气候变化领域集成服务门户(CCPortal): De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance

CCPortal

DOI	10.1186/s12870-021-03003-8
	De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance
	Wang, Jie; Li, Shiming; Lan, Lei; Xie, Mushan; Cheng, Shu; Gan, Xiaolong; Huang, Gang; Du, Guohua; Yu, Kang; Ni, Xuemei; Liu, Baolong; Peng, Guoxiong
通讯作者	Peng, GX (通讯作者)，Chongqing Univ, Genet Engn Res Ctr, Sch Life Sci, Chongqing 401331, Peoples R China. ; Ni, XM (通讯作者)，BGI Shenzhen, BGI Inst Appl Agr, Shenzhen 518120, Peoples R China. ; Liu, BL (通讯作者)，Chinese Acad Sci, Northwest Inst Plateau Biol, Key Lab Adaptat & Evolut Plateau Biota, Xining 810008, Qinghai, Peoples R China. ; Liu, BL (通讯作者)，Key Lab Crop Mol Breeding, Xining 810008, Qinghai, Peoples R China.
发表日期	2021
ISSN	1471-2229
卷号	21 期号:1
英文摘要	Background: Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. Results: Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. Conclusions: A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.
关键词	SETARIA-ITALICA RESISTANCE MODEL INFERENCE SEQUENCE PROVIDES PROGRAM INSIGHTS MUTATION VIRIDIS
英文关键词	Setaria italica; Genome; Comparative genomic analysis; Acetohydroxy acid synthase; Imazethapyr tolerance
语种	英语
WOS研究方向	Plant Sciences
WOS类目	Plant Sciences
WOS记录号	WOS:000660787100001
来源期刊	BMC PLANT BIOLOGY
来源机构	中国科学院西北生态环境资源研究院
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/254564
作者单位	[Wang, Jie; Xie, Mushan; Peng, Guoxiong] Chongqing Univ, Genet Engn Res Ctr, Sch Life Sci, Chongqing 401331, Peoples R China; [Wang, Jie; Li, Shiming; Lan, Lei; Cheng, Shu; Huang, Gang; Du, Guohua; Yu, Kang; Ni, Xuemei] BGI Shenzhen, BGI Inst Appl Agr, Shenzhen 518120, Peoples R China; [Wang, Jie; Li, Shiming; Huang, Gang; Yu, Kang] BGI Shenzhen, BGI Agro Seed Serv Wuhan Co Ltd, Wuhan 430090, Peoples R China; [Gan, Xiaolong; Liu, Baolong] Chinese Acad Sci, Northwest Inst Plateau Biol, Key Lab Adaptat & Evolut Plateau Biota, Xining 810008, Qinghai, Peoples R China; [Gan, Xiaolong; Liu, Baolong] Key Lab Crop Mol Breeding, Xining 810008, Qinghai, Peoples R China
推荐引用方式 GB/T 7714	Wang, Jie,Li, Shiming,Lan, Lei,et al. De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance[J]. 中国科学院西北生态环境资源研究院,2021,21(1).
APA	Wang, Jie.,Li, Shiming.,Lan, Lei.,Xie, Mushan.,Cheng, Shu.,...&Peng, Guoxiong.(2021).De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance.BMC PLANT BIOLOGY,21(1).
MLA	Wang, Jie,et al."De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance".BMC PLANT BIOLOGY 21.1(2021).