Evolution driven by repetitive regions in sea turtles

Studying genetic variability (for functional and ecological analyses) in species that have a very low number of informative sites (e.g. sea turtles) is very challenging. Thus, we will assemble a very high quality genome (chromosome level) of the green sea turtle and will develop the bioinformatics tools to search for other variability markers (such as repetitive units) in sea turtles and other vertebrate groups with a low number of informative sites.
 
Project details
Duration: 05/2019 – 04/2023
Third-party funded: yes
Involved Department(s): Dept Evolutionary Genetics/ BeGenDiv
Leibniz-IZW Project Leader(s):
Camila Mazzoni (BeGenDiv/Dept Evolutionary Genetics)

Leibniz-IZW Project Team:
Larissa Souza Arantes, Tomás Carrasco Valenzuela
(all: BeGenDiv/Dept Evolutionary Genetics)
Jörns Fickel (Dept Evolutionary Genetics)
Consortium Partner(s):
Yaron Tikochinski, Ruppin Academic Center, Israel
Current Funding Organisation: DAAD-CONICYT
Research Foci:
 
Population and evolutionary analyses of vertebrate species with low levels of polymorphism are chal­lenging because standard SNP identification and autosomal sequence multilocus analysis often do not provide enough genetically informative variation. These species either have a naturally slow mutation rate generating new SNPs of and/or have undergone dramatic losses in their genetic variation. Thus, studies involving such species may highly profit from another, non-standard assessment directed at genetic variation that evolves at a faster rate, such as repetitive units.
 

A group of species with a remarkably low frequency of polymorphisms are the Sea turtles. Even though more than 100 million years of evolution set them apart, the different species of sea turtles don’t display major divergences among their genomes: all sea turtles species have the same number of chromosomes and it has been shown that they possess relatively low divergence among their DNA sequences. Moreover, levels of variation within sea turtle species are very low compared with other vertebrate species. In a previous project involving five sea turtle species we identified the green sea turtle (Chelonia mydas) as the most polymorphic species among all Sea turtles, with heterozygosity levels of 0.3% (i.e. 3 variable positions per 1,000 bp). This value was at least similar to values found in the group of crocodilians, another group with low frequency polymorphisms.The leatherback sea turtle (Dermochelys coriacea), however, presented 10´ less variation than the green turtle, with only 3 variable positions per 10,000 bp.

In collaboration with the Vertebrate Genome Project (VGP), we aim to assemble the green sea turtle genome at the best quality possible, which is chromosome-level. Such high-quality and even partially phased genome (i.e. when both chromosome sequences from a diploid individual are distinguished from each other) will allow new and deep analyses of variation across the entire genome, and will also allow the direct comparison with the similarly high-quality leatherback sea turtle genome.

This project starts with the assembly of the green sea turtle chromosome-level genome and has three main goals:
  • Exploration of the whole genomes of two sea turtle species and analysis of reduced genome representation data from at least five additional sea turtle species to identify potential regions containing variable repetitive units,
  • Develop a pipeline for the identification of variation involving repetitive units across large genomes using sea turtles as a model, and
  • Compare the different patterns of repetitive units among complete genomes of vertebrate species with low frequencies of polymorphisms.