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The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success

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USDA ARS Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA
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Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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USDA ARS U.S. Arid-Land Agricultural Research Center, Maricopa, AZ 85138, USA
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Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budejovice, Czech Republic
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Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budejovice, Czech Republic
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Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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USDA ARS U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
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Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
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Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo 05508-000, SP, Brazil
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Institute of Biological Sciences, Federal University of Goiás, Av. Esperança s/n, Goiânia 74690-900, GO, Brazil
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Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
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A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI 54901, USA
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Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
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Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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School of Biological Sciences, The University of Queensland, Brisbane 4072, QLD, Australia
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Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
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USDA Agricultural Research Service, Commodity Protection and Quality Research, 9611 S. Riverbend Ave., Parlier, CA 93648, USA
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USDA Agricultural Research Service, Insect Control and Cotton Disease Research, 2771 F and B Road, College Station, TX 77845, USA
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USDA Agricultural Research Service, National Agricultural Library, 10301 Baltimore, Ave., Beltsville, MD 20705, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Erich Bornberg-Bauer
Genes 2022, 13(3), 446; https://doi.org/10.3390/genes13030446
Received: 30 December 2021 / Revised: 16 February 2022 / Accepted: 21 February 2022 / Published: 28 February 2022
(This article belongs to the Section Animal Genetics and Genomics)
The lesser grain borer, Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae), is a major global pest of cereal grains. Infestations are difficult to control as larvae feed inside grain kernels, and many populations are resistant to both contact insecticides and fumigants. We sequenced the genome of R. dominica to identify genes responsible for important biological functions and develop more targeted and efficacious management strategies. The genome was assembled from long read sequencing and long-range scaffolding technologies. The genome assembly is 479.1 Mb, close to the predicted genome size of 480.4 Mb by flow cytometry. This assembly is among the most contiguous beetle assemblies published to date, with 139 scaffolds, an N50 of 53.6 Mb, and L50 of 4, indicating chromosome-scale scaffolds. Predicted genes from biologically relevant groups were manually annotated using transcriptome data from adults and different larval tissues to guide annotation. The expansion of carbohydrase and serine peptidase genes suggest that they combine to enable efficient digestion of cereal proteins. A reduction in the copy number of several detoxification gene families relative to other coleopterans may reflect the low selective pressure on these genes in an insect that spends most of its life feeding internally. Chemoreceptor genes contain elevated numbers of pseudogenes for odorant receptors that also may be related to the recent ontogenetic shift of R. dominica to a diet consisting primarily of stored grains. Analysis of repetitive sequences will further define the evolution of bostrichid beetles compared to other species. The data overall contribute significantly to coleopteran genetic research. View Full-Text
Keywords: Bostrichidae; insect reference genome; insecticide resistance; insect genetics; lesser grain borer; Rhyzopertha dominica Bostrichidae; insect reference genome; insecticide resistance; insect genetics; lesser grain borer; Rhyzopertha dominica
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MDPI and ACS Style

Oppert, B.; Muszewska, A.; Steczkiewicz, K.; Šatović-Vukšić, E.; Plohl, M.; Fabrick, J.A.; Vinokurov, K.S.; Koloniuk, I.; Johnston, J.S.; Smith, T.P.L.; Guedes, R.N.C.; Terra, W.R.; Ferreira, C.; Dias, R.O.; Chaply, K.A.; Elpidina, E.N.; Tereshchenkova, V.F.; Mitchell, R.F.; Jenson, A.J.; McKay, R.; Shan, T.; Cao, X.; Miao, Z.; Xiong, C.; Jiang, H.; Morrison, W.R.; Koren, S.; Schlipalius, D.; Lorenzen, M.D.; Bansal, R.; Wang, Y.-H.; Perkin, L.; Poelchau, M.; Friesen, K.; Olmstead, M.L.; Scully, E.; Campbell, J.F. The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success. Genes 2022, 13, 446. https://doi.org/10.3390/genes13030446

AMA Style

Oppert B, Muszewska A, Steczkiewicz K, Šatović-Vukšić E, Plohl M, Fabrick JA, Vinokurov KS, Koloniuk I, Johnston JS, Smith TPL, Guedes RNC, Terra WR, Ferreira C, Dias RO, Chaply KA, Elpidina EN, Tereshchenkova VF, Mitchell RF, Jenson AJ, McKay R, Shan T, Cao X, Miao Z, Xiong C, Jiang H, Morrison WR, Koren S, Schlipalius D, Lorenzen MD, Bansal R, Wang Y-H, Perkin L, Poelchau M, Friesen K, Olmstead ML, Scully E, Campbell JF. The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success. Genes. 2022; 13(3):446. https://doi.org/10.3390/genes13030446

Chicago/Turabian Style

Oppert, Brenda, Anna Muszewska, Kamil Steczkiewicz, Eva Šatović-Vukšić, Miroslav Plohl, Jeffrey A. Fabrick, Konstantin S. Vinokurov, Igor Koloniuk, J. S. Johnston, Timothy P.L. Smith, Raul N.C. Guedes, Walter R. Terra, Clélia Ferreira, Renata O. Dias, Konstantin A. Chaply, Elena N. Elpidina, Valeriia F. Tereshchenkova, Robert F. Mitchell, Audra J. Jenson, Rachel McKay, Tisheng Shan, Xiaolong Cao, Zelong Miao, Chao Xiong, Haobo Jiang, William R. Morrison, Sergey Koren, David Schlipalius, Marcé D. Lorenzen, Raman Bansal, Yu-Hui Wang, Lindsey Perkin, Monica Poelchau, Kenlee Friesen, Morgan L. Olmstead, Erin Scully, and James F. Campbell. 2022. "The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success" Genes 13, no. 3: 446. https://doi.org/10.3390/genes13030446

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