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

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.

💡 Research Summary

The study investigates how transposable elements (TEs) have shaped the transcriptomes of non‑mammalian vertebrates and invertebrates, providing a comparative perspective with previously documented mammalian data. Five model organisms were examined: chicken (Gallus gallus), zebrafish (Danio rerio), sea squirt (Ciona intestinalis), fruit fly (Drosophila melanogaster), and nematode (Caenorhabditis elegans). Genome sequences, EST/cDNA alignments, and repeat annotations were obtained from the UCSC Genome Browser, allowing the authors to map each TE relative to annotated gene structures.

Key quantitative findings: In mammals, TEs occupy 37–55 % of the genome, whereas in the examined non‑mammalian species they cover roughly 10 % (with zebrafish as an outlier at 26.5 %). The composition of TE families differs markedly: chicken genomes are dominated by CR1 LINEs (≈79 % of all TEs), zebrafish by DNA transposons (>75 %), fruit fly by LTR elements (44 %), and C. elegans by DNA transposons (≈70 %). This compositional shift influences how TEs interact with host genes.

Insertion into introns: In humans and mice about 60 % of TEs reside within introns. In chicken, zebrafish, and sea squirt the corresponding percentages drop to 33.2 %, 47.3 %, and 39.4 % respectively. Fruit fly and C. elegans show similar overall intronic TE percentages to mammals, yet the proportion of introns that actually contain TEs is dramatically lower—1.7 % in fruit fly and 5.6 % in C. elegans—reflecting a strong selective barrier against TE integration in short introns.

Intronic length analysis reveals a positive correlation between median intron size and the fraction of introns harboring TEs. Median lengths of TE‑containing introns are ~3 kb in humans, mice, chicken, and zebrafish, but only ~700 bp in C. elegans and ~6 kb (after TE subtraction) in fruit fly, whose typical introns are only ~72 bp. This suggests that long introns provide a permissive environment for TE insertion and subsequent exonization, whereas short introns are protected by the “intron definition” mechanism.

Exonization events: The authors identified 70 TE‑derived exons in chicken and 253 in zebrafish, 9 in sea squirt, but none in fruit fly and only a single case in C. elegans (supported by a solitary individual). In mammals, thousands of TE‑derived exons have been reported; the lower numbers in non‑mammalian vertebrates indicate a reduced but still detectable contribution of TEs to transcriptome diversification. The majority of TE‑derived exons are alternatively spliced, mirroring the mammalian pattern and implying selective pressure to preserve the original mRNA while allowing novel isoforms. In chicken, many TE‑derived exons appear constitutively spliced, but limited EST coverage may bias this observation.

Orientation bias: Across the studied genomes, LTRs, DNA transposons, and LINEs preferentially insert in the antisense orientation relative to the host transcript, likely because sense‑oriented insertions would introduce ectopic promoters and be deleterious.

Coding‑region insertions: In fruit fly, three LINE insertions were found within internal coding exons, extending exon length dramatically (up to >4 kb) without disrupting the reading frame, a phenomenon not observed in mammals. In C. elegans, a DNA transposon contributed an alternatively spliced 73‑bp exon to a conserved gene, suggesting that exonization can also affect protein‑coding sequences in nematodes, albeit rarely.

Overall, the data support the authors’ central hypothesis: intron length is a key determinant of TE insertion frequency and subsequent exonization. The evolution of long introns in vertebrates created a “fertile ground” for TE‑driven transcriptome innovation, a process that intensified after the emergence of mammals. In contrast, the short‑intron architecture of many invertebrates restricts TE integration, resulting in minimal exonization. This work underscores that the impact of TEs on genome evolution is highly lineage‑specific, shaped by structural genome features and the balance between mutagenic risk and potential adaptive benefit.