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Sun Z, Chen Y, Chen Y, Lu Z, Gui F. Tracking Adaptive Pathways of Invasive Insects: Novel Insight from Genomics. Int J Mol Sci 2023; 24:ijms24098004. [PMID: 37175710 PMCID: PMC10179030 DOI: 10.3390/ijms24098004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Despite the huge human and economic costs of invasive insects, which are the main group of invasive species, their environmental impacts through various mechanisms remain inadequately explained in databases and much of the invasion biology literature. High-throughput sequencing technology, especially whole-genome sequencing, has been used as a powerful method to study the mechanisms through which insects achieve invasion. In this study, we reviewed whole-genome sequencing-based advances in revealing several important invasion mechanisms of invasive insects, including (1) the rapid genetic variation and evolution of invasive populations, (2) invasion history and dispersal paths, (3) rapid adaptation to different host plant ranges, (4) strong environmental adaptation, (5) the development of insecticide resistance, and (6) the synergistic damage caused by invasive insects and endosymbiotic bacteria. We also discussed prevention and control technologies based on whole-genome sequencing and their prospects.
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Affiliation(s)
- Zhongxiang Sun
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Yao Chen
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Yaping Chen
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Zhihui Lu
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Furong Gui
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
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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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Lata D, Coates BS, Walden KKO, Robertson HM, Miller NJ. Genome size evolution in the beetle genus Diabrotica. G3 (BETHESDA, MD.) 2022; 12:jkac052. [PMID: 35234880 PMCID: PMC8982398 DOI: 10.1093/g3journal/jkac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/22/2022] [Indexed: 11/20/2022]
Abstract
Diabrocite corn rootworms are one of the most economically significant pests of maize in the United States and Europe and an emerging model for insect-plant interactions. Genome sizes of several species in the genus Diabrotica were estimated using flow cytometry along with that of Acalymma vittatum as an outgroup. Genome sizes ranged between 1.56 and 1.64 gigabase pairs and between 2.26 and 2.59 Gb, respectively, for the Diabrotica subgroups fucata and virgifera; the Acalymma vittatum genome size was around 1.65 Gb. This result indicated that a substantial increase in genome size occurred in the ancestor of the virgifera group. Further analysis of the fucata group and the virgifera group genome sequencing reads indicated that the genome size difference between the Diabrotica subgroups could be attributed to a higher content of transposable elements, mostly miniature inverted-transposable elements and gypsy-like long terminal repeat retroelements.
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Affiliation(s)
- Dimpal Lata
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Nicholas J Miller
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
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Zhao Z, Elsik CG, E Hibbard B, S Shelby K. Detection of alternative splicing in western corn rootworm (Diabrotica virgifera virgifera LeConte) in association with eCry3.1Ab resistance using RNA-seq and PacBio Iso-Seq. INSECT MOLECULAR BIOLOGY 2021; 30:436-445. [PMID: 33955085 DOI: 10.1111/imb.12709] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
Alternative splicing is a common feature in eukaryotes that not only increases the transcript diversity, but also has functional consequences. In insects, alternative splicing has been found associated with resistance to pesticides and Bt toxins. Up to date, the alternative splicing in western corn rootworm (Diabrotica virgifera virgifera LeConte) has not been studied. To investigate its alternative splicing pattern and relation to Bt resistance, we carried out single-molecule real-time (SMRT) transcript sequencing and Iso-seq analysis on resistant, eCry3.1Ab-selected and susceptible, unselected, western corn rootworm neonate midguts which fed on seedling maize with and without eCry3.1Ab for 12 and 24 h. We present transcriptome-wide alternative splicing patterns of western corn rootworm midgut in response to feeding on eCry3.1Ab-expressing corn using a comprehensive approach that combines both RNA-seq and SMRT transcript sequencing techniques. The results showed genes in western corn rootworm are highly alternatively spliced, which happens on 67.73% of multi-exon genes. One of the alternative splicing events we identified was a novel peritrophic matrix protein with two alternative splicing isoforms. Analysis of differential exon usage between resistant and susceptible colonies showed that in eCry3.1Ab-resistant western corn rootworm, expression of one isoform was significantly higher than in the susceptible colony, while no significant differences between colonies were observed with the other isoform. Our results provide the first survey of alternative splicing in western corn rootworm and suggest that the observed alternatively spliced isoforms of peritrophic matrix protein may be associated with eCry3.1Ab resistance in western corn rootworm.
