Evolutionary genomics of host range expansion in aphid crop pests

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.

The proposed research in this fellowship is designed to understand how generalist insect pests have evolved to colonise diverse host plant species. The fellowship focuses on generalist and specialist aphid species, and aims to identify the genes and gene families underpinning generalism, the evolutionary processes shaping genetic variation of these genes, and validating the candidate genes identified using gene knockdown and host transfer experiments. The three main objectives of the proposal are:

The first objective is to generate comparative genomic resources for specialist and generalist aphids across the aphid phylogeny and launch an open access ensemble genome hub (OPENinsectVECTOR.org). In total, I will generate 24 new aphid genome assemblies with associated gene annotations.

My second objective is to identify genes associated with generalism based on comparative analysis of 26 aphid genomes from three aphid genera. I will investigate the relative contributions of positive selection, gene family expansion/contraction and adaptive introgression for the evolution of generalism. To accomplish this, estimate gene duplication and loss rates from reconciled gene trees, calculate dN/dS ratios in a phylogenetic framework, and test for evidence of recombination using ABBA-BABA tests and Patterson's D statistics.

In my third and final objective, I will validate the functional significance of the identified genes and gene families, testing their role in adaptation to novel host in a host swap experiment. To accomplish this, I will be using plant-mediated RNAi knockdown in the model generalist aphid M. persicae, and calculate the fitness after host transfer, studying survival and fecundity of RNAi aphids with the aim to identify causal genetic variants and genes enabling rapid host adaptation and generalism.

Aphids are economically important pests on a diverse range of crops grown in the UK and globally. These insects cause direct feeding damage and also transmit more than 300 different plant viruses and pathogens. Whereas the majority of aphids are specialized and colonize only one or a few related plant species, some aphid species can colonize diverse crops. It is thought that the generalist aphid species are particularly problematic, because they can acquire viruses from weeds and neighboring crops and transmit them to young seedlings, which are particularly susceptible to the pathogens and aphids. In the past approximately 15 years, seed companies and farmers have been able to protect the young seedlings via applications of neonicotinoid insecticides within the seed coating; this insecticide spreads systemically within the plant and protects the young seedlings for approximately 6 weeks upon emergence. However, there is evidence that neonicotinoids affect beneficial insects, including bees, leading to new legislations that have banned these insecticides from the market. In Europe, neonicotinoids are already not being used for flowering crops, such as oilseed rape, and next year they will also be forbidden for other crops, such as sugar beet. Since the discontinuation of neonicotinoids, oilseed rape productions have been seriously afflicted by aphid, flea beetle and slug outbreaks. It is expected that, for sugar beet, the ban of these insecticide will lead to more than 30% loss due to outbreaks of yellows viruses transmitted by aphids. This would make the production of sugar beet, and other crops, economically unviable in the UK.

With the research described in the Fellowship project, I hope to generate basic knowledge on the evolution of generalism in aphids. I expect generated knowledge will be valuable for the characterization of key aphid genes that enable aphids to colonize plant species and migrate from weed to crop and crop to crop. I believe this is important, because so far there is a general lack of knowledge about the biology of aphids and this is seriously affecting the development of novel methods to control these insect pests. Even though insecticides have been highly effective at controlling arthropod pests, they are damaging to the general environment. The knowledge generated in this project may reveal aphid pathways and genes that could serve as targets for new, more benign, control methods. Realistically, it is unlikely that I will be developing such novel methods within the time line of this project, but via my existing and future contacts with colleagues in industry I will be in a good position to take any discoveries made in this project forward to achieve strategic research goals in the future. Overall such achievements would benefit the nation's health and wealth by increasing crop yields and protection of the environment. Within this project, I wish to involve the general public as much as possible via providing basic information on aphids and other insect pests via the OPENInsectVECTOR.org hub, writing of blogs and interactions with journalists.