流式细胞术和K-mer分析联用法测定三花莸基因组大小与特征

doi:10.14088/j.cnki.issn0439-8114.2026.07.021

湖北农业科学 ›› 2026, Vol. 65 ›› Issue (7): 133-139.doi: 10.14088/j.cnki.issn0439-8114.2026.07.021

流式细胞术和K-mer分析联用法测定三花莸基因组大小与特征

邓玉杰^1a,1b, 张泽志², 游磊^1a,1b, 张勇洪^1a,1b, 郑兰兰^1a,1b

1.湖北医药学院,a.基础医学院/药用植物及进化遗传学十堰市重点实验室; b.生物医药研究院/武当特色中药研究湖北省重点实验室,湖北十堰 442000;
2.十堰市农业科学院, 湖北十堰 442000

收稿日期:2026-03-18 出版日期:2026-07-25 发布日期:2026-07-23
通讯作者: 游磊(1989-),男,副教授,主要从事植物药道地性和表观药理研究及RPA、纳米抗体等相关新型实用技术研发,(电子信箱)youlei@hbmu.edu.cn。
作者简介:邓玉杰(2001-),女,贵州遵义人,在读硕士研究生,研究方向为中药基原研究与表观药理,(电子信箱)2571951059@qq.com。
基金资助:
国家自然科学基金项目(32000609; 32200680); 湖北医药学院PI项目(HBMUPI202104); 湖北省高等学校优秀中青年科技创新团队计划项目(T2023016); “十四五”湖北省高等学校优势特色学科群(生物与医药)项目(2022BMXKQT4)

Combined flow cytometry and K-mer analysis for genome size estimation and genomic characterization of Schnabelia terniflora

DENG Yu-jie^1a,1b, ZHANG Ze-zhi², YOU Lei^{1a, 1b}, ZHANG Yong-hong^1a,1b, ZHENG Lan-lan^1a,1b

1a. School of Basic Medicine/Shiyan Key Laboratory of Medicinal Plants and Evolutionary Genetics; 1b .Bio-medicine Research Academy/Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000,Hubei,China;
2. Shiyan Academy of Agricultural Sciences, Shiyan 442000,Hubei,China

Received:2026-03-18 Published:2026-07-25 Online:2026-07-23

摘要/Abstract

摘要： 为了深入挖掘三花莸(Schnabelia terniflora)的遗传背景并促进其基因组资源的开发,利用流式细胞术对三花莸进行基因组大小估算,以玉米作为对照植物;同时利用Illumina测序平台对三花莸基因组进行测定,借助K-mer工具分析三花莸基因组杂合度、GC含量等遗传信息,并进行NT比对。结果表明,流式细胞术估测三花莸基因组大小约为1 210 Mb。利用Illumina测序平台获取103.77 Gb的高质量数据,平均测序深度为73×,经测算,三花莸的基因组容量约为1 220 Mb,其杂合度为1.18%,GC含量为38.04%,重复序列比例为80.20%。对比发现,利用K-mer分析法得出的基因组大小与流式细胞术的检测结果基本吻合。此外,根据NT数据库比对结果,在所有已知序列的物种中,三花莸与盔状黄芩(Scutellaria galericulata)的reads匹配度最高(17.82%),其次为三花莸自身(10.44%)、黑球花[(Ballota nigra), 4.77%]、少花三花莸[(Schnabelia oligophylla), 3.24%]等植物。三花莸基因组具有较低的杂合度以及较高的重复序列比例。

关键词: 三花莸(Schnabelia terniflora), 流式细胞术, K-mer分析, 基因组大小, 药用植物

Abstract: To further elucidate the genetic background of Schnabelia terniflora and promote the development of its genomic resources, flow cytometry was used to estimate the genome size of Schnabelia terniflora, with maize used as the reference plant. Meanwhile, the genome of Schnabelia terniflora was sequenced using the Illumina sequencing platform, and K-mer analysis was used to analyze the heterozygosity, GC content, and other genetic information of the Schnabelia terniflora genome, followed by NT alignment. The results showed that the genome size of Schnabelia terniflora estimated by flow cytometry was approximately 1 210 Mb. A total of 103.77 Gb of high-quality data was obtained using the Illumina sequencing platform, with an average sequencing depth of 73×. The genome size of Schnabelia terniflora was estimated to be approximately 1 220 Mb, with a heterozygosity rate of 1.18%, a GC content of 38.04%, and a repetitive sequence proportion of 80.20%. A comparison revealed that the genome size estimated by K-mer analysis was basically consistent with the results detected by flow cytometry. In addition, according to the NT database alignment results, among all species with known sequences, the sequencing reads of Schnabelia terniflora showed the highest matching rate with Scutellaria galericulata (17.82%), followed by Schnabelia terniflora itself (10.44%), Ballota nigra (4.77%), Schnabelia oligophylla (3.24%), and other plants. The genome of Schnabelia terniflora exhibited relatively low heterozygosity and a high proportion of repetitive sequences.

