G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation

摘要

Major projects now underway aim to sequence most of the multicellular organisms on earth (e.g., the Earth Biogenome Project). But obtaining this data is only the beginning. To understand these organisms and how they relate to each other, we need to annotate their genomes (i.e., identify the genes and other features). While computers are essential for this process, most annotation tasks still require or benefit from human analyses. Genome browsers allow annotators to quickly visualize and evaluate multiple lines of evidence to create the best gene models. Hence, annotation of large number of eukaryotic species requires efficient generation of genome browsers and recruitment of many volunteers to participate. We have previously developed a web-based platform (G-OnRamp) to reduce the technical barriers for creating genome browsers. Using the G-OnRamp browsers, we engaged 15 faculty and their students in a Course-based Undergraduate Research Experience (CURE) focused on genome annotation of parasitoid wasp species. We find that G-OnRamp browsers work well in the classroom, and these efforts are beneficial for students and researchers. Students gain research experience, learn about genes and genomes, and learn how to work with large datasets. Researchers obtain high-quality datasets that could not be generated in any other way.