Using comparative genomics to predict the epidemiology and evolution of R. solanacearum plant pathogen in the UK

植物病原菌危害农作物，在全球范围内造成相当大的经济损失。青枯病是由土传革兰氏阴性检疫菌青枯病引起的一种重要的细菌性作物病害。在英国，青枯病菌会引起马铃薯褐腐病。到目前为止，英国的所有疫情都与洪水或灌溉来自受污染的河流水源的马铃薯作物有关，在那里，它可以通过在次要寄主植物木兰花的根部越冬而持续存在。目前已知青枯菌的密度在7-9月水温较高时达到高峰，引起病害暴发的致病菌株与从马铃薯病田上游分离的环境菌株高度相关。虽然这些发现表明环境水库在病原体暴发中发挥了重要作用，但自1992年第一次疾病暴发以来，青枯病菌种群是如何扩散、扩展和进化的仍不清楚。本项目将利用种群基因组学和一系列时间采样的病原体分离物来了解青枯病在英国水系中的流行病学、扩散和进化。该研究将解决三个研究问题：1)扩散：将UK分离物与青枯病菌基因组现有序列数据库进行比较，以确定UK种群是否在遗传上是独特的和局部适应的，并估计国际传播的频率。2)毒力：环境分离物与疾病暴发期间收集的致病分离物是否不同？与环境菌株相比，某些特定的毒力基因是否更常与致病有关？3)进化动力学：自1992年以来英国的青枯病暴发期间，青枯病菌发生了多大程度的变化？我们能否利用全基因组关联方法(Gwas)来识别对病原菌和环境分离物重要的数量性状？所获得的结果将被用于开发一个基因组数据库，该数据库将有助于识别新的暴发菌株，推断其可能的地理来源，并针对给定的暴发菌株匹配特定的控制管理策略。该项目结合了基于实验室的直接实验、下一代基因组测序、生物信息学和进化生物学，以了解并发植物病原菌暴发的动态。你还将有机会发展微生物学、实验进化论、微生物生态学和假说引导的实验设计方面的技能。由于这是一个跨学科的项目，理想的应聘者将至少对一个主要学科领域有背景或表现出兴趣--例如微生物学、遗传学、生物信息学、发病机制--并愿意在其他领域发展技能。

Plant pathogenic bacteria cause considerable economic losses globally due to damage to crops. Bacterial wilt, caused by the soil-borne Gram-negative quarantine bacterium Ralstonia solanacearum, is one of the most important bacterial crop diseases. In the UK, R. solanacearum causes potato brown rot. Thus far, all UK outbreaks have been associated with flooding or irrigation of potato crops from contaminated river water sources where it can persist by overwintering in the roots of its secondary host plant, Woody Nightshade. It is currently known that R. solanacearum densities peak in July-September when the water temperatures are high and that the pathogenic strains driving disease outbreaks are highly related to the environmental strains isolated from upstream of the infested potato fields. While these findings suggest that environmental reservoirs play important roles in the pathogen outbreaks, it is still unclear how the R. solanacearum population has dispersed, expanded and evolved since the first disease outbreak in 1992.This project will use population genomics and a collection of time sampled pathogen isolates to understand the epidemiology, dispersal and evolution of R. solanacearum in the UK river system. The studentship will address three research questions:1) Dispersal: comparison of UK isolates with an existing sequence database of R. solanacearum genomes to determine whether the UK population is genetically unique and locally adapted and to estimate the frequency of international dispersal.2) Virulence: do the environmental isolates differ from the pathogenic isolates collected during disease outbreaks? Are some specific virulence genes more often associated with pathogenic compared to environmental isolates?3) Evolutionary dynamics: to what extent has R. solanacearum changed during the UK disease outbreaks since 1992? Can we identify quantitative traits that are important for pathogenic vs. environmental isolates by using genome-wide association approaches (GWAS)?The obtained results will be used to develop a genomic database that will help in identifying novel outbreak strains, to infer the likely geographic source of their origin and to match specific control management strategies against the given outbreak strain.The project combines laboratory-based direct experimentation, next-generation genome sequencing, bioinformatics and evolutionary biology to understand the dynamics of concurrent plant pathogen outbreaks. You will also have an opportunity to develop skills in microbiology, experimental evolution, microbial ecology and hypothesis-led experimental design. As this is an interdisciplinary project, ideal candidates will have a background in or a demonstrated interest in at least one of the main subject areas - e.g. microbiology, genetics, bioinformatics, pathogenesis - and be willing to develop skills in the other areas.