TBGR

TBGR integrates genomic assemblies, gene annotations, and comparative analyses to support comparative and functional genomics within the Brassicaceae family.

Key Features:

• Genome coverage: Contains 82 genome assemblies from 27 Brassicaceae species.
• Glucosinolate genes: Houses 4,096 annotated glucosinolate-related genes.
• Auxin-related genes: Houses 6,625 annotated auxin-related genes.
• Flowering genes: Houses 13,805 annotated flowering-related genes.
• Resistance genes: Houses 36,632 annotated resistance genes.
• Anthocyanin genes: Houses 1,939 annotated anthocyanin genes.
• m6A modification genes: Houses 1,231 annotated m6A modification genes.
• CRISPR guide sequences: Identifies and catalogs 1,174,049 CRISPR guide sequences.
• Transposable elements: Identifies and catalogs 5,856,479 transposable elements.
• Comparative genomics tools: Provides BLAST for sequence alignment, synteny analysis for conserved blocks, Primer Design for PCR, Seq_fetch for sequence retrieval, and JBrowse for genome visualization.
• Synteny, duplication, and orthologs: Reports conserved gene order (synteny), duplication events, and orthologous relationships among the 27 species.
• Gene annotation sources: Annotations are derived from TrEMBL, Swiss-Prot, Nr, GO, and Pfam.

Scientific Applications:

• Comparative genomics: Comparative analyses of synteny, orthology, and gene family expansions across Brassicaceae species.
• Functional genomics: Investigation of gene families involved in glucosinolate biosynthesis, auxin signaling, flowering, resistance, anthocyanin production, and m6A modification.
• Evolutionary biology: Study of duplication events, transposable element dynamics, and evolutionary relationships within the Brassicaceae.
• Plant breeding and trait analysis: Identification of candidate genes and genomic regions relevant to breeding and trait improvement within Brassicaceae.

Methodology:

Uses BLAST, synteny analysis, Primer Design, Seq_fetch, and JBrowse; annotations mapped from TrEMBL, Swiss-Prot, Nr, GO, and Pfam; identifies/catalogs CRISPR guide sequences (1,174,049) and transposable elements (5,856,479); computes synteny, duplication events, and orthologous relationships across 27 species.