De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids

doi:10.1093/dnares/dsac034

	De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids
	Zhou, Tao ; Bai, Guoqing 1,2; Hu, Yiheng 3; Ruhsam, Markus 4; Yang, Yanci 5; Zhao, Yuemei 6
	2022
发表期刊	DNA RESEARCH
ISSN	1340-2838
卷号	29 期号:6
摘要	Gentiana macrophylla is a perennial herb in the Gentianaceae family, whose dried roots are used in traditional Chinese medicine. Here, we assembled a chromosome-level genome of G. macrophylla using a combination of Nanopore, Illumina, and Hi-C scaffolding approaches. The final genome size was similar to 1.79 Gb (contig N50 = 720.804 kb), and 98.89% of the genome sequences were anchored on 13 pseudochromosomes (scaffold N50 = 122.73 Mb). The genome contained 55,337 protein-coding genes, and 73.47% of the assemblies were repetitive sequences. Genome evolution analysis indicated that G. macrophylla underwent two rounds of whole-genome duplication after the core eudicot. genome triplication event. We further identified candidate genes related to the biosynthesis of iridoids, and the corresponding gene families mostly expanded in G. macrophylla. In addition, we found that root-specific genes are enriched in pathways involved in defense responses, which may greatly improve the biological adaptability of G. macrophylla. Phylogenomic analyses showed a sister relationship of asterids and rosids, and all Gentianales species formed a monophyletic group. Our study contributes to the understanding of genome evolution and active component biosynthesis in G. macrophylla and provides important genomic resource for the genetic improvement and breeding of G. macrophylla.
关键词	medicinal plant Gentiana macrophylla genome assembly whole-genome duplication iridoid biosynthesis
学科领域	Genetics & Heredity
DOI	10.1093/dnares/dsac034
收录类别	SCI
语种	英语
WOS关键词	DENDROBIUM-OFFICINALE ; TRANSPOSABLE ELEMENTS ; GENE ; ALIGNMENT ; ANNOTATION ; ACCURATE ; IDENTIFICATION ; REVEALS ; PROGRAM ; TOOL
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000911859500001
出版者	OXFORD UNIV PRESS
文献子类	Article
出版地	OXFORD
EISSN	1756-1663
资助机构	National Natural Science Foundation of China [31900273, 31800554] ; Outstanding Youth Scientific Research Project of Shaanxi Academy of Sciences [2017K-12] ; Scientific Research Project of Shaanxi Province Bureau of Traditional Chinese Medicine [610902] ; National Traditional Chinese Medicine Resources Survey Project in 2017 [2017-66] ; Scottish Government's Rural and Environment Science and Analytical Services Division
作者邮箱	zhoutao196@mail.xjtu.edu.cn ; yezi19820320@163.com
作品OA属性	gold, Green Published
引用统计	被引频次：9[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/28701
专题	系统与进化植物学国家重点实验室
作者单位	1.Xi An Jiao Tong Univ, Sch Pharm, Xian 710061, Peoples R China 2.Inst Bot Shaanxi Prov, Xian Bot Garden Shaanxi Prov, Shaanxi Engn Res Ctr Conservat & Utilizat Bot Res, Xian 710061, Peoples R China 3.Shaanxi Eins Ecol Sci & Technol Co Ltd, Xian, Peoples R China 4.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 5.Royal Bot Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Midlothian, Scotland 6.Baotou TeachersColl, Sch Biol Sci & Technol, Baotou, Peoples R China 7.Guizhou Educ Univ, Sch Biol Sci, Guiyang, Peoples R China
推荐引用方式 GB/T 7714	Zhou, Tao,Bai, Guoqing,Hu, Yiheng,et al. De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids[J]. DNA RESEARCH,2022,29(6).
APA	Zhou, Tao,Bai, Guoqing,Hu, Yiheng,Ruhsam, Markus,Yang, Yanci,&Zhao, Yuemei.(2022).De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids.DNA RESEARCH,29(6).
MLA	Zhou, Tao,et al."De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids".DNA RESEARCH 29.6(2022).

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