Location: Corn Insects and Crop Genetics Research
Project Number: 5030-22000-018-08-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Oct 1, 2015
End Date: Feb 14, 2018
To sequence the western corn rootworm (Diabrotica virgifera virgifera) genome and use the information about gene content to compare the genes involved in successful attack of corn by Diabrotica larvae versus those involved when attacking Miscanthus and switchgrass.
We will sequence the 2.6 Gb D. virgifera genome using Roche pyrosequencing (providing long 700 bp reads for contig building) and ILLUMINA sequencing-by-synthesis (providing deep coverage with 100 bp reads that correct homopolymer errors in the 454 reads). Paired-end libraries of 3, 8, and 20 kb lengths will also be sequenced with ILLUMINA to provide scaffolding information. Long-range scaffolding and mapping will be facilitated with additional sequencing using the Pacific Biosciences SMRT "strobe" method, as well as Sanger end-sequencing of BACs from an existing library, and a SNP-based linkage map currently underway in Iowa. The assembled genome (Illinois) will be annotated using MAKER (Utah) using on-going and additional transcriptome sequencing, and made available via GMOD tools (INRA, France). We will compare gene expression in root-feeding larvae on corn versus Miscanthus and switchgrass using RNA-seq with ILLUMINA (Iowa/Nebraska).