Key words: Schnabelia terniflora, flow cytometry, K-mer analysis, genome size, medicinal plant

中图分类号:

Q949.777.6

邓玉杰, 张泽志, 游磊, 张勇洪, 郑兰兰. 流式细胞术和K-mer分析联用法测定三花莸基因组大小与特征[J]. 湖北农业科学, 2026, 65(7): 133-139.

DENG Yu-jie, ZHANG Ze-zhi, YOU Lei, ZHANG Yong-hong, ZHENG Lan-lan. Combined flow cytometry and K-mer analysis for genome size estimation and genomic characterization of Schnabelia terniflora[J]. HUBEI AGRICULTURAL SCIENCES, 2026, 65(7): 133-139.

参考文献

[1] CANTINO P D,WAGSTAFF S J,OLMSTEAD R G.Caryopteris (Lamiaceae) and the conflict between phylogenetic and pragmatic considerations in botanical nomenclature[J].Systematic botany,1998,23(3):369-386.
[2] 冉先德. 冉氏释名本草[M].长沙:湖南科学技术出版社,2008.
[3] 王红霞,王露露,郑岩,等.三花莸的生药学鉴别及微性状研究[J].中药材,2016,39(2):295-298.
[4] 张永红,陈革林,陈崇宏,等.三花莸的化学成分研究[J].中草药,2005,36(4):501-502.
[5] 国家中医药管理局《中华本草》编委会.中华本草-9[M].上海:上海科学技术出版社,1999.
[6] 郑晓珂,颜慧,李丹丹,等.三花莸的化学成分研究[J].中国药学杂志,2013,48(23):1997-2001.
[7] ZHAO Y, LIU Y X, ZHOU H X, et al.Characterisation and skin protection activities of polysaccharides from Schnabelia terniflora[J].Natural product research, 2024, 38(23): 4191-4195.
[8] WU Q G,YANG H L,SUN Y X,et al.Organogenesis and high-frequency plant regeneration in Caryopteris terniflora Maxim. using thidiazuron[J].In vitro cellular & developmental biology-plant,2021,57(1):39-47.
[9] 钟国跃,秦松云,钟廷渝,等. 羌族民间药用莸属植物的生药学鉴定[J].中国中药杂志,1993(7):392-394,446.
[10] 周印锁,李兆琳,朱加亮,等.三花莸挥发油化学成分的研究[J].植物研究,1993,13(4):394-398.
[11] 李阳,王杰敏,古军霞,等.人参叶绿体基因组密码子偏好性分析[J].分子植物育种,2025,23(3):926-934.
[12] 谢欣,贺黎铭,蔡凌,等.灵芝基因组学及其功能基因研究进展[J].农业生物技术学报,2025,33(4):898-910.
[13] MOURI H,TATSUMI M,NISHINO T,et al.The complete chloroplast genome of Taraxacum albidum (Asteraceae), a Japanese endemic dandelion[J].Mitochondrial DNA part B,2024,9(8):1015-1019.
[14] WEI S N,YING J N,LU M X,et al.Plastome comparison and phylogenomics of Chinese endemic Schnabelia (Lamiaceae): Insights into plastome evolution and species divergence[J].BMC plant biology,2025,25:600.
[15] ZHOU P,ZHANG Q,LI J,et al.A first insight into the genomic background of Ilex pubescens (Aquifoliaceae) by flow cytometry and genome survey sequencing[J].BMC genomics,2023,24(1):270.
[16] 于福来,黄梅,张影波,等.裸花紫珠基因组调研及SSR特征分析[J].中国中药杂志,2019,44(18):3974-3978.
[17] HARDIE D C,GREGORY T R,HEBERT P D N. From pixels to picograms: A beginners' guide to genome quantification by Feulgen image analysis densitometry[J].The journal of histochemistry and cytochemistry,2002, 50(6):735-749.
[18] DOLEŽEL J,BARTOŠ J. Plant DNA flow cytometry and estimation of nuclear genome size[J].Annals of botany,2005,95(1):99-110.
[19] 王利虎,张琼,陈凯,等.流式细胞术在植物倍性鉴定及基因组大小估测中的应用策略[J].分子植物育种,2021,19(17):5833-5841.
[20] DOLEŽEL J, GREILHUBER J, SUDA J. Estimation of nuclear DNA content in plants using flow cytometry[J]. Nature protocols, 2007, 2(9): 2233-2244.
[21] SHARMA S,KUMAR K,ARPITA K,et al.Flow cytometry and K-mer-based approach for genome size estimation of clusterbean: A case study[A].JAIN M,GARG R. Legume genomics[M].New York, NY,USA: Humana,2025.281-296.
[22] HESSE U.K-mer-based genome size estimation in theory and practice[A].HEITKAM T,GARCIA S. Plant cytogenetics and cytogenomics[M].New York,NY,USA:Humana,2023.79-113.
[23] 游磊,石宪铭,郑兰兰,等.联合流式细胞术和K-mer分析法测定活血丹基因组大小[J/OL].分子植物育种,1-11[2026-03-10].https://link.cnki.net/urlid/46.1068.S.20240903.0912.002.
[24] 罗湘胤,游磊,叶峥秀,等.药用植物冷水花DNA条形码分析和基因组大小测定[J].湖北医药学院学报,2024,43(1):13-17.
[25] 李琳,张泽志,罗湘胤,等.药用植物虎耳草的DNA条形码鉴定及基因组大小评估[J].湖北医药学院学报,2024,43(3):247-251.
[26] CHEN Y X,CHEN Y S,SHI C M,et al. SOAPnuke: A MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data[J].GigaScience, 2018, 7(1): gix120.
[27] 陈志威,张泽志,游磊,等.联合流式细胞术和K-mer分析法测定高粱泡基因组大小[J/OL].分子植物育种,1-12[2026-03-10].https://link.cnki.net/urlid/46.1068.S.20250418.0923.002.
[28] DE SENA BRANDINE G,SMITH A D.Falco:High-speed FastQC emulation for quality control of sequencing data[J].F1000Research,2019,8:1874.
[29] MARÇAIS G,KINGSFORD C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers[J].Bioinformatics,2011,27(6):764-770.
[30] LIU B H,SHI Y J,YUAN J Y,et al.Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects[J].Quantitative biology, 2013, 35(s1-3):62-67.
[31] 马秋月,王玉虓,李倩中,等.基于流式细胞术和K-mer方法测定6种槭属植物基因组大小[J].南京林业大学学报(自然科学版),2023,47(1):163-170.
[32] SUN S L,ZHOU Y S,CHEN J,et al.Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes[J].Nature genetics,2018,50(9):1289-1295.
[33] 朱楚然,徐娇,都明理,等.三岛柴胡基因组Survey分析及SSR位点挖掘[J].中国中药杂志,2019,44(18):3960-3966.
[34] TECHEN N,PARVEEN I,PAN Z Q,et al.DNA barcoding of medicinal plant material for identification[J]. Current opinion in biotechnology, 2014, 25: 103-110.
[35] PALHARES R M,GONÇALVES DRUMMOND M,DOS SANTOS ALVES FIGUEIREDO BRASIL B,et al. Medicinal plants recommended by the World Health Organization: DNA barcode identification associated with chemical analyses guarantees their quality[J].PLoS one,2015,10(5):e0127866.
[36] 石宪铭,张泽志,叶峥秀,等.联合流式细胞术和K-mer分析法测定半蒴苣苔基因组大小[J/OL].分子植物育种,1-10[2026-03-10].https://link.cnki.net/urlid/46.1068.S.20240914.1600.004.
[37] MONDEGO J M,CARAZZOLLE M F,COSTA G G,et al.A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao[J].BMC genomics,2008,9(1):548.
[38] 翟兆东,黄彦钧,赵泓,等.马齿苋的基因组大小估算及基因组调查测序[J].分子植物育种,2023,21(2):464-471.
[39] ZHOU P,LI J,HUANG J,et al.Genome survey sequencing and genetic background characterization of Ilex chinensis Sims (Aquifoliaceae) based on next-generation sequencing[J].Plants,2022, 11(23):3322.
[40] TIMP W,FEINBERG A P.Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host[J].Nature reviews cancer,2013,13(7):497-510.

