Abstract
The tuatara (Sphenodon punctatus)—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2—is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
Highlights
It is a species of importance in other contexts
To provide insights into the biology of the tuatara, we have sequenced its genome in partnership with Ngātiwai, the Māori iwi who hold kaitiakitanga over the tuatara populations located on islands in the far north of New Zealand
We find that the tuatara genome—as well as the animal itself—is an amalgam of ancestral and derived characteristics
Summary
Example, RSPO1 and WNT4) gene networks to promote testicular or ovarian development, respectively[24]. 659 of the 4,284 orthologues we tested had significantly different ω values (ratios of non-synonymous to synonymous substitutions, dN/dS) on the tuatara branch relative to the birds and other reptiles we tested (Supplementary Information 17) None of these orthologues had ω values suggestive of strong positive selection (that is, >1), the results do indicate that shifts in patterns of selection are affecting many genes and functional categories of genes across the tuatara genome, including genes involved in RNA regulation, metabolic pathways, general metabolism and sex determination. Our results support the distinctiveness of the North Brother Island tuatara, which has variously been described as S. punctatus or Sphenodon guntheri[3,32] This population is highly inbred and shows evidence of a severe bottleneck, which most probably reflects a founder event around the time of the last glaciation[34]. Each partnership is unique, we provide a template agreement (Supplementary Information 20) that we hope will be useful to others
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