In silico identification and assessment of insecticide target sites in the genome of the small hive beetle, Aethina tumida

Abstract

Background: The small hive beetle, Aethina tumida, is a rapidly emerging global pest of honey bee colonies. Small hive beetle infestation can be extremely destructive, which may cause honey bees to abscond and render colony infrastructure unusable. Due to the impacts small hive beetles have on honey bees, a wide variety of physical, cultural, and chemical control measures have been implemented to manage small hive beetle infestations. The use of insecticides to control small hive beetle populations is an emerging management tactic. Currently, very little genomic information exists on insecticide target sites in the small hive beetle. Therefore, the objective of this study is to utilize focused in silico comparative genomics approaches to identify and assess the potential insecticide sensitivity of the major insecticide target sites in the small hive beetle genome.

Results: No previously described resistance mutations were identified in any orthologs of insecticide target sites. Alternative exon use and A-to-I RNA editing were absent in AtumSC1. The ryanodine receptor in small hive beetle (Atum_Ryr) was highly conserved and no previously described resistance mutations were identified. A total of 12 nAChR subunits were identified with similar alternative exon use in other insects. Alternative exon use and critical structural features of the GABA-gated chloride channel subunits (Atum_RDL, Atum_GRD, and Atum_LCCH3) were conserved. Five splice variants were found for the glutamate-gated chloride channel subunit. Exon 3c of Atum_GluCl may be a beetle-specific alternative exon. The co-occurrence of exons 9a and 9b in the pH-sensitive chloride channel (Atum_pHCl) is a unique combination that introduces sites of post-translational modification. The repertoire and alternative exon use for histamine-gated chloride channels (Atum-HisCl), octopamine (Atum_OctR) and tyramine receptors (Atum_TAR) were conserved.

Conclusions: The recently published small hive beetle genome likely serves as a reference for insecticide-susceptible versions of insecticide target sites. These comparative in silico studies are the first step in discovering targets that can be exploited for small hive beetle-specific control as well as tracking changes in the frequency of resistance alleles as part of a resistance monitoring program. Comparative toxicity alongside honey bees is required to verify these in silico predictions.

Keywords: Honey bee; Insecticide; Pest management; Small hive beetle; Target-site.

Fig. 1

Phylogenetic relationship of the cys-loop ligand gated ion channel superfamily of the small hive beetle, Aethina tumida (green), red flour beetle, Tribolium castaneum (red), and honey bee, Apis mellifera (black). Genbank accession numbers for the sequences mentioned in this figure can be found in Additional file 1: Table S1

Fig. 2

Alternative splicing of nicotinic acetylcholine receptor subunits (nAChRs) in the small hive beetle, Aethina tumida. a Variation in the intron acceptor splice site in Atumα3 that adds 12 nucleotides to the 5′ end of exon 11. Amino acids shown in bold appear under the first base of the codon. Exon sequences are shown within borders. The shaded sequence represents the alternative intron splice site sequence that is added in XM_020016025.1. Dashes represent intron 10 of Atumα3 (not to scale). b Predicted transcript from Atumα6. Alternatively-spliced exons 3a/3b and 8a/8b/8c are shaded black and gray, respectively. The conserved exon 8b is not present in the genomic sequence and appears as a box with dotted border. Exons are shown as boxes and sizes are approximately proportional to nucleotide length. Introns shown as lines connecting the boxes are not to scale. c Schematic diagram of missing genomic region of Atumα7 compared to Tcasα7. Atumα7 is lacking equivalents of exons 6 and 7 from Tcasα7. Letters and numbers at the top of the diagram represent the approximate locations of ligand binding loops and transmembrane domains, respectively. Exons are shown as boxes and sizes are approximately proportional to nucleotide length. Introns shown as lines connecting the boxes are not to scale

Fig. 3

Transcript variants of Atum_pHCl. a Amino acid sequence of splice variants due to alternative splicing of exon 9 in Atum_pHCl compared to Tcas_pHCl [45]. Sequence motifs in bold are protein kinase-C phosphorylation sites, underlined motifs are casein kinase II phosphorylation sites, and shaded motifs are N-myristoylation sites. b Amino acid sequence of splice variants due to alternative splicing of intron 10 in Atum_pHCl. The corresponding sequence in Tcas_pHCl is identical to the regular splice variant

Fig. 4

Phylogenetic relationship of octopamine and tyramine receptors in small hive beetle, Aethina tumida (green), red flour beetle, Tribolium castaneum (red), honey bee, Apis mellifera (black), fruit fly, Drosophila melanogaster (blue), and silk worm, Bombyx mori (purple). Genbank accession numbers for the sequences mentioned in this figure can be found in Additional file 1: Table S1