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

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	De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids
	Zhou, Tao ; Bai, Guoqing 2,3; Hu, Yiheng 6; Ruhsam, Markus 7; Yang, Yanci 1; Zhao, Yuemei 5
刊名	DNA RESEARCH
	2022
卷号	29 期号:6
关键词	medicinal plant Gentiana macrophylla genome assembly whole-genome duplication iridoid biosynthesis
ISSN号	1340-2838
DOI	10.1093/dnares/dsac034
文献子类	Article
英文摘要	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.
学科主题	Genetics & Heredity
电子版国际标准刊号	1756-1663
出版地	OXFORD
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)
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000911859500001
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
内容类型	期刊论文
源URL	[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.Royal Bot Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Midlothian, Scotland 2.Inst Bot Shaanxi Prov, Xian Bot Garden Shaanxi Prov, Shaanxi Engn Res Ctr Conservat & Utilizat Bot Res, Xian 710061, Peoples R China 3.Xi An Jiao Tong Univ, Sch Pharm, Xian 710061, Peoples R China 4.Guizhou Educ Univ, Sch Biol Sci, Guiyang, Peoples R China 5.Baotou TeachersColl, Sch Biol Sci & Technol, Baotou, Peoples R China 6.Shaanxi Eins Ecol Sci & Technol Co Ltd, Xian, Peoples R China 7.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, 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).