ABSTRACT Background The host shift in insects has been considered a key process with potential to collaborate with ecological 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 effects, since they use a wide-range of cacti as hosts, and many species have cacti-hosts preference. Despite the potential adaptive role of TEs by generating genetic variability between species and populations, the extent of TEs’ contribution to host shift remains unexplored. Results Here, we performed genomics and transcriptomics analyses in seven genomes of cactophilic species/subspecies to investigate how TEs interact with genes likely to be associated with host shift. Our results revealed transposition bursts between species, and an enrichment of TEs at promoter regions of host shift-related genes. Pairwise differential expression analysis between species with different preferential hosts in larvae and head tissues demonstrated divergence on gene expression associated with host location in head, whereas for the larvae we found higher differential expression of genes related to usage/detoxification. Although TEs’ presence does not affect overall gene expression, we observed 2.1% of genes generating gene-TE chimeric transcripts, including those with function affecting host preference. In addition, Helitrons were often observed interacting with genes as a cis -regulatory element. Conclusions Our combined genomics and transcriptomics approaches provide new insights regarding the evolutionary role of TEs on the context of ecological speciation.

Transposable elements as evolutionary driving force to ecological speciation in cactophilicDrosophilaspecies