Abstract
ABSTRACT Background The host shift in insects has been considered a key process with potential to collaborate with reproductive isolation and speciation. Both genomics and transcriptomics variation has been attributed to such process, in which gene families with functions for host location, acceptance and usage have been proposed to evolve. In this context, cactophilic Drosophila species are an excellent model to study host shift evolution, since they use a wide-range of cacti as hosts, and many species have different preferences. Transposable elements are engines of genetic novelty between populations and species, driving rapid adaptive evolution. However, the extent of TEs’ contribution to host shift remains unexplored. Results We performed genomic and transcriptomic analysis in seven genomes of cactophilic species/subspecies to investigate how TEs interact with genes associated with host shift. Our results revealed enrichment of TEs at promoter regions of host shift-related genes, with Helitrons representing ∼60% of the cases, demonstrating an unprecedented putative cis - regulatory role of Helitrons in Drosophila . Differential expression analysis between species with different preferred hosts demonstrated divergence on gene expression in head and larvae tissues. Although TEs’ presence does not affect overall gene expression, we observed 1.31% of genes generating gene-TE chimeric transcripts, including those with function affecting host preference. Conclusions Our combined genomic and transcriptomic approaches provide evidence of TE-driven divergence between species, highlighting the evolutionary role of TEs in the context of host shift, a key adaptive process that can cause reproductive isolation.