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

作者：Sen Wang, Shenghan Gao, Jingyi Nie, Xinyu Tan, Junhua Xie, Xiaochun Bi, Yan Sun, Sainan Luo, Qianhui Zhu, Jianing Geng, Wanfei Liu, Qiang Lin, Peng Cui, Songnian Hu, Shuangyang Wu · 发表于：Frontiers in Plant Science · 年份：2022 · DOI：10.3389/fpls.2021.769700 · 被引用次数：19 · 研究领域：Genomics and Phylogenetic Studies、Genetic Mapping and Diversity in Plants and Animals、Plant Disease Resistance and Genetics

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.