Variants in the mitochondrial genome sequence of Rhyzopertha dominica (Fabricius)(Coleoptera: Bostrycidae)

Authors: Perkin, Lindsey; Smith, Timothy - Tim; Oppert, Brenda; POELCHAU, MONICA - US Department Of Agriculture (USDA)

Submitted to: Insects
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/26/2021
Publication Date: 4/27/2021
Citation: Perkin, L.C., Smith, T.P., Oppert, B.S., Poelchau, M. 2021. Variants in the mitochondrial genome sequence of Rhyzopertha dominica (Fabricius)(Coleoptera: Bostrycidae). Insects. 12(5). Article 387. https://doi.org/10.3390/insects12050387. LOG NO. 378692
DOI: https://doi.org/10.3390/insects12050387

Interpretive Summary: The lesser grain borer is one of the leading beetle pests of stored grains worldwide. The major control method for this beetle is phosphine fumigation, but the increase in resistant populations may limit the ability of phosphine to be effective. The insect mitochondria is the major source of energy production, and some phosphine-resistant insects have reduced energy production. Therefore we want to understand whether changes in the mitochondrial genome may promote phosphine resistance in insects. From an inbred laboratory strain of the lesser grain borer, we extracted and sequenced genomic DNA. Those sequences were assembled and annotated to identify mitochondrial sequences, and the assembled sequence was manually verified. The mitochondrial genome sequence for the lesser grain borer was a total length of 15,724 bp, similar to other insects, and encoded typical mitochondrial genes. We compared our predicted mitochondrial genome sequence to that of another lesser grain borer strain from Jingziguan (China) that was recently published. While there was mostly agreement among the two sequences, key differences may suggest mutations in the two populations related to phosphine control pressure, but differences also could be the result in different genome interpretations. We will use this as a research tool to examine the expression of mitochondrial genes in phosphine-susceptible and -resistant insect populations.

Technical Abstract: The lesser grain borer, Rhyzopertha dominica Fabricius, is a coleopteran pest of stored grains worldwide. The major control method for R. dominica is phosphine fumigation, but the increase in resistant populations threatens efficacy. Some phosphine-resistant insects have reduced respiration, and thus studying the mitochondrial genome may provide additional information regarding resistance. Genomic DNA from an inbred laboratory strain of R. dominica was extracted and sequenced with both short (Illumina) and long (Pac Bio) read technologies. Short read sequences were assembled and annotated by open software to identify mitochondrial sequences, and the assembled sequence was manually annotated and verified by long read sequences. The mitochondrial genome sequence for R. dominica was a total length of 15,724 bp and encoded 22 trna genes, 2 rRNA genes, 13 protein coding genes (7 nad subunits, 3 cox, 2 atp, and 1 cytB), flanked by a long control region. We compared our predicted mitochondrial genome to that of another R. dominica strain from Jingziguan (China) that was recently published. While there was mostly agreement among the two assemblies, key differences may suggest mutations in the two populations related to insecticide control pressure, mainly that of phosphine. Additionally, differences in sequence data, assembly, and annotation may result in different genome interpretations.