Key points
- Eleven undergraduate students at the University of Florida are the first to assemble the pignut hickory tree genome.
- The work was done as part of a hands-on research course open to all majors and taught by instructors at the Florida Museum of Natural History.
- The hickory tree selected for genome sequencing and assembly grows in the McCarty Woods conservation area on the University of Florida’s main campus.
- The completed genome was recently published in the peer-reviewed journal G3 Genes|Genomes|Genetics, where it is freely available for other scientists to access and study. A photo of the tree used for genome sequencing was selected by the journal’s editorial staff as the cover image for this issue.
If you take a stroll through the oldest and busiest part of the University of Florida’s main campus in Gainesville, you’ll likely pass by or through a 2.9-acre forest full of gnarled and wizened trees. The forest is just north of the Florida Museum of Natural History’s dry collection building, and the spongy footpath that meanders through it starts out beneath the broad and dark green canopy of two pignut hickory trees (Carya glabra).
The trees are a regular sight for Audrey Tucker, an undergraduate student at the University of Florida majoring in biology, and as of April of 2025, her name and those of 10 other students decorate a plaque staked at the base of one of the hickories. All eleven students were members of a 2025 independent research course in which they assembled the pignut hickory’s genome for the first time. This course was part of a collection of Course-Based Undergraduate Research Experience (CURE) classes organized by the UF Center for Undergraduate Research to give students, especially freshmen, the opportunity to learn through structured inquiry and investigation.
“I walk past that tree probably every day, and just seeing that I was able to be a part of something bigger than a regular class was really special,” Tucker said.
The course, called Plant Genome Assembly and Annotation, was offered during the 2025 spring semester and taught by Pamela and Douglas Soltis, both distinguished professors at the Florida Museum; Shengchen Shan, a staff scientist at the museum; Edgardo Ortiz Valencia, a computational biologist for the Soltis research team; and Alex Harkess, a faculty investigator at the HudsonAlpha Institute for Biotechnology.
“When Pam and Doug heard that Alex was organizing this course, they thought of McCarty Woods right away,” Shan said.
For the last several years, the Soltises have organized a grassroots effort to conserve and revitalize McCarty Woods. Once a month, they gather with a group of volunteers and a few boxes of doughnuts on Saturday morning and spend an hour or two pulling up invasive species, planting natives, picking up trash, and laying down pine straw to add nutrients to the soil and cushion the trails.
The idea behind the course was to give students the opportunity to assemble the genome of a plant species that previously lacked one. The course was part of a broader initiative developed by Harkess and Leslie Goertzen of Auburn University to sequence genomes from trees on college campuses across the nation. There’s no end to things scientists can do with this type of data. Genomes are used to determine how species are related to each other, how genes function, how life evolves, how to cure or treat diseases, how best to protect endangered species, how organisms interact with their environments, how to improve crop yields…the list goes on.
Knowing that being able to see and touch the tree would add special significance to the project, the instructors collected leaves from a venerable swamp chestnut oak (Quercus michauxii) that grows in McCarty Woods and sent them to Harkness for DNA extraction and sequencing. But there was a delay in sequencing the material, and the work couldn’t be completed before the start of the semester.
“We were planning to do the oak tree first,” Shan said. “All oaks are diploids, so we knew their genomes would be comparatively easy to assemble.
An organism’s ploidy level refers to how many copies of DNA it has tucked inside its genome. Humans and many other animals are diploid, meaning they have two sets of DNA. When two diploids sexually reproduce, one copy from the mother and one from the father is passed down to the offspring. But some organisms have extra copies of their DNA. Tetraploids have four, hexaploids have six, and so on all the way up to the netted adder’s-tongue fern (Ophioglossum reticulatum), which has 48 copies of its DNA.
Fortunately, the instructors had also sent in pignut hickory leaves for sequencing, and those data were ready to go the first day of class.
