GGDB

GGDB relates duplicated genes and gene collinearity across 29 well-assembled Gramineae genomes to analyze polyploidization, speciation, and structural genome evolution.

Key Features:

• Hierarchical gene relationship analysis: Systematically relates duplicated genes in collinear regions to specific evolutionary events such as polyploidization and speciation to separate duplicates originating from distinct events.
• Comprehensive paralog and ortholog lists: Provides curated lists of paralogous and orthologous genes across 29 well-assembled Gramineae genome sequences for comparative genomics analyses.
• Homologous gene comparison and phylogenetics: Compares homologous genes among selected plants, generates genome-scale and localized alignment figures, and constructs gene-based phylogenetic trees corrected using gene collinearity.
• Structural-change visualization: Visualizes genome structural changes to detect effects of paleo-polyploidy on genome structure and function.

Scientific Applications:

• Evolutionary reconstruction: Resolve evolutionary histories of Gramineae genomes by linking duplicated genes to specific polyploidization and speciation events using gene collinearity.
• Polyploidy and genetic diversity: Investigate the impact of polyploidy and duplicated-gene retention on genetic diversity and potential implications for crop improvement in Gramineae.
• Comparative genomics: Enable cross-species analyses of paralogs and orthologs to study gene retention, loss, structural rearrangements, and functional innovation across Gramineae.

Methodology:

Analyzed up-to-date genome sequences from 29 Gramineae species, established relationships between duplicated genes and specific evolutionary events using gene collinearity, and generated alignment figures and gene-based phylogenetic trees corrected by collinearity.