Wang Sen, Gao Shenghan, Nie Jingyi, Tan Xinyu, Xie Junhua, Bi Xiaochun, Sun Yan, Luo Sainan, Zhu Qianhui, Geng Jianing, Liu Wanfei, Lin Qiang, Cui Peng, Hu Songnian, Wu Shuangyang
Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
Front Plant Sci. 2022 Jan 21;12:769700. doi: 10.3389/fpls.2021.769700. eCollection 2021.
In 2002, the first crop genome was published using the rice cultivar 93-11, which is the progenitor of the first super-hybrid rice. The genome sequence has served as a reference genome for the cultivars, but the assembly has not been updated. In this study, we update the 93-11 genome assembly to a gap-less sequence using ultra-depth single molecule real-time (SMRT) reads, Hi-C sequencing, reference-guided, and gap-closing approach. The differences in the genome collinearity and gene content between the 93-11 and the Nipponbare reference genomes confirmed to map the cultivar sequencing data to the 93-11 genome, instead of the reference. Furthermore, time-course transcriptome data showed that the expression pattern was consistently correlated with the stages of seed development. Alternative splicing of starch synthesis-related genes and genomic variations of make it a novel resource for targeted breeding. Collectively, the updated high quality 93-11 genome assembly can improve the understanding of the genome structures and functions of groups in molecular breeding programs.
2002年，首个作物基因组以水稻品种93-11为材料发表，93-11是首个超级杂交水稻的亲本。该基因组序列一直作为这些品种的参考基因组，但组装尚未更新。在本研究中，我们使用超深度单分子实时（SMRT）测序 reads、Hi-C测序、参考引导和缺口闭合方法，将93-11基因组组装更新为无缺口序列。93-11与日本晴参考基因组之间的基因组共线性和基因含量差异证实，应将这些品种的测序数据映射到93-11基因组，而非参考基因组上。此外，时间进程转录组数据表明，表达模式与种子发育阶段始终相关。淀粉合成相关基因的可变剪接和基因组变异使其成为定向育种的新资源。总体而言，更新后的高质量93-11基因组组装能够增进对分子育种计划中这些群体的基因组结构和功能的理解。
