Creating a Microbial Genome Analysis Project using Publically Available Genome Sequences and Online Bioinformatics Programs

 

Tested Studies in Laboratory Teaching, 2016, Volume 37

Lori R. Scott, Todd C. Nickle, Stephen Koury, Brad Goodner, Katherine Houmeil, Ben McFarland, Jennifer Tenlen, Andrew Lumpe, Kimberly Murphy, D. Rhoads, D. Wood, & Daihong Chen

Abstract

The Department of Energy's Joint Genome Institute (DOE JGI) has sequenced the genomes of more than 200 microbes from across the Tree of Life as part of the Genome Encyclopedia of Bacteria and Archaea (GEBA) project. The original GEBA project was completed in collaboration with the Leibniz-Institut DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH). In the pilot study, the DOE JGI sequenced 53 bacterial and three archaeal novel and highly diverse genomes, representing a first step towards a phylogenetically balanced set of sequenced genomes across the microbial tree of life (Wu et al., 2009). An additional approximately 200 GEBA genomes have since been sequenced (DOE JGI, 2015). Most of these organisms are poorly represented in the scientific literature, thereby creating the opportunity for undergraduate and high school students to make significant contributions to our understanding of microbial genome structure and function. Students make these contributions by: 1) manually annotating open reading frames (ORFs) predicted by automated bioinformatics programs for the purpose of expanding the original annotation and identifying errors; and/or 2) performing functional genomics studies to confirm the computer-based function predictions.

Keywords:  bioinformatics, genomics, web-based

Boston University (2015)