Rice Gene Index

Rice Gene Index provides integrated pan-genome and comparative genomics resources for Asian rice, consolidating reference genomes and transcriptome data to enable analysis of genetic diversity and gene function.

Key Features:

• Pan-Genome Integration: Consolidates genomic information from 16 platinum standard reference genomes together with supplementary transcriptome data to represent the rice pan-genome.
• Ortholog Gene Indices: Identifies and catalogs 112,658 Ortholog Gene Indices across rice accessions for comparative and evolutionary analyses.
• GeneCard Pages: Associates each gene with a GeneCard page containing genomic, transcriptomic, and homology information.
• Search Capabilities: Provides multiple search modalities including keyword-based, sequence-based, and relationship-based searches for locating genes and gene relationships.
• Visualization Tools: Enables visualization of gene relationships at local and global scales via Microcollinearity and Macrocollinearity modules for studying structural variation and synteny.

Scientific Applications:

• Comparative Genomics: Supports cross-accession comparisons to identify conserved and variable genomic regions among rice varieties.
• Functional Genomics: Facilitates association of gene models with transcriptomic and homology data to investigate gene function.
• Evolutionary Biology: Enables analysis of evolutionary relationships and synteny across rice accessions using ortholog indices and collinearity visualizations.
• Agronomic Trait Discovery: Assists identification of candidate genes associated with agronomic traits through integrated genomic and transcriptomic evidence.
• Pan-Genome and Diversity Studies: Supports characterization of genetic diversity and structural variation across the rice pan-genome.

Methodology:

Integration and comparative analyses of multiple reference genomes and transcriptome datasets, including consolidation of 16 platinum standard reference genomes and supplementary transcriptome data.