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Title: BeetleBase in 2010: Revisions to Provide Comprehensive Genomic Information for Tribolium castaneum

Author
item KIM, HEE SHIN - Kansas State University
item MURPHY, TERENCE - Kansas State University
item XIA, JING - Kansas State University
item CARAGEA, DOINA - Kansas State University
item PARK, YOONSEONG - Kansas State University
item Beeman, Richard
item Lorenzen, Marce
item MANAK, J.ROBERT - University Of Iowa
item BUTCHER, STEPHEN - University Of Iowa
item BROWN, SUSAN - Kansas State University

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/14/2009
Publication Date: 10/9/2009
Citation: Kim, H., Murphy, T., Xia, J., Caragea, D., Park, Y., Beeman, R.W., Lorenzen, M.D., Manak, J., Butcher, S., Brown, S.J. 2010. BeetleBase in 2010: Revisions to Provide Comprehensive Genomic Information for Tribolium castaneum. Nucleic Acids Research. 38: D437-D442.

Interpretive Summary: The red flour beetle genome sequence has created the most comprehensive body of genomic information available for any agricultural pest species, but access to the data can be cumbersome and difficult. We have created “BeetleBase”, a user-friendly website for easy access and recovery of all types of genetic and genomic information about this pest insect for use by scientists, researchers, and others. The current version of BeetleBase is of greatest use to genetics and biology researchers, but future versions will include general literature on flour beetles and related insects that will be of interest to pest control specialists, educators, and the general public.

Technical Abstract: BeetleBase (http://www.beetlebase.org) has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum. The database contains genomic sequence scaffolds mapped to 10 linkage groups (genome assembly release Tcas_3.0), genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The database was reconstructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL-based Chado data model and visualized on tracks in GBrowse. The updated genetic map is visualized in CMAP. We have also enhanced usability by integrating these tools with BLAST and BLAT database search capabilities. BeetleBase serves as a long-term repository for Tribolium genomic data, and is compatible with other model organism databases.