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

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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.