A near-chromosome level genome assembly of the European hoverfly, Sphaerophoria rueppellii (Diptera: Syrphidae), provides comparative insights into insecticide resistance-related gene family evolution

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dc.contributor.authorBailey, Emma
dc.contributor.authorField, Linda
dc.contributor.authorRawlings, Christopher
dc.contributor.authorKing, Rob
dc.contributor.authorMohareb, Fady
dc.contributor.authorPak, Keywan‑Hassani
dc.contributor.authorHughes, David
dc.contributor.authorWilliamson, Martin
dc.contributor.authorGanko, Eric
dc.contributor.authorBuer, Benjamin
dc.contributor.authorNauen, Ralf
dc.date.accessioned2022-03-25T11:57:15Z
dc.date.available2022-03-25T11:57:15Z
dc.date.issued2022-03-12
dc.description.abstractBackground 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.en_UK
dc.description.sponsorshipBiotechnology and Biological Sciences Research Council (BBSRC): Bayer Crop Science and Syngenta AG.en_UK
dc.identifier.citationBailey E, Field L, Rawlings C, et al., (2022) A near-chromosome level genome assembly of the European hoverfly, Sphaerophoria rueppellii (Diptera: Syrphidae), provides comparative insights into insecticide resistance-related gene family evolution, BMC Genomics, Volume 23, March 2022, Article number 198en_UK
dc.identifier.eissn1471-2164
dc.identifier.issn1471-2164
dc.identifier.urihttps://doi.org/10.1186/s12864-022-08436-5
dc.identifier.urihttp://dspace.lib.cranfield.ac.uk/handle/1826/17683
dc.language.isoenen_UK
dc.publisherBioMed Centralen_UK
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectSphaerophoria rueppelliien_UK
dc.subjectHoverfyen_UK
dc.subjectPacBioen_UK
dc.subjectIlluminaen_UK
dc.subjectHi-Cen_UK
dc.subjectWhole genome sequencingen_UK
dc.subjectBenefcial predatoren_UK
dc.subjectInsecticide resistanceen_UK
dc.subjectComparative genomicsen_UK
dc.subjectDipteraen_UK
dc.subjectSyrphidaeen_UK
dc.subjectCrop pestsen_UK
dc.titleA near-chromosome level genome assembly of the European hoverfly, Sphaerophoria rueppellii (Diptera: Syrphidae), provides comparative insights into insecticide resistance-related gene family evolutionen_UK
dc.typeArticleen_UK

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