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High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan

文献类型： 外文期刊

作者： Zhang, Hui 1 ; Wang, Yuexing 3 ; Deng, Ce 1 ; Zhao, Sheng 1 ; Zhang, Peng 1 ; Feng, Jie 1 ; Huang, Wei 2 ; Kang, Shujing; 1 ;

作者机构： 1.Chinese Acad Agr Sci, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr, Genome Anal Lab,Minist Agr,Agr Genom Inst Shenzhe, Shenzhen 518120, Peoples R China

2.South China Agr Univ, Coll Life Sci, State Key Lab Conservat & Utilizat Subtrop Agrobi, Guangzhou 510642, Peoples R China

3.China Natl Rice Res Inst, State Key Lab Rice Biol, Hangzhou 310006, Peoples R China

4.Henan Agr Univ, Coll Agron, Natl Key Lab Wheat & Maize Crop Sci, Zhengzhou 450002, Peoples R China

5.Guangxi Univ, Coll Life Sci & Technol, Nanning 530004, Peoples R China

6.Nanjing Agr Univ, Plant Phen Res Ctr, Nanjing 210095, Peoples R China

关键词： de novo genome assembly; high-quality; PacBio; Nanopore; variation; rice

期刊名称：SCIENCE CHINA-LIFE SCIENCES （ 影响因子：6.038； 五年影响因子：4.754 ）

ISSN： 1674-7305

年卷期：

页码：

收录情况： SCI

摘要： High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding. Tian-you-hua-zhan has been a leading hybrid in China over the past decade. Here, de novo genome assembly strategy optimization for the rice indica lines Huazhan (HZ) and Tianfeng (TF), including sequencing platforms, assembly pipelines and sequence depth, was carried out. The PacBio and Nanopore platforms for long-read sequencing were utilized, with the Canu, wtdbg2, SMARTdenovo, Flye, Canu-wtdbg2, Canu-SMARTdenovo and Canu-Flye assemblers. The combination of PacBio and Canu was optimal, considering the contig N50 length, contig number, assembled genome size and polishing process. The assembled contigs were scaffolded with Hi-C data, resulting in two "golden quality" rice reference genomes, and evaluated using the scaffold N50, BUSCO, and LTR assembly index. Furthermore, 42,625 and 41,815 non-transposable element genes were annotated for HZ and TF, respectively. Based on our assembly of HZ and TF, as well as Zhenshan97, Minghui63, Shuhui498 and 9311, comprehensive variations were identified using Nipponbare as a reference. The de novo assembly strategy for rice we optimized and the "golden quality" rice genomes we produced for HZ and TF will benefit rice genomics and breeding research, especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.

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