A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect

Brad S. Coates, Kimberly K.O. Walden, Dimpal Lata, Neetha Nanoth Vellichirammal, Robert F. Mitchell, Martin N. Andersson, Rachel McKay, Marcé D. Lorenzen, Nathaniel Grubbs, Yu Hui Wang, Jinlong Han, Jing Li Xuan, Peter Willadsen, Huichun Wang, B. Wade French, Raman Bansal, Sammy Sedky, Dariane Souza, Dakota Bunn, Lance J. MeinkeNicholas J. Miller, Blair D. Siegfried, Thomas W. Sappington, Hugh M. Robertson

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Adaptations by arthropod pests to host plant defenses of crops determine their impacts on agricultural production. The larval host range of western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is restricted to maize and a few grasses. Resistance of D. v. virgifera to crop rotation practices and multiple insecticides contributes to its status as the most damaging pest of cultivated maize in North America and Europe. The extent to which adaptations by this pest contributes to host plant specialization remains unknown. Results: A 2.42 Gb draft D. v. virgifera genome, Dvir_v2.0, was assembled from short shotgun reads and scaffolded using long-insert mate-pair, transcriptome and linked read data. K-mer analysis predicted a repeat content of ≥ 61.5%. Ortholog assignments for Dvir_2.0 RefSeq models predict a greater number of species-specific gene duplications, including expansions in ATP binding cassette transporter and chemosensory gene families, than in other Coleoptera. A majority of annotated D. v. virgifera cytochrome P450s belong to CYP4, 6, and 9 clades. A total of 5,404 transcripts were differentially-expressed between D. v. virgifera larvae fed maize roots compared to alternative host (Miscanthus), a marginal host (Panicum virgatum), a poor host (Sorghum bicolor) and starvation treatments; Among differentially-expressed transcripts, 1,908 were shared across treatments and the least number were between Miscanthus compared to maize. Differentially-expressed transcripts were enriched for putative spliceosome, proteosome, and intracellular transport functions. General stress pathway functions were unique and enriched among up-regulated transcripts in marginal host, poor host, and starvation responses compared to responses on primary (maize) and alternate hosts. Conclusions: Manual annotation of D. v. virgifera Dvir_2.0 RefSeq models predicted expansion of paralogs with gene families putatively involved in insecticide resistance and chemosensory perception. Our study also suggests that adaptations of D. v. virgifera larvae to feeding on an alternate host plant invoke fewer transcriptional changes compared to marginal or poor hosts. The shared up-regulation of stress response pathways between marginal host and poor host, and starvation treatments may reflect nutrient deprivation. This study provides insight into transcriptomic responses of larval feeding on different host plants and resources for genomic research on this economically significant pest of maize.

Original languageEnglish (US)
Article number19
JournalBMC genomics
Volume24
Issue number1
DOIs
StatePublished - Dec 2023

Keywords

  • Differential expression
  • Genome assembly
  • Host plant specialization

ASJC Scopus subject areas

  • Genetics
  • Biotechnology

Fingerprint

Dive into the research topics of 'A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect'. Together they form a unique fingerprint.

Cite this