Functional Genomics of Aphid Adaptation to Plant Species

1.背景：绿色桃蚜Myzus persicae（GPA）是一种全球性的重要农业害虫，可以定殖来自50多个植物科的400多种不同植物物种，并且保持杀虫剂抗性机制的世界纪录，对至少70种不同的合成化合物显示抗性。此外，GPA具有显著的可塑性，使得由基因相同的雌性组成的一个克隆可以在广泛的植物物种上生存和繁殖。这与大多数其他蚜虫物种形成对比，包括豌豆蚜（Acyrthosiphon pisum），它已经适应了一个植物家族中的一个或几个相关植物物种。大问题：GPA表型可塑性的遗传控制机制是什么？这种可塑性是否与GPA在过去60年中进化出对至少70种不同合成化合物的杀虫剂抗性的能力有关，即“进化眨眼”？3.假设：我们假设GPA的表型可塑性是由于其（1）基因组适应的形式，某些多基因家族的扩展是重要的毒力，结合（2）影响基因家族成员的基因表达水平的表观遗传调控。根据对植物宿主和杀虫剂的暴露，基因家族中的某些成员被差异性地上调或下调，为寄生虫提供了一个通用的“遗传工具箱”。支持性数据：Hogenhout实验室已经为GPA克隆“O”开发了研究工具，该克隆在英国占主导地位，近年来对多种作物造成了损害。我们保持这个克隆作为基因相同的女性，可以生存和繁殖的不同植物物种，包括例如白菜和烟草植物，产生不同的防御化合物，是有毒的蚜虫。GPA克隆O全基因组序列目前正在使用基因表达数据进行组装和注释。我们有证据表明，特定基因家族的成员，如组织蛋白酶和角质层蛋白，在GPA对植物物种的表型适应中发挥作用。我们还对细胞色素450单加氧酶（P450）感兴趣，这是植物化学物质和农药等有机物质的解毒酶。最后，我们开发了植物介导的RNA干扰（RNAi）技术，可以研究特定GPA基因的敲除对不同植物物种GPA存活和繁殖的影响.目的：在第一个目的中，我们将推进物理基因组图谱的构建，鉴定编码序列并对GPA克隆O的基因家族成员进行进化分析。在第二个目标中，我们将评估哪些基因在GPA克隆O中受到差异调节，GPA克隆O在不同植物物种上饲养并暴露于各种农药。我们还将对其他GPA克隆的基因组进行测序，这些克隆对农药敏感和耐药，并确定差异表达的基因是否具有高突变频率。在第三个目标中，我们使用植物介导的RNAi来敲低特定基因的表达，以评估它们对GPA在不同植物物种和杀虫剂暴露后生存能力的影响。我们将评估DNA甲基化是否参与GPA表型可塑性。6.影响：在这个项目完成后，我们将有一个更好的了解如何GPA适应多种植物物种，如果这涉及到GPA的杀虫剂抗性的发展机制。我们还将阐明GPA克隆对农药敏感和耐药的基因组变异水平。这项研究对我们全面了解昆虫如何适应环境至关重要。最终，这可能对作物害虫控制中日益严重的杀虫剂抗药性演变问题产生实际影响。

1. The Background: The green peach aphid (GPA) Myzus persicae, an agronomically important pest worldwide, can colonize over 400 different plant species from more than 50 plant families and holds the world record of insecticide resistance mechanisms, showing resistance to at least 70 different synthetic compounds. Moreover, GPA is remarkably plastic such that one clone consisting of genetically identical females can survive and reproduce on a wide range of plant species. This is in contrast to majority of other aphid species, including the pea aphid (Acyrthosiphon pisum), which has adapted to one or a few related plant species within one plant family.2. The Big Questions: What are the genetic control mechanisms that underlie the phenotypic plasticity of GPA? Is this plasticity related to GPA ability to evolve insecticide resistance to at least 70 different synthetic compounds in the last 60 years, i.e. an "evolutionary blink-of-an-eye"?3. The Hypotheses: We hypothesize that the phenotypic plasticity of GPA is due to its (1) genomic adaptations in the form of the expansion of certain multigene families that are important for virulence, in combination with (2) epigenetic regulation affecting gene expression levels of gene family members. Depending on exposure to plant hosts and pesticides, certain members within gene families are differentially up or down-regulated, providing the parasite with a versatile "genetic toolbox".4. The Supportive Data: The Hogenhout lab has developed research tools for GPA clone "O", which has predominated in the UK, causing damage to diverse crops in recent years. We maintain this clone as genetically identical females that can survive and reproduce on diverse plant species, including for example Chinese cabbage and tobacco plants, which produce different defense compounds that are toxic to aphids. The GPA clone O whole genome sequence is currently being assembled and annotated using gene expression data. We have evidence that members of specific gene families, such as cathepsins and cuticular proteins, play a role in the phenotypic adaptation of GPA to plant species. We are also interested in cytochrome 450 monooxygenases (P450s), which are detoxification enzymes of organic substances such as phytochemicals and pesticides. Finally, we have developed the plant-mediated RNA interference (RNAi) technology enabling studies of the effect of the knock down of specific GPA genes on GPA survival and reproduction on various plant species.5. The Objectives:In the first objective we will advance the construction of a physical genomic map, identify coding sequences and conduct evolutionary analysis of gene family members of GPA clone O. In the second objective we will assess which genes are differentially regulated in GPA clone O reared on different plant species and exposed to various pesticides. We will also sequence the genomes of additional GPA clones that are susceptible and resistant to pesticides and determine if differentially expressed genes are subject to high mutation frequencies. In the third objective we use plant-mediated RNAi to knock down the expression of specific genes to assess their effect on the ability of GPA to survive on different plant species and upon insecticide exposure. We will assess if DNA methylation is involved in GPA phenotypic plasticity. 6. The Implications: At completion of this project we will have gained a better understanding of how GPA adapts to multiple plant species and if this relates to mechanisms involved in the development of insecticide resistance of GPA. We will also have elucidated the level of genomic variation amongst GPA clones susceptible and resistant to pesticides. This research is fundamentally important to our overall understanding of how insect adapt to their environments. Ultimately, this could have practical implications for the increasing problem of the evolution of insecticide resistance in crop-pest control.