The collections of rice germplasm are an important source of genetic diversity for modern breeding, but the gene resources remains largely unexplored. Now we report the establishment and in-depth analysis of a pan-genome dataset for the O. sativa-O. rufipogon species complex, by sequencing and de novo assembly of 66 phylogenetically representative accessions.. Rice pan-genome data

The samples included 22 accessions of O. sativa temperate japonica, 5 of O. sativa tropical japonica, 1 of O. sativa aromatic, 19 of O. sativa indica, 6 of O. sativa aus and 13 of O. rufipogon, representing all major genetically distinct clusters in O. sativa and O. rufipogon. The genomic DNA of each accession was sequenced with an average of 115x using Illumina technology, generating totally 3.1 Tb of raw sequence reads. The 66 rice genomes was all de novo assembled. The final assemblies had the contig N50 sizes ranging from 21 kb to 75 kb in different accessions.