Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics

文献类型： 外文期刊

第一作者： Wang, Sen

作者： Wang, Sen;Xie, Junhua;Liu, Wanfei;Lin, Qiang;Cui, Peng;Gao, Shenghan;Nie, Jingyi;Tan, Xinyu;Bi, Xiaochun;Sun, Yan;Luo, Sainan;Zhu, Qianhui;Geng, Jianing;Hu, Songnian;Wu, Shuangyang

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关键词： time course transcriptome; alternative splicing; waxy; 93-11; chromosome level

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：6.627； 五年影响因子：7.255 ）

ISSN： 1664-462X

年卷期： 2022 年 12 卷

页码：

收录情况： SCI

摘要： 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 indica 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 indica 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 waxy 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 Oryza groups in molecular breeding programs.

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