The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates

TL;DR

This study compares the impact of transposable elements on the transcriptomes of mammals, non-mammalian vertebrates, and invertebrates, revealing a correlation between intron length and TE exonization across species.

Contribution

It provides the first extensive comparative analysis of TE effects on transcriptomes across diverse non-mammalian species, highlighting evolutionary differences.

Findings

Lower TE exonization in invertebrates compared to vertebrates.

Exonized TEs are mostly alternatively spliced in vertebrates.

TE exonization correlates with intron length and evolutionary complexity.

Abstract

Background: Transposable elements (TEs) have played an important role in the diversification and enrichment of mammalian transcriptomes through various mechanisms such as exonization and intronization (the birth of new exons/introns from previously intronic/exonic sequences, respectively), and insertion into first and last exons. However, no extensive analysis has compared the effects of TEs on the transcriptomes of mammalian, non-mammalian vertebrates and invertebrates. Results: We analyzed the influence of TEs on the transcriptomes of five species, three invertebrates and two non-mammalian vertebrates. Compared to previously analyzed mammals, there were lower levels of TE introduction into introns, significantly lower numbers of exonizations originating from TEs and a lower percentage of TE insertion within the first and last exons. Although the transcriptomes of vertebrates exhibit a significant level of exonizations of TEs, only anecdotal cases were found in invertebrates. In vertebrates, as in mammals, the exonized TEs are mostly alternatively spliced, indicating selective pressure maintains the original mRNA product generated from such genes. Conclusions: Exonization of TEs is wide-spread in mammals, less so in non- mammalian vertebrates, and very low in invertebrates. We assume that the exonization process depends on the length of introns. Vertebrates, unlike invertebrates, are characterized by long introns and short internal exons. Our results suggest that there is a direct link between the length of introns and exonization of TEs and that this process became more prevalent following the appearance of mammals.