AI Article Synopsis

  • Modern taxonomic classification of fungi often relies on molecular markers, but this study employs phylogenomics to analyze 710 fungal genomes and reconstruct evolutionary relationships.
  • * The research generated a new set of 1,362 high-quality molecular markers and found that about 7.59% of the fungal strains were previously misidentified, highlighting the need for better population-level sampling in species classification.
  • * The findings indicate that using genomic data can significantly improve the accuracy of identifying fungal species and help resolve ongoing taxonomic debates, ultimately supporting the construction of a more precise Tree of Life.

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 . To do so, we generated a novel set of 1,362 high-quality molecular markers specific for 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.IMPORTANCEIdentification 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 . Our evolutionary genomic analyses revealed that nearly 8% of publicly available 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.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10986620PMC
http://dx.doi.org/10.1128/spectrum.03980-23DOI Listing

Publication Analysis

Top Keywords

molecular markers
12
fungal species
12
genomic data
12
phylogenomics species
8
species populations
8
data set
8
set 710
8
strains fungal
8
publicly genomes
8
multiple strains
8

Similar Publications

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!