AUTHOR=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 TITLE=Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics JOURNAL=Frontiers in Plant Science VOLUME=12 YEAR=2022 URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.769700 DOI=10.3389/fpls.2021.769700 ISSN=1664-462X ABSTRACT=

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.