TVIR

TVIR provides a curated genomic and transcriptomic database covering 59 vegetable species to support comparative genomics, gene function analysis, and molecular breeding research.

Key Features:

• Extensive Gene Repositories: Contains functional gene counts including 5,215 auxin-related genes, 2,437 anthocyanin genes, 15,002 flowering genes, 79,830 resistance genes, and 2,639 glucosinolate genes.
• N6-Methyladenosine (m6A) Genes: Identifies 2,597 m6A-related genes categorized as 513 writers, 1,058 erasers, and 1,026 readers.
• CRISPR and miRNA Data: Provides 2,101,501 CRISPR guide sequences and 17,377 microRNAs for genetic engineering and functional genomics analyses.
• Gene Synteny and Orthology: Includes information on gene synteny, duplication, and orthologs across the included vegetable species.
• Comprehensive Annotations: Contains 2,346,850 gene annotations sourced from Swiss-Prot, TrEMBL, Gene Ontology (GO), Pfam, and Non-redundant (Nr) databases.
• Bioinformatics Tools: Integrates synteny analysis, primer design, BLAST searches, and JBrowse genome visualization.
• Transcriptome Data: Compiles transcriptome datasets from 98 vegetables annotated with species, tissue type, and growth stage.

Scientific Applications:

• Comparative Genomics: Enables cross-species comparisons using synteny, orthology, and duplication data.
• Functional Genomics: Supports gene function inference using m6A classifications, miRNAs, annotations, and transcriptome profiles.
• Genome Editing and Molecular Breeding: Facilitates design and evaluation of CRISPR guides and primers for editing and breeding experiments.
• Gene Expression Studies: Supports analysis of expression patterns across species, tissues, and growth stages using compiled transcriptome data.

Methodology:

Includes synteny analysis, primer design, BLAST searches, and JBrowse genome visualization.