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Coates BS, Walden KKO, Lata D, Vellichirammal NN, Mitchell RF, Andersson MN, McKay R, Lorenzen MD, Grubbs N, Wang YH, Han J, Xuan JL, Willadsen P, Wang H, French BW, Bansal R, Sedky S, Souza D, Bunn D, Meinke LJ, Miller NJ, Siegfried BD, Sappington TW, Robertson HM. A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect. BMC Genomics 2023; 24:19. [PMID: 36639634 PMCID: PMC9840275 DOI: 10.1186/s12864-022-08990-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/04/2022] [Indexed: 01/15/2023] Open
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.
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Affiliation(s)
- Brad S. Coates
- grid.508983.fCorn Insects & Crop Genetics Research Unit, USDA-ARS, 2310 Pammel Dr, 532 Science II, Iowa State University, Ames, IA 50011 USA
| | - Kimberly K. O. Walden
- grid.35403.310000 0004 1936 9991Roy J. Carver Biotechnology Center, University of Illinois at Champaign-Urbana, Urbana, IL USA
| | - Dimpal Lata
- grid.62813.3e0000 0004 1936 7806Department of Biology, Illinois Institute of Technology, Chicago, IL USA
| | | | - Robert F. Mitchell
- grid.267474.40000 0001 0674 4543University of Wisconsin Oshkosh, Oshkosh, WI USA
| | - Martin N. Andersson
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
| | - Rachel McKay
- grid.267474.40000 0001 0674 4543University of Wisconsin Oshkosh, Oshkosh, WI USA
| | - Marcé D. Lorenzen
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Nathaniel Grubbs
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Yu-Hui Wang
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Jinlong Han
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Jing Li Xuan
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Peter Willadsen
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Huichun Wang
- grid.24434.350000 0004 1937 0060Department of Entomology, University of Nebraska, Lincoln, NE USA
| | - B. Wade French
- grid.508981.dIntegrated Crop Systems Research Unit, USDA-ARS, Brookings, SD USA
| | - Raman Bansal
- grid.512850.bUSDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA USA
| | - Sammy Sedky
- grid.512850.bUSDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA USA
| | - Dariane Souza
- grid.15276.370000 0004 1936 8091Department of Entomology, University of Florida, Gainesville, FL USA
| | - Dakota Bunn
- grid.62813.3e0000 0004 1936 7806Department of Biology, Illinois Institute of Technology, Chicago, IL USA
| | - Lance J. Meinke
- grid.24434.350000 0004 1937 0060Department of Entomology, University of Nebraska, Lincoln, NE USA
| | - Nicholas J. Miller
- grid.62813.3e0000 0004 1936 7806Department of Biology, Illinois Institute of Technology, Chicago, IL USA
| | - Blair D. Siegfried
- grid.15276.370000 0004 1936 8091Department of Entomology, University of Florida, Gainesville, FL USA
| | - Thomas W. Sappington
- grid.508983.fCorn Insects & Crop Genetics Research Unit, USDA-ARS, 2310 Pammel Dr, 532 Science II, Iowa State University, Ames, IA 50011 USA
| | - Hugh M. Robertson
- grid.35403.310000 0004 1936 9991Department of Entomology, University of Illinois at Champaign-Urbana, Urbana, IL USA
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Zhao Z, Meihls LN, Hibbard BE, Ji T, Elsik CG, Shelby KS. Differential gene expression in response to eCry3.1Ab ingestion in an unselected and eCry3.1Ab-selected western corn rootworm (Diabrotica virgifera virgifera LeConte) population. Sci Rep 2019; 9:4896. [PMID: 30894586 PMCID: PMC6427003 DOI: 10.1038/s41598-019-41067-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 02/26/2019] [Indexed: 01/09/2023] Open
Abstract
Diabrotica virgifera virgifera LeConte, the western corn rootworm (WCR) is one of the most destructive pests in the U.S. Corn Belt. Transgenic maize lines expressing various Cry toxins from Bacillus thuringiensis have been adopted as a management strategy. However, resistance to many Bt toxins has occurred. To investigate the mechanisms of Bt resistance we carried out RNA-seq using Illumina sequencing technology on resistant, eCry3.1Ab-selected and susceptible, unselected, whole WCR neonates which fed on seedling maize with and without eCry3.1Ab for 12 and 24 hours. In a parallel experiment RNA-seq experiments were conducted when only the midgut of neonate WCR was evaluated from the same treatments. After de novo transcriptome assembly we identified differentially expressed genes (DEGs). Results from the assemblies and annotation indicate that WCR neonates from the eCry3.1Ab-selected resistant colony expressed a small number of up and down-regulated genes following Bt intoxication. In contrast, unselected susceptible WCR neonates expressed a large number of up and down-regulated transcripts in response to intoxication. Annotation and pathway analysis of DEGs between susceptible and resistant whole WCR and their midgut tissue revealed genes associated with cell membrane, immune response, detoxification, and potential Bt receptors which are likely related to eCry3.1Ab resistance. This research provides a framework to study the toxicology of Bt toxins and mechanism of resistance in WCR, an economically important coleopteran pest species.
