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The gap-free rice genomes provide insights for centromere structure and function exploration and graph-based pan-genome construction

By Jia-Ming Song, Wen-Zhao Xie, Shuo Wang, Yi-Xiong Guo, Jesse Poland, Dal-Hoe Koo, Dave Kudrna, Evan Long, Yicheng Huang, Jia-Wu Feng, Wenhui Zhang, Seunghee Lee, Jayson Talag, Run Zhou, Xi-Tong Zhu, Daojun Yuan, Joshua Udall, Weibo Xie, Rod A. Wing, Qifa Zhang, Jianwei Zhang, Ling-Ling Chen

Posted 24 Dec 2020
bioRxiv DOI: 10.1101/2020.12.24.424073

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.

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