Editing Tuatara (section)

== Genomic characteristics ==
The most abundant [[Long interspersed nuclear element|LINE element]] in the tuatara is L2 (10%). Most of them are interspersed and can remain active. The longest L2 element found is 4 kb long and 83% of the sequences had ORF2p completely intact. The CR1 element is the second most repeated (4%). Phylogenetic analysis shows that these sequences are very different from those found in other nearby species such as lizards. Finally, less than 1% are elements belonging to L1, a low percentage since these elements tend to predominate in placental mammals.<ref name="Gemmell2020" /> Usually, the predominant LINE elements are the CR1, contrary to what has been seen in the tuatara. This suggests that perhaps the genome repeats of sauropsids were very different compared to mammals, birds and lizards.<ref name="Gemmell2020" />

The genes of the [[major histocompatibility complex]] (MHC) are known to play roles in disease resistance, [[mate choice]], and kin recognition in various vertebrate species. Among known vertebrate genomes, MHCs are considered one of the most polymorphic.<ref>{{cite journal |author=Sommer, S. |date=October 2005 |title=The importance of immune gene variability (MHC) in evolutionary ecology and conservation |journal=Frontiers in Zoology |volume=2 |issue=1 |page=16 |doi=10.1186/1742-9994-2-16 |pmc=1282567 |pmid=16242022 |doi-access=free}}</ref><ref>{{cite journal |vauthors=Rymešová D, Králová T, Promerová M, Bryja J, Tomášek O, Svobodová J, Šmilauer P, Šálek M, Albrecht T |date=2017-02-16 |title=Mate choice for major histocompatibility complex complementarity in a strictly monogamous bird, the grey partridge (''Perdix perdix'') |journal=Frontiers in Zoology |volume=14 |page=9 |doi=10.1186/s12983-017-0194-0 |pmc=5312559 |pmid=28239400 |doi-access=free}}</ref> In the tuatara, 56 MHC genes have been identified; some of which are similar to MHCs of amphibians and mammals. Most MHCs that were annotated in the tuatara genome are highly conserved, however there is large genomic rearrangement observed in distant [[lepidosaur]] lineages.<ref name="Gemmell2020" />

Many of the elements that have been analyzed are present in all [[amniote]]s, most are mammalian interspersed repeats or MIR, specifically the diversity of MIR subfamilies is the highest that has been studied so far in an amniote. 16&nbsp;families of [[Short interspersed nuclear element|SINEs]] that were recently active have also been identified.<ref name="Gemmell2020" />

The tuatara has 24&nbsp;unique families of [[DNA transposon]]s, and at least 30 subfamilies were recently active. This diversity is greater than what has been found in other amniotes and in addition, thousands of identical copies of these transposons have been analyzed, suggesting to researchers that there is recent activity.<ref name="Gemmell2020" />

The genome is the second largest known to reptiles. Only the [[Greek tortoise]] genome is larger.<ref>[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977179/ Did Lizards Follow Unique Pathways in Sex Chromosome Evolution?]</ref> Around 7,500&nbsp;[[LTR retrotransposon|LTRs]] have been identified, including 450&nbsp;[[endogenous retrovirus]]es (ERVs). Studies in other [[Sauropsida]] have recognised a similar number but nevertheless, in the genome of the tuatara it has been found a very old clade of retrovirus known as [[Spumavirus]].<ref name="Gemmell2020" />

More than 8,000&nbsp;[[non-coding RNA]]-related elements have been identified in the tuatara genome, of which the vast majority, about 6,900, are derived from recently active [[transposable element]]s. The rest are related to ribosomal, [[Spliceosome|spliceosomal]] and [[signal recognition particle RNA]].<ref name="Gemmell2020" />

The [[Mitochondrial DNA|mitochondrial genome]] of the genus ''Sphenodon'' is approximately 18,000&nbsp;bp in size and consists of 13&nbsp;protein-coding genes, 2&nbsp;[[ribosomal RNA]] and 22&nbsp;[[transfer RNA]] genes.<ref name="Gemmell2020" />

[[DNA methylation]] is a very common modification in animals and the distribution of [[CpG site]]s within genomes affects this methylation. Specifically, 81% of these CpG sites have been found to be methylated in the tuatara genome. Recent publications propose that this high level of methylation may be due to the amount of repeating elements that exist in the genome of this animal. This pattern is closer to what occurs in organisms such as zebrafish, about 78%, while in humans it is only 70%.<ref name="Gemmell2020" />