The gap-free rice genomes provide insights for centromere structure and function exploration and graph-based pan-genome construction
AbstractAsia 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.
Song, J.-M., Xie, W.-Z., Wang, S., Guo, Y.-X., Poland, J., Koo, D.-H., … Chen, L.-L. (2020). The gap-free rice genomes provide insights for centromere structure and function exploration and graph-based pan-genome construction. doi:10.1101/2020.12.24.424073