UNIVERSITY PARK, Pa. — Graduate students in Penn State’s College of Agricultural Sciences contributed to the first complete genome sequence of a harmful plant pathogen from an ornamental Prunushost through an active-learning activity in a plant disease diagnosis course.
The pathogen — Xanthomonas arboricola pv. pruni — is a bacterium that causes disease on species such as peach, apricot and plum trees, as well as on ornamental species such as cherry laurel. Having the full genome sequence from an ornamental host will help future diagnostic efforts, the researchers said.
The project was a collaboration among the students, faculty in the college, Penn State Extension, and the Plant Disease Clinic in the Department of Plant Pathology and Environmental Microbiology. Together, the team determined the complete genome sequence of the pathogen, publishing their work in the journal Microbiology Resource Announcements.
Verónica Román-Reyna, an assistant professor of plant pathology who led the genomic sequencing activity as part of the course and co-authored the resulting paper, said that in addition to providing key insights into the pathogen, the project was an opportunity to help train the next generation of scientists.
“These research techniques are vital for our students to understand,” she said. “And in addition to gaining valuable experience, we now have the full genome sequence to share with other plant pathologists as a resource for understanding what the bacterium can do, how it differs from other bacteria and what to investigate next. It also helps the clinic, because they now have the sequence to compare against if they see this pathogen again in the future.”
The project began through the Harbaugh Faculty Scholars program, which integrated a genomics module to a plant disease diagnosis course in collaboration with the lead instructor, assistant professor Sharifa Crandall.
“Students learn how to ID diseases, up close and personal, through observation of infected plant samples and via cutting-edge DNA diagnostic tools,” Crandall said. “Knowing which pathogen is which helps farmers and foresters make targeted disease management decisions.”
To find samples for the students to analyze, they collaborated with Penn State’s Plant Disease Clinic, a free service that provides clinical diagnoses of plant diseases submitted by Pennsylvania agricultural producers, urban gardeners and homeowners.
“The clinic received a plant sample with symptoms of a bacterial disease that we thought would be really interesting to investigate further,” said Sara May, head diagnostician and manager of the clinic and co-author on the paper. “It was on an ornamental Prunus species, a cherry laurel, and it was a pathogen that we’d seen before but didn't have good information as far as genetic sequencing of the whole genome. We knew it would be a great opportunity for the students to delve into.”
Richard González, dual-title doctoral student in plant pathology and microbiome sciences, said he was particularly interested in participating in the project because his own research focuses on Xanthomonas arboricola pv. pruni isolated from peaches and nectarines in Pennsylvania.
“In this project, Xap was isolated from a different host, which made it especially interesting and directly connected to my research interests,” he said. “I saw it as an opportunity not only to contribute my experience with Xap and antimicrobial resistance but also to learn more about bacterial genomics and how genomic data can be generated, analyzed and shared with the scientific community.”
The resulting genome sequence was uploaded to GenBank, an open-access public database of DNA sequences built by the National Center for Biotechnology Information, a part of the U.S. National Institutes of Health.
Lauren Carneal, doctoral student in plant pathology and environmental microbiology, said the experience allowed her to branch out from her typical research, which focuses on bacterial systems.
“I valued the chance to work with others in my department that I wouldn’t get the opportunity to collaborate with due to our different niches in the field,” she said. “The project allowed us to not only learn technical skills, but science communication and genomic analysis. Dr. Román-Reyna’s expertise truly allowed us to gain experience beyond the standard classroom expectations.”
González agreed, citing collaboration and incorporating next-generation sequencing into the learning process as some of his favorite parts of the project.
“Students are not only learning how to isolate bacteria, analyze genomes and interpret genomic information, but also contributing genome sequences and associated information that other scientists can use in future research,” he said. “I think this is a great example of how teaching, research and collaboration can come together in the same project.”
Luis Fernando Flores-Lopez, dual-title doctoral candidate in plant pathology and microbiome sciences at Penn State; Joshua Giesler, graduated master student; Damiana Rojas, graduated master student; and Sharifa Crandall, assistant professor of soilborne disease dynamics and management at Penn State, also co-authored the paper.
This research was funded by the U.S. Department of Agriculture's National Institute of Food and Agriculture Federal Appropriations under project numbers PEN04676 and PE04997. This content is solely the responsibility of the authors and does not necessarily represent the views of the funders.