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<p>Abstract</p> <p>Background</p> <p>The genomes of three major mosquito vectors of human diseases, <it>Anopheles gambiae</it>, <it>Aedes aegypti</it>, and <it>Culex pipiens quinquefasciatus</it>, have been previously sequenced. <it>C. p. quinquefasciatus</it> has the largest number of predicted protein-coding genes, which partially results from the expansion of three detoxification gene families: cytochrome P450 monooxygenases (P450), glutathione S-transferases (GST), and carboxyl/cholinesterases (CCE). However, unlike <it>An. gambiae</it> and <it>Ae. aegypti</it>, which have large amounts of gene expression data, <it>C. p. quinquefasciatus</it> has limited transcriptomic resources. Knowledge of complete gene expression information is very important for the exploration of the functions of genes involved in specific biological processes. In the present study, the three detoxification gene families of <it>C. p. quinquefasciatus</it> were analyzed for phylogenetic classification and compared with those of three other dipteran insects. Gene expression during various developmental stages and the differential expression responsible for parathion resistance were profiled using the digital gene expression (DGE) technique.</p> <p>Results</p> <p>A total of 302 detoxification genes were found in <it>C. p. quinquefasciatus</it>, including 71 CCE, 196 P450, and 35 cytosolic GST genes. Compared with three other dipteran species, gene expansion in <it>Culex</it> mainly occurred in the CCE and P450 families, where the genes of α-esterases, juvenile hormone esterases, and CYP325 of the CYP4 subfamily showed the most pronounced expansion on the genome. For the five DGE libraries, 3.5-3.8 million raw tags were generated and mapped to 13314 reference genes. Among 302 detoxification genes, 225 (75%) were detected for expression in at least one DGE library. One fourth of the CCE and P450 genes were detected uniquely in one stage, indicating potential developmentally regulated expression. A total of 1511 genes showed different expression levels between a parathion-resistant and a susceptible strain. Fifteen detoxification genes, including 2 CCEs, 6 GSTs, and 7 P450s, were expressed at higher levels in the resistant strain.</p> <p>Conclusions</p> <p>The results of the present study provide new insights into the functions and evolution of three detoxification gene families in mosquitoes and comprehensive transcriptomic resources for <it>C. p. quinquefasciatus</it>, which will facilitate the elucidation of molecular mechanisms underlying the different biological characteristics of the three major mosquito vectors.</p>