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Affiliation(s)
- Z Zhao
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - C G Elsik
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - B E Hibbard
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- USDA-ARS Plant Genetics Research Unit, Columbia, MO, USA
| | - K S Shelby
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- USDA-ARS Biological Control of Insects Research Laboratory, Columbia, MO, USA
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Guan DL, Hao XQ, Mi D, Peng J, Li Y, Xie JY, Huang H, Xu SQ. Draft Genome of a Blister Beetle Mylabris aulica. Front Genet 2020; 10:1281. [PMID: 32010178 PMCID: PMC6972506 DOI: 10.3389/fgene.2019.01281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/21/2019] [Indexed: 11/13/2022] Open
Abstract
Mylabris aulica is a widely distributed blister beetle of the Meloidae family. It has the ability to synthesize a potent defensive secretion that includes cantharidin, a toxic compound used to treat many major illnesses. However, owing to the lack of genetic studies on cantharidin biosynthesis in M. aulica, the commercial use of this species is less extensive than that of other blister beetle species in China. This study reports a draft assembly and possible genes and pathways related to cantharidin biosynthesis for the M. aulica blister beetle using nanopore sequencing data. The draft genome assembly size was 288.5 Mb with a 467.8 Kb N50, and a repeat content of 50.62%. An integrated gene finding pipeline performed for assembly obtained 16,500 protein coding genes. Benchmarking universal single-copy orthologs assessment showed that this gene set included 94.4% complete Insecta universal single-copy orthologs. Over 99% of these genes were assigned functional annotations in the gene ontology, Kyoto Encyclopedia of Genes and Genomes, or Genbank non-redundant databases. Comparative genomic analysis showed that the completeness and continuity of our assembly was better than those of Hycleus cichorii and Hycleus phaleratus blister beetle genomes. The analysis of homologous orthologous genes and inference from evolutionary history imply that the Mylabris and Hycleus genera are genetically close, have a similar genetic background, and have differentiated within one million years. This M. aulica genome assembly provides a valuable resource for future blister beetle studies and will contribute to cantharidin biosynthesis.
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Affiliation(s)
- De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Xiao-Qian Hao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Da Mi
- NextOmics Biosciences Institute, Wuhan, China
| | - Jiong Peng
- NextOmics Biosciences Institute, Wuhan, China
| | - Yuan Li
- NextOmics Biosciences Institute, Wuhan, China
| | - Juan-Ying Xie
- College of Computer Science, Shaanxi Normal University, Xi’an, China
| | - Huateng Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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6
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Adedipe F, Grubbs N, Coates B, Wiegmman B, Lorenzen M. Structural and functional insights into the Diabrotica virgifera virgifera ATP-binding cassette transporter gene family. BMC Genomics 2019; 20:899. [PMID: 31775611 PMCID: PMC6882327 DOI: 10.1186/s12864-019-6218-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The western corn rootworm, Diabrotica virgifera virgifera, is a pervasive pest of maize in North America and Europe, which has adapted to current pest management strategies. In advance of an assembled and annotated D. v. virgifera genome, we developed transcriptomic resources to use in identifying candidate genes likely to be involved in the evolution of resistance, starting with members of the ATP-binding cassette (ABC) transporter family. RESULTS In this study, 65 putative D. v. virgifera ABC (DvvABC) transporters were identified within a combined transcriptome assembly generated from embryonic, larval, adult male, and adult female RNA-sequence libraries. Phylogenetic analysis placed the deduced amino-acid sequences of the DvvABC transporters into eight subfamilies (A to H). To supplement our sequence data with functional analysis, we identified orthologs of Tribolium castaneum ABC genes which had previously been shown to exhibit overt RNA interference (RNAi) phenotypes. We identified eight such D. v. virgifera genes, and found that they were functionally similar to their T. castaneum counterparts. Interestingly, depletion of DvvABCB_39715 and DvvABCG_3712 transcripts in adult females produced detrimental reproductive and developmental phenotypes, demonstrating the potential of these genes as targets for RNAi-mediated insect control tactics. CONCLUSIONS By combining sequence data from four libraries covering three distinct life stages, we have produced a relatively comprehensive de novo transcriptome assembly for D. v. virgifera. Moreover, we have identified 65 members of the ABC transporter family and provided the first insights into the developmental and physiological roles of ABC transporters in this pest species.
