The SkateBase web portal supports the North East Bioinformatics Collaborative’s project to sequence the genome of the Little Skate. Provided is a clearinghouse for Little Skate Genome Project and other publicly available Skate and Ray (Batoidea) genome data, and tools for data visualization and analysis.
The little skate (Leucoraja erinacea) is a chondrichthyan (cartilaginous) fish native to the east coast of North America. Elasmobranchs (Skates, Rays, and Sharks) exhibit many fundamental vertebrate characteristics, including a neural crest, jaws and teeth, an adaptive immune system, and a pressurized circulatory system. These characteristics have been exploited to promote understanding about human physiology, immunology, stem cell biology, toxicology, neurobiology and regeneration. The development of standardized experimental protocols in elasmobranchs such as L. erinacea and the spiny dogfish shark (Squalus acanthias)has further positioned these organisms as important biomedical and developmental models. Despite this distinction, the only reported chondrichthyan genome is the low coverage (1.4x) draft genome of the elephant shark (Callorhinchus milii). To close the evolutionary gaps in available elasmobranch genome sequence data, and generate critical genomic resources for future biomedical study, the genome of L. erinacea is being sequenced by the North East Bioinformatics Collaborative (NEBC). As close evolutionary relatives, the little skate sequence will facilitate studies that employ dogfish shark and other elasmobranchs as model organisms.
Little Skate Genomic Contigs Build 2 (FASTA)
2,962,365 contigs; 1,555,444,314 bp (521 MB)
Wang, Q.*, C.N. Arighi*, B.L. King*, S.W. Polson*, J. Vincent*, C. Chen, H. Huang, B. Kingham, S.T. Page, M.F. Rendino, W.K. Thomas, D.W. Udwary, C.H. Wu, and the North East Bioinformatics Collaborative Curation Team. Community annotation and bioinformatics workforce development in concert – Little skate genome annotation workshops and jamborees. Database, 2012. doi:10.1093/database/bar064.
* authors contributed equally. PubMed PMCID:PMC3308154