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Background: The control of mosquitoes transmitting infectious diseases relies mainly on the use of chemical insecticides. However, mosquito control programs are now threatened by the emergence of insecticide resistance mechanisms. Hitherto, most research efforts have been focused on elucidating molecular basis of inherited resistance, but less attention has been paid to the short-term response of mosquitoes to insecticides and pollutants and yet this could have a significant impact on insecticide efficacy and may allow identifying mosquito genes involved in insecticide tolerance. Here, a combination of LongSAGE and Solexa sequencing was used to perform a deep transcriptome analysis of larvae of the yellow fever mosquito exposed for 48h to sub-lethal doses of three chemical insecticides and three anthropogenic pollutants. Results: Thirty millions of 20 bp cDNA tags were sequenced, mapped to mosquito genome and clustered, representing 6850 known genes and 4868 additional clusters not located within predicted genes. Differential transcriptome analysis revealed 453 genes and 250 additional clusters being differentially transcribed in mosquito larvae exposed to xenobiotics. Cross-validation of transcription profiles of 14 selected genes by RT-qPCR revealed a high correlation of transcription ratios obtained from the two techniques. Mosquitoes exposed to insecticides or anthropogenic pollutants showed considerable modifications of their transcriptome correlated to the molarity and chemical properties of xenobiotics. Genes encoding cuticular proteins, transporters, and enzymes involved in the mitochondrial respiratory chain and detoxification processes were particularly affected. Conclusion: Genes and molecular mechanisms potentially involved in xenobiotic response and insecticide tolerance were identified. Despite low concentrations and no apparent phenotypic effects, the significant impact of these xenobiotics on mosquito larvae transcriptome rise important questions about the ?hidden impact? of anthropogenic pollutants on ecosystems and consequences on vector control in polluted areas. At the technical level, the method used in the present study appears as a powerful approach for investigating transcriptome variations in genome-sequenced organisms and can provide useful informations for the detection of novel transcripts. |