The role of recombination in rapid adaptive evolution of fungal plant pathogens: Integrating demographic models, inferences of natural selection and population recombination maps

重组在真菌植物病原体快速适应性进化中的作用：整合人口模型、自然选择推论和种群重组图

• 批准号: 274402545
• 负责人: Professorin Dr. Eva Holtgrewe-Stukenbrock, Ph.D.
• 金额: --
• 依托单位: Botanisches Institut und Botanischer Garten
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2015
• 资助国家: 德国
• 起止时间: 2014-12-31 至 2021-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/274402545?language=en
• 关键词: role; recombination; rapid; adaptive; evolution

Antagonistic co-evolution between pathogens and their hosts can drive rapid adaptive changes in both partners. In this project we aim to understand the underlying mechanisms that drive rapid adaptation in two closely related fungal plant pathogenic species Zymoseptoria tritici (pathogen of cultivated wheat) and Zymoseptoria ardabiliae (pathogen of wild grasses). These two species differ not only in terms of host and environment (agro-ecosystem versus natural grassland) but also in terms of effective population size. We have previously shown that the effective population size is significantly higher in Z. tritici in spite of the strong directional selection pressure imposed to the pathogen in the wheat field. In the first phase of the SPP1819 we compared patterns of polymorphism and divergence to model the distribution of fitness effects across the genome of Z. tritici and to infer the proportion of adaptive mutations fixed by selection, α, as well as the overall rate of adaptation, ωA. In parallel, we used codon models of sequence evolution to detect genes evolving under balancing selection and to infer the strength of purifying selection acting on each gene. We furthermore correlated measures of adaptation with different parameters among others recombination rate, transposable element content, gene density and protein size. Based on α and ωA we find that adaptive evolution overall plays a strong role in protein evolution in Z. tritici and in particular affects genes encoding putative virulence factors. We also report a strong effect of recombination on the rate of adaptation, as well as pervasive background selection. In the second phase of the SPP we will further assess the impact of recombination on rapid adaptive evolution. We will do this by inferring the distribution of selective sweeps throughout the genome of Z. tritici and Z. ardabiliae using composite likelihood ratio (CLR) statistics. In this project we propose to develop new population genetic models that take the demography of the two plant pathogens species into account and include inferred genetic parameters and locus-specific recombination rates to infer maps of selective sweeps across the fungal genomes. This will allow us to compare the distribution of sweeps in the two species and rates of adaptive evolution. Finally, the project will investigate the underlining biological implications of rapid adaptive evolution by conducting functional analyses of selected candidate genes located in swept genome regions. In summary this project will provide novel insight into mechanisms of rapid adaptive evolution of plant pathogens, in particular the role of recombination rate variation. We will finally identify and describe the role of those genes that have experienced recent rapid adaptive evolution in these important plant pathogens.

病原体和宿主之间的对抗性共同进化可以推动双方的快速适应性变化。在这个项目中，我们的目标是了解驱动两个密切相关的真菌植物病原物种Zymoseptoria triploid（栽培小麦的病原体）和Zymoseptoria ardabiliae（野草的病原体）快速适应的潜在机制。这两个物种不仅在宿主和环境（农业生态系统与天然草地）方面不同，而且在有效种群规模方面也不同。我们以前已经证明，有效的人口规模是显着较高的Z。尽管在麦田中对病原体施加了强大的定向选择压力，但仍然可以抑制病原体的生长。在SPP 1819的第一阶段，我们比较了多态性和分歧的模式，以模拟Z基因组中适应性效应的分布。并推断出选择固定的适应性突变的比例α，以及适应的总体速率ωA。同时，我们使用序列进化的密码子模型来检测在平衡选择下进化的基因，并推断作用于每个基因的纯化选择的强度。此外，我们相关的措施，适应与不同的参数之间的重组率，转座因子的内容，基因密度和蛋白质的大小。基于α和ωA，我们发现适应性进化总体上在Z蛋白质进化中起着重要作用。tripetrin，特别是影响编码推定的毒力因子的基因。我们还报告了重组对适应率的强烈影响，以及普遍的背景选择。在SPP的第二阶段，我们将进一步评估重组对快速适应性进化的影响。我们将通过推断选择性扫描在整个Z基因组中的分布来做到这一点。trillium和Z. Ardabiliae使用复合似然比（composite likelihood ratio，RIB）统计。在这个项目中，我们建议开发新的种群遗传模型，考虑到两种植物病原体物种的人口统计学，并包括推断的遗传参数和位点特异性重组率，以推断真菌基因组的选择性扫描图。这将使我们能够比较两个物种的扫描分布和适应性进化的速度。最后，该项目将通过对位于扫描基因组区域的选定候选基因进行功能分析，研究快速适应性进化的重要生物学意义。总之，该项目将提供新的见解植物病原体的快速适应性进化的机制，特别是重组率变化的作用。 最后，我们将确定和描述这些重要的植物病原体中经历了最近的快速适应性进化的基因的作用。