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Affiliation(s)
- Folukemi Adedipe
- Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, 1566 Thomas Hall, Raleigh, NC, 27695-7613, USA
| | - Nathaniel Grubbs
- Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, 1566 Thomas Hall, Raleigh, NC, 27695-7613, USA
| | - Brad Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Brian Wiegmman
- Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, 1566 Thomas Hall, Raleigh, NC, 27695-7613, USA
| | - Marcé Lorenzen
- Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, 1566 Thomas Hall, Raleigh, NC, 27695-7613, USA.
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7
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Chu F, Klobasa W, Wu P, Pinzi S, Grubbs N, Gorski S, Cardoza Y, Lorenzen MD. Germline transformation of the western corn rootworm, Diabrotica virgifera virgifera. INSECT MOLECULAR BIOLOGY 2017; 26:440-452. [PMID: 28397990 DOI: 10.1111/imb.12305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The western corn rootworm (WCR), a major pest of maize, is notorious for rapidly adapting biochemically, behaviourally and developmentally to a variety of control methods. Despite much effort, the genetic basis of WCR adaptation remains a mystery. Since transformation-based applications such as transposon tagging and enhancer trapping have facilitated genetic dissection of model species such as Drosophila melanogaster, we developed a germline-transformation system for WCR in an effort to gain a greater understanding of the basic biology of this economically important insect. Here we report the use of a fluorescent-marked Minos element to create transgenic WCR. We demonstrate that the transgenic strains express both an eye-specific fluorescent marker and piggyBac transposase. We identified insertion-site junction sequences via inverse PCR and assessed insertion copy number using digital droplet PCR (ddPCR). Interestingly, most WCR identified as transgenic via visual screening for DsRed fluorescence proved to carry multiple Minos insertions when tested via ddPCR. A total of eight unique insertion strains were created by outcrossing the initial transgenic strains to nontransgenic WCR mates. Establishing transgenic technologies for this beetle is the first step towards bringing a wide range of transformation-based tools to bear on understanding WCR biology.
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Affiliation(s)
- F Chu
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
| | - W Klobasa
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
| | - P Wu
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
| | - S Pinzi
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
| | - N Grubbs
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
| | - S Gorski
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
| | - Y Cardoza
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
| | - M D Lorenzen
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
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8
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Coates BS, Abel CA, Perera OP. Estimation of long terminal repeat element content in the Helicoverpa zea genome from high-throughput sequencing of bacterial artificial chromosome pools. Genome 2016; 60:310-324. [PMID: 28177843 DOI: 10.1139/gen-2016-0067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The lepidopteran pest insect Helicoverpa zea feeds on cultivated corn and cotton across the Americas where control remains challenging owing to the evolution of resistance to chemical and transgenic insecticidal toxins, yet genomic resources remain scarce for this species. A bacterial artificial chromosome (BAC) library having a mean genomic insert size of 145 ± 20 kbp was created from a laboratory strain of H. zea, which provides ∼12.9-fold coverage of a 362.8 ± 8.8 Mbp (0.37 ± 0.09 pg) flow cytometry estimated haploid genome size. Assembly of Illumina HiSeq 2000 reads generated from 14 pools that encompassed all BAC clones resulted in 165 485 genomic contigs (N50 = 3262 bp; 324.6 Mbp total). Long terminal repeat (LTR) protein coding regions annotated from 181 contigs included 30 Ty1/copia, 78 Ty3/gypsy, and 73 BEL/Pao elements, of which 60 (33.1%) encoded all five functional polyprotein (pol) domains. Approximately 14% of LTR elements are distributed non-randomly across pools of BAC clones.
