How the mushroom lost its gills: phylogenomics and population genetics of a morphological innovation in the fungal genus Lentinus

蘑菇如何失去鳃：香菇属真菌形态创新的系统基因组学和群体遗传学

• 批准号: 2333266
• 负责人: David Hibbett
• 金额: $ 68.35万
• 依托单位: Clark University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2024
• 资助国家: 美国
• 起止时间: 2024-01-01 至 2026-12-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2333266&HistoricalAwards=false
• 关键词: How; mushroom; lost; its; gills

Fungi represent one of the few branches in the tree of life in which complex multicellular forms (i.e., mushrooms) have evolved. Mushrooms come in a dazzling array of shapes, from the classic “toadstool,” with a cap and stalk, to coral- and candelabra-shaped mushrooms, bird’s nest fungi, bracket fungi, puffballs, and others. Fungal biologists have learned a great deal about the historical patterns of changes in the shapes of mushrooms, but the genetic mechanisms that underlie changes in morphology (form) are obscure. This research will use genomic methods to understand patterns and mechanisms of morphological evolution in mushrooms in the genus Lentinus, which includes a mix of gilled mushrooms and polypores—mushrooms that form pores instead of gills. A particular focus will be the species Lentinus tigrinus (the “tiger sawgill”), which contains both gilled mushrooms and puffball-like “secotioid” forms, in which the gills are covered by a persistent layer of tissue. These two forms are so dissimilar that they were once thought to be different species, but they are capable of mating and they occur side-by-side in populations throughout North America. Lentinus tigrinus presents a case of “evolution caught in the act.” By studying the genetic basis of the switch from a gilled mushroom to the secotioid form in L. tigrinus, this project will shed light on the molecular mechanisms that contribute to the present diversity of mushrooms. This project will provide training for a graduate student and a Postdoctoral Fellow, and it has a significant outreach component, involving workshops on fungal biology for youths in the public schools of Worcester, Massachusetts, and mushroom forays for the general public. Undergraduates will be engaged through course activities that bring research into the classroom.This research will involve four main components: (1) Higher-level relationships of the genus Lentinus will be resolved, using phylogenomic approaches. Genome data will be collected from living cultures as well as herbarium specimens representing exemplars of previously recognized sections of Lentinus. (2) A detailed analysis of the section Tigrini (which contains L. tigrinus) will be conducted, with the aim of resolving species limits. Genomic data will be obtained from all species in section Tigrini, emphasizing populations of L. tigrinus in North America, Europe, and Asia. (3) Two approaches will be taken to identify the genetic region(s) responsible for the secotioid form: (a) a cross-population population-genomic analysis of secotioid and agaricoid (gilled) individuals will be conducted, using specimens collected from populations in Illiniois and Massachusetts, and (b) a genome-wide association study will be performed, using progeny of a cross between secotioid and agaricoid individuals from the Massachusetts population. (4) Population-genetic analyses will be conducted to assess whether the genetic region(s) responsible for the secotioid form is(are) under positive selection. Analyses of genotype frequencies will also be performed to determine if there is assortative mating among the secotioid and agaricoid forms. Collectively, the results of this research will reconstruct higher-level relationships in Lentinus and resolve the genetic bases and population-level dynamics of a morphological innovation in L. tigrinus.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

真菌是生命之树中为数不多的由复杂的多细胞形式（即蘑菇）进化而来的分支之一，蘑菇具有各种令人眼花缭乱的形状，从带有菌盖和茎的经典“伞菌”到珊瑚。烛台形蘑菇、燕窝真菌、支架真菌、马勃菌等真菌生物学家已经了解了大量关于蘑菇形状变化的历史模式，但遗传。这项研究将利用基因组方法来了解香菇属蘑菇的形态进化模式和机制，其中包括鳃蘑菇和多孔菌（形成孔而不是鳃的蘑菇）。特别关注的是 Lentinus tigrinus（“虎锯鳃”）物种，它含有鳃蘑菇和马勃状“secotioid”形式，鳃上覆盖着一层持久的组织。这两种形式非常不同，以至于它们曾经被认为是不同的物种，但它们能够交配，并且在整个北美的种群中并存。提出了一个“进化过程中的进化”的案例。通过研究虎纹蘑菇从带鳃蘑菇转变为裂蘑菇形式的遗传基础，该项目将揭示导致目前多样性的分子机制。该项目将为一名研究生和一名博士后研究员提供培训，其中一个重要的外展部分包括为马萨诸塞州伍斯特公立学校的年轻人举办真菌生物学研讨会，以及为广大本科生举办蘑菇生物学研讨会。通过将研究带入课堂的课程活动来参与。这项研究将涉及四个主要组成部分：（1）将使用系统发育学方法从活的文化中收集基因组数据来解决香菇属的高级关系。 (2) 将对 Tigrini 部分（包含 L. tigrinus）进行详细分析，目的是从所有物种中获得基因组数据。 Tigrini 部分，强调北美、欧洲和亚洲的 L. tigrinus 种群 (3) 将采用两种方法来确定负责 secotiid 形式的遗传区域： (a) 将使用从伊利诺伊州和马萨诸塞州的人群中收集的样本，对 secotioid 和 agaricoid (gilled) 个体进行跨群体群体基因组分析，以及 (b) 将使用以下物种的后代进行全基因组关联研究：来自马萨诸塞州种群的裂线型和伞形孢菌个体之间的杂交 (4) 将进行群体遗传分析，以评估负责裂线型形式的遗传区域是否处于阳性状态。还将进行基因型频率分析，以确定裂叶类和伞形孢类形式之间是否存在选型交配，这项研究的结果将重建香菇的更高层次的关系，并解决香菇的遗传基础和群体水平动态。 L. tigrinus 的形态创新。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。