Phylogenetic Taxonomy of Filamentous Fungi

Filamentous fungi exhibit astounding diversity and play vital roles in ecosystems, agriculture, industry and medicine. Phylogenetic taxonomy integrates molecular sequence data with morphological and biochemical characteristics to resolve evolutionary relationships among fungal taxa. By analysing conserved DNA regions such as the internal transcribed spacer (ITS) and protein-coding genes like beta-tubulin (BenA) and RNA polymerase II second largest subunit (RPB2), taxonomists can delineate monophyletic groups and define genera, sections and species with greater precision than traditional morphology alone. This approach has revealed hidden lineages, clarified species complexes and supported a stable classification under the ‘One Fungus – One Name’ principle. The integration of polyphasic methods—including molecular phylogenetics, extrolite profiling and detailed morphological assessment—ensures robust species hypotheses. This system underpins accurate identification, informs risk assessment of pathogenic species, guides bioprospecting for novel metabolites and enhances conservation efforts for rare taxa. Advances in high-throughput sequencing and bioinformatic pipelines continue to refine taxonomic frameworks, promoting global collaboration and data sharing within the mycological community.

Research from Nature Portfolio

Recent studies have described two novel taxa within the family Trichocomaceae, employing a multilocus phylogenetic framework and comprehensive morphological analysis. Strains isolated from clematis roots were subjected to four-gene sequencing, confirming the novelty of Rasamsonia chlamydospora and Talaromyces clematidis. Detailed characterisation of conidiophores, conidia and growth profiles on differential media reinforced their placement in distinct phylogenetic clades, illustrating the power of sequence data in uncovering cryptic diversity. In an earlier investigation into Penicillium section Sclerotiora, researchers combined ITS, BenA, CaM and RPB2 gene phylogenies with colony morphology and microscopic traits to delineate five new species. The study highlighted a well-supported subclade of biverticillate species and provided diagnostic keys to distinguish them from closely related taxa. These contributions demonstrate how targeted molecular markers and rigorous morphological scrutiny refine species boundaries and enrich our understanding of fungal evolution.

Phylogenetic Taxonomy of Filamentous Fungi publication trend

The graph below shows the total number of articles in phylogenetic taxonomy of filamentous fungi across all publications each year (not limited to Nature Index journals).

Technical terms

Internal transcribed spacer (ITS): A non-coding DNA region between ribosomal RNA genes used as a universal barcode for fungal identification.

Beta-tubulin (BenA): A protein-coding gene frequently sequenced in phylogenetic studies for resolving closely related fungal species.

RNA polymerase II second largest subunit (RPB2): A conserved gene providing phylogenetic resolution at genus and family levels.

Monophyletic group: A set of organisms that includes an ancestor and all its descendants, indicating a single evolutionary lineage.

Polyphasic approach: An integrative method combining molecular, morphological and chemical data to support robust species definitions.

Section: A taxonomic rank below genus, grouping species sharing common evolutionary characteristics.

References

1. Two new species of Trichocomaceae (Eurotiales), accommodated in Rasamsonia and Talaromyces section Bacillispori, from the Czech Republic. Scientific Reports (2023).
2. Phylogeny and morphological analyses of Penicillium section Sclerotiora (Fungi) lead to the discovery of five new species. Scientific Reports (2017).
3. Classification of Aspergillus, Penicillium, Talaromyces and related genera (Eurotiales): An overview of families, genera, subgenera, sections, series and species. Studies in Mycology (2020).
4. Morphological and phylogenetic analyses reveal two new Penicillium species isolated from the ancient Great Wall loess in Beijing, China. Frontiers in Microbiology (2024).
5. Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era – Past, present and future. Computational and Structural Biotechnology Journal (2018).