July 7, 2019  |  

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

Authors: Du, Huilong and Yu, Ying and Ma, Yanfei and Gao, Qiang and Cao, Yinghao and Chen, Zhuo and Ma, Bin and Qi, Ming and Li, Yan and Zhao, Xianfeng and Wang, Jing and Liu, Kunfan and Qin, Peng and Yang, Xin and Zhu, Lihuang and Li, Shigui and Liang, Chengzhi

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.

Journal: Nature communications
DOI: 10.1038/ncomms15324
Year: 2017

Read publication

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.