Recent expansion of Penelope-like retrotransposons in the leatherback turtle Dermochelys coriacea

Abstract

Abstract Transposable elements are known to induce variation in vertebrate genomes through their diversity and number, with related species usually presenting consistency in the proportion and abundance of TE families. Despite their ancient divergence times, sea turtles Chelonia mydas and Dermochelys coriacea show high levels of overall genomic synteny and gene collinearity, but there is still a lot to explore regarding their TE panorama. In light of this, we analysed high-quality reference genomes of these species, which represent the two different extant superfamilies of sea turtles - Dermochelyidae and Cheloniidae - to explore their mobilomes and compared them with the 13 available Testudines draft genomes. In line with previous genome-wide comparisons between the two distantly related sea turtle superfamilies, our analyses showcased that turtle genomes generally share similar mobilomes. Nonetheless, we identified that the main difference between these mobilomes is a much higher proportion of Penelope-like Elements (PLEs) and Long Interspersed Elements (LINEs) in D. coriacea. Finally, we identified a new PLE subfamily of Neptune-1 present in D. coriacea’s genome, with evidence for a substantial amount of recent insertions. These results show that despite the overall slow evolutionary pace of turtle genomes, at least D. coriacea exhibits an active mobilome.