Phylogenomics of the genus Hypoxylon based on 50 new high quality genomes and with special emphasis on the H. rubiginosum complex

Hypoxylon 属的系统基因组学基于 50 个新的高质量基因组，特别强调 H. rubiginosum 复合体

• 批准号: 350664738
• 负责人: Professor Dr. Russell J. Cox
• 金额: --
• 依托单位: Helmholtz-Zentrum für Infektionsforschung (HZI)
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/350664738?language=en
• 关键词: Phylogenomics; genus; Hypoxylon; based; 50

The genus Hypoxylon (Hypoxylaceae, Xylariales) and related genera have been the subject of intensive work regarding the evaluation of its taxonomy by polythetic methodology (comprising careful morphological studies, generation of secondary metabolite profiles by using HPLC/DAD-MS and multi-locus molecular phylogenies). Moreover, several unprecedented secondary metabolites were discovered from these fungi, many of those are chemotaxonomic markers and/or show strong bioactivities. In a currently ongoing project 13 genome sequences from species of the Hypoxylaceae and Xylaria hypoxylon were generated and annotated for secondary metabolite biosynthetic gene clusters (BGC), and over 600 BGC were found, which were mainly restricted to individual species. Furthermore, various methods for genome comparison (ANI- average nucleotide identity; AAI- average amino acid identity; POCP-percentage of conserved proteins), were firstly applied on a larger scale in fungi. In addition, a phylogenomic approach was realized at the family level for Sordariomycetes for the first time, and the resulting phylogeny based on the full genome sequences was found widely in accordance with the multi-locus phylogeny. This data matrix was complemented by a concurrently constructed HPLC-DAD/MS based compound library containing HPLC profiles of extracts from the strains that were sequenced. The library contains over 100 pure secondary metabolites from Hypoxylaceae and is therefore perfectly suited for dereplication (i.e., early stage identification of known metabolites by comparing their spectra and retention times in a standardized HPLC system. The follow-up project is intended to embark on these prerequisites, targeting the Hypoxylon rubiginosum complex, which comprises numerous endophytes and apparently rare, host-specific saprotrophs as well as ubiquitous ascomycetes that grow on angiosperm wood. In total, 50 representative strains of this complex will be selected. Some endophytes that appear phylogenetically closely related to the ascospore-derived strains will also be included. The strains will be subjected to genome sequencing and concurrently studied intensively for metabolite production The aims of the study will be: a) generate and annotate 50 genome sequences of various species of the genus Hypoxylon with emphasis on the H. rubiginosum complex; b) evaluate the utility of genome comparison parameters (ANI, AAI, POCP), to define species boundaries; c) stabilize the phylogeny of Hypoxylon based on phylogenomic approaches; d) study the genomes and secondary metabolome of endophytic vs. ascospore derived strains of the same species; e) further investigate evolutionary relationships between the BGC of closely related species; f) identify the BGC encoding some important chemotaxonomic marker molecules; and g) to discover and engineer hitherto unknown metabolites of Hypoxylon and their BGC.

炭团菌属（Hypoxylaceae，Xylariales）及其相关属的分类学研究一直是通过多元方法（包括仔细的形态学研究、利用HPLC/DAD-MS生成次级代谢产物谱和多位点分子生物学）对其进行分类学评价的深入研究的主题。此外，从这些真菌中发现了一些前所未有的次级代谢产物，其中许多是化学分类学标记和/或显示出强烈的生物活性。在目前正在进行的项目中，从Hypoxylaceae和Xylaria hypoxylon的物种中产生13个基因组序列并注释次级代谢物生物合成基因簇（BGC），并发现超过600个BGC，其主要限于单个物种。此外，用于基因组比较的各种方法（ANI-平均核苷酸同一性; AAI-平均氨基酸同一性; POCP-保守蛋白质的百分比）首次在真菌中大规模应用。此外，首次实现了对囊壳菌科水平的单基因组研究，并发现了基于全基因组序列的多位点单基因组遗传。该数据矩阵由同时构建的基于HPLC-DAD/MS的化合物库补充，该化合物库包含测序菌株提取物的HPLC图谱。该文库含有超过100种来自Hypoxylaceae的纯次级代谢产物，因此非常适合于去复制（即，通过在标准化HPLC系统中比较已知代谢物的光谱和保留时间，进行早期鉴定。 后续项目旨在着手解决这些先决条件，目标是红褐色炭团菌复合体，其中包括许多内生菌和显然罕见的宿主特异性腐养菌以及在被子植物木材上生长的普遍存在的子囊菌。总共将选择该复合物的50个代表性菌株。一些内生菌，似乎在遗传学上密切相关的子囊孢子衍生的菌株也将包括在内。这些菌株将进行基因组测序，同时对代谢产物的生产进行深入研究 本研究的主要目的是：a）获得并注释50个炭团菌属不同种的基因组序列，重点是H。Rubiginosum复合体; B）评估基因组比较参数的效用（ANI，AAI，POCP），以定义物种边界; c）基于基因组学方法稳定Hypoxylon的进化; d）研究相同物种的内生菌与子囊孢子衍生菌株的基因组和次级代谢物组; e）进一步研究密切相关物种的BGC之间的进化关系; f）鉴定编码一些重要的化学分类学标记分子的BGC;和g）发现和工程化迄今未知的炭团菌代谢物及其BGC。