Two gap-free reference genomes and a global view of the centromere architecture in rice

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

Research output: Contribution to journalArticlepeer-review

40 Scopus citations


Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome sequenced almost two decades ago. However, reference genomes for all higher organisms to date contain gaps and missing sequences. Here, we report the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, which are being used as a model system for studying heterosis and yield. Gap-free reference genomes provide the opportunity for a global view of the structure and function of centromeres. We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures. In addition, the similarity of CentO repeats in the same chromosome is higher than across chromosomes, supporting a model of local expansion and homogenization. Both genomes have over 395 non-TE genes located in centromere regions, of which ∼41% are actively transcribed. Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes. The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.

Original languageEnglish (US)
Pages (from-to)1757-1767
Number of pages11
JournalMolecular Plant
Issue number10
StatePublished - Oct 4 2021


  • MH63
  • ZS97
  • centromere architecture
  • hybrid rice
  • rice genome

ASJC Scopus subject areas

  • Molecular Biology
  • Plant Science


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