De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids
文献类型:期刊论文
作者 | Zhou, Tao; Bai, Guoqing2,3; Hu, Yiheng6; Ruhsam, Markus7; Yang, Yanci1; Zhao, Yuemei5 |
刊名 | DNA RESEARCH |
出版日期 | 2022 |
卷号 | 29期号:6 |
ISSN号 | 1340-2838 |
关键词 | medicinal plant Gentiana macrophylla genome assembly whole-genome duplication iridoid biosynthesis |
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 |
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). |
入库方式: OAI收割
来源:植物研究所
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