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

植物致病菌对农作物的危害在全球范围内造成了相当大的经济损失。青枯病是一种重要的作物细菌性病害，由土壤传播的革兰氏阴性检疫细菌（Ralstonia solanacearum）引起。在英国，R. solanacearum引起马铃薯褐腐病。到目前为止，所有的英国爆发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，它可以通过在其次生寄主植物龙葵的根部越冬而持续存在。目前已经知道，7 - 9月是水温度较高的时候，茄青霉的密度达到高峰，导致疾病爆发的致病菌株与侵染马铃薯地上游分离的环境菌株高度相关。虽然这些发现表明环境宿主在病原菌暴发中发挥了重要作用，但自1992年首次暴发以来，尚不清楚茄青霉种群是如何分散、扩大和进化的。该项目将使用种群基因组学和收集时间采样的病原体分离物来了解R. solanacearum在英国河流系统中的流行病学，传播和进化。该奖学金将解决三个研究问题：1)扩散：将英国分离株与现有的R. solanacearum基因组序列数据库进行比较，以确定英国种群是否具有遗传独特性和本地适应性，并估计国际扩散的频率。2)毒力：环境分离株与疾病暴发时收集的致病分离株是否不同？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：自1992年以来，在英国疾病爆发期间，R. solanacearum发生了多大程度的变化？我们能否通过使用全基因组关联方法（GWAS）来确定致病与环境分离的重要数量性状？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，并针对给定的爆发菌株匹配特定的控制管理策略。该项目结合了实验室直接实验、下一代基因组测序、生物信息学和进化生物学来了解并发植物病原体爆发的动态。你也将有机会发展微生物学、实验进化、微生物生态学和以假设为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具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-并愿意发展其他领域的技能。

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.