Interested in transposable elements in the Anolis genome? You should be!
As DNA sequences that can move about the genome, transposable elements – or TEs – are also called “jumping genes”. These are some of the most important components of genomes, accounting for much of the variation in genome size and structure across vertebrates. The activity of TEs add to the genetic variation of populations in neutral, deleterious, and sometimes adaptive ways. In the human genome, TEs can insert into genes and cause numerous genetic diseases such as muscular dystrophy (Cannilan and Batzer 2006).
We published a review in last month’s issue of Mobile Genetic Elements (Tollis & Boissinot 2011) describing the diversity and abundance of TEs found so far in the Anolis genome, and how they impact our understanding of genome evolution in reptiles and mammals. The Anolis genome contains an extraordinary diversity of TEs, including DNA transposons (“cut and paste” elements) and long terminal repeat (LTR) and non-LTR retrotransposons (“copy and paste” elements). Even though there are many different kinds of TEs in Anolis, within most TE families there are low copy numbers relative to the human genome, suggesting that purifying selection keeps tight control.
This is totally different than what is observed in mammalian genomes, where only the L1 retrotransposon has dominated. Forty percent of the human genome is due to the activity of this TE (Lander et al. 2001), the result of the accumulation of hundreds of thousands of copies over 100 million years of primate evolution (Khan et al. 2006).
Information coming in from other squamates suggest that reptiles and mammals may have different ways of dealing with their intragenomic parasites. A study of two snakes, copperhead and Burmese python, show that the diversity of TEs in snakes is similar to Anolis (Castoe et al. 2011). However, TE abundance differs in these snakes, even though they both have similarly small genomes (TE content is ~20% and ~40% of genome size in python versus copperhead, respectively).
We compare the TE profile of Anolis to other vertebrate models (including zebrafish, stickleback, pufferfish, Xenopus, zebra finch and chicken, human and other mammals) and place them in a phylogenetic context in order to understand genomic evolution since the tetrapod and amniote radiations. The most parsimonious model of amniote genome evolution is one in which the ancestor of mammals and reptiles contained a TE-diverse genome, just like Anolis.
Why do TE profiles differ within and between lineages? It could be due to metabolic demands, demographic histories of the host species, or regulation of TE activity of the host. My dissertation research is investigating the interaction between A. carolinensis‘s evolutionary history and the geographic distribution of TE polymorphisms across its natural range. It has involved field work and a lot of lab work including using the Anolis genome sequence. I hope to report my interesting results very soon!