Variants in the Mitochondrial Genome Sequence of Rhyzopertha dominica (Fabricius) (Coleoptera: Bostrycidae).

Lindsey C Perkin,Brenda Oppert,Timothy P L Smith

doi:10.3390/insects12050387

Abstract

Simple SummaryThe lesser grain borer damages grains in storage worldwide. The major control method for this beetle is phosphine fumigation, but the increase in resistant populations has led to a loss in phosphine efficacy. Insect mitochondria are the major source of energy, 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, but we need an accurate mitogenome sequence and annotation. We extracted and sequenced genomic DNA from a laboratory colony of the lesser grain borer and assembled and annotated the mitochondrial genome. The mitochondrial genome sequence was similar in structure to other insect mitochondria and encoded typical mitochondrial genes. We compared our predicted mitochondrial genome sequence to that of another lesser grain borer strain from Jingziguan (China). While there was mostly agreement among the two sequences, the data will be used to determine if key differences may suggest mutations in the two populations related to phosphine control pressure. However, differences also could be the result in different genome sequences and interpretations. The data will be useful as a research tool to examine the expression of mitochondrial genes in phosphine susceptible and -resistant insect populations.The lesser grain borer, Rhyzopertha dominica, is a coleopteran pest of stored grains and is mainly controlled by phosphine fumigation, but the increase in phosphine-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 (Pacific Biosciences) read technologies for whole genome sequence assembly and annotation. 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 had 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 from a R. dominica strain from Jingziguan (China). While there was mostly agreement between the two assemblies, key differences will be further examined to determine if mutations in populations are related to insecticide control pressure, mainly that of phosphine. Differences in sequence data, assembly, and annotation also may result in different genome interpretations.

Highlights

The lesser grain borer, Rhyzopertha dominica (Fabricius) (Coleoptera: Bostrycidae), is a major pest of stored grains and grain products [1]
Significant phosphine resistance occurs in insects with mutations in rph2, which encodes dihydrolipoamide dehydrogenase (DLD) [5]
MiSeq reads corresponding to the mitochondrial genome were separated from nuclear genomic reads, with approximately 0.39% of the 20,951,116 total reads (60,094 reads) representing putative mitochondrial reads

Summary

Introduction

The lesser grain borer, Rhyzopertha dominica (Fabricius) (Coleoptera: Bostrycidae), is a major pest of stored grains and grain products [1]. Phosphine fumigation is a major control method used in the management of infestations of stored product pests including. Phosphine is a cost-effective fumigant, and the low cost has increased its usage, resulting in the selection and propagation of resistant populations [2]. Two nuclear genes have been identified in R. dominica, rph and rph, that act synergistically to increase phosphine resistance when individuals carry both mutated genes [3,4]. Significant phosphine resistance occurs in insects with mutations in rph, which encodes dihydrolipoamide dehydrogenase (DLD) [5]. The second gene, rph, encodes cytochrome b5 fatty acid desaturase [6], and higher levels of resistance are found in insects with mutations in both genes

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