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Affiliation(s)
- Zixiao Zhao
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Lisa N Meihls
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA.,USDA-ARS, Columbia, MO, Columbia, MO, USA
| | - Bruce E Hibbard
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA.,USDA-ARS, Columbia, MO, Columbia, MO, USA
| | - Tieming Ji
- Department of Statistics, University of Missouri, Columbia, MO, USA
| | - Christine G Elsik
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA.,Division of Animal Sciences, University of Missouri, Columbia, MO, USA.,MU Informatics Institute, University of Missouri, Columbia, MO, USA
| | - Kent S Shelby
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA. .,USDA-ARS, Columbia, MO, Columbia, MO, USA.
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Long-Term Population Studies Uncover the Genome Structure and Genetic Basis of Xenobiotic and Host Plant Adaptation in the Herbivore Tetranychus urticae. Genetics 2019; 211:1409-1427. [PMID: 30745439 DOI: 10.1534/genetics.118.301803] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/02/2019] [Indexed: 01/11/2023] Open
Abstract
Pesticide resistance arises rapidly in arthropod herbivores, as can host plant adaptation, and both are significant problems in agriculture. These traits have been challenging to study as both are often polygenic and many arthropods are genetically intractable. Here, we examined the genetic architecture of pesticide resistance and host plant adaptation in the two-spotted spider mite, Tetranychus urticae, a global agricultural pest. We show that the short generation time and high fecundity of T. urticae can be readily exploited in experimental evolution designs for high-resolution mapping of quantitative traits. As revealed by selection with spirodiclofen, an acetyl-CoA carboxylase inhibitor, in populations from a cross between a spirodiclofen-resistant and a spirodiclofen-susceptible strain, and which also differed in performance on tomato, we found that a limited number of loci could explain quantitative resistance to this compound. These were resolved to narrow genomic intervals, suggesting specific candidate genes, including acetyl-CoA carboxylase itself, clustered and copy variable cytochrome P450 genes, and NADPH cytochrome P450 reductase, which encodes a redox partner for cytochrome P450s. For performance on tomato, candidate genomic regions for response to selection were distinct from those responding to the synthetic compound and were consistent with a more polygenic architecture. In accomplishing this work, we exploited the continuous nature of allele frequency changes across experimental populations to resolve the existing fragmented T. urticae draft genome to pseudochromosomes. This improved assembly was indispensable for our analyses, as it will be for future research with this model herbivore that is exceptionally amenable to genetic studies.
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E. Pereira A, Souza D, Zukoff SN, Meinke LJ, Siegfried BD. Cross-resistance and synergism bioassays suggest multiple mechanisms of pyrethroid resistance in western corn rootworm populations. PLoS One 2017. [PMID: 28628635 PMCID: PMC5476265 DOI: 10.1371/journal.pone.0179311] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently, resistance to the pyrethroid bifenthrin was detected and confirmed in field populations of western corn rootworm, Diabrotica virgifera virgifera LeConte from southwestern areas of Nebraska and Kansas. As a first step to understand potential mechanisms of resistance, the objectives of this study were i) to assess adult mortality at diagnostic concentration-LC99 to the pyrethroids bifenthrin and tefluthrin as well as DDT, ii) estimate adult and larval susceptibility to the same compounds as well as the organophosphate methyl-parathion, and iii) perform synergism experiments with piperonyl butoxide (PBO) (P450 inhibitor) and S,S,S-tributyl-phosphorotrithioate (DEF) (esterase inhibitor) in field populations. Most of the adult field populations exhibiting some level of bifenthrin resistance exhibited significantly lower mortality to both pyrethroids and DDT than susceptible control populations at the estimated LC99 of susceptible populations. Results of adult dose-mortality bioassays also revealed elevated LC50 values for bifenthrin resistant populations compared to the susceptible control population with resistance ratios ranging from 2.5 to 5.5-fold for bifenthrin, 28 to 54.8-fold for tefluthrin, and 16.3 to 33.0 for DDT. These bioassay results collectively suggest some level of cross-resistance between the pyrethroids and DDT. In addition, both PBO and DEF reduced the resistance ratios for resistant populations although there was a higher reduction in susceptibility of adults exposed to PBO versus DEF. Susceptibility in larvae varied among insecticides and did not correlate with adult susceptibility to tefluthrin and DDT, as most resistance ratios were < 5-fold when compared to the susceptible population. These results suggest that both detoxifying enzymes and target site insensitivity might be involved as resistance mechanisms.
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Affiliation(s)
- Adriano E. Pereira
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
| | - Dariane Souza
- Department of Entomology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Sarah N. Zukoff
- Southwest Research and Extension Center, Kansas State University, Garden City, Kansas, United States of America
| | - Lance J. Meinke
- Department of Entomology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Blair D. Siegfried
- Department of Entomology & Nematology, University of Florida, Gainesville, Florida, United States of America
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