Today’s guest post was contributed by Neil Halterman, assistant professor in the Department of Molecular and Human Genetics at Baylor College of Medicine, who combines team science, genetics and neuroscience to study the mechanisms driving arthritis. Nelle is also passionate about science communication and advocacy: she is a freelance writer, edits a blog for early career scientists (ecrLife) and promotes open, reproducible science. You can follow Nele on LinkedIn.
How do you develop an accessible, equitable genomics class that builds student confidence in working with genomic datasets?
That’s the question botanist Alex Harkis, who studies the mechanisms of plant reproduction and sex determination, asked himself when he opened his research lab at the Hudson Alpha Institute for Biotechnology and began teaching a plant genomics class at Auburn University. By having her students draw real-world data about an organism (like the most famous tree on campus), she taught her class how to assemble genomes and interpret their structural organization. By structuring the class around writing a genome report, students walked away with a real publication that demonstrated their expertise and could help them apply for fellowships or grad school. One of these success stories, the genome assembly of southern live oak, was just published in G3: Genes
Harkis’ inspiration came from a class he developed in 2016 as a postdoc at the Donald Danforth Plant Science Center in St. Louis. At the time, Oxford Nanopore Technologies had just released a portable, affordable sequencing instrument (MINION), making sequencing more accessible to researchers. “It was an exciting time to be doing genomics, and I wanted to see if we could bring a nanopore sequencer into the classroom and do real genomics. [with it]” Herkis explained.
The organism in question? Duckweed, the small free-floating green plant you often see covering lakes. “Duckweed is among the fastest reproducing plants on the planet: it can clonally divide in 12 to 24 hours and is simply indestructible,” explains Harkis. “[They also have] Really small genomes, like 130 Mb for some of them, and they’re small, so you can bring them into classrooms, and people can interact with them. [it],” he adds. Fionn McLaughlin, a fellow postdoc at the University of Washington, liked the idea and suggested adding a proteomics component to the class. The class quickly turned into a true collaboration, with students loading sequencers and mass spectrometers, then analyzing the resulting data and recording each student as a public benefit. Along with the multi-omics experience, they also learned how a manuscript Write and add a publication to your CVs.
“When I asked a [my] The students who led her to become a grad student at her dream school told me she had manuscripts as an undergrad,” Harkis says. At the time, she realized that the doors to grad school can be closed to many students who can’t get research experience outside of their coursework because they have to support themselves financially. [students] Publish manuscripts as undergrad?
To do this, he needed funds to generate multi-omic datasets that students would use during his class. Auburn University, like many others, holds an annual fundraiser to benefit various community projects. The problem? Few people care as deeply about duckweed as Harkiss does, so he had to identify a different creature that could tug at people’s heartstrings and make them open their wallets.
To identify this plant we have to go back to the early 2000s, when two magnificent southern live oak trees (Quercus Virginia) climbed Toomer’s Corner, welcoming students to campus. “Tomer’s trees were iconic: every image or logo of the university [included] These two trees [and] After winning every football game, students would throw toilet paper into the trees,” says Harkis. Unfortunately, in 2009, an angry rival fan poisoned both trees after his team lost to Auburn, a double tree killing that shook the entire community. “It was heartbreaking,” Harkis adds.
Fast forward to 2020: Harkis learns about this story and realizes it would be a perfect candidate for his genomics class. To his surprise, a genetically identical clone of one of Toomer’s oaks was growing in the hands of Leslie Goertzen, who runs Auburn’s Herbarium and Arboretum. “Before the trees died, a handful of Auburn professors took clonal cuttings, but there was no significant effort. [plant] They said, so they disappeared all over Auburn. After finding the fresh biological material needed to generate high-quality multi-omic datasets for the class, the two developed their project together through an annual Auburn fundraiser. “In 24 hours, we [raised] $13,000 from alumni, including football coaches. Everyone put money in because that tree meant something to them,” Harkis recalled.
With everything he needed on hand, Harkis created long and short reading sequences for students to learn genome assembly, as well as HiC reads for them to study its structure. Before long, students began plugging away to collect the chloroplast and nuclear genomes of their beloved tree. The class was a huge success, and the results of the students’ hard work can be read in this month’s issue of G3.
Encouraged, Harkis parlayed his experiences into a career grant application to the National Science Foundation, presenting the American Campus Tree Genomes (ACTG) project, which will provide accessible, engaging and equitable classroom genomics education through the sequencing of one tree each year on college campuses. The project received funding, and before he knew it, Harkis was overwhelmed with requests to participate in the project. “I was getting about 50 [emails] “For a month, with these wonderful romantic stories about university campuses, sometimes not even a tree, but a plant of cultural, emotional, economic importance, like the WA38 “Cosmic Crisp™” apple at Washington State University, or the Emancipation Oak where President Lincoln delivered the first Emancipation Recitation,” says Harclam.
The project took off and became a classic example of open team science. Harkis’s lab generated the data, and his team trained teachers on genomic methods before the start of the semester. Huiting Zhang, faculty at Washington State University, developed a Docker workflow and accompanying Github instructions that walk people through the genome assembly process. Faculty also shared curriculum and built on each other’s work, significantly reducing the burden on incoming faculty. The students’ goal was to work toward a manuscript, and Harkis organized the class around writing a specific type of paper: “The G3 Genome Reports are a great model for a paper: it’s straightforward and has the same structure every time, no matter what species you’re working on,” Harkis explains. It has since partnered with G3 to reduce publication fees for student work, and ACTG-related publications have already served as the journal’s cover image three times. “It’s been very interesting, [especially] For students who have never published a paper, to get cover on their first paper,” he adds.
The success of this program cannot be understated, as hundreds of students have gained confidence and hands-on experience in genomic technologies. The ACTG community is also connected through Slack, and Harkess has found that many alumni have gone on to grad school and continue to apply the knowledge gained in class. Recently, the project even expanded, with Eli Armstrong at the University of California, Berkeley launching the Campus Mascot Genome Project and starting with the campus’s infamous banana slug.
So, what’s next? With enthusiasm and interest growing within the community, and a small but sustained level of funding needed for data production, Harkis is now evaluating the sustainability of this exciting teaching method. If you have an idea or want to create a similar class on your campus, be sure to reach out to this amazing community!
If you have your own genome report to submit, use this link or contact G3 at g3-gsa@thegsajournals.org.
