It’s Complicated: Rapid Publication of Genomes in
            <i>Microbiology Resource Announcements</i>
            Can Be Both Part of the Problem and the Solution to Fungal Taxonomic Resolution

Stevenson, Bradley S.; Stamps, Blake W.

doi:10.1128/mra.00458-21

Cited by 2 publications

(2 citation statements)

References 8 publications

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“…Next, orthologous sequences are inferred based on sequence similarity from databases such as the National Center for Biotechnology Information; then, software is used to infer phylogenetic trees for each sequence, representing a hypothesis of the evolutionary history of these species (Raja et al, 2017). Despite the potential for genome-scale data to facilitate fungal taxonomy, current practices typically do not rely on whole-genome data, in part because of sparse genome sequences available across the fungal tree of life (Xu, 2020; Aime et al, 2021; Arias et al, 2021; Fountain et al, 2021; Kanamasa, 2021; Kück and Dahlmann, 2021; Li and Yu, 2021; Ruiz and Radwan, 2021; Stevenson and Stamps, 2021; Venkateswaran et al, 2021; Yin et al, 2021). Here, we tested the hypothesis that phylogenomic approaches that leverage whole genome sequences will improve the accuracy of phylogenetic reconstructions that have be based on sequences from a small number of loci (Rokas et al, 2003; Jarvis et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

“…Aspergillus niger is an industrial workhorse and Aspergillus oryzae is used in the production of fermented foods like soy sauce and sake (Gibbons et al, 2012; Cairns et al, 2018). Accurate identification of Aspergillus fungi with barcode loci is often challenging (Houbraken et al, 2021; Li and Yu, 2021; Stevenson and Stamps, 2021; Venkateswaran et al, 2021; Yin et al, 2021), but important because even closely related species can differ in drug resistance profiles and ability to cause disease (dos Santos et al, 2020; Steenwyk et al, 2020c). For example, clinical strains of Aspergillus nomius and Aspergillus tamarii have been misidentified as Aspergillus flavus (Tam et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomics reveals extensive misidentification of fungal strains from the genusAspergillus

Steenwyk

Balamurugan

Raja

et al. 2022

Preprint

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Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. However, the use of one or few molecular markers can lead to inaccurate inferences of species history and errors in classification. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense dataset of 711 fungal genomes from the biomedically and technologically important genusAspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific forAspergillusand provide profile Hidden Markov Models for each, facilitating others to use these molecular markers. Examination of the resulting genome-scale phylogeny: (1) helped resolve ongoing taxonomic controversies and identified new ones; (2) revealed extensive strain misidentification, underscoring the importance of population-level sampling in species classification; and (3) identified novel lineages that may shed light on the early evolution of an important genus. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the tree of life.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Phylogenomics reveals extensive misidentification of fungal strains from the genusAspergillus

Steenwyk

Balamurugan

Raja

et al. 2022

Preprint

View full text Add to dashboard Cite

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Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

Steenwyk,

Balamurugan,

Raja

et al. 2024

Microbiol Spectr

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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. IMPORTANCE Identification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genus Aspergillus . Our evolutionary genomic analyses revealed that nearly 8% of publicly available Aspergillus genomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.

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It’s Complicated: Rapid Publication of Genomes in Microbiology Resource Announcements Can Be Both Part of the Problem and the Solution to Fungal Taxonomic Resolution

Cited by 2 publications

References 8 publications

Phylogenomics reveals extensive misidentification of fungal strains from the genusAspergillus

Phylogenomics reveals extensive misidentification of fungal strains from the genusAspergillus

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

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