The tuatara genome: insights into vertebrate evolution from the sole survivor of an ancient reptilian order
Preprint posted on December 08, 2019 https://www.biorxiv.org/content/10.1101/867069v1
Between 85-70 million years ago, the land mass now known as New Zealand (or Aotearoa, its Māori designation) parted from the supercontinent of Gondwana. A most notable lack of endemic mammal competitors, together with very late human colonization (it is thought that Māori people first arrived in New Zealand some 700-900 years ago), led to the extraordinary preservation of Gondwana-like fauna and flora in New Zealand. The reptile Sphenodon punctatus, also known as tuatara, is such a “living fossil” (Figure 1).
Tuatara are remarkably unique. These reptiles represent the only extant species of the ancient order Rhynchocephalia (Sphenodontia), which presumably originated in the Early Mesozoic, approximately 250 million years ago, and thrived throughout Gondwana. Nowadays, wild tuatara are restricted to 32 offshore islands in New Zealand, where their survival is challenged, for example, by ongoing climate change and predation by invasive mammal species. Their phylogenetic relationship amongst reptiles was ambiguous for a long time because of features shared with many groups. Nevertheless, tuatara have a set of fascinating adaptations that set them apart from other reptiles. For example, the tuatara can live for more than 100 years and have temperature-dependent sex determination (hence why climate change is a big issue). Māori find tuatara very significant, adding an extra cultural dimension to the relevance of this species. In fact, the Māori people give tuatara the status of taonga (meaning treasure) and consider them as the guardians of special places.
Now, Professor Neil J. Gemmell and colleagues report the sequencing and assembly of the tuatara genome, providing an amazing window into the past, namely into the early evolution of tetrapods, amniotes, and reptiles. Moreover, it provides an invaluable resource for the future conservation of this species.
- The tuatara genome is pretty up on the list of largest vertebrate genomes with an estimated 5 Giga base pairs (compared to 3 Giga base pairs in human).
- Phylogenetic analysis comparing the genome of tuatara with other amniotes reveals that tuatara shared a common ancestor with snakes and lizards around 250 million years ago.
- At least 64% of the tuatara genome is comprised of repetitive sequences, split between transposable elements (31%) and low copy number segmental duplications (33%). This high proportion of repeats is more similar to mammalian genomes, than reptilian genomes. The authors then took a closer look at the astonishing quantity and diversity of transposable elements, per family, identifying recent transposon activity and unique expansions.
- Using post-bisulfite adaptor tagging, whole-genome DNA methylation levels of the tuatara genome were set at around 81% of methylated CpG sites, the highest DNA methylation levels of amniotes. The authors propose that these high DNA methylation levels may be a result of the high proportion of transposable elements present in the tuatara genome.
- The authors identify ortholog and novel genes potentially related to the many adaptations of tuatara, regarding immunity, odor reception, thermal regulation, and selenium metabolism.
- Contrary to what was previously thought, the tuatara genome is evolving relatively slowly, judging by DNA substitution rates. In fact, the tuatara genome seems to be the slowest-evolving genome amongst lepidosauria, the group including tuatara, lizards, and snakes.
What I like about this preprint?
In a recent visit to New Zealand, I was very happy to learn about the tuatara, an iconic animal for New Zealanders. As a fan of transposable elements, I became even happier after finding this preprint and learning about the unprecedented diversity and quantity of transposable elements present in the tuatara genome. The genome of this extraordinary animal, whose ancestors once roamed in Gondwana, will undoubtedly be a treasure-trove of great biological insights.
The somewhat sterile scientific literary style typically leaves no room for reporting more human aspects of scientific research. Another aspect I really enjoyed about this preprint is its unusual human and cultural dimension. As stated in the preprint, to perform this work, researchers had to reach out to, and work with the indigenous Māori communities, especially the Ngātiwai and Ngāti Koata, the Māori iwi (tribes) holding kaitiakitanga (guardianship) of the tuatara. Indigenous communities and researchers had to get together to clearly and transparently define the common goal: to know more about the tuatara in order to ultimately prevent its extinction.
- With the bounty of information that this genome provides, what do you think are the next steps in tuatara research?
- With what you could already learn from its genome, which tuatara conservation strategies could be implemented? Given New Zealand’s strict conservation policies protecting its offshore islands, is reduction of inbreeding by introducing individuals from other islands an option?
- Is there an expansion of genomically encoded DNA methyltransferase genes in tuatara? It is plausible that an unusually high number of DNA methyltransferases is required to establish the observed high levels of DNA methylation. Alternatively, there may be some more highly processive DNA methyltransferase(s).
Want to know more?
Tuatara: Biology and Conservation of a Venerable Survivor, Cree, 2014
Tuatara, Jones & Cree, 2012.
Posted on: 20th December 2019Read preprint
Also in the evolutionary biology category:
Hedgehog signaling is required for endomesodermal patterning and germ cell development in Nematostella vectensis
|Selected by||Paul Gerald L. Sanchez and Stefano Vianello|
Bacterial FtsZ induces mitochondrial fission in human cells
|Selected by||Leeba Ann Chacko|
Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations
|Selected by||Alexa Sadier, Alexa Sadier|
Also in the genomics category:
CoolMPS™: Advanced massively parallel sequencing using antibodies specific to each natural nucleobase
|Selected by||Kerryn Elliott|
Hnf4a-mediated regulation of proximal tubule progenitors in the mouse kidney
|Selected by||Brooke Chambers|
Mutational signatures are jointly shaped by DNA damage and repair
|Selected by||Kerryn Elliott|
preListsevolutionary biology category:in the
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
|List by||Hiral Shah|
COVID-19 / SARS-CoV-2 preprints
List of important preprints dealing with the ongoing coronavirus outbreak. See http://covidpreprints.com for additional resources and timeline, and https://connect.biorxiv.org/relate/content/181 for full list of bioRxiv and medRxiv preprints on this topic
|List by||Gautam Dey, Zhang-He Goh|
SDB 78th Annual Meeting 2019
A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.
|List by||Alex Eve|
Pattern formation during development
The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.
|List by||Alexa Sadier|