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Published on: October 28, 2021
Evaluation of two novel barcodes for species recognition of opportunistic pathogens in Fusarium
Abdullah M S Al-Hatmi1, A H G Gerrits Van Den Ende2, J Benjamin Stielow2
1CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands; Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands; Directorate General of Health Services, Ibri Hospital, Ministry of Health, P.C.: 100, P.O. Box : 393, Ibri, Oman.
Abstract:
The genus Fusarium includes more than 200 species of which 73 have been isolated from human infections. Fusarium species are opportunistic human pathogens with variable aetiology. Species determination is best made with the combined phylogeny of protein-coding genes such as elongation factor (TEF1), RNA polymerase (RPB2) and the partial β-tubulin (BT2) gene. The internal transcribed spacers 1, 2 and 5.8S rRNA gene (ITS) have also been used, however, ITS cannot discriminate several closely related species and has nonorthologous copies in Fusarium. Currently, morphological approaches and tree-building methods are in use to define species and to discover hitherto undescribed species. Aftter a species is defined, DNA barcoding approaches can be used to identify species by the presence or absence of discrete nucleotide characters. We demonstrate the potential of two recently discovered DNA barcode loci, topoisomerase I (TOP1) and phosphoglycerate kinase (PGK), in combination with other routinely used markers such as TEF1, in an analysis of 144 Fusarium strains belonging to 52 species. Our barcoding study using TOP1 and PKG provided concordance of molecular data with TEF1. The currently accepted Fusarium species sampled were well supported in phylogenetic trees of both new markers.
Insights
New DNA barcodes, topoisomerase I (TOP1) and phosphoglycerate kinase (PGK), accurately identify Fusarium species. These markers, combined with elongation factor TEF1, improve fungal species determination in clinical diagnostics.
Area of Science:
- Mycology
- Molecular Biology
- Fungal Pathogenesis
Background:
- The genus Fusarium comprises over 200 species, with 73 identified in human infections.
- Fusarium species are opportunistic pathogens, necessitating accurate species identification for effective treatment.
- Current species determination relies on combined phylogenetic analysis of protein-coding genes (TEF1, RPB2, BT2) and morphological methods.
Purpose of the Study:
- To evaluate the efficacy of two novel DNA barcode loci, topoisomerase I (TOP1) and phosphoglycerate kinase (PGK), for Fusarium species identification.
- To assess the concordance of TOP1 and PGK markers with established markers like TEF1.
- To determine if these new markers can reliably support phylogenetic analyses of Fusarium species.
Main Methods:
- Phylogenetic analysis of 144 Fusarium strains from 52 species.
- Utilized DNA barcoding with TOP1 and PGK gene sequences.
- Compared results with TEF1 gene sequences and morphological data.
Main Results:
- TOP1 and PGK markers demonstrated concordance with TEF1, supporting molecular identification.
- Phylogenetic trees constructed using TOP1 and PGK well-supported currently accepted Fusarium species.
- The study confirmed the potential of TOP1 and PGK as reliable DNA barcodes for Fusarium.
Conclusions:
- TOP1 and PGK are effective DNA barcodes for Fusarium species identification.
- These markers enhance the accuracy and reliability of fungal species determination.
- The findings contribute to improved diagnostics and understanding of Fusarium pathogenesis.
