Dynamic mini-chromosomes: mechanisms of exchange, stability and causation of fungal pathogen adaptation

粮食作物不断受到已有病原体的新变种和新出现的病原体的威胁。稻瘟菌有很长的变异历史，以克服水稻作物中的抗性，1985年出现了一个新的稻瘟菌变种，在巴西小麦上造成了毁灭性的疾病。事实证明，小麦稻瘟病比稻瘟病更难控制，因为使用20世纪80年代的菌株确定的潜在抗性基因在控制最近的侵袭性菌株方面不再有效。这种疾病的全球传播和缺乏控制措施加剧了人们对全球粮食安全的担忧。最近的研究表明，来自稻瘟病田间分离物的多余染色体可能加速了适应进化，并有助于该真菌的毒力。额外染色体被认为在病原菌基因的进化中发挥作用，这些基因对寄主植物的抗性至关重要，包括植物种/属和作物品种水平上的寄主专一性。该项目将研究额外染色体，以了解它们的流行情况、菌株之间的移动、与核心染色体的DNA交换、稳定性以及对致病性和毒力的贡献。研究结果将有助于了解稻瘟病病原体的基因组动力学，并有助于揭示额外染色体在许多植物、动物和其他真菌中的作用。研究生和本科生将接受广泛的基因组学、生物信息学、分子植物-微生物相互作用和植物生物安全方面的培训。本科生将参加为期8周的植物病害诊断夏季研究体验，包括实地收集和使用尖端测序技术识别疾病生物体。稻瘟病菌在50多种牧草上引起稻瘟病，其中包括古老的稻瘟病和新出现的小麦稻瘟病。稻瘟病和不断进化的病原菌构成的全球农业威胁使得了解稻瘟病病原菌的基因组动态变得重要。BLAST真菌基因组包括数百个假定的效应基因，这些基因在宿主入侵期间特异表达，通常编码与促进疾病有关的小分泌蛋白。这些效应器的一个子集被宿主抗药性基因产物识别，从而触发抗药性并阻止宿主的感染。无论是在寄主物种/属水平上，还是在作物品种水平上，这些效应物都在决定稻瘟病菌的寄主专一性方面发挥着重要作用。最新的小麦稻瘟菌非必需额外染色体的基因组数据表明，这些额外染色体中含有许多在其他菌株不可或缺的核心染色体上经常发现的效应基因，以及其他可能在病原菌侵袭性中发挥作用的基因。该项目建议进一步了解额外染色体的流行率、菌株间的移动、与核心染色体的DNA交换、稳定性以及对致病性和毒力的贡献。这一假设将得到验证，即额外的染色体通过充当从核心染色体上删除的效应器基因的储存库，以及在调节它们在核心染色体上的重新定位来发挥作用。该项目将结合稻瘟病生物学的方法学，包括适应性进化策略、真菌菌株之间的无性转移、分子生物学、基因组学和细胞学。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Food crops are constantly threatened by new variants of established pathogens and by newly-emerged pathogens. The rice blast fungus Magnaporthe oryzae has a long history of variation to overcome resistance deployed in rice crops, and a new M. oryzae variant emerged in 1985 to cause devastating disease on wheat in Brazil. Wheat blast disease is proving even harder to control than rice blast because potential resistance genes identified using strains from the 1980s are no longer effective in controlling recent aggressive isolates. Global spread of the disease and lack of control measures enhance fears about global food security. Recent studies indicated that dispensable supernumerary chromosomes from blast field isolates might accelerate adaptive evolution and contribute to virulence of the fungus. Supernumerary chromosomes are hypothesized to play roles in the evolution of pathogen genes that are critical for resistance in host plants, including host specificity at the plant species/genus and the crop cultivar levels. The project will study supernumerary chromosomes to understand their prevalence, movement between strains, DNA exchange with core-chromosomes, stability, and contributions to pathogenicity and virulence. Outcomes will be valuable for understanding genomic dynamics of the blast pathogen and help reveal roles of supernumerary chromosomes in many plants, animals and other fungi. Graduate students and undergraduates will receive broad training in genomics, bioinformatics, molecular plant-microbe interactions, and plant biosecurity. Undergraduates will participate in an 8-week summer research experience in plant disease diagnostics involving collections in the field and identification of disease organisms using cutting edge sequencing technologies. The fungus Magnaporthe oryzae causes blast diseases on more than 50 grass species, which include the ancient rice blast and the newly emerged wheat blast. Global agricultural threats posed by blast diseases and evolving pathogens make it important to understand genome dynamics of blast pathogens. The blast fungal genome includes hundreds of putative effector genes that are specifically expressed during host invasion and that generally encode small secreted proteins involved promoting disease. A subset of these effectors is recognized by host resistance gene products, which triggers resistance and blocks infection of that host. Such effectors play a major role in determining host specificity in blast fungal pathogens, both at the host species/genus level, and at the crop cultivar level. The recent genomic data of dispensable supernumerary chromosomes from the wheat blast field isolates showed that the supernumerary chromosomes contain many effector genes that are often found on indispensable core-chromosomes in other strains, as well as other genes that may play a role in pathogen aggressiveness. This project proposes to further understand supernumerary chromosomes with respect to their prevalence, inter-strain movement, DNA exchange with core-chromosomes, stability, and contributions to pathogenicity and virulence. The hypothesis will be tested that supernumerary chromosomes play roles in effector mobility by serving as a repository for effector genes that are deleted from core-chromosomes, and a role in mediating their relocation on core-chromosomes. The project will combine methodologies in blast disease biology, including adaptive evolution strategies, parasexual transfer between fungal strains, molecular biology, genomics, and cytology.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.