Using Tobamoviruses for Phylogenetic Instruction in Undergraduate Biology Courses

Abstract

Microbial diversity and taxonomy instruction provide an ideal opportunity to introduce students to basic bioinformatics skills. There are many ways to illustrate evolutionary relationships between microorganisms using phylogenetic trees. Thought must be given to the method of presentation used in class because interpreting complex trees can be quite challenging for students. Here we present a simple activity that teaches the fundamental bioinformatics skills of multiple sequence alignments and phylogenetics by using Tropical soda apple mosaic virus and other tobamoviruses that produce trees that are easy to interpret. Tobamoviruses are important agricultural pathogens and have well defined phylogenetic groupings that correspond to the phylogenetic groupings of host plant families. This clear pattern illustrates the coevolution of the virus and host, and makes interpreting relationships based on these trees very straightforward. The organization of the trees also indicates related plants that a given virus may potentially infect, making this type of analysis useful for developing measures to limit spread and minimize economic impacts. The simplicity of the analysis, coupled with the real-world application in agricultural science, helps actively engage students in a topic that is challenging to learn. This activity is broadly adaptable, and can be introduced as a learning module in courses covering topics in microbiology, molecular biology, genetics and evolution. Completion of this activity provides students with key foundational skills for phylogenetic analysis and the confidence to utilize bioinformatics software.

Virology in the Classroom: Current Approaches and Challenges to Undergraduate- and Graduate-Level Virology Education

“…One example is a phylogenetics exercise from an introductory bioinformatics course. Fillmer et al (12) used MEGA7, ClustalW, and amino acid sequences from the replicase of 28 tobamoviruses to teach students sequence alignment and phylogenetics. This was done to help students understand evolution and the role of phylogenetic relationships therein.…”