Investigating the impact of whole genome duplication on transposable element evolution in ray-finned fishes

Abstract

Transposable elements (TEs) can make up more than 50% of any given vertebrates genome, with substantial variability in TE composition among lineages. TE variation is often linked to changes in gene regulation, genome size, and speciation. However, the role that genome duplication events have played in generating abrupt shifts in the composition of the mobilome over macroevolutionary timescales remains unclear. We investigated the degree to which the teleost genome duplication (TGD) shaped the diversification trajectory of the ray-finned fish mobilome. We integrate a new high coverage genome of Polypterus bichir with data from over 100 publicly available actinopterygian genomes to assess the macroevolutionary implications of genome duplication events on TE evolution. Our results provide no evidence for a substantial shift in mobilome composition following the TGD event. Instead, the diversity of the actinopterygian mobilome appears to have been shaped by a history of lineage specific shifts in composition that are not correlated with commonly evoked drivers of diversification such as body size, water column usage, or latitude. Collectively, these results provide a new perspective on the early diversification of the actinopterygian mobilome and suggest that historic ploidy events may not necessarily catalyze bursts of TE diversification and innovation.