Data_Sheet_1_Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics.ZIP

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.

2002年，首个作物基因组以水稻品种93-11为材料发表，该品种是首个超级杂交稻的亲本。该基因组序列长期作为籼稻品种的参考基因组，但原组装版本始终未得到更新。本研究利用超深度单分子实时测序（Single Molecule Real-Time, SMRT）读段、Hi-C测序技术，结合参考基因组引导与缺口填补方法，将93-11的基因组组装升级为无缺口序列。通过对比93-11与日本晴参考基因组的基因组共线性及基因组成差异，证实将籼稻品种的测序数据比对至93-11基因组，相较于比对至日本晴参考基因组更为合理。此外，时序转录组数据分析显示，基因表达模式与种子发育各阶段显著相关。淀粉合成相关基因的可变剪接事件以及蜡质基因的基因组变异，使该组装版本成为靶向育种的新型宝贵资源。综上，本次升级的高质量93-11基因组组装，可助力研究者在分子育种项目中更好地理解稻属（Oryza）类群的基因组结构与功能。