A pangenome reference of wild and cultivated rice

The wild rice Oryza rufipogon, progenitor of Asian cultivated rice O. sativa, is an important resource for rice breeding. Here we presented a wild-cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse O. rufipogon accessions and 16 diverse O. sativa varieties. This pangenome contains 3.87 Gb novel sequences absent in the japonica Nipponbare reference genome. We captured alternate assemblies that included heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes with 28,907 core-genes and 13,728 wild rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance gene analogs in wild rice compared to that in cultivars. Our analysis indicated that two cultivated subpopulations, intro-indica and basmati were generated through gene flows among cultivars in South Asia. We also provided strong evidence to support the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 SNPs and 13,853 PAVs differentiated between indica and japonica, which mainly be traced back to the divergence of their respective ancestors and a larger genetic bottleneck in japonica. This study provides reference resource for enhancing rice improvements and enriches our understanding of the origin and domestication process of rice.