Diversity and Evolution of Transposable Elements Across Four Anolis Lizard Genomes

Transposable elements are DNA sequences that can move from one genomic locus to another, and are essential and ubiquitous components of vertebrate genomes. Within mammals, the human genome is dominated by the autonomous L1 and non-autonomous Alu non-LTR retrotransposons, and the transposable element repertoires of other eutherians are similarly constrained. In contrast, the genomes of most fish and reptiles contain a diverse array of transposable elements, including multiple active clades of non-LTR and LTR retrotransposons as well as DNA transposons. Understanding why reptiles, as the sister taxon to mammals, differ so greatly in terms of their genomic parasites would shed light on the coevolution of genomes and their transposable elements. However, the divergence times of modern reptilian lineages are on average much older than those of modern mammals, and comparative studies have suffered from a lack of phylogenetic resolution. Here we describe and analyze the repetitive landscapes of three newly sequenced Anolis lizard genomes. Together with the genomic model A. carolinensis, these genomes represent a lineage whose diversification is limited to the Cenozoic Era. While the four Anolis genomes are similar in terms of transposable element diversity and abundance, we found evidence of differential accumulation of some DNA transposon families as well as differences in the average age of insertions of particular families between genomes. This suggests that while there has been at least some differential success between orthologous transposable element families subsequent to speciation, the repetitive profiles of Anolis genomes have remained relatively stable during the diversification process.