The cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. The rice pan-genome, the genome of rice species rather than an individual, has been constructed from 3K rice genomes with a medium sequencing coverage about 15X. This pan-genome contains ~370Mbp IRGSP genome and ~260Mbp novel sequences, which are almost the same size as an individual rice genome.
This database provides:
- Basic information of 3,010 rice accessions
- Sequences and gene annotations for the rice pan-genome
- Gene presence-absence variations (PAVs) of rice accessions
- Expression profiles for rice pan-genome
This database also provides:
- Basic search functions:
- Search a single gene to obtain its basic information, distributions, PAVs and gene functions
- Search a single rice to obtain its sequencing landscape and meta-information (source, classification, etc.)
- Search sequence(s) against pan-genome sequences
- Advanced search functions:
- Search multiple rice accessions to obtain their shared genes
- Search multiple genes to obtain rice accessions where they all present
- Visualization functions:
- A tree browser to view the phylogeny of 3K rice accessions
- A genome browser to view gene annotation and presence-absence variations (PAVs)
