GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data

Area of Science:

• Genomics
• Bioinformatics
• Plant Science

Background:

• Rice is a critical global food staple and a model organism for genetic research.
• There is a growing demand for comprehensive and accessible rice genomic data.

Purpose of the Study:

• To present GrameneOryza (version 8), an updated online resource for rice genomic data adhering to FAIR principles.
• To enhance accessibility and usability of diverse rice genomic information for researchers.

Main Methods:

• Integrated 28 Oryza genomes, including wild and domesticated types, with outgroup species.
• Generated 38K protein-coding gene family trees for ortholog and paralog identification.
• Collected and curated 66 million single-nucleotide variants (SNVs) and 1200 phenotypes.

Main Results:

• Version 8 includes 28 Oryza genomes and expanded genetic variation data with 66 million SNVs.
• Mapped RG3K reads to seven additional Asian rice genomes, yielding 19 million SNVs per genome.
• Introduced Oryza CLIMtools for studying genome adaptation and environmental impacts.

Conclusions:

• GrameneOryza version 8 offers a robust, FAIR-compliant platform for rice genomic research.
• The expanded dataset and new tools facilitate deeper understanding of rice genetics and adaptation.