Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis

Abstract

Food security is important for the ever-growing global population. Soybean, Glycine max (L.) Merr., is cultivated worldwide providing a key source of food, protein and oil. Hence, it is imperative to maintain or to increase its yield under different conditions including challenges caused by abiotic and biotic stresses. In recent years, the soybean pod-sucking stinkbug Riptortus pedestris has emerged as an important agricultural insect pest in East, South and Southeast Asia. Here, we present a genomics resource for R. pedestris including its genome assembly, messenger RNA (mRNA) and microRNA (miRNA) transcriptomes at different developmental stages and from different organs. As insect hormone biosynthesis genes (genes involved in metamorphosis) and their regulators such as miRNAs are potential targets for pest control, we analyzed the sesquiterpenoid (juvenile) and ecdysteroid (molting) hormone biosynthesis pathway genes including their miRNAs and relevant neuropeptides. Temporal gene expression changes of these insect hormone biosynthesis pathways were observed at different developmental stages. Similarly, a diet-specific response in gene expression was also observed in both head and salivary glands. Furthermore, we observed that microRNAs (bantam, miR-14, miR-316, and miR-263) of R. pedestris fed with different types of soybeans were differentially expressed in the salivary glands indicating a diet-specific response. Interestingly, the opposite arms of miR-281 (-5p and -3p), a miRNA involved in regulating development, were predicted to target Hmgs genes of R. pedestris and soybean, respectively. These observations among others highlight stinkbug's responses as a function of its interaction with soybean. In brief, the results of this study not only present salient findings that could be of potential use in pest management and mitigation but also provide an invaluable resource for R. pedestris as an insect model to facilitate studies on plant-pest interactions.

Keywords: Ecdysteroid; MicroRNA; Neuropeptide; Sesquiterpenoid; Soybean; Stinkbug; Transcriptome.

Fig. 1

A Schematic diagram showing the life cycle of stinkbug Riptortus pedestris. B Laboratory/culture setup of R. pedestris culture in the laboratory. C Genome assembly statistics. D Summary of transcriptome sequencing (mRNA and sRNA). E Phylogenetic tree based on single-copy orthologs among hemipteran insects with D. melanogaster as outgroup

Fig. 2

A Presence/absence of sesquiterpenoids pathway genes in R. pedestris (upper middle panel); gene expression (row Z-score) of sesquiterpenoid (lower left panel) and ecdysteroid (lower right panel) biosynthesis pathway genes across different developmental stages (egg/embryo, instars I to V and adult) and bean seed feeding (cultivated and wild soybeans C08, W05, respectively and common bean) comprised of organs head and salivary glands. B Annotation and copy number of neuropeptide genes in R. pedestris (left panel); gene expression (row Z-score) of neuropeptide genes across different developmental stages and upon bean seed feeding treatment (right panel)

Fig. 3

A miRNAs and their respective locations on the genome (scaffolds). B Presence/absence of predicted miRNAs on various hemipteran species

Fig. 4

A Schematic diagram of seed feeding experimental setup. B Differentially expressed miRNAs in salivary gland (upper) and head (lower) upon feeding. C miRNA-281:HMGS binding structure. Binding structure of miRNA:soybean HMGS is retrieved from psRNATarget; binding structure of miRNA:stinkbug HMGS is retrieved from RNAhybrid