The Bovine Genome Database (BGD)

The Bovine Genome Database (BGD) provides integrated bovine genomics resources for genome annotation, data integration, and comparative analyses across bovine and other ruminant assemblies.

Key Features:

• Genome Browsing: JBrowse and GBrowse support scaffold and chromosome coordinate systems and display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphisms, markers, quantitative trait loci (QTL), and alignments to complementary DNAs, ESTs, and protein homologs across assemblies including ARS-UCD1.2 and UMD3.1.1.
• Genome Annotation: The Apollo Annotation Editor connected to a Chado database enables editing and creation of gene models and includes the Locus-Specific Alternate Assembly (LSAA) plug-in to annotate potential assembly errors and structural variants.
• Data Integration and Mining: BovineMine provides integrated data retrieval and supports genomes and gene annotation datasets from non-bovine ruminants (goat and sheep), multi-assembly queries per organism, additional ontologies, and template queries.
• Sequence Database Searching: BLAST databases are provided to perform sequence searches for identification of homologous sequences across genomic datasets.
• Quantitative Trait Loci (QTL) Viewer: A QTL viewer integrated with the BGD Chromosome GBrowse enables localization of candidate genes associated with specific QTLs.
• Gene Pages: Each OGS gene model has a dedicated page containing gene structure, transcript variants, functional descriptions, gene symbols, Gene Ontology terms, annotator comments, and links to NCBI, Ensembl, and wiki pages.

Scientific Applications:

• Genome annotation and curation: Editing and creation of gene models using Apollo and Chado for improved OGS and annotation consistency.
• QTL and trait dissection: Integration of QTL viewer and genome annotations to identify candidate genes underlying quantitative traits.
• Comparative genomics across ruminants: Cross-assembly navigation and inclusion of goat and sheep genomes support comparative analyses and multi-assembly queries per organism.
• Functional annotation and homology inference: Use of RefSeq, Ensembl models, cDNA/EST and protein alignments, BLAST searches, and Gene Ontology terms to infer gene function and transcript variants.

Methodology:

Computational components explicitly include JBrowse and GBrowse for genome browsing; Apollo Annotation Editor connected to a Chado database with the LSAA plug-in for annotation; BovineMine for data mining; BLAST databases for sequence searches; and a QTL viewer integrated with Chromosome GBrowse.