|
Sequencing and De Novo Assembly of A Near Complete Indica Rice Genome
Huilong Du, Ying Yu, Yanfei Ma, Qiang Gao, Yinghao Cao, Zhuo Chen, Bin Ma, Ming Qi, Yan Li,
Xianfeng Zhao, Jing Wang, Kunfan Liu, Peng Qin, Xin Yang, Lihuang Zhu, Shigui Li & Chengzhi Liang
Nature Communications
Abstract
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-megabase 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 serves as a new reference for the discovery of genes and structural variations in rice.
|
论文编号: |
DOI:10.1038/ncomms15324 |
论文题目: |
Sequencing and De Novo Assembly of A Near Complete Indica Rice Genome |
英文论文题目: |
Sequencing and De Novo Assembly of A Near Complete Indica Rice Genome |
第一作者: |
Huilong Du, Ying Yu, Yanfei Ma, Qiang Gao, Yinghao Cao, Zhuo Chen, Bin Ma, Ming Qi, Yan Li,
Xianfeng Zhao, Jing Wang, Kunfan Liu, Peng Qin, Xin Yang, Lihuang Zhu, Shigui Li & Chengzhi Liang |
英文第一作者: |
Huilong Du, Ying Yu, Yanfei Ma, Qiang Gao, Yinghao Cao, Zhuo Chen, Bin Ma, Ming Qi, Yan Li,
Xianfeng Zhao, Jing Wang, Kunfan Liu, Peng Qin, Xin Yang, Lihuang Zhu, Shigui Li & Chengzhi Liang |
联系作者: |
|
英文联系作者: |
|
外单位作者单位: |
|
英文外单位作者单位: |
|
发表年度: |
2017-05-05 |
卷: |
|
期: |
|
页码: |
|
摘要: |
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-megabase 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 serves as a new reference for the discovery of genes and structural variations in rice. |
英文摘要: |
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-megabase 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 serves as a new reference for the discovery of genes and structural variations in rice. |
刊物名称: |
Nature Communications |
英文刊物名称: |
Nature Communications |
论文全文: |
|
英文论文全文: |
|
全文链接: |
|
其它备注: |
Huilong Du, Ying Yu, Yanfei Ma, Qiang Gao, Yinghao Cao, Zhuo Chen, Bin Ma, Ming Qi, Yan Li, Xianfeng Zhao, Jing Wang, Kunfan Liu, Peng Qin, Xin Yang, Lihuang Zhu, Shigui Li & Chengzhi Liang. Sequencing and De Novo Assembly of A Near Complete Indica Rice Genome. Nature Communications. DOI:10.1038/ncomms15324 |
英文其它备注: |
|
学科: |
|
英文学科: |
|
影响因子: |
|
第一作者所在部门: |
|
英文第一作者所在部门: |
|
论文出处: |
|
英文论文出处: |
|
论文类别: |
|
英文论文类别: |
|
参与作者: |
|
英文参与作者: |
|
|