ABSTRACT
Asia rice (Oryza sativa) is divided into two subgroups, indica/xian and japonica/geng, the former has greater intraspecific diversity than the latter. Here, for the first time, we report the assemblies and analyses of two gap-free xian rice varieties ‘Zhenshan 97 (ZS97)’ and ‘Minghui 63 (MH63)’. Genomic sequences of these elite hybrid parents express extensive difference as the foundation for studying heterosis. Furthermore, the gap-free rice genomes provide global insights to investigate the structure and function of centromeres in different chromosomes. All the rice centromeric regions share conserved centromere-specific satellite motifs but with different copy numbers and structures. Importantly, we show that there are >1,500 genes in centromere regions and ∼16% of them are actively expressed. Based on MH63 gap-free reference genome, a graph-based rice pan-genome (Os-GPG) was constructed containing presence/absence variations of 79 rice varieties. Compared with the other rice varieties, MH63 contained the largest number of resistance genes. The acquisition of ZS97 and MH63 gap-free genomes and graph-based pan-genome of rice lays a solid foundation for the study of genome structure and function in plants.
Competing Interest Statement
The authors have declared no competing interest.