HT-SuperSAGE of the gut tissue of a Vip3A-resistant Heliothis virescens F. (Lepidoptera: Noctuidae) strain provides insights into its evolution and toxin adaptation

Summary: Multi-toxins Bt-crops carrying insecticidal toxins with similar host spectrum and different mode of action e.g. Cry and Vip, are expected to improve resistance management in target pests. Control failure has been informed for Cry toxins but not for Vip3A, of which no mechanism of resistance has yet been identified. Here we applied HT-SuperSAGE to analyze the transcriptome profiling in the midgut tissue of a tobacco budworm Heliothis virescens (F.) strain laboratory-selected for Vip3A resistance. A total of 1324252 26-bp tags were sequenced representing 17751 unique transcripts (UniTags) from genetically similar Vip3A-resistant (Vip-Sel) strain and susceptible control (Vip-Unsel) strain. Differential expression was found significant (≥ 2.5-fold or ≤ 0.4) for 1845 unigenes that constitute 10.4% of the total number of UniTags, where 277 represented overexpressed (OE) and 1568 underexpressed (UE) genes in Vip-Sel compared to Vip-Unsel. BLASTN searches mapped 1141 of these UniTags to H. virescens EST sequences, of which, 816 (143 OE and 673 UE) were unambiguously annotated to proteins in NCBI non-redundant protein databases. Gene ontology revealed Vip3A adaptation induced major constitutive transcriptional differences in serine-proteases (SP)-mediated proteolysis, ribosome biogenesis and metabolic processes. Several unigenes homologous to a particular member of the REsponse to PAThogen (REPAT) family were found to be predominantly OE. Since UniTags related to SP and ribosomal proteins (RP) were the most represented in the libraries, they were further analyzed in details. Interestingly, UniTags related to the putative Vip3A-binding protein RpS2 were underexpressed, while, the tumorigenesis suppressor RpL37 accounted for the 35% of total overexpressed RP. A subset of unigenes was chosen to confirm the HT-SuperSAGE data by qRT-PCR. The present study is the first providing a lepidopteran gut transcriptome associated with Vip3A resistance and a foundation for future attempts to elucidate the resistance mechanism. Methods: Midgut transcriptional profiles of third-instar larvae from genetically similar Vip3A-resistant (Vip-Sel) and susceptible control (Vip-Unsel) strains were generated by HT-SuperSAGE. RNA pools of Vip-Sel and Vip-Unsel samples (five RNA preparations each) were prepared and used for the construction of SuperSAGE libraries HvR_GCCT and HvS_GCAC, respectively, according to the procedure described by [Matsumura et al., 2010]. Purified PCR products were mixed and applied to Illumina Genome Analyzer II sequencing with GEX (DpnII) primer in the sequencing reactions as recommended by the manufacturer. Sorting of sequence reads based on index sequences and the subsequent extraction of sequence tags from reads was conducted using a script written in Perl. Fold-change for each tag was calculated as in [Gilardoni et al., 2010]. qRT–PCR validation was performed using TaqMan and SYBR Green assays.