Coffee Genome Hub

Coffee Genome Hub provides centralized access to genomic, genetic, and breeding data for Coffea canephora (Robusta) to support genomic, comparative, and breeding research.

Key Features:

• Comprehensive Genomic Data: Hosts the complete Coffea canephora genome sequence with gene structure, gene product data, metabolic pathways, gene families, transcriptomic profiles, syntenic blocks, genetic markers, and genetic maps.
• Advanced Analysis Tools: Employs GMOD tools for querying, visualization, and data downloading to support diverse genomic analyses.
• Genome Browser with Community Annotation System: Provides a genome browser integrated with a Community Annotation System and an annotation editor to refine automatic gene annotations via community contributions.
• Interoperability and Integration: Integrates with South Green resources for phylogenomics and SNP data and supports analyses through the Galaxy workflow manager.

Scientific Applications:

• Translational and Applied Research: Centralizes genetic information and analysis resources to support breeding program improvement and trait-dissection studies in coffee.
• Comparative Genomics: Enables exploration of conserved chromosomal gene orders among asterid angiosperms and investigation of species-specific gene family expansions, including N-methyltransferases (NMTs) involved in caffeine biosynthesis, defense-related genes, and enzymes for secondary compound synthesis.
• Evolutionary Studies: Supports analyses of sequential tandem duplications and independent expansions of caffeine-related gene families relative to cacao and tea, informing the polyphyletic origins of caffeine in eudicots.

Methodology:

Uses GMOD tools for data querying and visualization, integrates with the Galaxy workflow manager for analyses, and employs a Community Annotation System with an annotation editor to refine automatic gene annotations.