Community Annotation and Bioinformatics Workforce Development in Concert -- Little Skate Genome Annotation

In this workshop you will learn:

• The scope and structure of the skate genome project

• Why skates are useful as model organisms

• How you can adopt the resource to teach gene and protein annotation

Skates are chondrichthyan fishes, a group comprised of elasmobranchs and holocephalans. Sharks and rays compose modern elasmobranchs and include the little skate, Leucoraja erinacea. Chondrichthyan fishes are important model organisms for comparative genomics because of their basal position in vertebrate evolutionary history and fundamental gnathostome characteristics including jaws, an adaptive immune system, neural crest, and a pressurized circulatory system. The little skate is one of eleven strategically selected non-mammalian organisms determined by a National Human Genome Research Institute (NHGRI) panel to have the greatest potential to fill crucial gaps in human biomedical knowledge. The Northeast Bioinformatics Collaborative (NEBC) built upon the Northeast Cyberinfrastructure Consortium (NECC; http://www.necyberconsortium.org), began a de novo sequencing project in 2010 with the goal of building cyberinfrastucture in the northeast corridor and developing a critical mass of informatic-savvy life scientists. Three workshops and an annotation jamboree were held to provide training in genome sequencing, annotation, and analysis. Additionally a model organism website, SkateBase (http://skatebase.org), was established as a nexus for project data and educational and curation activities. High throughput next generation sequencing data from both the transcriptome and genome are used in parallel to teach gene and protein annotation in bioinformatics classes at University of Delaware (2012 & 2013) and Georgetown University (2013). Annotated genes are reviewed by curators and subsequently displayed at SkateBase in conjunction with GO ontology terms, protein domain structure, orthology resources, and PubMed literature results. The translation of a classroom exercise into information suitable for distribution through the website represents a metric to measure the broader impact of the project and its mission to create a cyber-knowledgeable life science workforce. We are applying the physical and virtual infrastructure and lessons learned from these activities to refine genome annotation workflow. Future plans include an expansion of scope by including GenBank submission procedure in classroom lectures and student projects. We invite other institutions to leverage the educational resources at SkateBase in their curriculum as we look toward our continuing efforts for larger-scale functional and structural community annotation of the little skate genome.