RPAN: Rice Pan-genome Browser

Lab of Computational Genomics and Metagenomics, Shanghai Jiao Tong University

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences


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:

  1. Basic information of 3,010 rice accessions
  2. Sequences and gene annotations for the rice pan-genome
  3. Gene presence-absence variations (PAVs) of rice accessions
  4. Expression profiles for rice pan-genome

This database also provides:

  1. 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
  2. Advanced search functions:
    • Search multiple rice accessions to obtain their shared genes
    • Search multiple genes to obtain rice accessions where they all present
  3. 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)

Heatmap of Gene PAVs

The pevious heatmap was based on gene family PAV. It is based on gene PAV. Corrected on Feb 11,2018

Genome composition

pie charts

Geographical distribution



#Total sequencing bases 16.6Tbps
#Pan-genome size 641Mbps
#Total rice accessions 3,010
#Indica 1,764
#Japonica 801
#AUS 221
#ARO 101
#ADM 123
#High-quality accessions 453
#RNA-seq runs 226
#Total genes 50,995
#Core genes 23,914
#Candidate Core genes 4,986
#Distributed genes 22,095
#Subspecies-unbalanced genes 13,617
#Indica-dominant genes 5,579
#Japonica-dominant genes 6,038
#Subspecies-specific genes 853
#Indica-specific genes 587
#Japonica-specific genes 147
#AUS-specific genes 67
#ARO-specific genes 52
#Subgroup-unbalanced genes 11,581
#Indica-subgroup-unbalanced genes 9,816
#Japonica-subgroup-unbalanced genes 3,418
#Random genes 5,316

Terminology specification