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Background  Phlebotomine sand flies (Diptera, Nematocera) are important vectors of several pathogens, including  Leishmania  parasites, causing serious diseases of humans and dogs. Despite their importance as disease vectors, most aspects of sand fly biology remain unknown including the molecular basis of their reproduction and sex determination, aspects also relevant for the development of novel vector control strategies.    Results  Using comparative genomics/transcriptomics data mining and transcriptional profiling, we identified the sex determining genes in phlebotomine sand flies and proposed the first model for the sex determination cascade of these insects. For all the genes identified, we produced manually curated gene models, developmental gene expression profile and performed evolutionary molecular analysis. We identified and characterized, for the first time in a Nematocera species, the  transformer  ( tra ) homolog which exhibits both conserved and novel features. The analysis of the  tra  locus in sand flies and its expression pattern suggest that this gene is able to autoregulate its own splicing, as observed in the fruit fly  Ceratitis capitata  and several other insect species.    Conclusions  Our results permit to fill the gap about sex determination in sand flies, contribute to a better understanding of this developmental pathway in Nematocera and open the way for the identification of sex determining orthologs in other species of this important Diptera sub-order. Furthermore, the sex determination genes identified in our work also provide the opportunity of future biotechnological applications to control natural population of sand flies, reducing their impact on public health.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5898-4) contains supplementary material, which is available to authorized users.

Identification of sex determination genes and their evolution in Phlebotominae sand flies (Diptera, Nematocera)