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The fruit fly species,  Ceratitis rosa sensu stricto  and  Ceratitis quilicii , are sibling species restricted to the lowland and highland regions, respectively. Until recently, these sibling species were considered as allopatric populations of  C. rosa  with distinct bionomics. We used deep Next Generation Sequencing (NGS) technology on intact guts of individuals from the two sibling species to compare their transcriptional profiles and simultaneously understand gut microbiome and host molecular processes and identify distinguishing genetic differences between the two species. Since the genomes of both species had not been published previously, the transcriptomes were assembled  de novo  into transcripts. Microbe-specific transcript orthologs were separated from the assembly by filtering searches of the transcripts against microbe databases using OrthoMCL. We then used differential expression analysis of host-specific transcripts (i.e. those remaining after the microbe-specific transcripts had been removed) and microbe-specific transcripts from the two-sibling species to identify defining species-specific transcripts that were present in only one fruit fly species or the other, but not in both. In  C. quilicii  females, bacterial transcripts of  Pectobacterium spp .,  Enterobacterium buttiauxella, Enterobacter cloacae  and  Klebsiella variicola  were upregulated compared to the  C. rosa s.s . females. Comparison of expression levels of the host transcripts revealed a heavier investment by  C. quilicii  (compared with  C. rosa s.s .) in: immunity; energy production; cell proliferation; insecticide resistance; reproduction and proliferation; and redox reactions that are usually associated with responses to stress and degradation of fruit metabolites.

Species-specific transcriptional profiles of the gut and gut microbiome of Ceratitis quilicii and Ceratitis rosa sensu stricto