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Open Access Highly Accessed Correspondence

Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era

Robert Alan Edwards1, John Matthew Haggerty2, Noriko Cassman2, Julia Christine Busch23, Kristen Aguinaldo2, Sowmya Chinta2, Meredith Houle Vaughn4, Robert Morey1, Timothy T Harkins56, Clotilde Teiling5, Karin Fredrikson57 and Elizabeth Ann Dinsdale1*

Author Affiliations

1 Computer Sciences Department, San Diego State University, 5500 Campanile Dr., San Diego 92182, CA, USA

2 Biology Department, San Diego State University, 5500 Campanile Dr., San Diego 92182, CA, USA

3 Current Address: Scripps Institute of Oceanography, University of California, 9500 Gilman Drive, San Diego 92023, La Jolla, USA

4 School of Teacher Education, San Diego State University, 5500 Campanile Dr., San Diego 92182, CA, USA

5 Roche 454 Lifesciences, 15 Commercial Street, Branford 06405, CT, USA

6 Current Address: Life Technologies, Advanced Application Development, Beverly 01915, MA, USA

7 Current Address: Immun Array 800, East Leigh Street, Suite 15, Richmond 23219, VA, USA

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BMC Genomics 2013, 14:600  doi:10.1186/1471-2164-14-600

Published: 4 September 2013

Abstract

Background

The revolution in DNA sequencing technology continues unabated, and is affecting all aspects of the biological and medical sciences. The training and recruitment of the next generation of researchers who are able to use and exploit the new technology is severely lacking and potentially negatively influencing research and development efforts to advance genome biology. Here we present a cross-disciplinary course that provides undergraduate students with practical experience in running a next generation sequencing instrument through to the analysis and annotation of the generated DNA sequences.

Results

Many labs across world are installing next generation sequencing technology and we show that the undergraduate students produce quality sequence data and were excited to participate in cutting edge research. The students conducted the work flow from DNA extraction, library preparation, running the sequencing instrument, to the extraction and analysis of the data. They sequenced microbes, metagenomes, and a marine mammal, the Californian sea lion, Zalophus californianus. The students met sequencing quality controls, had no detectable contamination in the targeted DNA sequences, provided publication quality data, and became part of an international collaboration to investigate carcinomas in carnivores.

Conclusions

Students learned important skills for their future education and career opportunities, and a perceived increase in students’ ability to conduct independent scientific research was measured. DNA sequencing is rapidly expanding in the life sciences. Teaching undergraduates to use the latest technology to sequence genomic DNA ensures they are ready to meet the challenges of the genomic era and allows them to participate in annotating the tree of life.

Keywords:
Undergraduate education; DNA sequencing; Sea lion; Metagenome