Evolutionary multispecies transcriptomics to reveal genes that govern fungal spore germination and pathogenesis

项目摘要 人类的真菌病原体普遍存在于环境中，并经常与宿主接触 通过营养孢子的传播。虽然孢子萌发和随后的发育被认为是 对于真菌-宿主相互作用的启动至关重要，人们对控制这些事件的真菌基因知之甚少。 我们的目标是利用比较基因组学、进化生物学和真菌发病机制来定义基因 它们对孢子萌发、随后的生长和寄主在进化上的多样性是必不可少的 真菌群。我们选择了一系列具有致病能力的真菌，这些真菌的孢子与 哺乳动物宿主，包括主要的、机会性的和非致病的物种。我们将利用一个 高效和创新的管道，揭示其不断演变的角色导致表型的基因 这些物种之间的差异。PiS Trail和Townsend定义了一个范例，将 将比较基因组学、发育生物学和转录组学整合为一个单一的、统一的系统发育框架 这将确定控制这些真菌中孢子萌发和生长的关键基因。我们的关键是 方法是利用真菌之间的进化关系来推断其表达已被 在从祖先状态到现在的每个谱系的进化过程中发生了变化，从而允许特定的特征(如 作为发病机制)进化。在我们最近发表的工作和初步数据中，这种方法是巨大的 有效地识别其进化作用导致发育和表型差异的基因 真菌在(1)有性发育和(2)孢子萌发和早期感染期间的种类 植物的致病机理。 我们将使用一种常见的介质来萌发来自以下真菌的孢子：主要病原体 条件致病菌烟曲霉菌， 尖孢镰刀菌和毛壳菌，罕见的条件致病菌尼杜氏曲霉，以及 非致病性粗糙脉孢菌。我们将在一段时间内对这些真菌进行转录转录 在与萌发有关的温度条件下的萌发及其后续发育 环境对哺乳动物宿主的影响。我们将重建这些基因表达的进化变化 多个物种来识别最近经历了基因表达变化的基因，特别是 发生在共享的祖先分支上，其中关键特征(如定居哺乳动物的能力)具有 进化了。这些实验将产生一组高度可信的候选基因，其功能有望 对每种生物的孢子萌发和发育都是至关重要的。我们将使用基因敲除技术来 询问这些候选基因在孢子萌发和发育中的功能。这些研究将 确定无处不在的真菌感染的诊断、预防和疫苗干预的潜在目标 人类。

Project Summary Fungal pathogens of humans are prevalent in the environment, and commonly come into contact with hosts via dispersal of vegetative spores. Although spore germination and subsequent development are recognized as critical to the initiation of fungal-host interactions, little is known about the fungal genes that govern these events. Our goal is to leverage comparative genomics, evolutionary biology and fungal pathogenesis to define genes that are essential for spore germination, subsequent growth, and host colonization in an evolutionarily diverse group of fungi. We have chosen fungi with a range of abilities to cause disease upon interaction of spores with mammalian hosts, including primary, opportunistic, and nonpathogenic species. We will take advantage of a highly effective and innovative pipeline that reveals genes whose evolving roles have led to phenotypic differences among these species. PIs Trail and Townsend have defined a paradigm that brings together comparative genomics, developmental biology, and transcriptomics into a single, unified phylogenetic framework that will identify key genes that govern spore germination and outgrowth in these fungi. The linchpin of our approach is use of the evolutionary relationship between the fungi to infer genes whose expression has been altered during evolution from their ancestral state to each present-day lineage, thus allowing specific traits (such as pathogenesis) to evolve. In our recently published work and preliminary data, this approach was immensely powerful for identifying genes whose evolving role led to developmental and phenotypic differences among species during (1) fungal sexual development and (2) spore germination and early infection during fungal pathogenesis of plants. We will use a common medium to germinate spores from the following fungi: the primary pathogens Histoplasma capsulatum and Coccidioides posadasii, the opportunistic pathogens Aspergillus fumigatus, Fusarium oxysporum, and Chaetomium elatum, the infrequent opportunistic pathogen Aspergillus nidulans, and the non-pathogenic Neurospora crassa. We will subject these fungi to transcriptomics over a time-course of germination and subsequent development under temperature conditions relevant to germination in the environment vs. in a mammalian host. We will reconstruct evolutionary changes of gene expression across these multiple species to identify genes that have undergone recent shifts in gene expression, in particular shifts that occurred along the shared ancestral branches where key traits (such as the ability to colonize mammals) have evolved. These experiments will yield a high-confidence set of candidate genes whose function is expected to be critical for spore germination and development in each organism. We will use gene knock-out technology to interrogate the function of these candidate genes in spore germination and development. These studies will identify potential targets for diagnostic, prophylactic, and vaccine interventions for ubiquitous fungal infections of humans.