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.
Highlights
The family Bostrichidae mainly consists of species of wood-boring insects that feed on living trees, dead branches, and wood products
R. dominica feeds on grains that have a high content of starch, so we investigated the genome for expansion of α-amylases, maltases, and Glycoside hydrolases (GHs) relative to the genomes of other beetles that break down carbohydrate and di, tri, and oligosaccharides released from starch molecules
While over 300 chemoreceptor genes were identified in the genome, this beetle is unique among the studied Coleoptera with about 15% OR pseudogenes carrying a recently acquired single-point mutation, indicative of interbreeding in a closed system, such as granaries and relaxed selection on chemosensory genes
Summary
The family Bostrichidae mainly consists of species of wood-boring insects that feed on living trees, dead branches, and wood products. The species Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae) (lesser grain borer; Figure 1) was reported under the bark of Quercus suber (cork oak) and Cytisus spinosus (spiny broom) as early as 1849 [1] and more recently in other wooded environments [2–4]. The origin of R. dominica is speculated to be India, and most early citations were from India and Australia [5]. The insect has a cosmopolitan distribution and has been found in wood-based materials, leather stuffing, Genes 2022, 13, x FOR PEER REVIEWpharmaceuticals, and mud plaster [6]. Rhyzopertha dominica can be found in a3voaf r4i6ety of non-agricultural seed and fruits, with damaged acorns being a favorable host [6–8].
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