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Affiliation(s)
- Brad S Coates
- a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA.,b Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Craig A Abel
- a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Omaththage P Perera
- c USDA-ARS, Southern Insect Management Research Unit, 141 Experiment Station Road, P.O. Box 346, Stoneville, MS 38776, USA
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Coates BS, Alves AP, Wang H, Zhou X, Nowatzki T, Chen H, Rangasamy M, Robertson HM, Whitfield CW, Walden KK, Kachman SD, French BW, Meinke LJ, Hawthorne D, Abel CA, Sappington TW, Siegfried BD, Miller NJ. Quantitative trait locus mapping and functional genomics of an organophosphate resistance trait in the western corn rootworm, Diabrotica virgifera virgifera. INSECT MOLECULAR BIOLOGY 2016; 25:1-15. [PMID: 26566705 DOI: 10.1111/imb.12194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The western corn rootworm, Diabrotica virgifera virgifera, is an insect pest of corn and population suppression with chemical insecticides is an important management tool. Traits conferring organophosphate insecticide resistance have increased in frequency amongst D. v. virgifera populations, resulting in the reduced efficacy in many corn-growing regions of the USA. We used comparative functional genomic and quantitative trait locus (QTL) mapping approaches to investigate the genetic basis of D. v. virgifera resistance to the organophosphate methyl-parathion. RNA from adult methyl-parathion resistant and susceptible adults was hybridized to 8331 microarray probes. The results predicted that 11 transcripts were significantly up-regulated in resistant phenotypes, with the most significant (fold increases ≥ 2.43) being an α-esterase-like transcript. Differential expression was validated only for the α-esterase (ST020027A20C03), with 11- to 13-fold greater expression in methyl-parathion resistant adults (P < 0.05). Progeny with a segregating methyl-parathion resistance trait were obtained from a reciprocal backcross design. QTL analyses of high-throughput single nucleotide polymorphism genotype data predicted involvement of a single genome interval. These data suggest that a specific carboyxesterase may function in field-evolved corn rootworm resistance to organophosphates, even though direct linkage between the QTL and this locus could not be established.
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Affiliation(s)
- B S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, USA
| | - A P Alves
- University of Nebraska, Lincoln, NE, USA
| | - H Wang
- University of Nebraska, Lincoln, NE, USA
| | - X Zhou
- University of Nebraska, Lincoln, NE, USA
| | - T Nowatzki
- University of Nebraska, Lincoln, NE, USA
| | - H Chen
- University of Nebraska, Lincoln, NE, USA
| | | | | | | | - K K Walden
- University of Illinois, Champaign-Urbana, IL, USA
| | | | - B W French
- USDA-ARS, North-Central Agricultural Research Laboratory, Brooking, SD, USA
| | - L J Meinke
- University of Nebraska, Lincoln, NE, USA
| | - D Hawthorne
- University of Maryland, College Park, MD, USA
| | - C A Abel
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, USA
- Iowa State University, Ames, IA, USA
| | - T W Sappington
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, USA
- Iowa State University, Ames, IA, USA
| | | | - N J Miller
- University of Nebraska, Lincoln, NE, USA
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10
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Flagel LE, Bansal R, Kerstetter RA, Chen M, Carroll M, Flannagan R, Clark T, Goldman BS, Michel AP. Western corn rootworm (Diabrotica virgifera virgifera) transcriptome assembly and genomic analysis of population structure. BMC Genomics 2014; 15:195. [PMID: 24628835 PMCID: PMC4004143 DOI: 10.1186/1471-2164-15-195] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 03/04/2014] [Indexed: 02/04/2023] Open
Abstract
Background 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. Results 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. Conclusions 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. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-195) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Barry S Goldman
- Monsanto Company, 700 Chesterfield Parkway W, Chesterfield, MO 63017, USA.
