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

真菌是生命树中进化出复杂的多细胞形式(如蘑菇)的少数分支之一。蘑菇的形状五花八门，从经典的有盖有柄的“蘑菇”，到珊瑚和烛台形状的蘑菇、燕窝真菌、托槽真菌、马弗球等。真菌生物学家已经了解了蘑菇形状变化的历史模式，但形态(形式)变化背后的遗传机制尚不清楚。这项研究将使用基因组学方法来了解香菇属蘑菇的形态进化模式和机制，香菇属包括菌鳃和多孔的混合物-形成毛孔而不是鳃的蘑菇。一个特别的焦点将是虎鳃香菇(“老虎锯鳃”)，它既含有鳃蘑菇，也包含麻皮球状的“扇形”形态，在这种形态下，鳃被一层持久的组织覆盖。这两种形式如此不同，以至于它们曾经被认为是不同的物种，但它们能够交配，它们在整个北美的种群中并存。虎纹香菇呈现了一个“进化在行动中被抓住”的例子。通过研究虎纹伊蚊从鳃蘑菇转变为类扇形蘑菇的遗传基础，该项目将揭示导致目前蘑菇多样性的分子机制。该项目将为一名研究生和一名博士后研究员提供培训，并有一个重要的宣传部分，包括在马萨诸塞州伍斯特市的公立学校为年轻人举办真菌生物学讲习班，并为普通公众进行蘑菇探险。本科生将通过课程活动将研究带入课堂。这项研究将涉及四个主要部分：(1)利用系统基因组学方法解决香菇属更高层次的亲缘关系。基因组数据将从活的培养物以及代表先前识别的香菇部分样本的标本馆标本中收集。(2)将对底格里尼区(含有虎纹伊蚊)进行详细分析，以解决物种限制问题。基因组数据将从底格里尼组的所有物种中获得，重点是北美洲、欧洲和亚洲的虎纹伊蚊种群。(3)将采取两种方法来确定导致扇形的遗传区域(S)：(A)将利用从伊利诺伊斯和马萨诸塞州的群体中收集的标本，对扇形和木耳(鳃)个体进行跨种群基因组分析，以及(B)将利用来自马萨诸塞州的扇形和木耳类个体之间的杂交后代进行全基因组关联研究。(4)将进行群体遗传分析，以评估负责扇形的遗传区域(S)是否处于正选择状态。还将对基因频率进行分析，以确定在扇形和黑木耳类型之间是否存在分类交配。总而言之，这项研究的结果将重建香菇中更高级别的关系，并解决虎纹香菇形态创新的遗传基础和种群水平的动态。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.