ARS Scientists Develop Innovative Pipeline to Analyze Plant Pathogens
By: Tami Terella-Faram
Email: tami.terella-faram@usda.gov
ARS scientists in Corvallis, OR, in collaboration with Oregon State University, developed a disease surveillance platform that could improve U.S. agriculture by unlocking the future of plant health. PathogenSurveillance is an innovative, open-source software tool that can quickly analyze and identify novel microbial variants based on DNA sequences.
The automated PathogenSurveillance pipeline is an innovative workflow tool to help scientists respond in real-time to emerging, or re-emerging, invasive pathogens and pests. The surveillance platform will improve plant health and aid in reducing the spread of new and emerging diseases in agronomic, urban, and forest ecosystems.
“This genomics pipeline revolutionizes plant health, allowing us to identify any microbe, pest, or pathogen in just minutes-to-hours once there is a genome sequence,” said Nik Grunwald, ARS research plant pathologist at the Horticultural Crops Disease and Pest Management Research Unit in Corvallis. “The genomic pipeline can be used for real-time biosurveillance of known, or unknown, pathogens relatively quickly, which lessens the barrier to adoption and use of PathogenSurveillance drastically.”
A Camellia plant infected with Phytophthora nemorosa, which causes leaf blight. (Photo by Nik Grunwald, ARS plant pathologist).
Grunwald added that, since everything is sequence-based, this tool can be used to monitor the evolution of pest/pathogens in real-time, providing insights into how populations change, variations emerge, and new invasions occur. The platform can also be easily deployed to identify a specific pathogen, or to monitor the emergence of new disease strains or variants.
“Samples are sent to a local lab, and the resulting genome is sequenced and uploaded to the pipeline software system for identification,” Grunwald said. “Variation in genomes can thus be monitored over time and space by comparing genomes.”
This allows PathogenSurveillance to be used by labs or clinics with little computational experience, and it provides “unprecedented capability for in-field or point-of-care diagnosis of pests and pathogens,” according to Grunwald.
The PathogenSurveillance platform also enables scientists to input one to several hundred population samples of small-to-modest genome sizes, including bacteria, fungi, insects, and nematodes for pathogen surveillance and identification.
The program output is also intuitive for the user because it can provide graphs of genetic diversity and create reports in the form of an interactive HTML document.
“This will be a benefit to researchers, disease clinics, and diagnosticians in their work to identify clonal, or other types of variants such as the UG99 stem rust, or NA2 of sudden oak death,” added Grunwald.
Scientists can download the PathogenSurveillance software tool at: https://nf-co.re/pathogensurveillance/1.0.0/.