Coptis chinensis is a famous medicinal plant, which belongs to Coptis of Ranunculaceae. In China it has been applied for more than 2,000 years, and it is also one of the key medicinal plants worldwide with the whole plants and extract. The genome of Coptis chinensis was investigated in order to accelerate the completion of its genome sequencing, promote its research in molecular breeding, genetic evolution and the excavation of important medicinal plant gene resources. Based on high-throughput sequencing technology, two libraries with fragment sequences about 270 bp were constructed. After performing double-terminal 270 bp (PE 270) sequencing, 49.82 Gb raw data was obtained. It was estimated that Coptis chinensis genome size was 1.06 Gb, the repeat sequence content was about 71.46%, the heterozygosity was about 0.24%, and the GC content was about 39.50%. The study showed that Coptis chinensis had complex geome with repeat and large sequence data. Therefore, three generation sequencing technology is recommended to construcut a 20 Kb library and test 100× Pacbio data, and construcut the 270 bp small library and test 50× illumina data, which will contribute to the acquisiton of high-quality complete genome map of Coptis chinensis. This study also provides basic data for mining functional genes of C. chinensis.
| Published in | Asia-Pacific Journal of Pharmaceutical Sciences (Volume 1, Issue 3) |
| Page(s) | 24-27 |
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This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited. |
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Copyright © The Author(s), 2024. Published by Science Publishing Group |
Coptis chinensis, Genome Sequencing, Genomic Trait Assessment
| [1] | 中国药典. 一部[S]. 2015: 303。 |
| [2] | 孙红祥, 张昌禧, 吴远文. 黄连属药用植物的数量分类学研究[J]. 中国药学杂志, 1995, 30(1): 7。 |
| [3] | 陈红, 王海洋. 重庆石柱黄连叶形态分析初探[J]. 西南大学学报(自然科学版), 2007, 29(1): 31。 |
| [4] | 陈萍萍, 刘学医. 宣黄连的生态学和栽培研究[J]. 中国野生植物资源, 2012, 31(5): 75。 |
| [5] | 汪建云, 刘经伦, 施晓春, 等.云南黄连生物学特性和栽培管理初探[J]. 保山学院学报, 2013, 32(2): 1。 |
| [6] | 孙涛, 孔德英, 滕少娜, 等. 基于ITS2序列的黄连及其伪混品的分子鉴定[J]. 贵州农业科学, 2013, 41(9): 20。 |
| [7] | 李波, 刘俊, 闵道长, 等. 黄连属植物DNA条形码研究[J]. 江西农业大学学报, 2017, 39(6): 1089。 |
| [8] | 张春平, 何平, 胡世俊, 等. 药用三角叶黄连遗传多样性的ISSR分析[J]. 中国中药杂志, 2009, 34(24):3176。 |
| [9] | 陈大霞, 王钰, 张雪, 等. 黄连属部分药用植物遗传多样性与亲缘关系的SCoT分析[J]. 中国中药杂志, 2017, 42(3): 473. |
| [10] | He Y, Fan G, Gao J, et al. Correlation analyses between molecular perspective and phytochemical variations in Coptis chinensis, Franch [J]. Biochem Syst Ecol, 2015, 61: 143。 |
| [11] | 张春平，何平，何俊星，等. 药用峨眉野连遗传多样性的RAPD分析[J]. 中国中药杂志，2010, 35(2): 138-141。 |
| [12] | He Y, Xiao HT, Deng C, et al. Complete chloroplast genome sequence of Coptis chinensis Franch. and its evolutionary history [J]. BioMed Research International. 2017, doi: 10.1155/2017/8201836。 |
| [13] | 赵振宇. 黄连属植物物种鉴定及mini-barcode研究[M]. 2019, 中国中医科学院。 |
| [14] | Chen H, Deng C, Nie H, et al. Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes [J]. Peer J, 2007, DOI: 10.7717/peerj.3303。 |
| [15] | Chen S, Xu J, Liu C, et al. Genome sequence of the model medicinal mushroom Ganoderma lucidum [J]. Nat Commun, 2012, 3 (2): 913。 |
| [16] | Xu H, Song J, Luo H, et al. Analysis of the genome sequence of the medicinal plant Salvia miltiorrhiza [J]. Mol Plant, 2016, 9 (6): 949。 |
| [17] | Liang Y, Xiao W, Hui L, et al.The genome of Dendrobium officinale Illuminates the biology of the important traditional Chinese orchid herb [J]. Mol Plant, 2015, 8 (6): 922。 |
| [18] | Altschul S F, Gish W, Miller W, et al. Basic local alignment search tool [J]. J Mol Biol, 1990, 215: 403。 |
| [19] | 孙全, 何晓红, 牟军, 等. 黄连基因组勘测与分析[J].四川大学学报(自然科学版), 2014, 51(06): 1330。 |
APA Style
Hou Feixia, Wang Qihao, Peng Cheng, Gao Jihai. (2020). Genome Survey Sequencing of Coptis chinensis. Asia-Pacific Journal of Pharmaceutical Sciences, 1(3), 24-27.
