The evolutionary genomics of infectious phytopathogen emergence

传染性病原体给全球农业带来了沉重的负担，并导致发展中国家出现严重的粮食短缺。这一负担的大部分是由新出现的病原体造成的，这些病原体最近演变为对重要作物造成疾病。然而，令人惊讶的是，我们对使病原体出现并导致爆发的进化机制知之甚少。狄龙实验室的长期目标是了解新型传染病是如何通过关键致病基因（毒力因子）的多样化而出现的，以便我们能够更好地保护脆弱的作物免受毁灭性病原体的侵害。为了实现这一目标，我们利用植物病原体黄单胞菌来解决以下三个目标：1.表征关键毒力因子的分布和多样性。我们将分析一千多个基因组，以确定显示与宿主-病原体军备竞赛相关的进化特征的毒力因子。我们特别感兴趣的是在多个物种中发现的效应基因，因此能够产生跨物种的抗性屏障。2.从功能上评估毒力因子多样化在宿主-病原体相互作用中的作用。我们将测试候选毒力因子是否引起植物免疫，并将结果与我们的比较基因组分析联合收割机结合，以开发宿主特异性的定量模型。3.剖析新的传染病出现的进化途径。我们将实验性地进化出三种不同的X。campestris菌株的模式主机和表征的表型和遗传基础的疾病出现的时间。我们还将确定与疾病出现在替代主机，这将揭示脆弱性，是主机特定的适应的结果相关的进化权衡。我们的研究将捕获毒力因子如何在远亲病原体中传播，查明决定宿主-病原体相互作用命运的跨物种抗性因子，并首次直接洞察导致新植物疾病出现的进化途径。我们还将提供丰富的宿主抗性靶标新来源，并开发基因组使能的病原体诊断方法用于该领域。这项工作将直接使加拿大人受益，将这些资源用于正在进行的育种和监测计划，最终减轻加拿大农民的病原体负担和加拿大消费者的下游成本。未来五年，我还将为25名以上各级HQP提供高级多学科培训（B.Sc.，理学硕士，哲学博士、PDF），以填补学术界，工业界和政府的关键角色。随着我们不断变化的气候继续为病原体的成功创造有利条件，我们将帮助制定强有力的疾病控制战略，帮助改变宿主-病原体相互作用的平衡，以有利于我们脆弱的作物。

Infectious pathogens impose a substantial burden on the global agricultural industry and result in major food deficits in developing nations. Much of this burden is inflicted by emerging pathogens that have recently evolved to cause disease on important crops. However, we know surprisingly little about the evolutionary mechanisms that enable pathogens to emerge and cause outbreaks. The long-term goal of the Dillon Lab is to understand how novel infectious diseases emerge through diversification of critical disease-causing genes (virulence factors) so that we can better protect vulnerable crops from devastating pathogens. In pursuit of this goal, we are leveraging the plant pathogen Xanthomonas to address the following three objectives: 1.Characterize the distribution and diversification of critical virulence factors. We will analyze more than a thousand genomes to identify virulence factors displaying evolutionary signatures associated with the host-pathogen arms race. We are particularly interested in effector genes that are found in multiple species and are thus capable of generating cross-species resistance barriers. 2.Functionally assess the role of virulence factor diversification in the fate of host-pathogen interactions. We will test whether candidate virulence factors elicit plant immunity and combine the results with our comparative genomic analysis to develop quantitative models of host specificity. 3.Dissect the evolutionary pathways through which novel infectious diseases emerge. We will experimentally evolve three different X. campestris strains on a model host and characterize the phenotypic and genetic basis of disease emergence through time. We will also identify evolutionary tradeoffs associated with disease emergence on alternative hosts, which will reveal vulnerabilities that are a consequence of host specific adaptation. Our research will capture how virulence factors are disseminated across distantly related pathogens, pinpoint cross-species resistance factors that determine the fate of host-pathogen interactions, and produce the first direct insight into the evolutionary pathways that yield the emergence of new plant diseases. We will also provide a rich new source of host resistance targets and develop genome-enabled pathogen diagnostics for use in the field. This work will directly benefit Canadians by contributing these resources to ongoing breeding and surveillance programs, ultimately reducing the burden of pathogens on Canadian farmers and the downstream costs for Canadian consumers. In the next five years, I will also provide advanced multidisciplinary training for more than 25 HQP at all levels (B.Sc., M.Sc., Ph.D., PDF) to fill critical roles in academia, industry, and government. As our changing climate continues to create conditions conducive to pathogen success, we will help build robust disease-control strategies that help shift the balance of host-pathogen interactions in favour of our vulnerable crops.