ChimeraTE: A pipeline to detect chimeric transcripts derived from genes and transposable elements

Abstract

Transposable elements (TEs) are structural variants considered an important source of genetic diversity, which may arise in the transcriptome when TEs are transcribed in the same RNA molecule as genes, producing what we hereafter call chimeric transcripts. The presence of chimeric transcripts has been associated with adaptive traits in several species, but their identification remains hindered due to the lack of tools to detect them on a transcriptome-wide scale. Previous bioinformatics tools were developed to identify chimeric transcripts derived from TEs present in a reference genome. Nevertheless, different individuals/cells/strains might harbor different TE insertions generating such chimeric transcripts. Therefore, we have developed ChimeraTE, a pipeline that uses paired-end RNA-seq reads to identify chimeric transcripts with or without a reference genome, in a transcriptome-wide manner. ChimeraTE has two Modes: Mode 1 is a genome-guided approach that employs the canonical method of genome alignment, whereas Mode 2 identifies chimeric transcripts without a reference genome, being able to predict chimeras derived from fixed or polymorphic TEs. We have used both Modes with Illumina RNA-seq reads from ovarian tissues of Drosophila melanogaster wild-type strains, and found that ~3% of all genes generate chimeric transcripts. Approximately ~9% of all detected chimeras were absent from the D. melanogaster′s reference genome, corresponding to polymorphic insertions in the wild-type strains. ChimeraTE is the first pipeline with the ability to automatically uncover chimeric transcripts without a reference genome.

Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes acrossDrosophilanatural strains

“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted December 2, 2022. ; https://doi.org/10.1101/2022.12.02.518890 doi: bioRxiv preprint and AS insertions group (911 vs. 61 insertions, respectively). Note that a recent analysis by Oliveira et al 43 also found this same region of the roo consensus sequence to be the most abundant in chimeric gene-TE transcripts across four D. melanogaster strains 43 . The authors evaluated whether these short sequences were widespread repeats across the genome.…”

“…This short roo sequence is more common in the internal insertions group than in the overlap and AS insertions group (911 vs. 61 insertions, respectively). Note that a recent analysis by Oliveira et al 43 also found this same region of the roo consensus sequence to be the most abundant in chimeric gene-TE transcripts across four D. melanogaster strains 43 . The authors evaluated whether these short sequences were widespread repeats across the genome.…”

“…We argued that if these low complexity regions have a roo origin, we should find that at least some of them should also have a blast hit with a roo insertion. To test this, we used less strict blast parameters compared with Oliveira et al 43 and found that 57 of the low complexity regions have a roo element insertion as the second best hit and 148 have a roo insertion in the top 5 hits, suggesting that indeed some of these sequences have a clear roo origin (Table S5F). Furthermore, we also tested whether this low complexity region was present in the roo consensus sequence from a closely related species, D. simulans , and found that this was the case strongly suggesting that this low complexity sequence is an integral part of the roo element.…”

Transposable elements as evolutionary driving force to ecological speciation in cactophilicDrosophilaspecies

“…We used TRF v. 4.09 (161) in all TE insertions from each genome, with parameters 2, 5, 6, 75, 20, 50, 500, -m, -h, and removed TEs that had SSRs over more than 50% of their sequences. Such method has been previously used to remove TE copies that are indistinguishable from simple repeats (34,162).…”

“…Exaptation and domestication events can be often identified by the occurrence of chimeric transcripts, which are mRNAs with both gene and TE-derived sequences (33). A recent transcriptome-wide study has identified that ~1.12% of D. melanogaster genes produce chimeric transcripts (34). Among all genes, 76 produce polymorphic chimeric transcripts from TE insertions that were present in one strain, but absent in another, highlighting the potential of TEs as a source of genetic novelty between different natural Drosophila ecotypes.…”