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Background    Wolbachia  is a bacterial endosymbiont that naturally infects a wide range of insect species, and causes drastic changes to host biology. Stable infections of  Wolbachia  in mosquitoes can inhibit infection with medically important pathogens such as dengue virus and malaria-causing  Plasmodium  parasites. However, some native  Wolbachia  strains can enhance infection with certain pathogens, as is the case for the mosquito  Aedes fluviatilis , where infection with  Plasmodium gallinaceum  is enhanced by the native  w Flu  Wolbachia  strain. To better understand the biological interactions between mosquitoes and native  Wolbachia  infections, and to investigate the process of pathogen enhancement, we used RNA-Seq to generate the transcriptome of  Ae. fluviatilis  with and without  Wolbachia  infection.    Results  In total, we generated 22,280,160 Illumina paired-end reads from  Wolbachia -infected and uninfected mosquitoes, and used these to make a  de novo  transcriptome assembly, resulting in 58,013 contigs with a median sequence length of 443 bp and an  N50  of 2454 bp. Contigs were annotated through local alignments using BlastX, and associated with both gene ontology and KEGG orthology terms. Through baySeq, we identified 159 contigs that were significantly upregulated due to  Wolbachia  infection, and 98 that were downregulated. Critically, we saw no changes to Toll or IMD immune gene transcription, but did see evidence that  w Flu infection altered the expression of several bacterial recognition genes, and immune-related genes that could influence  Plasmodium  infection.  w Flu infection also had a widespread effect on a number of host physiological processes including protein, carbohydrate and lipid metabolism, and oxidative stress. We then compared our data set with transcriptomic data for other  Wolbachia  infections in  Aedes aegypti , and identified a core set of 15 gene groups associated with  Wolbachia  infection in mosquitoes.    Conclusions  While the scale of transcriptional changes associated with  w Flu infection might be small, the scope is rather large, which confirms that native  Wolbachia  infections maintain intricate molecular relationships with their mosquito hosts even after lengthy periods of co-evolution. We have also identified several potential means through which  w Flu infection might influence  Plasmodium  infection in  Ae. fluviatilis , and these genes should form the basis of future investigation into the enhancement of  Plasmodium  by  Wolbachia .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3441-4) contains supplementary material, which is available to authorized users.

The transcriptome of the mosquito Aedes fluviatilis (Diptera: Culicidae), and transcriptional changes associated with its native Wolbachia infection