The chromosome-scale genome of a gentle giant provides insight into the genetic health of a threatened population

The Aldabra giant tortoise is one of only two giant tortoise species left in the world and is currently on the Endangered Species List. Conservation efforts are ongoing, but more and better tools are urgently needed to improve the chances of long-term success. A study published today by an international team of researchers has provided such a tool: they have completed and published a very high-quality genome sequence that will help secure a future for this endangered species.

Gözde Çilingir of the University of Zurich and colleagues around the world have now provided precisely this information, using a number of state-of-the-art methods to achieve a ‘chromosome-scale’ representation of the genome of the Aldabra giant tortoise. This work will be published in the journal GigaScience.

Giant tortoises were once found on Madagascar and a variety of islands in the western Indian Ocean. Fossil records indicate that giant tortoises existed on every continent except Antarctica and Australia. Today only two giant tortoises exist: the Aldabra giant tortoise and the Galápagos giant tortoise. The Aldabra giant tortoise (Aldabrachelys gigantea) can reach a weight of up to 300 kg and typically lives more than 100 years, with an individual reportedly living to 250 years – if so, it would be the oldest recorded terrestrial vertebrate.

Aldabrachelys gigantea still lives in its natural habitat, the Aldabra Atoll northwest of Madagascar, but the gentle giant is “Vulnerable” according to the International Union for Conservation of Nature, meaning the species is critically endangered in the wild. Having more tools and resources, especially genetic information, is one of the best ways to ensure the long-term success of this amazing creature.

Lead researcher Çilingir emphasized this point, saying, “Genomic information is important to zoo breeding efforts to conserve the genetic diversity that exists in the wild.” may be useful, particularly on how they can aid in comparative studies with other tortoise and tortoise species, adding: “We have found that most of the genome is similar to other known genomes of Testudines (the order representing tortoises and includes tortoises).

The genome sequence data that the authors have generated here is at the forefront of what is being done in the genome sequencing arena, which performs “chromosome-scale” genome sequencing. This term is used when genome sequence data is a nearly complete representation of the sequence of more than two billion genetic “letters” and the sequences are aligned in the same order as they appear in the actual chromosomes. Not only did earlier genome sequences have many more gaps, but the sequence data was additionally placed in so-called “scaffolds,” sequences that are arranged in a relative order but not fully anchored in space with respect to the chromosome.

The current chromosome-scale genome sequences provide such fine-grained genomic information that it allows researchers to more closely follow genetic variation in wild and captive turtles. To demonstrate how the new reference genome can be used for practical conservation and breeding efforts, the authors sequenced thirty giant tortoises from the wild population and two individuals from Zurich Zoo. Using this data in combination with the high-quality reference genome, they were able to determine where the animals kept in zoos in the Aldabra Atoll originally came from.

The availability of a high-quality reference genome for this species will therefore help answer a number of biological questions – for example, to understand why the species grows to such an enormous size. With an appetite commensurate with their size, giant tortoises play an important role in shaping a typical island landscape due to the vast amount of vegetation they consume. In fact, after being reintroduced to their natural environment and helping them to thrive, giant tortoises could serve as ecological surrogates for the extinct giant tortoises on the western Indian Ocean islands due to their similar central roles in their ecosystems. Aldabra giant tortoises act as ecosystem engineers to restore degraded island habitats, even outside of their original home range.

Restoring natural conservation mechanisms is an essential building block to do much more than just reduce the risk of individual species becoming extinct.

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