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Isolation of Culturable Yeasts and Molds from Soils to Investigate Fungal Population Structure
Published on: May 27, 2022
A phylogenomic analysis of the Ascomycota
Barbara Robbertse1, John B Reeves, Conrad L Schoch
1Department of Botany and Plant Pathology, Oregon State University, Corvallis, 97333, USA. robberba@science.oregonstate.edu
Fungal Genetics and Biology : FG & B
|June 20, 2006
Summary
An automated method efficiently identifies fungal orthologous sequences for phylogenomic analysis. This approach resolves complex fungal evolutionary relationships, including problematic Ascomycota lineages.
Area of Science:
- Fungal genomics
- Bioinformatics
- Molecular evolution
Background:
- Phylogenetic analysis of fungal genomes is crucial for understanding fungal evolution.
- Previous methods for extracting orthologous sequences were often time-consuming and inefficient.
- Resolving deep divergences within the Ascomycota phylum has been challenging.
Purpose of the Study:
- To develop an automated procedure for extracting orthologous sequences from fungal genomes.
- To improve the efficiency and timeliness of phylogenomic analyses.
- To resolve problematic relationships within the Ascomycota phylogeny.
Main Methods:
- Developed an automated pipeline using all-versus-all BLASTP and Markov Clustering algorithm.
- Identified 854 single-copy, ubiquitously distributed protein clusters across 17 fungal proteomes.
- Generated a super alignment of 781 orthologous sequence clusters for phylogenetic analysis.
Main Results:
- Phylogenomic analyses using Neighbor-Joining and Maximum Likelihood methods yielded identical, highly supported topologies.
- The study resolved the placement of Leotiomycetes as sister to Sordariomycetes, a historically difficult phylogenetic problem.
- Phylogenetic analyses incorporating an unannotated genome (Coccidioides immitis) confirmed the robustness of the method and correctly placed the species.
Conclusions:
- The automated procedure is effective for identifying fungal orthologs and constructing robust phylogenomic datasets.
- The method successfully resolved challenging evolutionary relationships within the Ascomycota.
- This approach enables the incorporation of unannotated genomic data into phylogenetic studies, advancing fungal systematics.
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