Biology

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

Document Type

Article

Abstract

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life. © 2024 American Society for Microbiology. All rights reserved.

Publication Title

Microbiology Spectrum

Publication Date

4-2024

Volume

12

Issue

4

ISSN

2165-0497

DOI

10.1128/spectrum.03980-23

Keywords

Aspergillaceae, genomics, taxogenomics, pathogen; pathogenicity, Penicillium, plant pathogen, taxonomy, virulence

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