Genes (Feb 2022)
The Genome of <em>Rhyzopertha dominica</em> (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success
- Brenda Oppert,
- Anna Muszewska,
- Kamil Steczkiewicz,
- Eva Šatović-Vukšić,
- Miroslav Plohl,
- Jeffrey A. Fabrick,
- Konstantin S. Vinokurov,
- Igor Koloniuk,
- J. Spencer Johnston,
- Timothy P. L. Smith,
- Raul Narciso 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,
- James F. Campbell
Affiliations
- Brenda Oppert
- USDA ARS Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA
- Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
- Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
- Eva Šatović-Vukšić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
- Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
- Jeffrey A. Fabrick
- USDA ARS U.S. Arid-Land Agricultural Research Center, Maricopa, AZ 85138, USA
- Konstantin S. Vinokurov
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budejovice, Czech Republic
- Igor Koloniuk
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budejovice, Czech Republic
- J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
- Timothy P. L. Smith
- USDA ARS U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
- Raul Narciso C. Guedes
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Walter R. Terra
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo 05508-000, SP, Brazil
- Clélia Ferreira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo 05508-000, SP, Brazil
- Renata O. Dias
- Institute of Biological Sciences, Federal University of Goiás, Av. Esperança s/n, Goiânia 74690-900, GO, Brazil
- Konstantin A. Chaply
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
- Elena N. Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Valeriia F. Tereshchenkova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Robert F. Mitchell
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI 54901, USA
- Audra J. Jenson
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI 54901, USA
- Rachel McKay
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI 54901, USA
- Tisheng Shan
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
- Xiaolong Cao
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
- Zelong Miao
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
- Chao Xiong
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
- Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
- William R. Morrison
- USDA ARS Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA
- Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- David Schlipalius
- School of Biological Sciences, The University of Queensland, Brisbane 4072, QLD, Australia
- Marcé D. Lorenzen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
- Raman Bansal
- USDA Agricultural Research Service, Commodity Protection and Quality Research, 9611 S. Riverbend Ave., Parlier, CA 93648, USA
- Yu-Hui Wang
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
- Lindsey Perkin
- USDA Agricultural Research Service, Insect Control and Cotton Disease Research, 2771 F and B Road, College Station, TX 77845, USA
- Monica Poelchau
- USDA Agricultural Research Service, National Agricultural Library, 10301 Baltimore, Ave., Beltsville, MD 20705, USA
- Kenlee Friesen
- USDA ARS Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA
- Morgan L. Olmstead
- USDA ARS Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA
- Erin Scully
- USDA ARS Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA
- James F. Campbell
- USDA ARS Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA
- DOI
- https://doi.org/10.3390/genes13030446
- Journal volume & issue
-
Vol. 13,
no. 3
p. 446
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
- <i>Rhyzopertha dominica</i>