Evolution of fruiting body forms in the mushroom-forming Fungi (Agaricomycetes): a comparative phylogenetic, phylogenomic, and developmental approach

真菌是一大类具有深远经济和生态影响的生物，如腐生菌、病原体(包括人类在内的动植物)和互助者。真菌是工业生物产品(抗生素和酶)的重要来源，它们对发酵工业至关重要，包括生物燃料生产。然而，真菌的许多基本生物学知识仍然未知，包括关于真菌如何发育的知识。这个项目将研究蘑菇类真菌的发育和形态进化的历史模式和遗传机制。蘑菇类真菌是一大类真菌，包括鳃蘑菇、多孔菌、马弗球和其他复杂形式。这项研究的结果将提供关于真菌发育机制的基线信息，以及对基础和应用真菌生物学具有普遍意义的基因调控和其他过程。该项目将为博士生、博士后和本科生提供培训。教育和外展活动将把艺术和科学联系起来。对艺术和科学感兴趣的本科生将参加联合课程，发展观察技能，提高对真菌生物多样性的认识。该项目还将制作适合高中生的教育海报，说明真菌生物学和一般进化原理。海报和相关的教案将在一个项目网站上免费下载，并将在科学教育工作者的专业会议上通过研讨会分发。数以千计的真菌的基因序列已经公布，超过90个物种的完整基因组已经公布，而且还在增加。然而，这些数据还没有被组合和查询来理解真菌发育进化的过程。建议的研究包括(1)宏观进化分析，(2)系统发育分析，(3)发育分析。宏观进化分析将使用大规模的系统发育(多达4000个终端)，利用可公开获得的数据。将使用比较方法进行祖先状态重建，解决方向性趋势，并检验关键创新假设。系统基因组学分析将识别基因家族中拷贝数的变化，如转录因子、疏水素、凝集素和细胞壁生物发生酶，这可能与复杂形式的进化有关。发育分析将重点放在虎纹香菇上，通常是一种鳃蘑菇，但也有一种由单基因座(SEC)上的隐性等位基因赋予的、类似于马布麻球的“类扇形”形式。虎纹夜蛾有两个基因组序列，一个携带SEC+等位基因，另一个带有隐性SEC等位基因。将使用整体分离分析来确定Secocid基因座的身份。虎纹夜蛾菌盖的诱导需要光照，转录分析将被用来比较在光照或黑暗中产生的营养菌丝体和子实体中的基因表达模式。

Fungi represent a major group of organisms that have profound economic and ecological impacts as decayers, pathogens (of plants and animals, including humans), and mutualists. Fungi are important sources of industrial bioproducts (antibiotics and enzymes) and they are critical to the fermentation industry, including biofuel production. However, much of the basic biology of fungi remains unknown, including knowledge on how fungi develop. This project will address the historical patterns and genetic mechanisms of developmental and morphological evolution in Agaricomycetes, which is a large group of fungi that includes gilled mushrooms, polypores, puffballs, and other complex forms. The results of this research will provide baseline information on the mechanisms of fungal development, as well as gene regulation and other processes of general significance for basic and applied fungal biology. This project will provide training for a PhD student, a Postdoctoral Fellow, and undergraduates. Education and outreach activities will make connections between art and science. Undergraduates with interests in art and science will engage in joint classes that develop observational skills and raise awareness about fungal biodiversity. The project will also create educational posters appropriate for high school students that illustrate fungal biology and general evolutionary principles. Posters and associated lesson plans will be made available for free download on a project web site and will be distributed through workshops at professional conferences for science educators.Gene sequences for thousands of Agaricomycetes are available and complete genomes are available for over 90 species and increasing. However, these data have not been combined and queried to understand processes of fungal developmental evolution. The proposed research includes (1) macroevolutionary analyses, (2) phylogenomic analyses, and (3) developmental analyses. Macroevolutionary analyses will employ large-scale phylogenies (up to ca. 4000 terminals), drawing on publicly available data. Comparative methods will be used to perform ancestral state reconstruction, address directional trends, and test key innovation hypotheses. Phylogenomic analyses will identify shifts in copy number in gene families, such as transcription factors, hydrophobins, lectins and cell wall biogenesis enzymes, that may be correlated with evolution of complex forms. Developmental analyses will focus on Lentinus tigrinus, typically a gilled mushroom, but there is also a puffball-like "secotioid" form that is conferred by a recessive allele at a single locus (Sec). Two genome sequencs of L. tigrinus are available, one carrying the Sec+ allele and the other with the recessive sec allele. Bulk segregant analysis will be used to determine the identity of the secotioid locus. Pileus induction in L. tigrinus requires light and transcriptomic analyses will be used to compare gene expression patterns in vegetative mycelium and fruiting bodies produced in light or in darkness.