Using Nanopore Sequencing to Assemble and Compare Chloroplast Genomes: Introducing Genomics and Bioinformatics Into the Classroom

As rapidly emerging fields with broadening impacts on our everyday lives, recent calls have emphasized the need to incorporate bioinformatics and genomics within college science for training and scientific literacy purposes. Here, we describe a novel short-term bioinformatics and genomics module designed for adaptable implementation in early genetics courses to provide students a window as to how techniques and practices in these fields can be used to explore a scientific question from origination through analysis. Utilizing portable nanopore sequencing and a bioinformatics pipeline in a collaborative, free access web-based notebook, students gain experience with the sequencing, assembly, and comparison of chloroplast genomes from divergent genetic lineages of an herbaceous plant that exhibits cytonuclear genetic incompatibility. This approach increases the accessibility of genomics and bioinformatics to introductory genetics students by exposing them to the generation and analysis of next generation sequencing data on individual student machines using web-based tools that offset common computing limitations such as processing power and software compatibility. The module also adds to students’ general understanding of evolution by exploring the concepts of reproductive isolation, genetic causes of speciation, and the structure and function of organelle genomes. The module contains two components, the generation of sequence data and bioinformatics analysis, such that instructors without access to a sequencer can implement the bioinformatics analysis as a stand-alone unit. Student-reported data highlight the positive contributions of module participation to cognitive (knowledge, skills) and noncognitive (e.g., self-efficacy) gains related to next generation sequencing/bioinformatics as well as future academic and career interests. Primary Image: Using Nanopore sequencing to assemble and compare chloroplast genomes. Top left: Oxford Nanopore’s MK1D sequencer. Top right: examples of Campanula americana seedlings exhibiting cytonuclear genetic incompatibility. Bottom left: a C. americana individual exhibiting no genetic incompatibility. Bottom right: a C. americana chloroplast genome annotated by GeSeq.