Learning from the trees

Igniting a passion for science and learning

During the semester-long virtual course, Auburn students sequenced, assembled, and analyzed the genome of the Toomer’s Oak tree. Leaf tissue collected from one of the oak clones was sent to HudsonAlpha for sequencing in the HudsonAlpha Genome Sequencing Center. The raw data was returned to Auburn, where the students worked throughout the semester assembling and analyzing the sequencing data. 

The virtual nature of the class allowed students to work in real-time on their projects, getting help from each other and the instructors. A major issue with teaching bioinformatics is the availability of computational resources, such as supercomputing clusters. To solve this, the class used a teaching platform where every student had access to an Amazon AWS compute node, and all students could share data and analyses with each other. A key component of the class was that the end result was a publishable manuscript describing the genome assembly. 

Each week, one student was selected to push the manuscript on Google Docs forward by at least 300 words, and all other students helped edit and revise the text. The final project for the class was polished figures of a major analysis for the manuscript.  

“Nothing in this class is mindlessly push-button; it requires that students work both independently and as a group to grow as bioinformaticians, writers, plant biologists, and genome scientists," says Harkess. "In this sense, we hope that a single tree can act as a gateway for these students to use genomics to change the world.”

The benefits of ACTG extend beyond the traditional classroom setting, offering students a unique opportunity to develop advanced computational skills. These skills, previously reserved for specialized roles or postgraduate studies, are now being cultivated earlier, ensuring that the next generation of scientists can confidently navigate the complexities of modern data-driven disciplines. 

The first semester of the course was a success. All students contributed to the Quercus virginiana southern live oak genome manuscript, despite 70 percent having never written a manuscript, performed command line bioinformatics, or engaged in plant genomics molecular work. For several students, including Jill Abendroth, now a PhD student at the University of Wisconsin, the class helped drive them toward their graduate school journey.

“I don't think I can overstate how much the course helped shape the direction I'm going and helped instill a passion for something that was previously so intimidating to me,” says Jill, who is pursuing a PhD in plant breeding and plant genetics and plans to incorporate bioinformatics into her thesis project.

Auburn is not alone in having a beloved campus tree, and college campuses are not the only places where people make connections with trees. Everyone probably has a memory or a story about a tree that means something to them. A sturdy oak tree that served as a childhood jungle gym. Beautiful ginkgo trees that provided shade on your walk to college classes. Drs. Goertzen and Harkess turned iconic and historically impactful trees into the perfect subject to engage and excite students to learn bioinformatics and genomics. 

“Even though I'm not from Alabama and don't have the Auburn pride that goes with Toomer's Oaks, I think it's a compelling story," said Jill. "By the end of the semester, I was all in on the Toomer’s Oak, and I wanted to save this tree. I liked the history and drama of the story.”

What began as a single-semester course at Auburn University is expanding across the United States. Drs. Harkess and Goertzen built a framework so that other institutions can easily replicate the experience, from the crowdsource funding to the educational products to the actual science.

After the raw DNA sequencing data is returned from HudsonAlpha, Dr. Hancock’s students will begin analyzing and assembling the sequence data into chromosomes. Their class plans to compare their findings to the coconut, date palm, and oil palm genomes to identify unique traits of the Sabal palmetto species. By comparing the species, they can study how they grow and adapt to different environments.

The virtual nature of the course allows Dr. Hancock in South Carolina to provide the same standard of bioinformatics education the students at Auburn originally received. This model is also perfect for expanding the course outside the confines of a traditional four-year college or graduate school setting. 

“The program minimizes institutional barriers using the PRAXIS-AI teaching platform, which is entirely internet browser-based,” says Harkess. “It also allows teaching and learning to occur in non-traditional settings. If students can access the internet, they can do the coursework. We want students worldwide to be authentically trained in plant genomics, with access to the latest technologies, to broaden their scientific networks and career prospects.”

With the support of a recent $1,600,000 National Science Foundation CAREER grant, as well as partnerships with sequencing company Pacific Biosciences and with the journal G3: Genes, Genomes, Genetics, Harkess hopes to expand the program to reach 100 students per year, emphasizing the inclusion of HBCUs and community college students. 

ACTG is giving back to the scientific community in more ways than one. It creates a unique pipeline to train students and actively engage them in important bioinformatic work. As more schools join the program, more students will gain access to meaningful training while more high-quality genomes are being produced and released into the public domain. 

Just as Dr. Hancock’s class is comparing the Sabal palm to other palm species, the different tree and plant species sequenced through ACTG will give back to the science community by offering plant geneticists more species from which to draw meaningful conclusions about important features like drought tolerance, climate adaptation, and nutrient uptake.