Nature Communications
Nature Communications
5 years ago

Sequencing and de novo assembly of a near complete indica rice genome

Sequencing and de novo assembly of a near complete indica rice genome
Bin Ma, Shigui Li, Xin Yang, Peng Qin, Jing Wang, Kunfan Liu, Ying Yu, Yinghao Cao, Ming Qi, Huilong Du, Qiang Gao, Yan Li, Chengzhi Liang, Zhuo Chen, Yanfei Ma, Xianfeng Zhao, Lihuang Zhu
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.

Publisher URL: http://www.nature.com/articles/ncomms15324

DOI: 10.1038/ncomms15324

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