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Article

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

by
Brenda Oppert
1,*,
Anna Muszewska
2,
Kamil Steczkiewicz
2,
Eva Šatović-Vukšić
3,
Miroslav Plohl
3,
Jeffrey A. Fabrick
4,
Konstantin S. Vinokurov
5,
Igor Koloniuk
6,
J. Spencer Johnston
7,
Timothy P. L. Smith
8,
Raul Narciso C. Guedes
9,
Walter R. Terra
10,
Clélia Ferreira
10,
Renata O. Dias
11,
Konstantin A. Chaply
12,
Elena N. Elpidina
13,
Valeriia F. Tereshchenkova
14,
Robert F. Mitchell
15,
Audra J. Jenson
15,
Rachel McKay
15,
Tisheng Shan
16,
Xiaolong Cao
16,
Zelong Miao
16,
Chao Xiong
16,
Haobo Jiang
16,
William R. Morrison
1,
Sergey Koren
17,
David Schlipalius
18,
Marcé D. Lorenzen
19,
Raman Bansal
20,
Yu-Hui Wang
19,
Lindsey Perkin
21,
Monica Poelchau
22,
Kenlee Friesen
1,
Morgan L. Olmstead
1,
Erin Scully
1 and
James F. Campbell
1add Show full author list remove Hide full author list
1
USDA ARS Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA
2
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
3
Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
4
USDA ARS U.S. Arid-Land Agricultural Research Center, Maricopa, AZ 85138, USA
5
Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budejovice, Czech Republic
6
Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budejovice, Czech Republic
7
Department of Entomology, Texas A&M University, College Station, TX 77843, USA
8
USDA ARS U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
9
Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
10
Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo 05508-000, SP, Brazil
11
Institute of Biological Sciences, Federal University of Goiás, Av. Esperança s/n, Goiânia 74690-900, GO, Brazil
12
Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
13
A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
14
Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
15
Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI 54901, USA
16
Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
17
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
18
School of Biological Sciences, The University of Queensland, Brisbane 4072, QLD, Australia
19
Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
20
USDA Agricultural Research Service, Commodity Protection and Quality Research, 9611 S. Riverbend Ave., Parlier, CA 93648, USA
21
USDA Agricultural Research Service, Insect Control and Cotton Disease Research, 2771 F and B Road, College Station, TX 77845, USA
22
USDA Agricultural Research Service, National Agricultural Library, 10301 Baltimore, Ave., Beltsville, MD 20705, USA
 
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*
Author to whom correspondence should be addressed.
Genes 2022, 13(3), 446; https://doi.org/10.3390/genes13030446
Submission 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)
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Abstract

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.
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.; et al. 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, et al. 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. Spencer Johnston, Timothy P. L. Smith, and et al. 2022. "The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success" Genes 13, no. 3: 446. https://doi.org/10.3390/genes13030446

APA 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., ... Campbell, J. F. (2022). The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success. Genes, 13(3), 446. https://doi.org/10.3390/genes13030446

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