Evolutionary genomics of host range expansion in aphid crop pests

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Pest insects inflict significant economic damage to agricultural crops in the UK and across the world. Some pest insects have evolved the ability to colonise hundreds of different host plant species, whereas others are specialised on a single host plant. The former group of pest insects are called generalists, and they are particularly harmful because they can spread infectious diseases and pathogens across different host species. In addition, generalist pest insects have the propensity to rapidly evolve resistance to pesticides. An important question in biology is understanding the genetic underpinnings that enable generalist pest insects to exploit different host plant species. This fellowship combines comparative genomics and functional genomics approaches to identify these genetic adaptations. In particular, I will apply whole genome sequencing, assembly and annotating of the genomes of multiple specialist and generalist aphid species across the aphid phylogeny to identify the genes and the evolutionary mechanisms responsible for adaptation to a wide range of host plants. I will validate the bioinformatics and evolutionary genetic findings using a functional analyses, and test whether the identified genes and gene families impact the ability of aphids to adjust and survive on novel host plants. Specifically, this project has three objectives (1): Generate comparative genomic resources for 9 specialist aphids and 7 generalist aphids across the aphid phylogeny and launch an open access ensemble genome hub, (2) Identify genes under recurrent selection and gene families undergoing recent expansions or contractions in generalist aphid lineages, and (3) Test causal relationships between candidate genes and generalism using gene knockdown and host-swap experiments. The long-term goal of this fellowship is to understand how generalist insect pests have evolved to colonise diverse host plant species. This knowledge and understanding goes beyond the interest of entomologists, and is likely to be applicable to other generalist pathogens. As such, the proposed research in this fellowship is of interest to wider research community, including evolutionary biologists, ecologists, and geneticists working on a wide range of parasites and pathogens. Because this proposal transcends typical disciplinary boundaries, I will be engaging with entomologists and functional geneticist (Prof. Saskia Hogenhout) of the John Innes Centre (JIC), a genomicist (Dr. David Swarbreck) at the Earlham Institute (EI), and an evolutionary biologist (Prf. Cock van Oosterhout) at the University of East Anglia (UEA), and I will communicate my science on an interactive database in collaboration with Mark Blaxter at University of Edinburgh.The genomes sequenced in this project include many important crop pests and will represent a step change in the genomic resources available for aphids. These data will be made available to the community via a new genome hub - OPENinsectVECTOR.org - that will host the genomes, raise my profile in the field and serve as a future base for hosting comparative genome analyses of more sap-feeding insect species.