Students at San Diego State University are getting a unique experience: they are participating in a course with the goal of sequencing the genome of the California sea lion, Zalophus californianus, which is estimated to be almost as large as a human's. The class, which is being taught by Elizabeth Dinsdale, will give the students a chance to use Roche's Genome Sequencer FLX System and to do work that would normally be sent out for sequencing. "Students go from DNA extraction all the way through to preparing the libraries, amplifying the DNA, to actually running the machine. They see the whole process through," Dinsdale says. "This hasn't happened anywhere else. Undergrads aren't being taught the next generation of technology."
In the first four weeks of the class, the students generated more than 3 million DNA sequences from the sea lion, as well as from its kelp forest environment. Dinsdale says the students will sequence from "top to bottom," including sequencing microbial genomes they've found in the kelp, and conduct a metagenomic study of the surrounding seawater. "It's quite exciting for the students," she adds. "It's new, novel, and they're really contributing to a research project."
At the end of the spring semester, the students were in the process of annotating the genomes they've sequenced. They've got a good start, Dinsdale says, but they won't have time to annotate all the genomes before the end of the semester. Next year, though, the students will do a comparative genomic analysis of all their data, and then Dinsdale's collaborator Rob Edwards will teach a class in which the students will perform bio-enzymatic analyses on their data.
Dinsdale plans to offer the class again next year. "We won't have gotten anywhere close to doing all the bacterial genomes in that environment," she says. "Next year, we'll just select another set and continue the work."
The students, she adds, are not only getting a taste of the technical side of the project, but they're also helping to annotate the Tree of Life. "It makes the learning so much easier when they've gone through the process. They understand how the technology works and how to annotate," Dinsdale says. "They're gaining skills in hands-on genetics, and learning how genomics infiltrates every area of ecology, microbiology, and health. It's getting them ready to start their own research."