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

真菌代表了一个主要的有机体群体，作为腐烂物、病原体（植物和动物，包括人类）和互利共生者，具有深远的经济和生态影响。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（包括生物燃料生产）至关重要。然而，真菌的许多基本生物学仍然未知，包括真菌如何发展的知识。该项目将解决在Agaricomycetes，这是一个大组的真菌，包括鳃蘑菇，多孔菌，马勃菌，和其他复杂的形式的发育和形态进化的历史模式和遗传机制。这项研究的结果将提供有关真菌发育机制的基线信息，以及基因调控和其他对基础和应用真菌生物学具有普遍意义的过程。该项目将为一名博士生、一名博士后研究员和本科生提供培训。教育和推广活动将使艺术与科学联系起来。对艺术和科学感兴趣的本科生将参加联合课程，培养观察技能，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。海报和相关的课程计划将在一个项目网站上免费下载，并将通过科学教育工作者专业会议上的讲习班分发，可获得数千种伞菌的基因序列，并可获得90多个物种的完整基因组。然而，这些数据还没有被合并和查询，以了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）基因组分析，（3）发育分析。宏观进化分析将采用大规模的遗传学（高达约。4000个终端），利用公开可用的数据。比较方法将用于执行祖先状态重建，解决方向性趋势，并测试关键的创新假设。系统基因组分析将确定基因家族中拷贝数的变化，如转录因子、疏水蛋白、凝集素和细胞壁生物合成酶，这些可能与复杂形式的进化相关。发育分析将集中在香菇tigrinus，通常是一个鳃蘑菇，但也有一个马勃样的“secotioid”形式，这是由一个隐性等位基因在一个单一的基因座（Sec）。两个L.虎斑猫是可用的，一个携带Sec+等位基因，另一个携带隐性sec等位基因。将使用整体分离子分析来确定secotioid基因座的身份。毛状花序的诱导。tigrinus需要光和转录组学分析将用于比较营养菌丝体和子实体在光或黑暗中产生的基因表达模式。

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.