Phylogenetic Reconciliation of the Xylariales: Taxonomic systematics and beyond

• Applicant: Dr. Christopher Lambert
• Subject Area: Evolution and Systematics of Plants and Fungi ; Medical Microbiology and Mycology, Hygiene, Molecular Infection Biology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 575791605

Fungal taxonomy historically relied heavily on morphological characteristics, which is nowadays complemented by additional phenotypic characters in so-called polyphasic approaches. Such integration of morphological, chemical and genetic traits, amongst others, repeatedly showed that morphocentric species concepts are incongruent with these modern species concepts. Still, even polyphasic approaches are commonly limited by the resolution power of molecular phylogenetics, as state-of-the-art concatenation-based multi-gene phylogenies are often insufficient to fully resolve fungal taxa. This has in part been attributed to potential reticulation events such as incomplete lineage sorting and horizontal gene transfer, but investigations on the precise contribution of these events for lineage evolution and fungal speciation are scarce. With the advent of routine application of genome-level DNA-sequencing, this question can now be studied in unprecedented detail, which is for the benefit of not only fungal taxonomy, but also opens avenues for biotechnological applications. This project focuses on analyzing a set of 166 genome sequences available with taxa associated with the Xylariales (Ascomycyota). These fungi are extensively studied for their complex taxonomy and prolific secondary metabolism and will serve as an excellent model due to ample available data. Phylogenomics will be used to construct a species tree by following both concatenation and coalescence-based approaches and single-locus phylogenies used to evaluate the degree of reticulation in distinct lineages of the Xylariales. This knowledge will be utilized to propose an improved, comparative genomics-informed species concept for this polyphyletic group of fungi. In a second step, biosynthetic gene-clusters will be predicted and their distribution patterns analyzed in the light of the proposed reticulated history. This analysis will then be narrowed down to azaphilones, a class of highly conserved, chemotaxonomically informative pigments. Sequence information of experimentally validated azaphilone-producing biosynthetic core genes will be phylogenetically analyzed in a matrix containing anti-SMASH predicted biosynthetic gene clusters (BGCs) to facilitate BGC annotation. A synteny analysis will follow to track differences in BGC composition. A BLAST analysis of individual genes will be conducted to a) determine the origin of identified genes and b) control for missing or incomplete BGCs. Ultimately, this project aims to shed light on complex phylogenetic histories and how to exploit such information to predict the distribution of secondary metabolites in other larger fungal taxa. Moreover, this will lead to much needed insights into the evolution of the secondary metabolome of fungi and the mechanisms of gene flow, which will not only serve biodiversity research, but also bioengineering approaches to design new, bioactive compounds.

• DFG Programme: WBP Fellowship
• International Connection: Netherlands
• Host: Dr. Jérôme Collemare