Rice Genome Annotation Project (RGAP)

The Rice Genome Annotation Project (RGAP) provides updated resources for mining the rice genome, including improved annotation, gene expression data, and a genome browser to facilitate access for plant biologists.

Key Features:

• Genome Assemblies: The database includes 16 whole genome rice assemblies and sequence variants from multiple rice pan-genome projects including the 3000 Rice Genomes Project.
• Gene Expression Data: Gene expression abundance data was updated with 80 RNA-sequencing datasets.
• Gene Coexpression Analysis: Gene coexpression analysis was performed resulting in 39 coexpression modules that capture highly connected sets of co-regulated genes.
• Syntelog Identification: 32,335 syntelogs were identified between the Nipponbare reference genome and other rice genomes, and 19,371 syntelogs were identified between Nipponbare and four other Poaceae genomes.
• Genome Browser: An upgraded genome browser provides visualization and access to the datasets.

Scientific Applications:

• Gene Function Discovery: The coexpression modules facilitate discovery of gene function through identification of co-regulated gene sets.
• Comparative Genome Analysis: Syntelog identification between rice and other Poaceae genomes enables comparative genomic studies across grass species.
• Pan-Genome Studies: Sequence variants and multiple genome assemblies support pan-genome analyses of rice diversity.

Methodology:

Gene coexpression analysis was performed on 80 RNA-sequencing datasets to generate 39 coexpression modules. Syntelogs were identified between the Nipponbare reference genome and other rice genomes, and between Nipponbare and four other Poaceae genomes.