NEW YORK (GenomeWeb) – Researchers have sequenced the desert tortoise genome, which they hope will inform conservation approaches.
Agassiz's desert tortoise, Gopherus agassizii, is native to the Mojave Desert of the Western US and can live some 50 years in the wild. However, it is on the US endangered species list and is considered vulnerable by the International Union for Conservation of Nature. The tortoises' numbers have dwindled in part due to human impact on its habitat as well as a respiratory disease.
An Arizona State University-led team of researchers has sequenced the G. agassizii genome, and as it reported in PLOS One today, the team uncovered variants that appear to underpin its longevity and its adaption to an arid climate. The team also noted variants fixed among Gopherus species that are linked to the immune system.
"We don't know how the tortoise is handling the fact that it's also being threatened by an upper respiratory disease," first author Marc Tollis, a postdoc at ASU, said in a statement. "Decoding this genome will help us catalog which tortoise genes are evolving quickly enough to help them overcome this threat."
Tollis and his colleagues isolated DNA for sequencing from an Agassiz's desert tortoise, checking it against a database of STR repeats and mtDNA data to ensure it was G. agassizii and not a hybrid of G. agassizii and the closely related Morafka's desert tortoise, G. morafkai. They assembled the reads they generated into a 2.4 Gbp assembly.
At the same time, the researchers extracted RNA from lung, brain, and skeletal muscle for RNA sequencing, and they used the transcriptomic reads they generated to annotate the assembly.
In particular, the researchers noted that the G. agassizii assembly includes 20,172 protein-coding genes, which is in line with other published reptile genomes. Additionally, they reported that 43 percent of the G. agassizii genome comprises repeats, especially DNA transposons and long-terminal repeat elements, among others.
Tollis and his colleagues compared the G. agassizii genome to those of other sauropsids and chelonians, including the Chinese soft-shell turtle, American alligator, and the chicken, among others.
Chelonians — an order that includes turtles and tortoises — have accumulated fewer DNA substitutions over time than other sauropsids, the researchers reported. They noted that this could be the longer generation times of many chelonians.
Still, by comparing Agassiz's desert tortoise genome to that of the western painted tortoise, which is a temperate aquatic species, the researchers have pinpointed more than 50 genes that appeared to be under accelerated evolution in the desert tortoise.
For instance, one such gene was CD34, which encodes a protein involved in vascular repair following glomerular injury, while others were CSTA and SDR16C5, which are involved in keratinocyte differentiation and proliferation. Changes to genes like these, the researchers noted, could have enabled the tortoise to adapt to its arid environment.
Additionally, both Agassiz's desert tortoise and the green sea turtle also shared genes under accelerated evolution like BCL2A1 and GZMA that are involved in aging and apoptosis and could be linked to their longevity.
Tollis and his colleagues also examined SNPs that had become fixed in G. agassizii. Genes harboring such SNPs were enriched for gene ontology terms like RNA metabolism and processing, macromolecular modifications, and other metabolic processes. They also reported that three genes with fixed variants were linked to humoral or B-cell mediated immunity and nine overlapped with innate immune response.
As Agassiz's desert tortoise is susceptible to upper respiratory disease, the researchers noted that variants affecting immune response are of interest to potentially help manage disease.