  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.
