Western corn rootworm (Diabrotica virgifera virgifera) transcriptome assembly and genomic analysis of population structure

• Published in: BMC genomics Vol. 15; no. 1; p. 195
• Main Authors: Flagel, Lex E, Bansal, Raman, Kerstetter, Randall A, Chen, Mao, Carroll, Matthew, Flannagan, Ronald, Clark, Thomas, Goldman, Barry S, Michel, Andy P
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 14-03-2014; BioMed Central
• Subjects: Agricultural chemicals industry; Analysis; Animal behavior; Animals; Bioassays; Coleoptera - genetics; Computational Biology - methods; Crop rotation; Diabrotica virgifera virgifera; Genes; Genetic aspects; Genetic diversity; Genetic engineering; Genetically modified crops; Genetics, Population; Genomics; Genotype; Insecticides; Molecular Sequence Annotation; Physiological aspects; Polymorphism, Single Nucleotide; Population; R&D; Reproducibility of Results; Research & development; Studies; Transcriptome; Zea mays; United States; United States > US
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-15-195

Western corn rootworm (WCR) is one of the most significant insect pests of maize in North America. WCR has dramatically increased its range in the last century, invading key maize production areas in the US and abroad. In addition, this species has a history of evolving traits that allow it to escape various control options. Improved genetic and genomic resources are crucial tools for understanding population history and the genetic basis of trait evolution. Here we produce and analyze a transcriptome assembly for WCR. We also perform whole genome population resequencing, and combine these resources to better understand the evolutionary history of WCR.
The WCR transcriptome assembly presented here contains approximately 16,000 unigenes, many of which have high similarity to other insect species. Among these unigenes we found several gene families that have been implicated in insecticide resistance in other species. We also identified over 500,000 unigene based SNPs among 26 WCR populations. We used these SNPs to scan for outliers among the candidate genes, and to understand how population processes have shaped genetic variation in this species.
This study highlights the utility of transcriptomic and genomic resources as foundational tools for dealing with highly adaptive pest species. Using these tools we identified candidate gene families for insecticide resistance and reveal aspects of WCR population history in light of the species' recent range expansion.