An international collaboration published in the esteemed journal Nature features work by Shauna Vronces from her undergraduate research project in the Provart lab. Vronces took on this challenging BCB430 research project to develop a browser-based data visualizer for the Oat Pangenome.
Oats are considered particularly healthy. They provide fibre, lower cholesterol levels and are gluten-free. However, the genetic makeup of oats has been difficult to understand until now, mainly because it is particularly large and complex.
Professor Nicholas Provart‘s lab at the CSB addresses data complexity by developing user-friendly tools to visualize gene expression in different parts of the plant, from seed to stalk, and over time as the plant grows. Provart has developed the “eFP Browser”, a computational architecture for displaying colour-coded gene expression levels.
Compiling the oat pangenome meant refining data on 80,000 variable genes from 23 different strains of wild and domesticated oats over 504 different data points in time and space per gene. Each gene is present in 3 copies, as the oat genome is hexaploid.
The huge amount of data in the oat genome required Vronces to develop skills in SQL, database management, XML configuration, and even image editing. Vronces notes that “It was nice to learn computational skills that I hadn’t previously learned in any of my classes. Research projects are very different from when you are doing an assignment for a class.
“The main challenge I faced in adapting the pre-existing architecture for the eFP Browser was creating the XML file for the developmental map. It was actually really fun, and great experience, to figure out how to automate the process and all the troubleshooting that went along with it.”
Ending her fourth year with a computational biology project fit precisely with Vronces’ interests. She had been excited by her courses as a life sciences undergraduate but missed working with computers. Vronces realized she could combine her two interests when a fellow student told her about the Bioinformatics and Computational Biology specialization in the CSB department.
Vronces completed her project, graduating in 2023, and the international research team behind the Oat Pangenome has collated their complex results for publication as “A pangenome and pantranscriptome of hexaploid oat” in one of the world’s top scientific journals, Nature.
Vronces now has her name included in a high-profile research paper. “When I found out I was listed as a co-author, I was shocked, honestly – I didn’t think I would be mentioned at all. The first people I told were all family; everyone was really happy, proud and excited.
“The guidance and support in the CSB from Professor Provart, Vincent Lau, Asher Pasha, and from our collaborators played a massive role in helping me grow technically and gain confidence in my programming and research capabilities.”
Vronces is now studying for her Master of Science in Data Science and Analytics at TMU. “I am having a wonderful time! I hope to continue to play around with data visualization and develop creative solutions for researchers and non-researchers alike so they can engage with and understand data.”
Congratulations on this impactful paper, Shauna Vronces!