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Nandety RS, Kamita SG, Hammock BD, Falk BW. Sequencing and de novo assembly of the transcriptome of the glassy-winged sharpshooter (Homalodisca vitripennis). PLoS One 2013; 8:e81681. [PMID: 24339955 PMCID: PMC3858241 DOI: 10.1371/journal.pone.0081681] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/15/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The glassy-winged sharpshooter Homalodisca vitripennis (Hemiptera: Cicadellidae), is a xylem-feeding leafhopper and important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce's disease of grapevines. The functional complexity of the transcriptome of H. vitripennis has not been elucidated thus far. It is a necessary blueprint for an understanding of the development of H. vitripennis and for designing efficient biorational control strategies including those based on RNA interference. RESULTS Here we elucidate and explore the transcriptome of adult H. vitripennis using high-throughput paired end deep sequencing and de novo assembly. A total of 32,803,656 paired-end reads were obtained with an average transcript length of 624 nucleotides. We assembled 32.9 Mb of the transcriptome of H. vitripennis that spanned across 47,265 loci and 52,708 transcripts. Comparison of our non-redundant database showed that 45% of the deduced proteins of H. vitripennis exhibit identity (e-value ≤1(-5)) with known proteins. We assigned Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains to each transcript isoform. In order to gain insight into the molecular basis of key regulatory genes of H. vitripennis, we characterized predicted proteins involved in the metabolism of juvenile hormone, and biogenesis of small RNAs (Dicer and Piwi sequences) from the transcriptomic sequences. Analysis of transposable element sequences of H. vitripennis indicated that the genome is less expanded in comparison to many other insects with approximately 1% of the transcriptome carrying transposable elements. CONCLUSIONS Our data significantly enhance the molecular resources available for future study and control of this economically important hemipteran. This transcriptional information not only provides a more nuanced understanding of the underlying biological and physiological mechanisms that govern H. vitripennis, but may also lead to the identification of novel targets for biorationally designed control strategies.
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Affiliation(s)
- Raja Sekhar Nandety
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Shizuo G. Kamita
- Department of Entomology and UC Davis Comprehensive Cancer Research Center, University of California Davis, Davis, California, United States of America
| | - Bruce D. Hammock
- Department of Entomology and UC Davis Comprehensive Cancer Research Center, University of California Davis, Davis, California, United States of America
| | - Bryce W. Falk
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- * E-mail:
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Wang H, Coates BS, Chen H, Sappington TW, Guillemaud T, Siegfried BD. Role of a γ-aminobutryic acid (GABA) receptor mutation in the evolution and spread of Diabrotica virgifera virgifera resistance to cyclodiene insecticides. INSECT MOLECULAR BIOLOGY 2013; 22:473-484. [PMID: 23841833 DOI: 10.1111/imb.12037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The western corn rootworm, Diabrotica virgifera virgifera, is a damaging pest of cultivated corn that was controlled by applications of cyclodiene insecticides from the late 1940s until resistance evolved ∼10 years later. Range expansion from the western plains into eastern USA coincides with resistance development. An alanine to serine amino acid substitution within the Rdl subunit of the gamma-aminobutyric acid (GABA) receptor confers resistance to cyclodiene insecticides in many species. We found that the non-synonymous single nucleotide polymorphism (SNP) G/T at the GABA receptor cDNA position 838 (G/T(838)) of D. v. virgifera resulted in the alanine to serine change, and the codominant SNP allele T(838) was genetically linked to survival of beetles in aldrin bioassays. A phenotypic gradient of decreasing susceptibility from west to east was correlated with higher frequencies of the resistance-conferring T(838) allele in the eastern-most populations. This pattern exists in opposition to perceived selective pressures since the more eastern and most resistant populations probably experienced reduced exposure. The reasons for the observed distribution are uncertain, but historical records of the range expansion combined with the distribution of susceptible and resistant phenotypes and genotypes provide an opportunity to better understand factors affecting the species' range expansion.
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MESH Headings
- Aldrin/toxicity
- Animals
- Biological Assay/methods
- Chromosomes, Artificial, Bacterial/drug effects
- Chromosomes, Artificial, Bacterial/genetics
- Coleoptera/genetics
- Coleoptera/metabolism
- Evolution, Molecular
- Hydrocarbons, Chlorinated/toxicity
- Insecticide Resistance/genetics
- Insecticide Resistance/physiology
- Insecticides/toxicity
- Mutation
- North America
- Polymorphism, Single Nucleotide/drug effects
- Receptors, GABA/genetics
- Receptors, GABA/physiology
- Sequence Analysis, DNA
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Affiliation(s)
- H Wang
- University of Nebraska, Department of Entomology, Lincoln, NE, USA
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