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

植物病原菌对农作物的危害在全球范围内造成了巨大的经济损失。青枯病是由土传的革兰氏阴性检疫细菌青枯菌（Ralstonia solanacearum）引起的一种重要的细菌性作物病害。在英国，R。青枯菌引起马铃薯褐腐病。到目前为止，英国所有的疫情都与被污染的河流水源的洪水或灌溉马铃薯作物有关，在那里它可以通过在其第二宿主植物Woody Nightshade的根部越冬而持续存在。目前已知R.青枯菌密度在水温高的7 - 9月达到高峰，导致病害暴发的致病菌株与从受侵染的马铃薯田上游分离的环境菌株高度相关。虽然这些研究结果表明，环境水库发挥重要作用的病原体爆发，目前还不清楚如何R。自1992年第一次青枯病爆发以来，青枯菌种群发生了扩散、扩展和进化。英国河流系统中的青枯菌该研究项目将解决三个研究问题：1）扩散：将英国分离株与现有的R。青枯菌的基因组，以确定是否英国人口是遗传独特的和当地适应，并估计国际传播的频率。2）毒力：环境分离物不同的致病性分离物收集在疾病爆发？与环境分离株相比，某些特定的毒力基因是否更常与致病性相关？3)进化动力学：R。自1992年以来，青枯菌在英国疾病爆发期间发生了变化？我们能否通过全基因组关联方法（GWAS）来识别对致病性和环境分离株重要的数量性状？所获得的结果将用于开发一个基因组数据库，该数据库将有助于确定新的爆发菌株，推断其起源的可能地理来源，并针对特定的爆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，以了解同时发生的植物病原体爆发的动态。您还将有机会发展微生物学，实验进化，微生物生态学和假设主导的实验设计方面的技能。由于这是一个跨学科的项目，理想的候选人将在至少一个主要学科领域的背景或表现出兴趣-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.