correctly organized and annotated the genetic data, several surprises were unveiled by the combined efforts of the research groups of Camila Mazzoni, one of the paper's two senior authors and group leader of Evolutionary and Conservation Genomics at the Leibniz-IZW and the Berlin Center for Genomics in Biodiversity Research (BeGenDiv) and Lisa Komoroske, Professor of Environmental Conservation at UMass and the paper’s other senior author. The first is that, though green and leatherback turtles diverged from a common ancestor about 60 million years ago, their genomes are remarkably similar. Similar, but not the same. And it’s those differences that may hold the key to each species’ survival, especially considering that populations of both green and leatherback turtles have seen precipitous declines due to human activity.

It turns out that green turtles have evolved more genes dedicated to immunity, suggesting an immune system that is better prepared for new pathogens, as well as more olfactory receptors – they have better senses of smell. The leatherback genome also shows that they have historically had lower population levels. "This is both a blessing and a curse," says Komoroske, "because it means that, while leatherbacks are a resilient species, there isn’t much genetic diversity for them to evolve to meet the challenges of their rapidly changing environment." Insights such as these will help conservationists make more informed decisions about how best to protect these animals as they face the challenges of adapting to our rapidly changing planet.

“The only way we could do this work at all was through an incredible collaborative network that brought scientists from different fields together with organizations like the Vertebrate Genome Project and NOAA Fisheries' Southwest Fisheries Science Center, supported by funders from around the world,” says Komoroske. Indeed, the research was supported by the National Science Foundation, National Oceanic and Atmospheric Administration, Max Planck Institute of Molecular Cell Biology and Genetics, National Institutes of Health, Howard Hughes Medical Institute, Vertebrate Genomes Project, Sanger Institute, São Paolo Research Foundation, German Federal Ministry of Education and Research, Generalitat de Catalunya, la Caixa Foundation, Vienna Science and Technology Fund, City of Vienna, Welsh Government Sêr Cymru II, European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant, the Florida Sea Turtle Grants Program, and individual international donors.