Tooth Pseudogenes | johnabramyan

I was also fortunate to be part of the first turtle genome sequencing consortium to sequence the genome of the western painted turtle Chrysemys picta bellii. I was particularly interested in identifying the genes associated with tooth development in turtles. Turtles lost the ability to form teeth approximately 150- 200 million years ago, making them the oldest extant edentulous lineage of tetrapods (birds lost teeth approxi- mately 80-100 million years ago).

Previous studies in birds and edentulous mysticete (baleen) whales demon- strated that tooth loss is closely associated with the pseudogenization and subsequent degradation of the tooth-specific genes enamelin (ENAM), amelogenin (AMEL), ameloblastin (AMBN), dentin sialophosphoprotein (DSPP), and enamelysin (MMP20). I identified the majority of turtle pseudo-exons in their chromosomally syntenic regions when compared to other amniotes, consistent with the very slow rate of genomic change seen in chelonians. Turtle ENAM, AMEL, and MMP20 all contain premature stop codons (exons 5, 3, and 2, respectively) in addition to highly degenerated sequences. AMBN, while somewhat more conserved, has a premature stop codon in exon 7. While DSPP exons 1 and 2 are relatively conserved, all subsequent exons were unidentifiable.

Sequence identity scores between pseudogene exons identified in turtle and chicken were not significantly different from each other compared to their functional orthologs in crocodilians, even though turtles lost their teeth approximately 50-100 million year earlier. This extremely conservative pattern of tooth-loss pseudogenization across amniotes is consistent with a single evolutionary origin (and regulatory network) of teeth, and suggests that the deterioration of this pathway evolved independently (that is, is homoplastic) in turtles, whales, and birds. This is also consistent with the fossil record, as early members of all three lineages are known to be toothed. However, concordant with their overall slow rate of molecular evolution, the tooth-specific genes in turtles have accumulated mutations at roughly half the rate of accumulation found in birds.

I am currently working on more detailed analyses of these pseudogenes in collaboration with Prof. Brad Shaffer.

Manuscripts:

Shaffer, H. B., Minx, P., Warren, D. E., Shedlock, A. M., Thomson, R. C., Valenzuela, N., Abramyan, J.,... & Schwartz, T. (2013). The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol, 14(3), R28.