Tested Studies for Laboratory Teaching (ABLE Proceedings)

Title:

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

Url:

http://www.ableweb.org/volumes/vol-37/v37reprint.php?ch=21

Author:

Brad Goodner
Stephen Koury
Katherine Houmiel
Ben McFarland
Jennifer Tenlen
Andrew Lumpe
Lori Scott
Daihong Chen
Todd Nickle
Kimberly Murphy
D. Wood
D. Rhoads

Author's Address:

Mount Royal University
Augustana College, Biology Department, Rock Island, IL
University at Buffalo, Buffalo NY
Seattle Pacific University, Department of Biology, Seattle, WA
Hiram College, Department of Biology, OH
California State University, Department of Biology, San Bernardino, CA

Email Address:

loriscott@augustana.edu

Description: 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:

web-based
bioinformatics
genomics

Topic:

Microbiology
Bioinformatics

BEN Subject/Discipline Taxonomy:

Microbiology
Bioinformatics

Learning Resource Type:

Laboratory exercise (DCMI Type Vocabulary)

Context:

Undergraduate upper division 15-16

Format:

pdf