Transgenic corn and cotton produce crystalline (Cry) proteins derived from the soil bacterium Bacillus thuringiensis (Bt) that are toxic to lepidopteran larvae.  Helicoverpa zea, a key pest of corn and cotton in the U.S., has evolved widespread resistance to these proteins produced in Bt corn and cotton.  While the genomic targets of Cry selection and the mutations that produce resistant phenotypes are known in other lepidopteran species, little is known about how selection by Cry proteins shape the genome of H. zea.  We scanned the genomes of Cry1Ac-selected and unselected H. zea lines, and identified twelve genes on five scaffolds that differed between lines, including cadherin-86C (cad-86C), a gene from a family that is involved in Cry1A resistance in other lepidopterans.  Although this gene was expressed in the H. zea larval midgut, the protein it encodes has only 17 to 22% identity with cadherin proteins from other species previously reported to be involved in Bt resistance.  An analysis of midgut-expressed cDNAs showed significant between-line differences in the frequencies of putative nonsynonymous substitutions (both SNPs and indels).  Our results indicate that cad-86C is a likely target of Cry1Ac selection in H. zea.  It remains unclear, however, whether genomic changes at this locus directly disrupt midgut binding of Cry1Ac and cause Bt resistance, or indirectly enhance fitness of H. zea in the presence of Cry1Ac by some other mechanism.  Future work should investigate phenotypic effects of these nonsynonymous substitutions and their impact on fitness of H. zea larvae that ingest Cry1Ac.  

There are three data types associated with this data set. 

The first is raw Pacific Biosciences (PacBio) long read sequences produced from PCR amplified cad-86C cDNAs (m54163_180608_183238.subreads.bam).  We have also provided the barcodes that can be used to demultiplex these PacBio data using the demulti_bbduk.sh script provided at https://github.com/rguo1990/Hzea_PacBio_sequencing. 

The second is a pair of fasta files containing amplicon sequences produced by cad-86C primer pairs 1b and 2b.

The third is an excel spreadsheet containing the raw qPCR data used to test whether cad-86C was expressed in the H. zea larval midgut.

In order to demultiplex the PacBio dataset, please use the barcodes provided in the barcode file along with the demulti_bbduk.sh script provided at https://github.com/rguo1990/Hzea_PacBio_sequencing.