"What's really curious about tuatara is it has these features in the genome which are deeply ancestral," Gemmell said.
These lineages stretched back hundreds of millions of years.
"It has affinities with turtles, crocodilians, snakes and lizards, but there are also components of the genome that have closest affinity to genetic elements found in mammals, including humans," he said.
"So it's a real mish-mash of features that are likely a combination of the primitive and quite derived."
Much about the tuatara has been an enigma to scientists: it's still uncertain today whether the species is actually two sub-species, as has been maintained for the past two decades, or one.
The sequencing research had involved researchers from at least 25 laboratories around the world - such was the global interest in tuatara - along with input from Northland iwi Ngati Wai.
"It's a big genome, and it has got a lot of repetitive sequences that have never been described before," Gemmell said.
"So normally, when you sequence a genome, and particularly with mammals, you've got a reasonable idea of what you're going to find, in terms of sequence types.
"But because tuatara are so unusual, we've found all of these completely unique elements that are new to science."
One part of the project had been focused on how tuatara determined the sex of offspring.
"The simple answer to that at the moment is we just don't know how that works yet at a molecular level," he said.
"But it's important because we know tuatara have temperature dependent sex determination: at higher temperatures, they produce males, but at lower temperatures they produce females.
"And of course, with global warming, there are concerns that populations of tuatara will become more and more male-biased, which will probably lead to them becoming locally extinct, unless they can adapt by digging deeper burrows - but there is obviously a limit to how much that would help."
Pin-pointing the key gene or genes involved in sex determination might eventually allow scientists to ultimately inhibit or stimulate it to help tuatara populations maintain healthy sex ratios, he said.
"If we could get this information, there may be potential genetic approaches we could consider in the future that would enable us to help this species to persist."
Clive Stone of Ngati Wai said working with the researchers on the project had been a "fascinating journey" for the iwi, which treasured the tuatara as an "absolute taonga".
"It's given us a much better appreciation of the whakapapa of the species, and our objective has been to get a better understanding of what it means to us in the future," he said.
"We hold the tuatara in reverence - the mana it has is part of our story - so we very much value any information we get about its well-being."
Gemmell expected to finish writing the project's results by the end of the year.
Our tuatara taonga
• Adults range from about 300g to 1kg.
• Are the only surviving members of the order Sphenodontia, which was well represented by many species during the age of the dinosaurs, some 200 million years ago. All species except for the tuatara declined and eventually became extinct about 60 million years ago.
• Are recognised internationally and within New Zealand as species in need of active conservation management.
How DNA has redefined our native species
The yellow-eyed penguin
DNA analysis and carbon dating led to findings published last year that revealed a changeover between the yellow-eyed penguin and another penguin species that became extinct around the same time as the moa.
An Otago University team showed the waitaha, which was slightly smaller than the yellow-eyed penguin, vanished within 200 years of Polynesian settlement of New Zealand, before 1500AD.
In one of the most rapid biological transition events documented, the yellow-eyed penguin, or hoiho - considered one of the world's rarest penguin species with a population of between 6000 and 7000 - moved to the mainland from the Sub-Antarctic islands and replaced the waitaha within just a few decades, in the early 1500s.
The New Zealand sea lion
That research had fascinating parallels with the fate of a pre-historic species of New Zealand sea lion, which once dominated South Island shores before they became extinct as recently as between 1300 and 1500AD, soon after Polynesian settlement.
DNA analysis reported in 2014 showed their place on the New Zealand mainland was quickly taken by today's modern population, which was previously limited to the cold waters of the Sub-Antarctic.
The kiwi
2014 was also the year that scientists corrected the shocking suggestion that our national bird arrived here when its winged ancestor flew in from Australia.
The 150-year-old mystery was finally solved by DNA sequencing that revealed the bird was more closely related to the extinct, 2.3m tall elephant bird, a native of Madagascar.
The moa
A separate study in 2014 put even more genetic distance between the extinct moa and their old bush mates, the kiwi.
DNA-based research led by New Zealand scientist Professor Allan Baker suggested the giant birds were more closely related to a flying South American bird still alive today than our national icon.
The South American tinamous, one of the world's most ancient living groups of bird, can fly and are not categorised as ratites, but are considered close relatives because of the shared structure of their palate bones.
