To immerse undergraduate students in the genomic era, San Diego State University undertook a project to sequence the California Sea lion. The project has two major components and associated courses; a “hands on” sequencing courses and a bioinformatic course. The sequencing course teaches students to prepare DNA and sequence it on a Roche 454 Lifesciences flx machine. The students conduct the entire process from DNA extraction to loading the plate and running the machine. At the end of 13 weeks the students had sequenced 24 billion base pairs of sea lion genome. The students chose several contigs to investigate as part of their assessment. The Sea lion genome was assembled on Newbler, and 1.3 million contigs with an average length of 1,434 Bp were generated. The assembled DNA totals 1,951,532,210 bp with 13,352,265 bp in contigs > 10kb, and 972,007 bp in contigs > 15 kb. The N50 sizes are 2,127 bp for all contigs, 11,249 for the 10 kb contigs, and 16,472 for the 15 kb contigs
The assembled genome was turned over to the bioinformatic undergraduate class at San Diego State University and National Autonomous University of Mexico to start the annotation process. These students enjoyed the challenge of tackling this large dataset and describing the wealth of information that it contained. The bioinformatic students conducted a number of analyses including identifying the repeat regions, phylogenetic analysis, and gene identification using Artimis, Genescan, Genemark, Glimmer and gene annotation using Artemis and Blast2Go.
Both classes have been a huge success with students providing very positive feedback and learning a large sweep of new techniques. Many biology students were influenced to take the bioinformatics course, something they were unlikely to do prior to taking the sequencing course. Several of the students have been employed because of the experience that they gained in the course.
Photo credit: Elizabeth Dinsdale. Copyright Elizabeth Dinsdale, 2010