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

蘑菇形成真菌（伞形孢菌）子实体形式的进化：比较系统发育、系统发育和发育方法

• 批准号: 1456588
• 负责人: David Hibbett
• 金额: $ 33.94万
• 依托单位: Clark University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-04-01 至 2022-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1456588&HistoricalAwards=false
• 关键词: Evolution; fruiting; body; forms; mushroom

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.

真菌代表了一个主要的生物体群体，它们作为腐烂者、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，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，包括有关真菌如何发育的知识。该项目将研究伞形孢菌发育和形态进化的历史模式和遗传机制，伞形孢菌是一大类真菌，包括鳃蘑菇、多孔菌、马勃菌和其他复杂形式。这项研究的结果将为真菌发育机制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提供基线信息。该项目将为博士生、博士后研究员和本科生提供培训。教育和推广活动将在艺术和科学之间建立联系。对艺术和科学感兴趣的本科生将参加联合课程，以培养观察技能并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。海报和相关课程计划将在项目网站上免费下载，并将通过专业会议上的研讨会向科学教育者分发。数千种伞形孢菌的基因序列可供使用，并且完整的基因组可用于 90 多个物种，并且还在不断增加。然而，这些数据尚未被合并和查询以了解真菌发育进化的过程。拟议的研究包括（1）宏观进化分析，（2）系统发育分析，以及（3）发育分析。宏观进化分析将采用大规模系统发育（最多约 4000 个终端），并利用公开数据。将使用比较方法来重建祖先状态，解决方向趋势，并测试关键的创新假设。系统基因组分析将识别转录因子、疏水蛋白、凝集素和细胞壁生物发生酶等基因家族拷贝数的变化，这些变化可能与复杂形式的进化相关。发育分析将重点关注香菇（Lentinus tigrinus），通常是一种带鳃的蘑菇，但也有一种马勃状的“secotioid”形式，由单个位点的隐性等位基因赋予（Sec）。虎斑虎有两种基因组序列，一种带有 Sec+ 等位基因，另一种带有隐性 sec 等位基因。批量分离分析将用于确定裂切样基因座的身份。虎斑菌的菌毛诱导需要光，转录组分析将用于比较在光或黑暗下产生的营养菌丝体和子实体的基因表达模式。