| 基于本草基因组学应用流式细胞术和高通量测序技术检测人参基因组大小 |
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| 引用本文： | 张小燕,刘志香,廖保生,肖水明,徐江,盛玮. 基于本草基因组学应用流式细胞术和高通量测序技术检测人参基因组大小[J]. 世界科学技术-中医药现代化, 2017, 19(10): 1724-1728 |
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| 作者姓名： | 张小燕 刘志香 廖保生 肖水明 徐江 盛玮 |
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| 作者单位： | 1. 淮北师范大学生命科学学院 淮北 235000；2. 中国中医科学院中药研究所北京100700,2. 中国中医科学院中药研究所 北京 100700,2. 中国中医科学院中药研究所 北京 100700,2. 中国中医科学院中药研究所 北京 100700,2. 中国中医科学院中药研究所 北京 100700,1. 淮北师范大学生命科学学院 淮北 235000； |
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| 基金项目： | 国家自然科学基金项目（81503469）：基于微生态调节干预的人参皂苷代谢指征与肠道全微生物组关联分析（MiWAS）研究，负责人：肖水明；国家自然科学基金项目（81403053）：VeA蛋白协同调控灵芝有性发育与三萜类成分积累的机制研究，负责人：徐江。 |
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| 摘 要： | 人参（Ginseng）是五加科植物人参（Panax ginseng C. A. Mey.）的干燥根和根茎。由于其基因组数据的缺乏制约了人参基础研究和产业发展。本实验以水稻（Oryza sativa ssp. Nipponbare）和大豆（Glycine max(L.) Merrill）为内参，通过流式细胞术检测人参基因组大小约为3.42 Gb；同时，分别构建人参基因组插入片段大小为250 bp和500 bp的鸟枪法（shotgun）文库，利用Illumina Hiseq X Ten平台进行双端PE 150高通量测序，过滤原始测序数据后获得183.82 Gb高质量数据，K-mer分析法预估人参基因组大小为3.35 Gb，测序深度为54.87 X。本研究采用流式细胞术结合K-mer分析法测定人参基因组大小，为人参全基因组测序以及本草基因组学的研究提供基础数据。
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| 关 键 词： | 人参 基因组大小 流式细胞术 高通量测序 本草基因组学 |
| 收稿时间： | 2017-08-11 |
| 修稿时间： | 2017-10-20 |
Estimation of Genome Size of Ginseng Based on Herbgenomics by Flow Cytometric Analysis and High-throughput Sequence |
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| Zhang Xiaoyan,Liu Zhixiang,Liao Baosheng,Xiao Shuiming,Xu Jiang and Sheng Wei. Estimation of Genome Size of Ginseng Based on Herbgenomics by Flow Cytometric Analysis and High-throughput Sequence[J]. World Science and Technology—Modernization of Traditional Chinese Medicine and Materia Medica, 2017, 19(10): 1724-1728 |
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| Authors: | Zhang Xiaoyan Liu Zhixiang Liao Baosheng Xiao Shuiming Xu Jiang Sheng Wei |
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| Affiliation: | 1. College of Life Science, Huaibei Normal University, Huaibei 235000, China;2. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China,2. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China,2. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China,2. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China,2. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China and 1. College of Life Science, Huaibei Normal University, Huaibei 235000, China; |
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| Abstract: | Ginseng is the dried root and rhizome of Panax ginseng. The lack of genomic data has restricted thedevelopment of ginseng industry and basic research. The genome size of P. ginseng was estimated to be 3.42 Gb by usingthe genome data of Oryza sativa ssp. Nipponbare and Glycine max (L.) Merrill as the reference and the flow cytometricanalysis. Meanwhile, shotgun libraries with the insert size of 250 bp and 500 bp were constructed, and sequenced fordouble terminal PE 150 by using Illumina Hiseq X Ten platform. Totally, 183.82 Gb high quality data was obtained afterfiltering the raw data. The genome size of P. ginseng was 3.35 Gb and the sequencing depth was 54.87 X by K-meranalysis. In this study, flow cytometry and K-mer analysis were used to identify the genome size of ginseng, whichprovided basic data for the further whole genome sequencing and herbgenomics studies. |
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| Keywords: | Panax ginseng genome size flow cytometric analysis high-throughput sequence herbgenomics |
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