BeetleBase

BeetleBase provides integrated genomic data and analysis resources for the red flour beetle, Tribolium castaneum, to support genomic, genetic, and functional studies.

Key Features:

• Genomic Sequence Scaffolds: Includes genomic sequence scaffolds mapped to 10 linkage groups based on genome assembly release Tcas_3.0.
• Genetic Linkage Maps: Provides detailed genetic linkage maps for analysis of gene order and recombination.
• Official Gene Set and RefSeq: Contains the official gene set and NCBI Reference Sequences (RefSeq) for Tribolium castaneum.
• Predicted Gene Models: Includes predicted gene models to support gene identification and annotation.
• Expressed Sequence Tags (ESTs): Contains EST data for gene expression profiling across developmental stages.
• Whole-Genome Tiling Array Data: Includes whole-genome tiling array datasets representing several developmental stages.
• Data Storage: Stores genomic data in a PostgreSQL relational database using the Chado schema.
• Visualization Tools: Implements GBrowse for genomic track visualization and CMAP for comparative genetic map visualization.
• Search Integration: Integrates BLAST and BLAT search tools with GMOD modules for sequence querying.
• GMOD Reconstruction: Reconstructed and updated using upgraded Generic Model Organism Database (GMOD) modules.

Scientific Applications:

• Evolutionary Biology: Enables comparative and evolutionary analyses of genome structure and gene content in Tribolium castaneum.
• Developmental Genetics: Supports analysis of gene expression and genomic changes across developmental stages using ESTs and tiling array data.
• Functional Genomics: Facilitates functional annotation and gene model validation using RefSeq, predicted gene models, ESTs, and tiling arrays.
• Comparative Genomics: Supports comparative analyses with other model organisms through mapped scaffolds, RefSeq, and GMOD-compatible data structures.

Methodology:

Database content was updated and reconstructed using upgraded GMOD modules; genomic scaffolds were mapped to 10 linkage groups based on genome assembly Tcas_3.0; data are stored in PostgreSQL using the Chado schema; GBrowse and CMAP are used for genomic and comparative map visualization, and BLAST and BLAT are integrated for sequence search.