DISSERTATION RESEARCH: Systematics, diversification, and functional maintenance of trophic mode in Russula (Russulales)

来自真菌物种的比较基因组序列数据开始为真菌在自然界中扮演的关键生态角色提供见解。最近的研究表明，与植物相关的一大类真菌作为根共生体，称为外生菌根真菌，可能影响自然界中有机碳的循环。这项研究试图调查不同真菌科真菌分解有机化合物的能力的进化。该项目将产生整个家族物种的基因组序列数据，以测试红菇科中的物种和群体是如何相互联系的，这些真菌在自然界中扮演的生态角色，以及支配这些生态角色的特征是如何进化的。一名研究生将接受培训，一系列研讨会将培训本科生新的分子方法和基因组分析技术。这项研究还将通过欧洲、加拿大、亚洲和美国科学家之间建立的国际网络促进跨学科合作。这项研究的基因组数据有可能导致在真菌中生产生物燃料的进展。该项目将通过应用系统发育和系统发育学的方法，为红菇属、红菇科和红菇目建立一个新的分子系统框架，这将使新的多样性分类能够用于更多的系统研究。这项研究还将确定绿豆目基因组中编码氧化还原酶的基因，并能够分解纤维素、半纤维素、木质素和其他结构植物分子。来自红豆科代表性物种的基因组序列数据将由联合基因组研究所生成，并将通过MycoCosm管道进行组装。功能基因预测将由先前对已知腐生菌的降解基因组成的研究提供信息，特别是那些来自鲁苏拉目的成员。研究人员将研究整个谱系的功能变异，强调II类过氧化物酶、CAZymes和/或漆酶的多样性。功能基因的进化将通过基因家族系统发育和祖先状态重建方法来推断。

Comparative genomic sequence data from fungal species are beginning to provide insights into the crucial ecological roles fungi serve in nature. Recent studies suggest a major class of fungi that associate with plants as root symbionts, called ectomycorrhizal fungi, likely influence the cycling of organic carbon in nature. This research seeks to investigate the evolution of the ability to decompose organic compounds in the diverse fungal family, Russulaceae. The project will produce genome sequence data from species across the family to test how species and groups within the Russulaceae are related to each other, the ecological roles these fungi serve in nature, and how the traits that govern these ecological roles have evolved. One graduate student will be trained and a series of workshops will train undergraduates in new molecular methods and genome analysis techniques. This research will also promote interdisciplinary collaboration through established international networks between scientists in Europe, Canada, Asia, and the U.S. Genomic data from this study has the potential to lead to advances in biofuel production within fungi. This project will produce a new molecular systematic framework for Russula, Russulaceae, and Russulales through the application of phylogenetic and phylogenomic methods, which will enable the classification of novel diversity for additional systematic studies. This study will also identify genes within the genomes of the Russulales that encode oxidoreductases and are capable of breaking down cellulose, hemicellulose, lignin, and other structural plant molecules. Genomic sequence data from representative species across the Russulaceae will be generated by the Joint Genome Institute and will be assembled through the MycoCosm pipeline. Functional gene prediction will be informed by previous studies on degradative gene composition of known saprotrophs, with particular focus on those members from Russulales. Researchers will investigate functional variation throughout the lineage, emphasizing the diversity of class II peroxidases, CAZymes, and/or laccases. Evolution of functional genes will be inferred using gene family phylogenies and ancestral state reconstruction methods.