The sequencing of the human genome in 2001 marked the beginning of the genomic era [1, 2] and since then sequencing technology has undergone major improvements and cost reductions [3, 4]. The “next generation of sequencers” enables the sequencing of an ever increasing range of genomes quickly, cheaply and with a high degree of accuracy. Bold sequencing projects, such as the 1,000 bacteria genomes, and the 10,000 vertebrate genomes are revolutionizing life science research and medicine. In medicine, the community is preparing for personal, whole human genomes to become a part of routine care, while a trend to sequence gene panels in human increase until this happens. Even the effects of the human microbial community on human health have been described by DNA sequencing [5–7]. In the environmental sciences, microbes have been identified that are associated with different ecological processes, and the functional profile of microbial communities can be compared across environments [8, 9]. In the pharmaceutical industry, sequencing is used in all aspects research and development. Graduates competent in next generation sequencing technologies are needed to support each of these research endeavors, as highlighted in the National Research Council discussion of metagenomics, Clinical Pathologists call to action, and Nature’s discussion on the requisites in genome-jobs [10–12].
While the potential application for genomics is extensive, accelerating our scientific discoveries and simultaneously revolutionizing human lives, the training of the next generation of researchers is lagging . Genomic courses at undergraduate level have been taught at a small number of institutions, however the opportunity for students to gain hands on experience of preparing samples and operating the sequencers is rare. A key aspect in a young scientists’ development is to learn good experimental design practices, which is best achieved by providing experiences across the entire project work flow. In many courses, DNA sequences are obtained from projects available on the web  or third party resources, and the students annotate new genes, but do not do any of the sequencing process. Other courses enable the students to extract the DNA, which is sent to a genome center for technicians to sequence [15, 16], and the students annotate the new genomes. While annotation has been shown to engage students in analytical thinking, and can allow significant numbers of students to participate in the scientific process [14, 17, 18] there could be pedagogical and practical value in providing students with opportunities to participate in the whole process, including the sequencing per se. Here we test a new way to engage students, having them work directly with next-generation instrumentation to conduct the DNA sequencing process from the beginning, then annotating the novel genome they sequenced. We invite the scientific community to consider what might be accomplished by the distributed community of undergraduate scientists using this approach.
The most effective way to teach science is to participate in the scientific process . Molecular biology has proven adaptable to educational settings. Cloning projects have allowed students to become technically proficient and learn other important skills of science, such as critical thinking, troubleshooting and adapting protocols to become independent researchers . The development of the “phage hunter” course, where student isolate new phages, obtain sequence data, explore the genomic data, and get to name their phage has been highly successful in training students in scientific discovery and providing new data to science [19, 21]. We have built on this excitement of discovery and developed a course that allows undergraduate students to extract, sequence, and analyze novel genomes to become part of sequencing and annotating the tree of life.
The first series of courses in ecological genomics was taught in 2010 at San Diego State University. In the Ecological Metagenomics course, 21 students sequenced novel DNA from microbes, metagenomes and marine mammals. The students were provided with interdisciplinary training in genomics, experience in research, and generated data that is being used by an international consortium to investigate the genomic signature of cancers in the California sea lions. As a template for others to generate next generation DNA sequencing courses, here we describe the ecological metagenomics course, results of student affective surveys, learning outcomes, data quality, and initial findings of the first marine mammal genome sequenced and annotated by undergraduate students.