State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 Beichen West Road No. 2, Beijing 100101, China.
College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
Nat Commun. 2017 May 4;8:15324. doi: 10.1038/ncomms15324.
A high-quality reference genome is critical for understanding genome structure, genetic variation and evolution of an organism. Here we report the de novo assembly of an indica rice genome Shuhui498 (R498) through the integration of single-molecule sequencing and mapping data, genetic map and fosmid sequence tags. The 390.3 Mb assembly is estimated to cover more than 99% of the R498 genome and is more continuous than the current reference genomes of japonica rice Nipponbare (MSU7) and Arabidopsis thaliana (TAIR10). We annotate high-quality protein-coding genes in R498 and identify genetic variations between R498 and Nipponbare and presence/absence variations by comparing them to 17 draft genomes in cultivated rice and its closest wild relatives. Our results demonstrate how to de novo assemble a highly contiguous and near-complete plant genome through an integrative strategy. The R498 genome will serve as a reference for the discovery of genes and structural variations in rice.
高质量的参考基因组对于理解生物的基因组结构、遗传变异和进化至关重要。在这里，我们通过整合单分子测序和映射数据、遗传图谱和fosmid 序列标签，报告了籼稻品种 Shuhui498（R498）的从头组装。这个 390.3 Mb 的组装估计覆盖了 R498 基因组的 99%以上，比目前粳稻品种 Nipponbare（MSU7）和拟南芥（TAIR10）的参考基因组更加连续。我们在 R498 中注释了高质量的蛋白质编码基因，并通过与栽培稻及其最接近的野生近缘种的 17 个草案基因组进行比较，鉴定了 R498 和 Nipponbare 之间的遗传变异和存在/缺失变异。我们的结果展示了如何通过整合策略从头组装一个高度连续和近乎完整的植物基因组。R498 基因组将成为在水稻中发现基因和结构变异的参考。
