Evolutionary genomics of host range expansion in aphid crop pests

害虫给英国和世界各地的农作物造成了巨大的经济损失。一些害虫已经进化出了在数百种不同寄主植物上定居的能力，而另一些害虫则专门针对一种寄主植物。前一类害虫被称为多面手，它们特别有害，因为它们可以在不同的宿主物种之间传播传染病和病原体。此外，多面手害虫有迅速进化出抗药性的倾向。生物学中的一个重要问题是了解使多面手害虫能够利用不同寄主植物物种的遗传基础。本奖学金结合比较基因组学和功能基因组学方法来确定这些遗传适应。特别是，我将应用全基因组测序，组装和注释跨蚜虫系统发育的多个专业和通用蚜虫物种的基因组，以确定基因和进化机制负责适应广泛的寄主植物。我将使用功能分析验证生物信息学和进化遗传学的发现，并测试鉴定的基因和基因家族是否影响蚜虫在新寄主植物上的适应和生存能力。具体来说，该项目有三个目标：(1)：在蚜虫的系统发育过程中，为9种专业蚜虫和7种通才蚜虫生成比较基因组资源，并启动一个开放获取的集合基因组中心；(2)在通才蚜虫谱系中，鉴定在循环选择下的基因和近期扩张或收缩的基因家族；(3)通过基因敲低和宿主交换实验，检验候选基因与通才性之间的因果关系。这项研究的长期目标是了解害虫是如何进化到在不同的寄主植物物种中定居的。这种认识和理解超出了昆虫学家的兴趣范围，很可能适用于其他多面手病原体。因此，该奖学金的拟议研究引起了更广泛的研究界的兴趣，包括研究各种寄生虫和病原体的进化生物学家、生态学家和遗传学家。由于这一提议超越了典型的学科界限，我将与约翰英尼斯中心（JIC）的昆虫学家和功能遗传学家（Saskia Hogenhout教授）、厄尔勒姆研究所（EI）的基因组学家（David Swarbreck博士）以及进化生物学家(Prf。东英吉利大学（UEA）的Cock van Oosterhout教授，我将与爱丁堡大学的Mark Blaxter合作，在一个互动数据库上交流我的科学。该项目中测序的基因组包括许多重要的作物害虫，这将代表着蚜虫基因组资源的一个重大变化。这些数据将通过一个新的基因组中心（openentomtvector.org）提供给社区，该中心将承载基因组，提高我在该领域的知名度，并作为未来承载更多取食汁液的昆虫物种的比较基因组分析的基地。

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.