| 基于流式细胞术和K-mer分析的苦豆子基因组大小估测 |
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| 引用本文： | 黄阿晶,周佳熠,李天泽,邢怡德,高飞,周宜君.基于流式细胞术和K-mer分析的苦豆子基因组大小估测[J].中草药,2019,50(24):6098-6102. |
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| 作者姓名： | 黄阿晶 周佳熠 李天泽 邢怡德 高飞 周宜君 |
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| 作者单位： | 中央民族大学生命与环境科学学院, 北京 100081,中央民族大学生命与环境科学学院, 北京 100081,中央民族大学生命与环境科学学院, 北京 100081,中央民族大学生命与环境科学学院, 北京 100081,中央民族大学生命与环境科学学院, 北京 100081,中央民族大学生命与环境科学学院, 北京 100081 |
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| 基金项目： | 国家自然科学基金资助项目（31370356）；国家自然科学基金资助项目（31670335）；中央民族大学学术团队建设项目（2015C8）；国家大学生创新训练计划（SHSY2016120010） |
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| 摘 要： | 目的 采用流式细胞术与K-mer分析方法对苦豆子基因组大小及杂合率进行估测，为其全基因组测序提供参考。方法 以大豆为内标，通过流式细胞仪检测大豆与苦豆子细胞DNA含量的倍数关系，计算苦豆子的基因组大小。采用二代测序技术进行苦豆子基因组调查测序，使用K-mer分析估测苦豆子基因组大小与杂合率。结果 采用流式细胞术测得苦豆子基因组大小约为1 749 Mb。K-mer分析结果表明，苦豆子基因组大小约为1 648 Mb，基因组杂合率为1.12%，杂合率较高。结论 苦豆子基因组大小约为1.7 Gb，杂合率较高，后续研究可采用三代PacBio进行80~100 X深度的测序开展全基因组测序研究。
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| 关 键 词： | 苦豆子 流式细胞术 K-mer分析 基因组大小 杂合率 |
| 收稿时间： | 2019/6/3 0:00:00 |
Flow cytometry and K-mer analysis estimates of genome size of Sophora alopecuroides |
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| HUANG A-jing,ZHOU Jia-yi,LI Tian-ze,XING Yi-de,GAO Fei and ZHOU Yi-jun.Flow cytometry and K-mer analysis estimates of genome size of Sophora alopecuroides[J].Chinese Traditional and Herbal Drugs,2019,50(24):6098-6102. |
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| Authors: | HUANG A-jing ZHOU Jia-yi LI Tian-ze XING Yi-de GAO Fei and ZHOU Yi-jun |
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| Institution: | College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China and College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China |
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| Abstract: | Objective In this study, flow cytometry and K-mer analysis were used to estimate genome size and hybridity percentage of Sophora alopecuroides, so as to provide reference for its genome sequencing. Methods Glycine max served as an internal reference, the multiple relationship between DNA content in Glycine max and S. alopecuroides cells was detected by flow cytometry, and the genome size of S. alopecuroides was calculated. Genome sequencing of S. alopecuroides was carried out using NGS technology, genome size and hybridity percentage of S. alopec uroides were estimated by K-mer analysis. Results The genome size of S. alopecuroides was about 1 749 Mb measured by flow cytometry. K-mer analysis showed that the genome size of S. alopecuroides was about 1 648 Mb, the hybridity percentage was 1.12%, and the percentage of repetitive sequence was high. Conclusion The genome size of S. alopecuroides was about 1.7 Gb with high hybridity percentage. The technology of combining Illumina and PacBio is recommended for future genome sequencing. |
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| Keywords: | Sophora alopecuroides L flow cytometry K-mer anaylsis genome size hybridity percentage |
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