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A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data
Han,Bangxing1; Jing,Yi2; Dai,Jun1; Zheng,Tao2,3; Gu,Fangli1; Zhao,Qun1; Zhu,Fucheng1; Song,Xiangwen1; Deng,Hui1; Wei,Peipei1; Song,Cheng1; Liu,Dong1; Jiang,Xueping1; Wang,Fang1; Chen,Yanjun1; Sun,Chuanbo1; Yao,Houjun1; Zhang,Li1; Chen,Naidong1; Chen,Shaotong1; Li,Xiaoli1; Wei,Yuan4; Ouyang,Zhen4; Yan,Hui5; Lu,Jiangjie6; Wang,Huizhong6; Guo,Lanping7; Kong,Lingdong8; Zhao,Jing9; Li,Shaoping9; Luo,Lifen10; Kristiansen,Karsten3; Feng,Zhan2; Sun,Silong2; Chen,Cunwu1; Yue,Zhen2; Chen,Naifu1
2020-12-06
Source PublicationGenome biology and evolution
ISSN1759-6653
Volume12Issue:12Pages:2486-2490
Abstract

Dendrobium huoshanense is used to treat various diseases in traditional Chinese medicine. Recent studies have identified active components. However, the lack of genomic data limits research on the biosynthesis and application of these therapeutic ingredients. To address this issue, we generated the first chromosome-level genome assembly and annotation of D. huoshanense. We integrated PacBio sequencing data, Illumina paired-end sequencing data, and Hi-C sequencing data to assemble a 1.285 Gb genome, with contig and scaffold N50 lengths of 598 kb and 71.79 Mb, respectively. We annotated 21,070 protein-coding genes and 0.96 Gb transposable elements, constituting 74.92% of the whole assembly. In addition, we identified 252 genes responsible for polysaccharide biosynthesis by Kyoto Encyclopedia of Genes and Genomes functional annotation. Our data provide a basis for further functional studies, particularly those focused on genes related to glycan biosynthesis and metabolism, and have implications for both conservation and medicine.

KeywordAnnotation De Novo Assembly Genome Hi-c Assembly Orchid
DOI10.1093/gbe/evaa215
URLView the original
Indexed BySCIE
WOS Research AreaEvolutionary Biology ; Genetics & Heredity
WOS SubjectEvolutionary Biology ; Genetics & Heredity
WOS IDWOS:000606568300022
Scopus ID2-s2.0-85097570556
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Cited Times [WOS]:3   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionUniversity of Macau
Corresponding AuthorHan,Bangxing; Chen,Cunwu; Yue,Zhen; Chen,Naifu
Affiliation1.Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory,West Anhui University,230036,China
2.BGI Genomics,BGI-Shenzhen,Shenzhen,518083,China
3.Department of Biology,University of Copenhagen,
4.School of Pharmacy,Jiangsu University,Zhenjiang,212013,China
5.School of Biotechnology,Jiangsu University of Science and Technology,Zhenjiang,China
6.Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants,College of Life and Environmental Science,Hangzhou Normal University,Hangzhou,311121,China
7.State Key Laboratory Breeding Base of Dao-di Herbs,National Resource Center for Chinese Materia Medica,China Academy of Chinese Medical Sciences,100700,China
8.School of Life Sciences,Nanjing University,Nanjing,210093,China
9.State Key Laboratory of Quality Research in Chinese Medicine,Institute of Chinese Medical Sciences,University of Macau,Macao
10.Shenzhen Maternity and Child Healthcare Hospital,Shenzhen,China
Recommended Citation
GB/T 7714
Han,Bangxing,Jing,Yi,Dai,Jun,et al. A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data[J]. Genome biology and evolution,2020,12(12):2486-2490.
APA Han,Bangxing.,Jing,Yi.,Dai,Jun.,Zheng,Tao.,Gu,Fangli.,Zhao,Qun.,Zhu,Fucheng.,Song,Xiangwen.,Deng,Hui.,Wei,Peipei.,Song,Cheng.,Liu,Dong.,Jiang,Xueping.,Wang,Fang.,Chen,Yanjun.,Sun,Chuanbo.,Yao,Houjun.,Zhang,Li.,Chen,Naidong.,...&Chen,Naifu.(2020).A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data.Genome biology and evolution,12(12),2486-2490.
MLA Han,Bangxing,et al."A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data".Genome biology and evolution 12.12(2020):2486-2490.
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