| Summary: | <p>The larval midgut of diamondback moth,<i> Plutella xylostella</i>, is a dynamic tissue that interfaces with a diverse array of physiological and toxicological processes, including nutrient digestion and allocation, xenobiotic detoxification, innate and adaptive immune response, and pathogen defense. Despite its enormous agricultural importance, the genomic resources for <i>P. xylostella</i> are surprisingly scarce. In this study, a <i>Bt</i> resistant <i>P. xylostella</i> strain was subjected to the in-depth transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes in the <i>P. xylostella</i> larval midgut.</p><p>Using Illumina deep sequencing, we obtained roughly 40 million reads containing approximately 3.6 gigabases of sequence data. <i>De novo</i> assembly generated 63,312 ESTs with an average read length of 416bp, and approximately half of the <i>P. xylostella</i> sequences (45.4%, 28,768) showed similarity to the non-redundant database in GenBank with a cut-off E-value below 10<sup>-5</sup>. Among them, 11,092 unigenes were assigned to one or multiple GO terms and 16,732 unigenes were assigned to 226 specific pathways. In-depth analysis indentified genes putatively involved in insecticide resistance, nutrient digestion, and innate immune defense. Besides conventional detoxification enzymes and insecticide targets, novel genes, including 28 chymotrypsins and 53 ABC transporters, have been uncovered in the <i>P. xylostella</i> larval midgut transcriptome; which are potentially linked to the <i>Bt </i>toxicity and resistance. Furthermore, an unexpectedly high number of ESTs, including 46 serpins and 7 lysozymes, were predicted to be involved in the immune defense.</p><p>As the first tissue-specific transcriptome analysis of <i>P. xylostella</i>, this study sheds light on the molecular understanding of insecticide resistance, especially <i>Bt</i> resistance in an agriculturally important insect pest<i>,</i> and lays the foundation for future functional genomics research. In addition, current sequencing effort greatly enriched the existing <i>P. xylostella</i> EST database, and makes RNAseq a viable option in the future genomic analysis.</p>
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