Scientists from the UAB and Iowa State University have generated the genome assemblies of two hidden-neck turtles, unpublished until now. The results, which revealed a new three-dimensional structure of the genome within the phylogenetic group of reptiles, birds and mammals, will contribute to the development of more effective turtle conservation strategies, and to the study of the evolution of the genome and chromosomal organisation of vertebrates.
The study was led by researchers Aurora Ruiz-Herrera (UAB) and Nicole Valenzuela (Iowa State University), with the participation of researchers from the Institute of Evolutionary Biology (CSIC-UPF) and Earlham College. Published in Genome Research, it highlights the important role of chromatin, a three-dimensional structure into which genetic material folds and is packaged within the cell nucleus, in the regulation of gene function and its impact on evolution and speciation.
The researchers generated de novo assemblies (with no previous reference model) of the complete genome of two cryptodiran turtle species, commonly named short-necked turtles, by combining gene sequencing and expression techniques. The two turtles represent two lineages in which the sex chromosomes have evolved independently: one with XX/XY chromosomes, the type humans and other mammals have, and another with ZZ/ZW, present in birds and butterflies. In addition, researchers identified a new three-dimensional chromatin conformation in both lineages: beyond the fusion/fission events in linear genomes, they detected a chromosomal folding pattern that allows for centromere-telomere interactions. These discoveries provide new clues on the 3D chromatin structure in amniotes, a phylogenetic group to which reptiles, birds and mammals belong.
“We suggest that the divergent pattern found in the turtles originated from an existing amniote ancestral state defined by a nuclear configuration with extensive associations between its chromosomes that were preserved during linear genome reshuffling in turtles and other vertebrates,” states Nicole Valenzuela, researcher in the Department of Ecology, Evolution and Organismal Biology at Iowa State University.
“These findings broaden our knowledge about the evolution of sex chromosomes and provide a solid foundation for future research on genome evolution and chromosome organisation in vertebrates,” highlights Aurora-Ruiz Herrera, researcher in the Department of Cell Biology, Physiology and Immunology and the Institute of Biotechnology and Biomedicine (IBB) of the UAB.
Key model for scientific research
The researchers note in the article that the study of turtle genomes provides crucial information that could transform our understanding of biology and evolution. With their longevity and resistance to disease, they offer a unique model for scientific studies ranging from biomedicine to species conservation. Deciphering their genome is key to identifying the genes responsible for these traits, and could advance human medicine, especially in areas such as ageing and disease resistance.
In addition, the turtle genome offers a unique window into evolution: these reptile species have existed for more than 250 million years, surviving mass extinction events and adapting to diverse environments. Studying their DNA helps better to understand the mechanisms of adaptation and survival, which are key to the conservation of both, the turtles themselves and other species.
The first turtle genome assemblies were published more than a decade ago. Since then, twelve Chelonian genome assemblies have been reported, nine of them with their gene sequence identified. “The newly generated assemblies are now added to this list and reflect the importance of high-quality genomic resources for the advancement of evolutionary and developmental biology,” concludes Aurora Ruiz-Herrera.