ACS Style
Hou Feixia; Wang Qihao; Peng Cheng; Gao Jihai. Genome Survey Sequencing of Coptis chinensis. Asia-Pac. J. Pharm. Sci. 2020, 1(3), 24-27.
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Download@article{10045248,
author = {Hou Feixia and Wang Qihao and Peng Cheng and Gao Jihai},
title = {Genome Survey Sequencing of Coptis chinensis},
journal = {Asia-Pacific Journal of Pharmaceutical Sciences},
volume = {1},
number = {3},
pages = {24-27},
url = {https://www.sciencepublishinggroup.com/article/10045248},
abstract = {Coptis chinensis is a famous medicinal plant, which belongs to Coptis of Ranunculaceae. In China it has been applied for more than 2,000 years, and it is also one of the key medicinal plants worldwide with the whole plants and extract. The genome of Coptis chinensis was investigated in order to accelerate the completion of its genome sequencing, promote its research in molecular breeding, genetic evolution and the excavation of important medicinal plant gene resources. Based on high-throughput sequencing technology, two libraries with fragment sequences about 270 bp were constructed. After performing double-terminal 270 bp (PE 270) sequencing, 49.82 Gb raw data was obtained. It was estimated that Coptis chinensis genome size was 1.06 Gb, the repeat sequence content was about 71.46%, the heterozygosity was about 0.24%, and the GC content was about 39.50%. The study showed that Coptis chinensis had complex geome with repeat and large sequence data. Therefore, three generation sequencing technology is recommended to construcut a 20 Kb library and test 100× Pacbio data, and construcut the 270 bp small library and test 50× illumina data, which will contribute to the acquisiton of high-quality complete genome map of Coptis chinensis. This study also provides basic data for mining functional genes of C. chinensis.},
year = {2020}
}
TY - JOUR T1 - Genome Survey Sequencing of Coptis chinensis AU - Hou Feixia AU - Wang Qihao AU - Peng Cheng AU - Gao Jihai Y1 - 2020/03/06 PY - 2020 T2 - Asia-Pacific Journal of Pharmaceutical Sciences JF - Asia-Pacific Journal of Pharmaceutical Sciences JO - Asia-Pacific Journal of Pharmaceutical Sciences SP - 24 EP - 27 PB - Science Publishing Group UR - http://www.sciencepg.com/article/10045248 AB - Coptis chinensis is a famous medicinal plant, which belongs to Coptis of Ranunculaceae. In China it has been applied for more than 2,000 years, and it is also one of the key medicinal plants worldwide with the whole plants and extract. The genome of Coptis chinensis was investigated in order to accelerate the completion of its genome sequencing, promote its research in molecular breeding, genetic evolution and the excavation of important medicinal plant gene resources. Based on high-throughput sequencing technology, two libraries with fragment sequences about 270 bp were constructed. After performing double-terminal 270 bp (PE 270) sequencing, 49.82 Gb raw data was obtained. It was estimated that Coptis chinensis genome size was 1.06 Gb, the repeat sequence content was about 71.46%, the heterozygosity was about 0.24%, and the GC content was about 39.50%. The study showed that Coptis chinensis had complex geome with repeat and large sequence data. Therefore, three generation sequencing technology is recommended to construcut a 20 Kb library and test 100× Pacbio data, and construcut the 270 bp small library and test 50× illumina data, which will contribute to the acquisiton of high-quality complete genome map of Coptis chinensis. This study also provides basic data for mining functional genes of C. chinensis. VL - 1 IS - 3 ER -
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