NEW YORK (GenomeWeb) – A study online this week in the Proceedings of the National Academy of Sciences described findings from a genome sequencing study of the Tibetan Plateau frog Nanorana parkeri — just the second frog species to have its full genome sequenced.
Researchers from the US, China, Canada, Saudi Arabia, Denmark, Hong Kong, and elsewhere did de novo sequencing and assembly on the Tibetan Plateau frog, coupled with transcriptome sequencing on several tissue types. They then compared it with sequences from five other vertebrate species, including another previously sequenced frog species.
The analysis provided clues to features shared between the distantly related frogs, the team explained. More broadly, the draft genome assembly is expected to serve as a resource for studying vertebrate evolution, particularly the transition from land to water, as well as the adaptations that allow Tibetan frogs to thrive in high-altitude, low-oxygen conditions that impede other forms of life.
"This genome greatly broadens our understanding of the evolution of tetrapod genomes by providing additional comparative resources for the water-to-land transitional vertebrates," co-senior author Ya-Ping Zhang, a researcher affiliated with the Chinese Academy of Sciences and Yunnan University, and colleagues wrote.
The amphibian lineage has features that are expected to be crucial to understanding tetrapod vertebrate evolution, the researchers explained. But while most of the 7,000 or so frog species described so far have aquatic tadpole forms and an adult stage adapted to life on land, the only frog species sequenced so far represents a derived genus called Xenopus that spends all of its life in water.
For their new study, the investigators focused on N. parkeri, a species that has a well-defined terrestrial adult stage and has adapted to life at elevations that reach up to 5,000 meters (more than 16,400 feet).
The team used the Illumina HiSeq 2000 to tackle the 2.3-billion-base genome, producing 83-fold average sequence depths and at least 20-fold coverage across 94 percent of the resulting assembly. On top of that, the group generated almost 170 million bases of RNA sequence data from Tibetan frog brain, liver, ovary, and skin tissue samples.
The draft N. parkeri genome came in at 2 billion bases, the researchers noted, eclipsing that of the previously sequenced frog Xenopus tropicalis by hundreds of thousands of bases.
Nevertheless, their annotation suggested both frog genomes house roughly 20,000 predicted protein-coding genes — 23,408 genes in the case of N. parkeri — and share widespread synteny, despite falling in distinct branches of the frog family tree.
Many of the remaining Tibetan Plateau frog sequences were made up of transposable elements, the team noted, which made up some 50 percent of the N. parkeri genome.
Compared with the other four other vertebrate animals sequenced so far, the Xenopus and N. parkeri frog genomes contained relatively few rearrangements between different chromosomes, though rearrangements within individual chromosomes occurred at roughly the same rate.
Although 832 gene families were distinct to the Tibetan frogs and another 161 were only found in Xenopus, the researchers also tracked down more than 9,400 gene families that appeared to be shared across all six vertebrates.
The team selected nearly 4,300 single-copy gene orthologs from the latter set for a phylogenetic analysis of the animals — a tree that pointed to a divergence time of around 266 million years ago for Xenopus and N. parkeri frogs.
The Tibetan frog tended to show expansions to parts of the genome coding for smell receptor genes and components of other signaling pathways, while the Xenopus genome contained smooth muscle- and immune-related genes not present in the genome of its terrestrial cousin.