Abstract
BackgroundTransposable 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 mammals, non-mammalian vertebrates and invertebrates.ResultsWe 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 significant levels of exonization of TEs, only anecdotal cases were found in invertebrates. In vertebrates, as in mammals, the exonized TEs are mostly alternatively spliced, indicating that selective pressure maintains the original mRNA product generated from such genes.ConclusionsExonization of TEs is widespread 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.
Highlights
IntroductionTransposable 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
Transposable elements (TEs) have played an important role in the diversification and enrichment of mammalian transcriptomes through various mechanisms such as exonization and intronization, and insertion into first and last exons
Genome-wide analysis of TE insertions within the transcriptomes of five non-mammalian species To evaluate the effect of TEs on the transcriptomes of non-mammals, we analyzed the genomes of five nonmammalian vertebrates and invertebrates: G. gallus, D. rerio, C. intestinalis, D. melanogaster and C. elegans
Summary
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. Transposable elements (TEs) are mobile genetic sequences that comprise a large fraction of mammalian genomes: 45%, 37% and 55% of the human, mouse and opossum genomes are made up of these elements, respectively [1,2,3,4,5,6]. TEs are distinguished by their mode of propagation. TEs are not just 'junk' DNA but rather are important players in mammalian evolution and speciation through mechanisms such as exonization and intronization [8,9,10,11]. Alternative splicing of exonized TEs can be tissue specific [12,13] and
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