Transcriptional dynamics and tissue-specific expression patterns of transposable elements in orthopteran insects

Abstract

Transposable elements (TEs) are prevalent in the genomes of orthopteran insects, contributing significantly to their genome evolution and diversity. In light of the existing gap in our understanding of TEs transcript dynamics in orthopteran insects, we recognize the critical need to undertake comprehensive analyses in this area. Therefore, we have decided to delve into the characterization of TE transcripts, their abundance profiles, and the formation of chimeric transcripts using RNA-seq data and genome assemblies. The transcript analysis of TEs across various species revealed significant differences in TE abundance and expression patterns. In particular, Schistocerca americana exhibited twice the number of transcripts within the genus Schistocerca compared to the average of other species, while Gryllus bimaculatus displayed the lowest number of transcripts. Despite this, all Schistocerca species shared similar fractions of TE transcripts at the clade level, with DNA transposons (45%) being the most abundant, followed by LINE (19%) and LTR elements (18%). Interestingly, Acrida cinerea displayed different TE abundance patterns compared to Schistocerca species, particularly with an increased proportion of LTR transcripts, accounting for 31% of the total transcripts. Further analysis revealed tissue-specific transcriptional activity of TE clades, with notable differences between male and female specimens. In Gryllus bimaculatus, TEs were highly transcribed across ovaries and gut tissues in females compared to male testes and gut. Conversely, Gastrimargus marmoratus displayed higher TE transcription in male tissues compared to females, indicating species-specific expression patterns. A similar pattern has been observed in Acrida cinerea, except in female gonads, where 4618 TEs were transcribed compared to 3757 in male gonads. Despite these variations, no correlation was found between genome size and TE transcript abundance. Additionally, highly conserved TEs were involved in the formation of chimeric transcripts, indicating potential regulatory roles in gene expression. The expression quantification analysis of chimeric TEs and genes revealed tissue-specific expression patterns, and TEs do not control the overall expression of all genes except some, suggesting regulatory roles of TEs in gene expression. Overall, our study underscores tissue-specific variations in TE expression and transcript abundance among different species. Additionally, our findings suggest the involvement of highly conserved TEs in the formation of chimeric transcripts across different species.