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的第一个资助期内，我们专注于黑粉菌目的杂交和物种界定问题。以前的研究表明，已经分离了数百万年的黑粉菌目中的物种能够开始有性生殖。基于几个新基因组测序的物种，我们现在可以表明杂交是宿主特异性植物寄生虫这一谱系的共同特征，并且很可能是整个谱系进化过程中的一个重要特征。这使得物种的概念，如生物物种的概念（交配人口的兼容的个人产生可行的后代）或系统发育的物种的概念（结合为基础的方法）和物种识别的基础上，这些概念很难应用于这一谱系。因此，我们希望在本后续建议中研究和测试宿主特异性对物种识别和划界的相关性。我们将比较两个密切相关的科，即黑粉菌科和炭疽科的成员，以分析不同的不同方面有关的植物寄生虫的分类。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（如编码效应子的基因）对宿主特异性的贡献及其在杂交事件中的命运。(2)我们将利用全基因组信息、寄主特异性和共源性来了解黑粉菌科不同进化层次中相关基因的谱系排序。(3)基于目标富集的方法将研究最近的物种形成的种群的四个兄弟物种的Anthracoideaceae。因此，我们将有助于植物寄生虫的物种概念和物种界定的讨论，传统的物种概念，如形态，生物或系统发育的物种概念无法提供一个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.