假丝酵母属与相关属分类系统重建和系统基因组学研究

Candida is the largest genus of yeasts, and its species represent nearly half of all known ascomycetous yeasts. This genus not only includes many of human opportunistic pathogens, but also its many species have served as important industrial and agricultural vehicles for artisanal and industrial processes, food regulations, enzyme production, substrate specificities. Phylogenetic analyses of LSU rRNA D1/D2 and ITS sequences have demonstrated that Candida is highly polyphyletic, and species of Candida are distributed throughout the Saccharomycotina (Ascomycota). However, the D1/D2 and ITS regions used in phylogenetic analysis of Candida is relatively short and the phylogenetic resolution from the sequences is often inadequate for assignment of species representing well isolated monophyletic lineages to genera, which demonstrated the need for more extensive datasets to resolve those chaotic taxonomic problems. . The revising and reestablishment of the taxonomic system of the genus Candida will be carried out by the new Code (International Code of Nomenclature for algae, fungi, and plants, Melbourne Code, 2012) using phylogenomics framework based on next generation sequence data and the multi-gene analyses with 18S rDNA gene, internal transcribed spacer (ITS) region including 5.8S rDNA gene, 26S rDNA gene, Elongation factor 1-a (EF1-a)、RNA polymerase I (RPB1)RNA and polymerase II (RPB2) in this project. And then employ these data to explore the evolution of mating type system of Candida and related sexual genera and address the evolutionary relationship between those genera. This project will also explore the species diversity of Candida in China. This project will establish a new classification system of Candida and related genera based on a phylogenomics approach, which will benefit for the application of this group in biotechnology fields.

假丝酵母属是酵母菌中最大的属，其物种数几乎占了已知子囊菌酵母的一半。该属既包含了一些人类重要条件致病菌，也包括了很多重要的工农业生产菌。近年来酵母菌分子系统发育学的研究表明该属是一个高度异源的属，其当前的定义对酵母菌多样性研究和生产利用造成了很大的阻碍。所以，无论从分类学的角度还是从生产应用的角度都非常有必要对该属进行重新界定。. 本项目将在系统开展国内假丝酵母属物种多样性研究的基础上，在新的《国际藻类、真菌、植物命名法规》的框架下，通过多基因序列分析和系统基因组学方法对假丝酵母属进行重新界定和划分，通过比较基因组学方法阐明假丝酵母属和相关有性属的演化关系，并从进化基因组学的角度去探讨子囊菌酵母在属及以上分类单元，特别是科级分类单元的演化关系。本研究将会建立一个基于系统基因组学的假丝酵母及相关属的新分类系统，从而促进该类群被非分类学家在生物技术等领域的快速挖掘与应用。

假丝酵母属既包含人类重要条件致病菌，也包括很多重要的工农业生产菌。近年来酵母菌分子系统学的研究表明该属是一个高度异源的属，其当前的定义对酵母菌多样性研究和利用造成了的阻碍。本项目从三个方面开展了研究：1）系统开展国内假丝酵母属物种多样性研究；2）构建假丝酵母属多基因系统发育树；3）假丝酵母属和相关有性属的系统基因组和比较基因组研究。在新的《国际藻类、真菌、植物命名法规》的框架下，通过多基因序列分析和系统基因组学方法对假丝酵母属进行重新界定和划分。. 本项目从国内外10多个省市自治区采集树皮、腐木、花和果实等标本1965份，分离到5000余株酵母菌，现已完成1400多株代表性菌株的26S和ITS序列的测定，并对其中的500多株进行了18S、EF1-α、RPB1和RPB2序列测定，分析结果显示：这些地区的子囊菌酵母有292个种，隶属于92个属，假丝酵母63个种。另外，发现了103个包括假丝酵母在内的疑似子囊菌酵母新种。. 本项目通过对假丝酵母和相关类群的500多个酵母菌的26S、ITS、18S、EF1-α、RPB1和RPB2多基因分析，对高度异源的假丝酵母进行了处理。研究显示228个假丝酵母种应该被划归到31个已知属内，55个种将被划分在26个拟新建属内，而假丝酵母属本身将只保留46种。该研究结果不仅可以建立假丝酵母及相关属新的分类系统，而且还会促进该类群被非分类学家在生物技术等领域的快速挖掘与应用。. 本项目已经完成了100多个假丝酵母和相关物种的二代基因组的测定，并完成了基因组的组装。本项目特别对耳道假丝酵母分支内的8个近缘种的临床和野生菌株进行了研究，通过对相关菌株基因组的比较获知，耳道假丝酵母分支内的种存在两种不同的交配型，这预示该分支内物种可能进行有性生殖，这些数据将为阐明它们耐药机制、传播方式和进化途径提高很好的数据支撑。.