RT Journal Article SR Electronic T1 Assembly and Validation of Two Gap-free Reference Genomes for Xian/indica Rice Reveals Insights into Plant Centromere Architecture JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.12.24.424073 DO 10.1101/2020.12.24.424073 A1 Jia-Ming Song A1 Wen-Zhao Xie A1 Shuo Wang A1 Yi-Xiong Guo A1 Dal-Hoe Koo A1 Dave Kudrna A1 Yicheng Huang A1 Jia-Wu Feng A1 Wenhui Zhang A1 Yong Zhou A1 Andrea Zuccolo A1 Evan Long A1 Seunghee Lee A1 Jayson Talag A1 Run Zhou A1 Xi-Tong Zhu A1 Daojun Yuan A1 Joshua Udall A1 Weibo Xie A1 Rod A. Wing A1 Qifa Zhang A1 Jesse Poland A1 Jianwei Zhang A1 Ling-Ling Chen YR 2021 UL http://biorxiv.org/content/early/2021/01/01/2020.12.24.424073.abstract AB Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome completed almost two decades ago. However, all sequenced genomes to date contain gaps and missing sequences. Here, we report, for the first time, the assembly and analyses of two gap-free reference genome sequences of the elite O. sativa xian/indica rice varieties ‘Zhenshan 97 (ZS97)’ and ‘Minghui 63 (MH63)’ that are being used as a model system to study heterosis. Gap-free reference genomes also provide global insights into the structure and function of centromeres. All rice centromeric regions share conserved centromere-specific satellite motifs but with different copy numbers and structures. Importantly, we demonstrate that >1,500 genes are located in centromere regions, of which ~15.6% are actively transcribed. The generation and release of both the ZS97 and MH63 gap-free genomes lays a solid foundation for the comprehensive study of genome structure and function in plants and breed climate resilient varieties for the 21st century.Competing Interest StatementThe authors have declared no competing interest.