Going back in time to predict the evolution of future plant pathogen

马铃薯褐腐病是一种全球性的重要作物病害，由植物致病菌Ralstonia solanacearum引起，在英国属于最高经济风险类别。到目前为止，英国所有的疫情都与受污染的河流水源的洪水或灌溉马铃薯作物有关，在那里，病原体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，Fera Science通过每年在全英国范围内对河流进行采样来监测病原体的存在，以确定哪些河流将被禁止使用，不能用于灌溉。这个采样程序产生了一个有价值的菌株收集跨越35年病原体进化在其自然环境。该项目将使用基因组学、生物信息学和直接实验来确定在过去的三十年里，R. solanacearum的毒力是如何在英国河流网络中进化的。本项目将结合生物信息学、微生物学和植物生物学来确定茄青霉在环境库中进化时毒力的机制和遗传变化。工作将基于现有的200株Fera收集，这些收集已经与人共享并进行了测序。现在将对该集合进行表型表征，并链接回元数据（样本位置和年份），具体侧重于：目标1。比较关键毒力基因的变异，重点关注snp、缺失、插入序列和前噬菌体运动的影响。Friman实验室进一步开发了一种基因组尺度模型，可用于模拟不同变异对毒力基因网络的影响，从而允许对病原体表型进行计算机预测。目标2。比较关键毒力性状的变异，包括运动性、附着性、代谢、趋化性、耐受性、三型效应蛋白、胞外多糖产生、铁载体等。一部分分离株将在表达水平上使用转录组学进行表征。该数据将用于验证在目标1中获得的硅表型预测。目标3。植物病原菌毒力的定量变异。Friman实验室开发了植物分析方法，利用番茄分析来量化病原体毒力的变化，这将用于描述整个菌株收集的特征。这将允许在英国鉴定新的潜在的毒性病原体基因型标记基因，可用于快速流行病学诊断。

Potato brown rot, caused by Ralstonia solanacearum plant pathogenic bacterium, is a globally important crop disease, belonging to the highest economic risk category in the UK. Thus far, all UK outbreaks have been associated with flooding or irrigation of potato crops from contaminated river water sources where the pathogen can persist by overwintering in the roots of its secondary host plant, Woody Nightshade.Pathogen presence is currently monitored through annual, UK-wide river sampling by Fera Science to identify contaminated rivers that will be banned and cannot be used for irrigation. This sampling program has produced a valuable strain collection spanning 35 years of pathogen evolution in its natural environment. This project will use genomics, bioinformatics, and direct experimentation to establish how the virulence of R. solanacearum has evolved in the UK river network during the past three decades.This project will use a combination of bioinformatics, microbiology, and plant biology to identify mechanisms and genetic changes in R. solanacearum virulence when evolving in environmental reservoirs. Work will be based on an existing 200-strain Fera collection, which has already been shared with and sequenced. This collection will now be characterised phenotypically and linked back to metadata (sample location and year) specifically focusing on:Objective 1. Comparing variation in key virulence genes, focusing on effects of SNPs, deletions, and insertion sequence and prophage movement using bioinformatics. Friman lab has further developed a genome-scale model that can be used to model the effect of different variants on virulence gene networks, allowing in silico prediction of pathogen phenotypes.Objective 2. Comparing variation in key virulence traits, including motility, attachment, metabolism, chemotaxis, stress tolerance, type three effector proteins, exopolysaccharide production, siderophores and several others. A subset of isolates will be characterised at the expression level using transcriptomics. This data will be used to validate in silico phenotype predictions obtained in objective 1.Objective 3. Quantifying variation in pathogen virulence in planta. Friman lab has developed in planta assays to quantify changes in pathogen virulence using tomato assays, which will be used to characterise the whole strains collection. This will allow the identification of new potential marker genes for virulent pathogen genotypes in the UK that could be used to rapid epidemiological diagnostics.