Using population 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相当大的经济损失。由革兰氏阴性检疫菌青枯菌引起的细菌性青枯病是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。英国疫情的爆发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，它可以通过在其次要宿主植物WoodyNightshade的根中越冬而持续存在。目前已知青枯病菌的密度在水温较高的7-9月达到高峰，从疫病暴发中分离到的菌株与从受侵染的马铃薯田上游的水和替代寄主分离的环境菌株高度相关。虽然这些发现表明环境水库在疾病暴发中发挥了重要作用，但自1992年发现第一种疾病以来，青枯病种群是如何分散、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株来了解英国河流系统青枯病的流行病学和基因组进化。这项研究将涉及三个研究领域：1)全球病原体传播：将UK分离株与现有的青枯病菌基因组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)进化动力学：自1992年以来英国青枯病菌暴发期间，青枯病菌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)来识别对致病菌株和环境分离株重要的数量性状？我们能否利用基因组差异来推断病原体在环境水库中的生态和适应情况以及青枯病菌在英国仍在进化？3)青枯病菌基因的时空分布：我们将开发一个基因组数据库，帮助识别新的暴发菌株，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暴发的动态。

Plant pathogenic bacteria cause considerable economic losses globally due to damage to crops.Bacterial wilt, caused by the Gram-negative quarantine bacterium Ralstonia solanacearum, is one ofthe most important bacterial crop diseases. In the UK, R. solanacearum causes potato brown rot. UKoutbreaks have been associated with flooding or irrigation of potato crops from contaminated riverwater sources where it can persist by overwintering in the roots of its secondary host plant, WoodyNightshade. It is currently known that R. solanacearum densities peak in July-September when thewater temperatures are high and that the strains isolated from disease outbreaks are highly related tothe environmental strains isolated from water and alternative hosts upstream of the infested potatofields. While these findings suggest that environmental reservoirs play important roles in the diseaseoutbreaks, it is still unclear how the R. solanacearum population has dispersed, expanded and evolvedsince the first disease finding in 1992.This project will use population genomics and a collection of time sampled pathogen isolates tounderstand the epidemiology and genomic evolution of R. solanacearum in the UK river system. Thestudentship will address three research areas:1) Global pathogen dispersal: comparison of UK isolates with an existing sequence database of R.solanacearum genomes to determine whether the UK population is genetically unique and locallyadapted and to estimate the frequency of international dispersal.2) Evolutionary dynamics: to what extent has R. solanacearum changed during the UK diseaseoutbreaks since 1992? Can we identify quantitative traits that are important for pathogenic vs.environmental isolates by using genome-wide association approaches (GWAS)? Can we use genomedifference to infer something about pathogen ecology and adaptation in environmental reservoirs andis R. solanacearum still evolving in the UK?3) Spatial and temporal distribution of R. solanacearum genotypes: We will develop a genomicdatabase that will help in identifying novel outbreak strains, to infer the likely geographic source of their2origin and to match specific control management strategies against the given outbreak strain.The project combines next-generation genome sequencing, bioinformatics and evolutionary biology tounderstand the dynamics of concurrent plant pathogen outbreaks.