How Scientists Are Mapping Phytophthora's Evolution to Protect Global Food Security
In the 1840s, a mysterious blight wiped out Ireland's potato crops, leading to famine, mass starvation, and one of the most devastating chapters in agricultural history. The culprit, later identified as Phytophthora infestans, translates fittingly to "plant destroyer" 9 . Today, scientists are fighting back with an innovative digital tool—a dynamic family tree that promises to revolutionize how we track and combat these destructive pathogens 1 .
The Irish Potato Famine caused by Phytophthora infestans resulted in approximately 1 million deaths and forced another million to emigrate.
Approximately 150 new Phytophthora species have been identified since 2000 alone, highlighting the need for better classification tools 9 .
The Tree-Based Alignment Selector (T-BAS) toolkit is essentially a digital family tree for plant pathogens that researchers across the globe can access, query, and update in real-time 1 . Developed by researchers at North Carolina State University, this tool provides a comprehensive framework for understanding Phytophthora evolution and relationships.
Allows scientists to place unknown isolates on a curated phylogeny of all Phytophthora species.
Provides data from several locations on the genome of each species for accurate identification.
"The real key to preventing disease outbreaks is to grab the signals before the outbreak occurs. T-BAS could be useful as a tool for disease surveillance and for figuring out the next new lineage that might emerge."
Phytophthora species continue to wreak havoc across the globe, causing severe diseases on food crops, forest trees, and ornamental plants 3 . These pathogens are present in air, soil, and water, enabling them to spread rapidly through diverse environments 9 .
Responsible for Sudden Oak Death, which still plagues West Coast oak populations 9 .
A generalist species with a remarkably wide host range, infecting almost 5000 plant species worldwide 2 .
Causes black pod disease of cacao, threatening chocolate production in Western Africa 3 .
A global threat to cacao production 3 .
The traditional approach to identifying Phytophthora species relied heavily on morphological characteristics - examining physical features under a microscope 3 . However, with the exponential discovery of new species and their subtle differences, this method has become increasingly impractical for accurate identification.
In a comprehensive study published in PLOS ONE in 2023, researchers detailed their ambitious effort to create the most complete Phytophthora phylogeny to date 3 . The team recognized that while multilocus sequencing generates robust phylogenies, the resulting trees often lack the biological information researchers need.
"The current phylogenetic system and curated knowledge on the Phytophthora genus is disjointed, with molecular phylogenies and biological information being presented in disparate resources" 3 .
The team mined publicly available sequence data for described Phytophthora species from nine different loci (28S, 60SL10, Btub, EF1α, Enl, HSP90, TigA, ITS, and CoxI) from GenBank, drawing on previous phylogenetic works and species descriptions 3 .
They assembled a dataset representing 192 formally described Phytophthora species and 33 informal taxa, making it the most comprehensive phylogeny of its kind 1 3 .
Using the T-BAS toolkit, they inferred the phylogenetic tree with the RAxML maximum likelihood method, which estimates the most probable evolutionary relationships based on genetic sequence data 3 .
The team enriched the phylogeny with crucial metadata including clade designations, host species, substrate preferences, sexual characteristics, geographic distribution, and reference literature 1 .
They developed a search engine to identify microsatellite genotypes of P. infestans based on genetic distance to known lineages, addressing the need for tracking specific disease strains 3 .
| Category | Number | Notes |
|---|---|---|
| Formally described species | 192 | - |
| Informal taxa | 33 | Not yet formally described |
| Nuclear genes sequenced | 8-9 | Varies by species |
| Total taxa in phylogeny | 225 | Combined formal and informal |
| Year | Species Count | Reference |
|---|---|---|
| 2000 | 50 species | Cooke et al. |
| 2014 | 90 formally described + 17 provisional | Martin et al. |
| 2017 | 142 formally described + 43 informal | Yang et al. |
| 2023 | 192 formally described + 33 informal | Coomber et al. |
The resulting open-access phylogeny provides an unprecedented resource for researchers worldwide 3 . Perhaps most innovatively, the tool allows the global Phytophthora community to upload sequences and determine the phylogenetic placement of new isolates within the larger phylogeny 1 . This "living" aspect means the tree continuously evolves as new species are discovered, addressing a critical limitation of previous static phylogenies.
| Tool/Resource | Function | Application in Phytophthora Research |
|---|---|---|
| T-BAS Web Portal | Visualization framework | Places unknown isolates on curated phylogeny |
| Eight nuclear genes | Molecular markers | Species identification and relationship mapping |
| RAxML program | Maximum likelihood analysis | Infers evolutionary relationships |
| Microsatellite search engine | Genotype identification | Tracks P. infestans lineages |
| Metadata database | Biological information storage | Links species to hosts, geography, and traits |
Used for investigating pathogenicity and resistance mechanisms in Phytophthora species 6 .
Includes handheld biosensors and smartphone-integrated systems for field detection 8 .
Used to clarify evolutionary relationships among closely related species 4 .
By providing an open-access resource, the tool enables researchers worldwide to identify potential threat species quickly. "Researchers can place emerging threat species into the open-access tree and look at which groups are expanding and evolving," notes Ristaino 9 . This capability is crucial for early detection and rapid response to new pathogenic threats.
The tool helps clarify confusion around closely related species. For example, a 2025 study of the Phytophthora 1a subclade (including P. cactorum, P. pseudotsugae, and P. hedraiandra) used mitogenome analysis to better understand their evolutionary relationships 4 . Such clarity is essential for accurate identification and management.
Recent experimental evolution studies show that P. infestans can develop resistance to multi-site fungicides like mancozeb within approximately 200 days of continuous exposure 5 7 . The T-BAS tool provides a framework for monitoring such adaptations across different populations.
The discovery that fungicide resistance can be reversible - declining when selection pressure is removed - offers new strategies for chemical rotation in agriculture 5 . This finding, combined with phylogenetic tools, supports more sustainable disease management approaches.
The T-BAS phylogeny for Phytophthora represents more than just a scientific achievement - it embodies a shift toward open science and global collaboration in tackling plant diseases.
"Collaboration and sharing data makes much more sense than being secretive" 9 .
This living phylogenetic resource continues to grow as researchers across the world contribute new data. For a genus known as "the plant destroyer," such collaborative tools offer hope for protecting global food security and natural ecosystems from these relentless pathogens. As new species emerge and climates change, this digital tree of life may prove instrumental in preventing the next great plant pandemic - before it has a chance to begin.