Revision of the phylogeny of the genus Hypoxylon (Xylariales) using a polyphasic approach and high-quality genome data
Creators: name: Cedeño–Sanchez, Marjorie
Publisher: name: Zenodo
Year: 2024

description: Xylariales is an order of fungi within the Phylum Ascomycetes, known for its ecological diversity and significant secondary metabolite production. Despite extensive studies, achieving a monophyletic and stable classification of Xylariales remains challenging because of the complexity of its morphological traits. Due to its prolific secondary metabolism and complex taxonomy, the Hypoxylaceae has attracted particular attention among these fungi, with the genus Hypoxylon playing a key role. Even after extensive research,Hypoxylon remains paraphyletic, which requires deeper studies using a polyphasic approach. To studyHypoxylon, this thesis incorporates morphological, chemotaxonomic, and genomic data to address these challenges.

A comprehensive study of theHypoxylon fuscum species complex, with specimens collected from Iran and Europe, led to a clearer delimitation of the species and the description of the new speciesH. eurasiaticum and H. pseudofuscum. Additionally, high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS-DAD) revealed the presence of two unknown stromatal compounds, which were isolated and characterized using NMR spectroscopy as 3′-malonyl-daldinin F and pseudofuscochalasin A. The new cytochalasin compound serves as a chemotaxonomic marker forH. pseudofuscum and the absence of both for H. fuscum sensu stricto.

A new species collected from the Democratic Republic of the Congo was studied using a polyphasic approach, resulting in the description of a new species that morphologically resembles Hypoxylon papillatum. A multi-gene phylogenetic analysis correlated that both species cluster together at the base of the Hypoxylaceae in their own clade. Based on these findings, a new genus namedParahypoxylon was introduced, comprising two species: Parahypoxylon papillatum andParahypoxylon ruwenzoriense.

Since not all species ofHypoxylon have been sequenced, it is not possible to study them using a complete polyphasic approach, particularly for species collected before the molecular era. Recent studies from 2010 and 2015 identified severalHypoxylon species from the Neotropics using exclusively morphological traits. The analyzes of their stromatal secondary metabolite profiles supported their classification within Xylariales and provided important data for these species.

Additionally, a comprehensive analysis of rDNA cistrons in 44 high-quality genomes of Hypoxylaceae was conducted, highlighting significant intragenomic polymorphisms, including deep paralogs in some of these species. Additionally, protein-coding genes were evaluated, and we recommend using theTUB2 gene as a more reliable barcoding marker for these fungi.

The integration of morphological, chemical, and genetic data has refined the taxonomy and phylogenetic relationships within the genusHypoxylon and related genera. This approach underscores the potential of these fungi as a valuable source of novel secondary metabolites, which could lead to the development of new drugs with innovative modes of action.

Another study on Xylariales demonstrated that when a holotype strain description before the molecular era is sequenced, drastic changes can occur. For example,Induratia apiospora from New Zealand was sequenced for the first time, revealing phylogenetic affinities with the Barrmaeliaceae, not with Induratiaceae where it was previously classified. Based on these findings, Induratia apiospora was classified within Barrmaeliaceae and resurrecting the genusMuscodor was resurrectedwithin Xylariaceae.