Today’s guest post was contributed by Nele Haelterman, assistant professor at Baylor College of Medicine’s Molecular and Human Genetics department, who combines team science, genetics, and neuroscience to study the mechanisms that drive joint pain. Nele 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 (reproducibility 4 everyone). You can follow Nele on LinkedIn.

How do you develop an accessible, equitable genomics class that builds students’ confidence in working with genomic datasets?

That is the question Alex Harkess—a botanist who studies the mechanisms of plant reproduction and sex determination—asked himself when he opened his research lab at HudsonAlpha Institute for Biotechnology and started to teach a plant genomics class at Auburn University. By pulling in real-world data about an organism his students care about (like the most iconic tree on campus), he taught his class how to assemble genomes and interpret their structural organization. By structuring the class around writing a genome report, students walked away with an actual publication that showed their expertise and could help them apply for fellowships or grad school. One of these success stories, the genome assembly of the Southern live oak, was just published in G3: Genes|Genomes|Genetics, and Harkess’ class gained such popularity that it spread to campuses around the U.S., untangling the genomes of nearly 15 organisms so far.

Harkess’ 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 (the minION), making sequencing more accessible to researchers. “It was an exciting time to do genomics, and I wanted to see if we could bring a nanopore sequencer into the classroom and do actual genomics [with it],” Harkess explains. 

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 as little as 12 to 24 hours and is just invincible,” explains Harkess. “[They also have] really tiny genomes, like 130 Mb for some of them, and they are small, so you can bring them into classrooms, and people can interact with [it],” he adds. Fionn McLaughlin, a fellow Washington University postdoc, loved this idea and proposed adding a proteomics component to the class. The class quickly turned into a true collaboration, with the students loading sequencers and mass spectrometers, then analyzing the resulting data and recording them in a publication that included each student as a co-author. Students didn’t just gain hands-on multi-omics experience, they also learned how to write a manuscript and got to add a publication to their CVs.

“When I asked one of [my] students what led her to become a grad student at her dream school, she told me she had manuscripts as an undergrad,” Harkess says. At that moment, he realized that the gateways to grad school may be closed for the many students who can’t gain research experience outside of their coursework because they have to financially support themselves. Harkess wondered, “ Could genomics reduce these inequities and help [students] publish manuscripts as undergrads?” 

To make this work, he needed funding to generate the multi-omic datasets that students would use during his class. Auburn University, like many others, has an annual fundraiser to benefit various community projects. The problem? Few people care as deeply about duckweed as Harkess does, so he had to identify a different organism that could tug at people’s heartstrings and would get them to open up their wallets. 

To identify this plant, we have to travel back in time to the early 2000s, when two majestic Southern live oak trees (Quercus virginiana) towered over Toomer’s Corner, welcoming students to the campus. “The Toomer’s trees were iconic: every university photo or logo [included] these two trees, [and] after every football game win, students would throw toilet paper in the trees,” Harkess explains. Unfortunately, a disgruntled fan from a rival team poisoned both trees in 2009 after his team lost to Auburn, in a double tree murder that shook the entire community. “It was heartbreaking,” Harkess adds. 

Fast forward to 2020: Harkess learned about this story and realizes this would be the perfect candidate for his genomics class. To his surprise, a genetically identical clone of one of the 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 wasn’t a focused effort to [plant] them somewhere, so they kind of disappeared throughout Auburn.” Having found the fresh biological material he needed to generate high-quality multi-omic datasets for the class, the two teamed up and pitched their project through the annual Auburn fundraiser. “In 24 hours, we [raised] $13,000 from alumni, including football coaches. Everyone put in money because that tree meant something to them,” Harkess remembers.

Having everything he needed in hand, Harkess generated long– and short–read sequences for students to learn genome assembly as well as HiC reads for them to study its structure. In no time, students started plugging away at assembling 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.  

Emboldened, Harkess wrapped his experiences into a CAREER grant application to the National Science Foundation, pitching the American Campus Tree Genomes (ACTG) project, which would offer accessible, engaging, and equitable classroom genomics education by sequencing one tree per year at a college campus. The project received funding, and before he knew it, Harkess was overwhelmed with requests to participate in the project. “I was getting about 50 [emails] a month from all over, with these amazing romantic stories about university campuses that have, not even a tree sometimes, but a plant that has cultural, emotional, economic significance, like the WA38 “Cosmic Crisp™” apple at Washington State University, or the Emancipation Oak where President Lincoln gave the first reciting of the emancipation proclamation in the South,” Harkess says. 

The project took off and became a prime example of open team science. Harkess’ lab generated the data, and his team trained teachers on genomic methods ahead of the semester’s start. Huiting Zhang, faculty at Washington State University, built Docker workflows and accompanying Github instructions that walk people through the genome assembly process. Faculty also shared the curriculum and built on each other’s work, significantly reducing the burden for incoming new faculty. The goal for the students was to work towards a manuscript, and Harkess structured the class around writing a specific type of paper: “G3 Genome Reports are an excellent model for a paper: it’s straightforward and has the same structure every time, no matter what species you’re working on,” Harkess explains. He then partnered with G3 to reduce publication fees for the students’ work, and ACTG-related publications have already served as the journal’s cover image three times. “It has been so exciting, [especially] for students who’ve never published a paper, to get the 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 experiences in genomic technologies. The ACTG community also remains connected through Slack, and Harkess has learned that several former students have entered grad school and continue to apply the knowledge they gained in class. Recently, the project even expanded, with Ellie Armstrong at the University of California, Berkeley initiating the campus mascot genome project and starting things off with the campus’s infamous banana slug. 

So, what’s next? Enthusiasm and interest within the community continue to grow, and as a small but continuous level of funding is needed for data generation, Harkess is now evaluating the sustainability of this engaging teaching method. If you have any ideas or would like to build out a similar class on your campus, make sure to get in touch with this amazing community!  

If you have your own Genome Report to submit, use this link or contact G3 at g3-gsa@thegsajournals.org. 

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