The pest status of A. gossypii in Australian cotton has steadily increased since the 1990’s when it was considered a late season secondary pest suppressed by insecticides used against other insect species (Wilson 1996). The introduction of Bt-transgenic cotton into Australia in the 1990’s, which contains a toxin deadly to the primary cotton insect pest Helicoverpa spp., significantly reduced the number of insecticide sprays required for their control (Fitt 2003). These sprays were inadvertently controlling secondary pest populations including A. gossypii, which consequently increased (Wilson 1996). In the late 1990s significant damage from A. gossypii via the transmission of the poleovirus Cotton Bunchy Top (CBT) disease (Reddall et al. 2004) led to reduced aphid tolerance by growers, and an increase in the number of targeted sprays against them. These sprays led to resistance in pest populations of A. gossypii that have caused the chemical control to fail. Spray failures against aphids can permanently tarnish Australia’s reputation for producing high quality lint if failures lead to ‘sticky cotton’. Failures also increase grower costs and the likely hood of unforeseen environmental consequences.

The aim of this study was to investigate insecticide resistance mechanisms associated with neonicotinoid resistant A. gossypii from Australian cotton. In the present de novo assembly, a total of 132,159,760 clean reads from the pooled transcriptomes of thiamethoxam resistant and susceptible A. gossypii strains were generated resulting in a dramatically increased repertoire of resistance-related genes in A. gossypii under thiamethoxam stress. Clean reads were assembled into 37,167 contigs and from this 31,042 unigenes were assembled of which 23,372 matched known genes. Therefore, this study has generated a comprehensive transcriptome resource for A. gossypii that has characterized the expression of numerous important transcripts encoding proteins involved in insecticide resistance. Consequently, this study will contribute to future research relating to molecular characterization of insecticide resistance mechanisms of A. gossypii and other insect pests.