Comprehensive annotation and phylogenetic analysis of chemosensory genes in Plodia interpunctella (Lepidoptera: Pyralidae)

Insect chemosensory genes play vital roles in food location, mating behavior, oviposition, and other behaviors in insects. These genes belong to several distinct families, including those that encode odorant receptors (ORs), gustatory receptors (GRs), ionotropic receptors (IRs), odorant binding proteins (OBPs), chemosensory proteins (CSPs), and sensory neuron membrane proteins (SNMPs). Although these gene families have been well annotated in several lepidopteran species, Plodia interpunctella (Lepidoptera: Pyralidae), a common pantry pest, remains understudied. In this study, we performed automated gene predictions using NCBI’s Eukaryotic Annotation Pipeline on a chromosome-scale assembly of P. interpunctella with RNA-seq expression data from chemosensory tissues to identify putative gene models of the transmembrane-bound receptors. We then manually corrected and curated all chemosensory gene models using a combination of RNA-Seq data and comparative recursive tblastn searches, which is essential for accurate identification of species-specific chemosensory genes and exons that may diverge significantly from those that have been previously annotated in close relatives. Thus far, we have found 63 ORs, 23 IRs, and 16 GRs, of which 17, 3, and 0 of the respective gene types are yet to be described in this species. Maximum likelihood phylogenetic trees revealed orthologous chemosensory genes shared among lepidopterans; however, we identified novel genes that are likely to allow this species to successfully exploit a wide range of resources under various environmental conditions. Our work helps lay a foundation for later exploitation of these genes to support pest management for P. interpunctella.