Plant Pathogen Tree of Life Assembled

Researchers at North Carolina State University have developed a new online tool—reportedly the first of its kind for plant pathogens—to help researchers across the globe identify, detect, and monitor species of Phytophthora, which have been responsible for plant diseases ranging from the devastating 1840s Irish potato famine to sudden oak death that still plagues the West Coast oak population.

The new pathogen “tree of life” provides information about each of the more than 192 formally described species, including their evolutionary history and relationships within groups, as well as more than 30 other informally described taxa. It also includes genetic sequence data from several locations on genome of each species. Other data include the global locations of each species, the plants that host the pathogen, and where the pathogen resides in, or on, its plant hosts.

“We’re taking all known Phytophthora species and putting them into a living ‘tree of life’ using the Tree-Based Alignment Selector (T-BAS) toolkit that was developed by my colleague Ignazio Carbone,” says Jean Ristaino, PhD, William Neal Reynolds Distinguished Professor of Plant Pathology at North Carolina State University and corresponding author of a paper “An open-access T-BAS phylogeny for emerging Phytophthora species” in PLOS ONE that describes the tool. “Researchers can place emerging threat species into the open-access tree and look at which groups are expanding and evolving.”

The new tool will allow researchers to update plant disease information in real time, according to Ristaino.

“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,” write the investigators.

“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.”

The real key to preventing disease outbreaks is to grab the signals before the outbreak occurs,” continued Ristaino, who directs NC State’s Emerging Plant Disease and Global Food Security cluster. “T-BAS could be useful as a tool for disease surveillance and for figuring out the next new lineage that might emerge. Researchers can query this database and the tree will incorporate the new species.”