An open-access T-BAS phylogeny for emerging Phytophthora species

Area of Science:

• Phytopathology and Bioinformatics
• Oomycete genomics and phylogenetics

Background:

• Phytophthora species are significant pathogens affecting diverse crops.
• The genus Phytophthora has over 190 described species, necessitating better identification tools.
• Existing sequence data and metadata are fragmented across various sources.

Purpose of the Study:

• To develop an open-access phylogenetic tool for Phytophthora species.
• To centralize diverse sequence data and associated metadata for improved research and identification.
• To create a dynamic and updatable phylogenetic resource for the global Phytophthora research community.

Main Methods:

• Utilized the Tree-Based Alignment Selector Toolkit (T-BAS) to construct a phylogeny.
• Inferred the phylogenetic tree using sequences from eight nuclear genes for 192 species and 33 informal taxa.
• Developed a search engine for identifying Phytophthora infestans microsatellite genotypes.
• Integrated metadata including host, substrate, distribution, and references.

Main Results:

• A comprehensive phylogeny of 192 Phytophthora species and 33 informal taxa was generated.
• The T-BAS tool provides a visualization framework for placing unknown isolates on the phylogeny.
• A search engine for P. infestans microsatellite genotypes was developed.
• The tool includes downloadable metadata and allows real-time updates as new species are described.

Conclusions:

• The T-BAS web portal offers a centralized, dynamic, and metadata-rich phylogenetic resource for Phytophthora.
• This tool facilitates data sharing, enhances species identification, and supports global research efforts.
• The T-BAS framework is adaptable for creating similar phylogenetic resources for other plant pathogens.