“I said great! And we rushed into the analysis so we could get the course underway. Later on, we discovered that it’s a tetraploid, and there was a moment of panic,” Shan said.
With twice as much DNA to assemble than they anticipated, the instructors worried the students wouldn’t have time to complete the project. But rather than viewing the situation as a setback, they used it as a learning opportunity.
“It was kind of a fun surprise,” Shan said. “We got to introduce the topic of polyploidy and how important it is to agriculture and medicine.”
Pignut hickories are native and abundant in eastern North America. They’re graceful trees known for their slow rate of growth and remarkably thick wood. In “A Natural History of Eastern and Central North America,” the botanist Donald Peattie wrote that “…Hickory is stronger than steel, weight for weight, more elastic, less brittle, less heat conductive. It is not possible to imagine another wood which could replace our Hickories if all of them were depleted.”
The task of assembling a genome is as complex and varied as the motivations of the people who undertake it. A quick glance at the roster shows this was true of the students in the Plant Genome Assembly and Annotation course.
“There were students from multiple different majors,” Shan said. “There were biology students who wanted a career related to genetics, but there were also English, chemistry, engineering and computer science majors. No matter what their career path, I think the coolest part of the experience for everyone was getting to learn by doing and working with real-world data to create something novel.”
The class met twice a week and usually began with a short lecture by one of the instructors. After that, students broke up into groups and worked on one of several tasks, with Shan moving between them to help out whenever someone got stuck.
“He would work us through it, step by step, and it never felt like it was a pressure to learn. It felt like it was an opportunity and something that I was really excited to be a part of,” Tucker said.
The first step to assembling a genome is to sort through the raw sequence data, which comes in hundreds of thousands of small segments.
“The basic procedure is just like piecing together a puzzle,” Shan said. The sequences are screened to filter out low-quality data; then the fragments are pieced together by matching up sections of overlapping DNA. This might sound like a simple procedure, but these two steps alone took the entire semester to complete, which is fast compared to how long it would have taken just a few years ago. The first human genome to be sequenced and assembled took hundreds of scientists from several countries and 13 years to complete.
“This field is changing rapidly,” Shan said. “People can spend four or five years as a doctoral student assembling a genome, but now it’s one semester with 11 undergraduate students because of advancements in technology.”
But assembling a genome is really just the beginning. Before it can be published and used by scientists, the assembled genome must be annotated to identify the tens of thousands of genes inside it, predict their functions, and compare them with those of closely related species.
Shan could have wrapped things up on his own, but he invited students who were interested to continue working on the genome over the summer. Tucker was among the five students who had the time to see things through. She’s now a student volunteer in the Soltis Lab, where she’s helping to assemble the original swamp chestnut genome that had originally been selected for the course. She plans on attending graduate school and a possible career in genetic counseling, a medical profession in which doctors use genetic sequences to find the root cause of certain illnesses.
Wherever her path takes her, she’ll have a peer-reviewed publication under her belt, the knowledge she gained from working on it and the satisfaction of a job well done.
The authors published their study in the journal G3 Genes|Genomes|Genetics.
Edgardo Ortiz, Baylee Klein, Arthur Oganisyan, Gia Serrano, Bryanna Stults, Rubina Torkzadeh, Ezra Linnan, Benjamin Pringle, Tyler Radtke, Moumita Hoque Rainy, Lia Swanson, and Gabrielle Vines of the University of Florida, Lauren Whitt of the HudsonAlpha Institute for Biotechnology, and Huiting Zhang of Washington State University are also co-authors of the study.
The study was funded in part by the National Science Foundation (grant nos. IOS-1923234, DEB-2043478, DBI-2320251 and IOS-PGRP CAREER-2239530).
Sources: Shengchen Shan, shan158538@ufl.edu;
Audrey Tucker, audreytucker@ufl.edu
Media contact: Jerald Pinson, jpinson@flmnh.ufl.edu, 352-294-0452