Alternaria section Alternaria: Species, formae speciales or pathotypes?
J H C Woudenberg1, M F Seidl2, J Z Groenewald3
1CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
Studies in Mycology
|March 9, 2016
Summary
This study reveals that Alternaria sect. Alternaria comprises only 11 phylogenetic species and one species complex, not 35 previously described morphospecies. Molecular data clarifies fungal species identification within this important genus.
Area of Science:
- Mycology
- Fungal Genomics
- Phylogenetics
Background:
- The fungal genus Alternaria is divided into 26 sections, with sect. Alternaria containing numerous small-spored species, many of which are significant pathogens.
- Species within Alternaria sect. Alternaria have been historically classified based on morphology and host specificity, but molecular variation is minimal, leading to taxonomic ambiguity.
Purpose of the Study:
- To investigate the molecular basis of species delineation within Alternaria sect. Alternaria.
- To determine if existing morphospecies are supported by genomic and transcriptomic data.
- To establish a clear and stable species classification for Alternaria sect. Alternaria.
Main Methods:
- Whole-genome sequencing of nine Alternaria morphospecies and transcriptome sequencing of 12 morphospecies.
- Multi-gene sequencing of 168 Alternaria isolates.
- Comparative genomic analysis, including whole-genome alignments and single nucleotide polymorphism (SNP) analysis.
- Phylogenetic tree construction using whole-genome, transcriptome, and multi-gene sequence data.
Main Results:
- Alternaria sect. Alternaria genomes exhibit high identity (96.7-98.2%) and low repeat content (1.4-2.7%).
- Molecular phylogenies confirmed that Alternaria sect. Alternaria comprises only 11 phylogenetic species and one species complex.
- Thirty-five morphospecies were synonymized under Alternaria alternata due to indistinguishable molecular variation.
Conclusions:
- Morphological species concepts are insufficient for accurate delineation within Alternaria sect. Alternaria.
- Genomic and transcriptomic data provide a robust framework for resolving species complexes in Alternaria.
- This study establishes a refined taxonomic classification for Alternaria sect. Alternaria, aiding in pathogen identification and management.
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