Generating beneficial predator genomes to provide comparative insights into insecticide resistance-related gene families.

Abstract

With a rapidly growing population to feed, finding ways to increase crop yields has become more important than ever. Insect pests contribute hugely to yield losses every year and finding methods to effectively control pest levels is therefore crucial to reduce these losses. Insecticide use alone is no longer a viable solution, due to ever increasing levels of resistance developing amongst crop pests, as well as the environmental concerns associated with their overuse. Biological control – the use of natural predators to keep pest populations under control – has proven to be a highly effective method of pest control and generally has less severe environmental impacts than pesticides (although introducing non-native species can result in undesirable changes to local biodiversity). Biological control agents are therefore a key component of Integrated Pest Management (IPM) strategies, which aim to manage pest populations in a sustainable and economical manner. IPM programs prioritise selective insecticides which target the pest species and are harmless to the beneficial predators. However, the numbers of reported insecticide resistance cases are far lower in beneficial predators as opposed to crop pests. As a result, insecticide application often harms beneficial predator populations and reduces their biological control capabilities, which may allow resistant pest populations to surge after application. Genomic information is readily available for a multitude of crop pest species, however, when this project began, there was minimal genomic data available for beneficial predators. By increasing the availability of genomic data for beneficial predators, we can perform comparative analyses between crop pests and their predators of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance. These analyses may help uncover whether there is any genomic basis for the reduced number of insecticide resistance cases in beneficial predators compared to crop pests. The aim of this project was to firstly sequence and assemble the genomes of key beneficial predators for which no genomic information is currently available. This included Orius laevigatus (minute pirate bug), Sphaerophoria rueppellii (European hoverfly) and Microctonus brassicae (parasitoid wasp). Next, these genomes were annotated and manual curation of resistance-associated detoxification genes was performed. The resultant detoxification gene sets were then used to perform comparative analyses between beneficial predators and crop pests. The results from the comparative analysis suggest a greater degree of detoxification family gene expansion within crop pests compared to beneficial predators. This difference was particularly apparent in the families associated with detoxification of plant xenobiotics and suggests that the plant-based diet of crop pests provided increased selection pressure for resistance mechanisms prior to the introduction of insecticides. Once insecticides were introduced, crop pests may therefore have had an advantage over beneficial predators in terms of developing insecticide resistance. In addition, variation in the levels of resistance between different beneficial predators correlated to some extent with gene expansion, with several factors having likely had some influence on this, including diet, migration and length of commercial use. The knowledge gained from this project could contribute to our understanding of insecticide resistance from a genomic perspective and aid in the development of successful IPM strategies.