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

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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.