Functional parasite epigenomics and transcriptomics for improving honey-bee health in a global pollination crisis

花粉是一种非常重要的生态系统服务，不仅有助于维持野生生态系统的生物多样性，而且对于满足不断增长的农业需求以维持全球粮食安全也是不可或缺的。蜜蜂是世界范围内最重要的传粉者之一，但近几十年来面临着相当大的下降，这导致了全球授粉危机[1]。蜜蜂健康受到寄生螨狄斯瓦螨和广泛病毒的复杂三方共生的严重影响[2]。瓦螨在几乎所有的蜂群中普遍存在，并且是蜜蜂数量减少的主要原因之一，因为它们传播导致致命疾病的病毒（最突出的是变形翼病毒DWV）。这些影响在紧张的环境条件下加剧，其中瓦螨属感染成为殖民地的真实的负担。虽然蜜蜂对病毒感染的功能性分子反应得到了很好的研究，但对功能性分子过程如何影响瓦螨属行为和病毒传播以及环境背景如何影响这些分子动力学还知之甚少[3]。本项目旨在发展对瓦螨属和DWV之间相互作用所涉及的功能性表观基因组和转录组分子过程的机制理解。要解决的广泛问题是：1）从不同的生态环境（例如，不同的季节）和/或具有不同的病毒载量收集的瓦螨是否在全基因组表观遗传信息（如核苷酸甲基化）方面存在差异？2)基因表达和生理途径调节的哪些变化与表观遗传信息的变化相关？3)如何操纵和利用瓦螨属的表观遗传机制来改善蜜蜂的健康？这些问题将通过一系列基于候选基因和全基因组表观基因组学和转录组学分析来解决。狄斯瓦螨的注释参考基因组是可用的，这将确保数据可以根据功能骨架进行解释，并可以得出有意义的推论。该项目将特别适合于对功能表观遗传学，基因组学和生物信息学感兴趣的学生。学生将接受该项目各个方面的全面培训，包括野外样本收集，螨类显微解剖，实验室螨类维护，广泛的分子生物学方法（DNA/RNA提取，PCR，qPCR等）。以及与项目期间生成的高通量测序数据类型相关的广泛生物信息学培训（Illumina，Oxford NanoPore）。贝尔法斯特女王大学的基因组核心技术单位（GCTU）和阿伯丁大学的基因组生物学和医学中心（CGEBM）提供了最先进的高通量测序以及高性能计算设施和正式的生物信息学培训。这种出色的基因组学和生物信息学支持确保除了全面的实用分子生物学技能外，还将获得一套全面的可转移数字技能。

Pollination is an immensely important ecosystem service that not only contributes to maintaining biodiversity in wild ecosystems but is also indispensable for meeting ever-increasing demands on agriculture to sustain global food security. Honey bees are among the most important pollinators world-wide but have faced a considerable decline in recent decades, which is contributing to a global pollination crisis [1].Honey-bee health is critically affected by an intricate three-way symbiosis with the parasitic mite Varroa destructor and a broad range of viruses [2]. Varroa mites are ubiquitous in virtually all bee colonies and are one of the main causes of honey-bee decline because they transmit viruses that cause deadly diseases (most prominently deformed-wing virus DWV). These impacts are exacerbated under stressful environmental conditions, where Varroa infection becomes a real burden for the colony. While the functional molecular responses of bees to viral infection are well-examined, it is poorly understood how functional molecular processes may affect Varroa behaviour and viral transmission and how environmental context may affect these molecular dynamics [3].This project aims to develop mechanistic understanding of functional epigenomic and transcriptomic molecular processes involved in the interactions between Varroa and DWV. The broad questions to be addressed are: 1) Do Varroa mites collected from different ecological contexts (e.g, different seasons) and/or having different viral loads differ in genome-wide epigenetic information such as nucleotide methylation? 2) What changes in gene expression and regulation of physiological pathways are associated with changes in epigenetic information? 3) How could the epigenetic machinery of Varroa be manipulated and harnessed to improve honey-bee health?These questions will be addressed with a range of candidate-gene based and genome-wide epigenomic and transcriptomic assays. An annotated reference genome of Varroa destructor is available, which will ensure that data can be interpreted against a functional backbone and meaningful inferences can be drawn. The project will be particularly suitable to a student with interests in functional epigenetics, genomics and bioinformatics. The student will receive full training in all aspects of the project, including collection of field samples, microdissection of mites, maintenance of mites in the lab, a broad range of molecular biology methods (DNA/RNA extraction, PCR, qPCR etc.) and extensive bioinformatics training relevant to the types of high-throughput-sequencing data generated during the project (Illumina, Oxford NanoPore). The Genomics Core Technology Unit (GCTU) at Queen's University Belfast and the Centre of Genome-Enabled Biology and Medicine (CGEBM) at the University of Aberdeen provide access to state-of-the-art high-throughput sequencing as well as high-performance computing facilities and formal bioinformatics training. This excellent genomics and bioinformatics support ensures that a comprehensive set of transferrable digital skills will be obtained in addition to a well-rounded set of practical molecular biology skills.