Genome evolution, commensalism and pathogenicity in the diploid fungus Candida albicans

真菌病原体表现出相当大的遗传可塑性，微变异和染色体水平 重新排列经常使适应主机和环境的压力。几个属 真菌是重要的人类病原体，侵袭性真菌感染导致死亡， 全球每年大约有150万到200万人。念珠菌属是最突出的原因 侵袭性真菌病在美国，主要的主角是白色念珠菌。这是一个高度 适应性物种的能力，占据不同的壁龛在人体内，无论是作为一个良性的 或者作为一种侵入性的机会致病菌。 该项目旨在定义C.白念珠菌二倍体基因组在相对较短的时间 在体外生长期间或在感染哺乳动物宿主期间鳞片。梭白色念珠菌基因组由 8条杂合染色体，可能发生从头突变、杂合性丢失（洛），或 包括染色体拷贝数变化的大规模重排。来定义微进化 变化，将在不同的小鼠模型中传代前后对临床分离株进行测序， 感染和通过深度测序分析确定的全谱遗传变化。初步 实验已经确定了哺乳动物感染期间较高的突变率， in C.白色念珠菌是由强大的净化选择塑造的。分析表明，“微观”变化是关键 微进化的驱动因素，包括频繁的从头突变和短的洛缺失事件。该项目旨在 在这些研究的基础上，利用C.白色念珠菌作为模型物种，以了解 杂合二倍体真核生物的遗传多样性。 拟议的实验将解决遗传变化如何驱动宿主适应，包括改变 在健康和毒性方面。将在传代前后检查基因表达变化， 宿主适应的基本机制将从遗传学角度进行剖析。令人兴奋的初步数据表明， 洛缺失和非整倍体是C.白色念珠菌容易适应宿主的小生境。 该提案还寻求开发新的工具，包括确定真菌生长速率的方法。 哺乳动物宿主，二倍体基因组的定相，以及用于高分辨率分析的生物信息学管道 杂合基因组这些实验将提供一个详细的洞察如何C。白色念珠菌适应 它的宿主，以及基因组变异驱动微进化的能力。

Fungal pathogens exhibit considerable genetic plasticity, with both microvariation and chromosomelevel rearrangements frequently enabling adaptation to host and environmental pressures. Several genera of fungi are important human pathogens, with invasive fungal infections responsible for the death of approximately 1.5 to 2 million people worldwide each year. Candida species are the most prominent cause of invasive fungal disease in the US, with the major protagonist being Candida albicans. This is a highly adaptive species with the ability to occupy diverse niches in the human body, either as a benign commensal or as an invasive opportunistic pathogen. This project seeks to define microevolution of C. albicans diploid genomes over relatively short time scales during growth in vitro or during infection of the mammalian host. The C. albicans genome consists of eight heterozygous chromosomes that can undergo de novo mutation, loss of heterozygosity (LOH), or large scale rearrangements including variations in chromosome copy number. To define microevolutionary changes, clinical isolates will be sequenced before and after passaging in different murine models of infection and the full spectrum of genetic changes determined by deep-sequencing analysis. Preliminary experiments have established higher mutation rates during mammalian infection and that genome evolution in C. albicans is shaped by strong purifying selection. Analyses reveal that ‘micro-scale’ changes are key drivers of microevolution, including frequent de novo mutations and short LOH events. This project looks to build on these studies and to use C. albicans as a model species for understanding the generation of genetic diversity in a heterozygous diploid eukaryote. The proposed experiments will address how genetic change drives host adaptation, including changes in fitness and virulence. Gene expression changes will be examined before and after passaging and mechanisms underlying host adaptation will be genetically dissected. Exciting preliminary data suggests that LOH and aneuploidy are important mechanisms by which C. albicans readily adapts to host niches. This proposal also seeks to develop new tools, including methods to define fungal growth rates in the mammalian host, phasing of diploid genomes, as well as bioinformatic pipelines for high resolution analysis of heterozygous genomes. These experiments will provide a detailed insight into how C. albicans adapts to its host, and the capacity for genomic variation to drive microevolution.