<i>Phytophthora urerae</i> sp. nov., a new clade 1c relative of the Irish famine pathogen <i>Phytophthora infestans</i> from South America

Grünwald, Niklaus J.; Forbes, G. A.; Perez‐Barrera, W.; Stewart, Jane E.; Fieland, Valerie J.; Larsen, Meredith M.

doi:10.1111/ppa.12968

Cited by 2 publications

References 31 publications

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An open-access T-BAS phylogeny for EmergingPhytophthoraspecies

Coomber

Saville

Carbone

et al. 2022

Preprint

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Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1875, it has expanded to comprise over 190 formally described species. There is a need for an open access bioinformatic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood method. A search engine was also developed to identify genotypes of P. infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, this resource can be updated in real-time to keep pace with new species descriptions. The tool contains metadata such as clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for diverse populations of pathogens.

show abstract

An open-access T-BAS phylogeny for EmergingPhytophthoraspecies

Coomber

Saville

Carbone

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

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

et al. 2023

View full text Add to dashboard Cite

Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1876, it has expanded to comprise over 190 formally described species. There is a need for an open access phylogenetic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood program. A search engine was also developed to identify microsatellite genotypes of P. infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, the tree can be updated in real-time as new species are described. The tool contains metadata including clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for other Oomycete, bacterial or fungal pathogens.

show abstract

Phytophthora urerae sp. nov., a new clade 1c relative of the Irish famine pathogen Phytophthora infestans from South America

Cited by 2 publications

References 31 publications

An open-access T-BAS phylogeny for EmergingPhytophthoraspecies

An open-access T-BAS phylogeny for EmergingPhytophthoraspecies

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

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