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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
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Codon-based phylogenetics introduces novel flagellar gene markers to oomycete systematics
Gregg P Robideau1, Nicolas Rodrigue2, C André Lévesque1
1Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; Department of Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada.
Molecular Phylogenetics and Evolution
|April 22, 2014
Summary
New flagellar genes, PF16 and OCM1, offer robust phylogenetic reconstruction and species identification in oomycetes. Analysis using a codon substitution model supports current evolutionary views and zoospore ontology.
Area of Science:
- Oomycete systematics
- Molecular evolution
- Phylogenetics
Background:
- Traditional oomycete systematics relies on ribosomal RNA and mitochondrial cytochrome oxidase sequences.
- Limitations exist in current molecular markers for oomycete phylogenetic reconstruction.
Purpose of the Study:
- To evaluate the utility of two single-copy protein-coding flagellar genes, PF16 and OCM1, for oomycete systematics.
- To assess their effectiveness in phylogenetic reconstruction and species identification.
Main Methods:
- Phylogenetic analysis using PF16 and OCM1 gene sequences.
- Application of a mutation-selection model of codon substitution.
- Development of PCR primers for gene amplification across oomycete genera.
Main Results:
- Phylogenetic relationships inferred from flagellar genes align with current oomycete evolutionary understanding when using a codon model.
- Nucleotide- and amino acid-level models yielded biologically implausible reconstructions.
- PF16 and OCM1 provided ample and robust resolution for species identification, respectively.
- Parallels were observed between flagellar gene phylogeny and zoospore ontology.
Conclusions:
- PF16 and OCM1 are valuable molecular markers for oomycete systematics.
- A rich codon substitution model is crucial for accurate phylogenetic inference.
- These genes enhance the molecular toolbox for oomycete research and identification.
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