The genomic basis of host specificity as tool for species recognition and delimitations in Ustilaginales - a parasite group with high gene flow

在1991年SPP的第一个资助期，我们主要研究了紫穗草属植物的杂交和种界划分问题。先前的研究表明，分离了数百万年的Ustilaginales物种能够开始有性繁殖。基于几个新基因组测序的物种，我们现在可以证明杂交是这个寄主特异性植物寄生虫谱系的一个共同特征，并且很可能是整个谱系进化过程中的一个重要特征。这使得物种概念，如生物学物种概念（产生可存活后代的相容个体的交配种群）或系统发育物种概念（基于聚结的方法）以及基于这些概念的物种识别难以应用于该谱系。因此，我们希望在后续的提案中研究和测试宿主特异性与物种识别和划界的相关性。我们将比较两个密切相关的科，即木菇科和炭疽科的成员，以分析与植物寄生虫分类相关的不同方面。我们计划研究以下几个方面：(1)我们将研究与感染过程相关的基因（如编码效应器的基因）在宿主特异性方面的贡献及其在杂交事件中的命运。(2)利用全基因组、宿主特异性和共系统发育等信息，了解菌科不同进化层次相关基因的谱系分选。(3)利用靶富集方法对炭疽科4个兄弟种种群的近期物种形成进行研究。因此，我们将有助于讨论植物寄生虫的物种概念和物种划分，而传统的物种概念，如形态学、生物学或系统发育的物种概念，迄今未能提供令人满意的分类概念。

During the first funding period of the SPP 1991 we were focusing on questions of hybridization and species delimitation in Ustilaginales. Previous work has shown that species within the Ustilaginales that have been separated for millions of years are able to initiate sexual reproduction. Based on several newly genome sequenced species, we could now show that hybridization is a common feature in this lineage of host specific plant parasites and most probably was an important feature during the evolution of the whole lineage. This makes species concepts, such as the biological species concept (mating population of compatible individuals producing viable offspring) or the phylogenetic species concept (coalescent based approaches) and species recognition based on these concepts difficult to apply in this lineage. Thus we would like to study and test the relevance of host specificity for species recognition and delimitation in this follow-up proposal. We will compare members of two closely related families namely the Ustilaginaceae and Anthracoideaceae to analyze different different aspects relevant for taxonomy of plant parasites. We plan to study the following aspects: (1) We will study the contribution of genes linked to the infection process (such as genes coding for effectors) with respect to host specificity and their fate during hybridization events. (2) We will use information of full genomes, host specificity and co-phylogeny to understand lineage sorting of relevant genes in different evolutionary strata in the Ustilaginaceae. (3) Based on a target-enrichment approach will study recent speciation in populations of four sibling species of Anthracoideaceae. Thereby we will contribute to the discussion of species concepts and species delimitation in plant parasites, where traditional species concepts like the morphological, biological or phylogenetic species concepts fail to provide a satisfying taxonomic concept so far.