Transposable elements and gene expression variation in the intraspecific hybrids of Capsella rubella

Transposable elements (TEs) are prevalent components of diverse genomes, and play an important role on the genomic stability and expression regulation of their adjacent genes. It is interesting to know the variation of TE expression and the effects of the presence/absence of TEs on gene expression after hybridization. Here we assessed the expression variation of TEs and the impacts of TEs on expression of nearby genes after hybridization based on comparisons of three pairs of reciprocal F-1 hybrids and four parents in Capsella rubella. Of the 480 TE families expressed in all the four parents and six F-1 hybrids, 7-23 (1.5%-4.2%) TE families were significantly differentially expressed between in silico and real F-1 hybrids, indicating the expression levels of these TE families were affected during hybridization. In particular, there was a Copia TE superfamily and a non-long terminal repeat (non-LTR) TE differentially expressed between the reciprocal F-1 hybrids of 879 and 86IT1, indicating maternal effects may have impacts on expression of TEs in these F-1 hybrids. Besides the impacts on the expression of TE families of the hybridization, genes adjacent to polymorphic TEs tended to show a higher proportion (24.83%) of allele-specific expression (ASE) in F-1 hybrids. Overall, our results highlight the impacts of hybridization on the expression level variation of TEs, and the effects of TEs on ASE after hybridization.