Origin and diversity of mushrooms in Eastern Canada and phylogenomics of selected groups

了解生物多样性的起源和分布是生物学的基础。我的研究计划的长期目标是在全球范围内调查真菌(担子菌门，真菌)中的物种丰富度和进化关系，特别是在蘑菇目中。后者包括大部分蘑菇形成真菌，由全世界描述的大约10,000个物种组成，尽管可能存在更多物种。几个问题影响了我们对全球和局部真菌多样性和物种分布的估计，特别是：(1)缺乏全面的区域或国家植物区系，(2)缺乏对大多数类群的现代分类处理(专著)，以及(3)存在许多形态相似的(隐晦的)物种。为了帮助解决这三个问题中的每一个，我建议在未来五年进行以下工作：(1)基于文献、草本植物和其他收集数据的历史记录，结合安大略省和魁北克省近十年来收集的1000个有良好记录的安大略省和魁北克省的蘑菇，并在我的实验室用ITS和LSU序列对DNA进行条形码编码，完成加拿大东部蘑菇的汇编。这将对加拿大东部的蘑菇多样性进行第一次现实的评估，在许多情况下，还允许在系统发育的背景下进行分类修订。后一项工作非常适合本科生的多个小项目。(2)在系统基因组框架内为Amanita组Caesaria和Vaginateae以及灵芝属准备世界专著；这将允许推断属于这些组的加拿大东部种的起源(S)和分类学。每组包含大约120种已知物种，其中许多要么已经在我手中，要么可以从各种来源获得(非洲材料除外)。初步数据表明，5个基因(ITS、EF1-α、LSU、RPB1和RPB2)的组合并不能完全解决系统发育关系。(3)北美鹅膏菌种群基因组研究和隐蔽种的检测。这组可食用的外生菌根真菌被认为由4-5种组成，但种的界限尚不清楚。这个群体的成员广泛分布在美国南部和阿巴拉契斯山脉沿线。在加拿大，魁北克南部的几个地区报告了雅克森氏原虫，最近才在安大略省南部发现。我建议比较至少60个集合的全基因组序列，这些集合代表了这个物种群体整个地理和生态范围内的种群。到目前为止，我们已经完成并注释了两个菌株的基因组(一个来自安大略省，一个来自墨西哥)；此外，新材料的重新收集正在进行中。这项研究应该解决这个物种复合体中的物种识别问题，并揭示蘑菇的物种形成过程。

Understanding the origin and distribution of biological diversity is fundamental to biology. The long-term goals of my research program are to investigate species richness and evolutionary relationships in the Agaricomycetes (Basidiomycota, Fungi) in a global scale, more particularly in the Agaricales. The latter includes the bulk of mushroom-forming fungi, and consists of about 10,000 species described worldwide, although many more probably exist. Several problems affect our estimates of fungal diversity and species distribution both globally and locally, particularly: (1) the scarcity of comprehensive regional or national flora, (2) the lack of modern taxonomic treatment (monographs) for most groups, and (3) the existence of many morphologically similar (cryptic) species. To help fix each of these three problems I propose to conduct the following work in the next five years: (1) Completion of a compendium of eastern Canada mushrooms based on historical records from the literature, herbaria, and other collection data, in combination with > 1,000 well-documented collections from Ontario and Quebec that were made in the last ten years and DNA-barcoded in my lab with both ITS and LSU sequences. This will produce a first realistic assessment of mushroom diversity in eastern Canada, and also, in many cases, permit taxonomic revisions in a phylogenetic context. This latter work is very well suited for multiple small projects for undergraduate students. (2) Preparation of world monographs for Amanita sections Caesarea and Vaginateae and for the genus Ganoderma in a phylogenomic framework; this will permit to infer the origin(s) and taxonomy of the eastern Canadian species belonging to these groups. Each group contains about 120 known species, many of which being either already in my possession or readily available from various sources (except material from Africa). Preliminary data indicates that a combination of 5 genes (ITS, EF1-alpha, LSU, RPB1 and RPB2) does not fully resolve phylogenetic relationships. (3) Population genomic studies and detection of cryptic species within the Amanita jacksonii species complex in North America. This species group of edible, ectomycorrhizal fungi is thought to consist of 4-5 species, but species delimitation is unclear. Members of this group are widespread in the southern U.S. and along the Appalaches. In Canada, A. jacksonii has been reported from few localities in southern Quebec, and has only been discovered recently in southern Ontario. I propose to compare whole genome sequences of at least 60 collections reprsentative of populations across the whole geographic and ecological range of this species group. To date, we have completed and annotated the genomes of two strains (one from Ontario, and one from Mexico); also, de novo collecting of fresh material is underway. This study should resolve species recognition within this species complex and shed light into speciation processes in mushrooms.