Browsing by Author "Bailey, Emma"
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Item Open Access Generating beneficial predator genomes to provide comparative insights into insecticide resistance-related gene families.(Cranfield University, 2022-01) Bailey, Emma; Mohareb, Fady R.; Hassani-Pak, Keywan; King, RobertWith 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.Item Open Access A near-chromosome level genome assembly of the European hoverfly, Sphaerophoria rueppellii (Diptera: Syrphidae), provides comparative insights into insecticide resistance-related gene family evolution(BioMed Central, 2022-03-12) Bailey, Emma; Field, Linda; Rawlings, Christopher; King, Rob; Mohareb, Fady; Pak, Keywan‑Hassani; Hughes, David; Williamson, Martin; Ganko, Eric; Buer, Benjamin; Nauen, RalfBackground Sphaerophoria rueppellii, a European species of hoverfly, is a highly effective beneficial predator of hemipteran crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest management (IPM) programmes. It is also a key pollinator of a wide variety of important agricultural crops. No genomic information is currently available for S. rueppellii. Without genomic information for such beneficial predator species, we are unable to perform comparative analyses of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance, between crop pests and their predators. These metabolic mechanisms include several gene families - cytochrome P450 monooxygenases (P450s), ATP binding cassette transporters (ABCs), glutathione-S-transferases (GSTs), UDP-glycosyltransferases (UGTs) and carboxyl/choline esterases (CCEs). Methods and findings In this study, a high-quality near-chromosome level de novo genome assembly (as well as a mitochondrial genome assembly) for S. rueppellii has been generated using a hybrid approach with PacBio long-read and Illumina short-read data, followed by super scaffolding using Hi-C data. The final assembly achieved a scaffold N50 of 87Mb, a total genome size of 537.6Mb and a level of completeness of 96% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 14,249 protein-coding genes. Comparative analysis revealed gene expansions of CYP6Zx P450s, epsilon-class GSTs, dietary CCEs and multiple UGT families (UGT37/302/308/430/431). Conversely, ABCs, delta-class GSTs and non-CYP6Zx P450s showed limited expansion. Differences were seen in the distributions of resistance-associated gene families across subfamilies between S. rueppellii and some hemipteran crop pests. Additionally, S. rueppellii had larger numbers of detoxification genes than other pollinator species. Conclusion and significance This assembly is the first published genome for a predatory member of the Syrphidae family and will serve as a useful resource for further research into selectivity and potential tolerance of insecticides by beneficial predators. Furthermore, the expansion of some gene families often linked to insecticide resistance and selectivity may be an indicator of the capacity of this predator to detoxify IPM selective insecticides. These findings could be exploited by targeted insecticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably and effectively controlling pests without impacting beneficial predator populations.Item Open Access A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus (Hemiptera: Anthocoridae), and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests(BioMed Central, 2022-01-11) Bailey, Emma; Field, Linda; Rawlings, Christopher; King, Rob; Mohareb, Fady; Pak, Keywan‑Hassani; Hughes, David; Williamson, Martin; Ganko, Eric; Buer, Benjamin; Nauen, RalfBackground: Orius laevigatus, a minute pirate bug, is a highly effective beneficial predator of crop pests including aphids, spider mites and thrips in integrated pest management (IPM) programmes. No genomic information is currently available for O. laevigatus, as is the case for the majority of beneficial predators which feed on crop pests. In contrast, genomic information for crop pests is far more readily available. The lack of publicly available genomes for beneficial predators to date has limited our ability to perform comparative analyses of genes encoding potential insecticide resistance mechanisms between crop pests and their predators. These mechanisms include several gene/protein families including cytochrome P450s (P450s), ATP binding cassette transporters (ABCs), glutathione S-transferases (GSTs), UDP-glucosyltransferases (UGTs) and carboxyl/cholinesterases (CCEs). Methods and findings: In this study, a high-quality scaffold level de novo genome assembly for O. laevigatus has been generated using a hybrid approach with PacBio long-read and Illumina short-read data. The final assembly achieved a scaffold N50 of 125,649 bp and a total genome size of 150.98 Mb. The genome assembly achieved a level of completeness of 93.6% using a set of 1658 core insect genes present as full-length genes. Genome annotation identified 15,102 protein-coding genes - 87% of which were assigned a putative function. Comparative analyses revealed gene expansions of sigma class GSTs and CYP3 P450s. Conversely the UGT gene family showed limited expansion. Differences were seen in the distributions of resistance-associated gene families at the subfamily level between O. laevigatus and some of its targeted crop pests. A target site mutation in ryanodine receptors (I4790M, PxRyR) which has strong links to diamide resistance in crop pests and had previously only been identified in lepidopteran species was found to also be present in hemipteran species, including O. laevigatus. Conclusion and significance: This assembly is the first published genome for the Anthocoridae family and will serve as a useful resource for further research into target-site selectivity issues and potential resistance mechanisms in beneficial predators. Furthermore, the expansion of gene families often linked to insecticide resistance may be an indicator of the capacity of this predator to detoxify selective insecticides. These findings could be exploited by targeted pesticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably, environmentally-friendly and effectively control pests without impacting beneficial predator populations.