The gap-free rice genomes provide insights for centromere structure and function exploration and graph-based pan-genome construction
Wing, Rod Anthony
Permanent link to this recordhttp://hdl.handle.net/10754/666733
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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.
CitationSong, 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
SponsorsWe sincerely thank 1) Pacific Biosciences of California, Inc. for sequencing of MH63, 520 2) Wuhan Frasergen Bioinformatics Co., Ltd. for sequencing of ZS97 and 3) Dr. 521 Jiming Jiang at MSU for his critical comments and constructive suggestions on our 522 centromere analyses.
PublisherCold Spring Harbor Laboratory