Introducing Undergraduate Students to Gene and Genome Structure through Gene Annotation

This session will describe how undergraduate genetics students can build a solid set of foundational bioinformatics skills and experience first hand the concepts of gene and genome structure as they identify and annotate genes within small regions of plant and animal genomes.  During multi-week investigative laboratory experiences, students use the iPlant Collaborative’s DNA Subway Red Line to build their own genome browser views of up to a 150,000 bp region of the genome under investigation. They then use the genome annotation tool Apollo to refine their gene models.  Furthermore, by importing available bioinformatics and experimental data students can produce evidence-based gene models.  Additional bioinformatics tools beyond the DNA Subway suite, such as InterProScan and Integrative Genomics Viewer, are used to support the gene annotation effort.  The investigative laboratory experience can be designed such that each student’s annotation region overlaps two other students’ sequences.  Thus, students can ultimately produce and discuss a combined lab “contig” annotation that can subsequently be combined with the efforts of other lab sections of the same course.  This larger scale view helps students’ focus shift from the details of individual gene structure to a genome organizational point of view.  A description of types of investigative projects that could potentially be scaled up for use in large multi-laboratory sectioned courses will be presented.