They weigh up to 250 kilograms and can live well over 100 years: next to their relatives from the Galapagos Islands, Aldabra giant tortoises are the only giant tortoises still alive today. However, due to climate change and the loss of their habitat, they are threatened with extinction. A research team has now almost completely sequenced and published the genome of an Aldabra giant tortoise. The data can serve as a reference genome when designing effective conservation programs. They also help to unravel mysteries such as the extraordinary size and longevity of the species.
For targeted species protection programs it is important to know as much as possible about the species to be protected. Genomic data can help plan matings in breeding programs, alert for potential genetic diseases in a population and, for captive animals, determine where they originally came from. A so-called reference genome is particularly helpful here: This is a high-quality, representative example of the genome of a species that can serve as a basis for comparing future sequencing of lower quality with it. Of all 44 turtle species still alive today, however, only three reference genomes have been available so far - and this despite the fact that numerous representatives are on the list of endangered species.
Zoo turtle as a blood donor
A team led by Gözde Çilingir from the University of Zurich has now created such a reference genome for the Aldabra giant tortoise (Aldabrachelys gigantea). The species is named after its place of origin, the Aldabra Atoll in the Seychelles north of Madagascar. Aside from a few released specimens on other islands, it is only found in the wild on Aldabra Atoll. "Due to its limited distribution and the threat of climate change, the species is classified as vulnerable on the list of threatened species," explains Çilingir.
"Genomic information is important to zoo breeding efforts to maintain genetic diversity in the wild."
As the starting material for the genome sequencing, the research team used a blood sample from an Aldabra giant tortoise named Hermania, which has lived at Zurich Zoo since 1955 and from which a blood sample was due as part of a routine veterinary examination anyway. Using modern DNA sequencing methods, Çilingir and her colleagues decoded the genome at the chromosome level. Compared to other sequencing, such a genome sequence is almost complete and it shows on which chromosomes the respective genetic sections are located.
Commonalities and mutations identified
"We found that most of the genome is similar to other known genomes of members of the tortoise order," says Çilingir. "All tortoise species that exist today are closely related evolutionarily, and therefore our data will be of great use not only for the Aldabra tortoise but for all East African and Malagasy tortoises."
Çilingir and her colleagues demonstrated a potential use of the new reference genome by sequencing 32 more lower-resolution genomes - 30 from wild Aldabra giant tortoises and two from other specimens from Zurich Zoo - and comparing them to the reference genome. Since the individual pieces of DNA from the additional sequencing could be precisely classified using the reference genome, the researchers were able to determine from which region of the Aldabra Atoll the two Zurich individuals probably originally came. "We also identified putative deleterious mutations that should be monitored," the authors said. "The findings are relevant to genetic diversity management and reintroduction efforts."
basis for further research
In future studies, the reference genome could also help investigate the genetic basis of the species' extraordinarily long lifespan. The presumed oldest Aldabra tortoise, which died at Kolkata Zoo in 2006, was probably 256 years old. If the corresponding records are correct, it was the oldest known land vertebrate. The question of which genetic traits are responsible for the giant growth of the species could also be clarified using the new genome data.
Source: Gözde Çilingir (University of Zurich) et al., GigaScience, doi: 10.1093/gigascience/giac090