A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data. / 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, Shaotong; Li, Xiaoli; Wei, Yuan; Ouyang, Zhen; Yan, Hui; Lu, Jiangjie; Wang, Huizhong; Guo, Lanping; Kong, Lingdong; Zhao, Jing; Li, Shaoping; Luo, Lifen; Kristiansen, Karsten; Feng, Zhan; Sun, Silong; Chen, Cunwu; Yue, Zhen; Chen, Naifu.

In: Genome Biology and Evolution, Vol. 12, No. 12, 2020, p. 2486-2490.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Han, B, Jing, Y, Dai, J, Zheng, T, Gu, F, Zhao, Q, Zhu, F, Song, X, Deng, H, Wei, P, Song, C, Liu, D, Jiang, X, Wang, F, Chen, Y, Sun, C, Yao, H, Zhang, L, Chen, N, Chen, S, Li, X, Wei, Y, Ouyang, Z, Yan, H, Lu, J, Wang, H, Guo, L, Kong, L, Zhao, J, Li, S, Luo, L, Kristiansen, K, Feng, Z, Sun, S, Chen, C, Yue, Z & Chen, N 2020, 'A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data', Genome Biology and Evolution, vol. 12, no. 12, pp. 2486-2490. https://doi.org/10.1093/gbe/evaa215

APA

Han, B., Jing, Y., Dai, J., Zheng, T., Gu, F., Zhao, Q., Zhu, F., Song, X., Deng, H., Wei, P., Song, C., Liu, D., Jiang, X., Wang, F., Chen, Y., Sun, C., Yao, H., Zhang, L., Chen, N., ... Chen, N. (2020). A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data. Genome Biology and Evolution, 12(12), 2486-2490. https://doi.org/10.1093/gbe/evaa215

Vancouver

Han B, Jing Y, Dai J, Zheng T, Gu F, Zhao Q et al. A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data. Genome Biology and Evolution. 2020;12(12):2486-2490. https://doi.org/10.1093/gbe/evaa215

Author

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, Shaotong ; Li, Xiaoli ; Wei, Yuan ; Ouyang, Zhen ; Yan, Hui ; Lu, Jiangjie ; Wang, Huizhong ; Guo, Lanping ; Kong, Lingdong ; Zhao, Jing ; Li, Shaoping ; Luo, Lifen ; Kristiansen, Karsten ; Feng, Zhan ; Sun, Silong ; Chen, Cunwu ; Yue, Zhen ; Chen, Naifu. / A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data. In: Genome Biology and Evolution. 2020 ; Vol. 12, No. 12. pp. 2486-2490.

Bibtex

@article{6ebbb01b42314d0aa94a2682e63f8f6d,
title = "A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data",
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.",
keywords = "annotation, de novo assembly, genome, Hi-C assembly, orchid",
author = "Bangxing Han and Yi Jing and Jun Dai and Tao Zheng and Fangli Gu and Qun Zhao and Fucheng Zhu and Xiangwen Song and Hui Deng and Peipei Wei and Cheng Song and Dong Liu and Xueping Jiang and Fang Wang and Yanjun Chen and Chuanbo Sun and Houjun Yao and Li Zhang and Naidong Chen and Shaotong Chen and Xiaoli Li and Yuan Wei and Zhen Ouyang and Hui Yan and Jiangjie Lu and Huizhong Wang and Lanping Guo and Lingdong Kong and Jing Zhao and Shaoping Li and Lifen Luo and Karsten Kristiansen and Zhan Feng and Silong Sun and Cunwu Chen and Zhen Yue and Naifu Chen",
year = "2020",
doi = "10.1093/gbe/evaa215",
language = "English",
volume = "12",
pages = "2486--2490",
journal = "Genome Biology and Evolution",
issn = "1759-6653",
publisher = "Oxford University Press",
number = "12",

}

RIS

TY - JOUR

T1 - A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data

AU - Han, Bangxing

AU - Jing, Yi

AU - Dai, Jun

AU - Zheng, Tao

AU - Gu, Fangli

AU - Zhao, Qun

AU - Zhu, Fucheng

AU - Song, Xiangwen

AU - Deng, Hui

AU - Wei, Peipei

AU - Song, Cheng

AU - Liu, Dong

AU - Jiang, Xueping

AU - Wang, Fang

AU - Chen, Yanjun

AU - Sun, Chuanbo

AU - Yao, Houjun

AU - Zhang, Li

AU - Chen, Naidong

AU - Chen, Shaotong

AU - Li, Xiaoli

AU - Wei, Yuan

AU - Ouyang, Zhen

AU - Yan, Hui

AU - Lu, Jiangjie

AU - Wang, Huizhong

AU - Guo, Lanping

AU - Kong, Lingdong

AU - Zhao, Jing

AU - Li, Shaoping

AU - Luo, Lifen

AU - Kristiansen, Karsten

AU - Feng, Zhan

AU - Sun, Silong

AU - Chen, Cunwu

AU - Yue, Zhen

AU - Chen, Naifu

PY - 2020

Y1 - 2020

N2 - 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.

AB - 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.

KW - annotation

KW - de novo assembly

KW - genome

KW - Hi-C assembly

KW - orchid

U2 - 10.1093/gbe/evaa215

DO - 10.1093/gbe/evaa215

M3 - Journal article

C2 - 33045048

AN - SCOPUS:85097570556

VL - 12

SP - 2486

EP - 2490

JO - Genome Biology and Evolution

JF - Genome Biology and Evolution

SN - 1759-6653

IS - 12

ER -

ID: 254666590