流式细胞术和K-mer分析联用法测定三花莸基因组大小与特征

Combined flow cytometry and K-mer analysis for genome size estimation and genomic characterization of Schnabelia terniflora

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 10

编辑推荐

Metrics

本文评价

[1]	张鹏, 张泽志, 游磊, 郑兰兰, 张勇洪. 蒲儿根基因组大小评估与特征分析[J]. 湖北农业科学, 2026, 65(5): 214-220.
[2]	游磊, 朱哲慧, 石宪铭, 张泽志, 郑兰兰, 张勇洪. 基于ImageJ的药用植物黄精染色体核型分析[J]. 湖北农业科学, 2025, 64(4): 24-30.
[3]	李加太. 敦煌本吐蕃医学文献中的药用植物多样性研究[J]. 湖北农业科学, 2021, 60(7): 90-94.
[4]	苟文博, 杨中铎, 周格格. 四种药用植物内生真菌的分离及抗单胺氧化酶的活性研究[J]. 湖北农业科学, 2021, 60(3): 56-59.
[5]	郝俊霄, 靳文戈, 李良波, 黄荣韶, 唐辉, 甘凤琼. 四种药用植物在喀斯特生境下的生理特征及适生性[J]. 湖北农业科学, 2020, 59(9): 77-82.
[6]	肖冰, 余洁, 李雪银, 马跃灵, 李绍婷, 徐燃. 鄂西地区54种药用植物食用价值调查[J]. 湖北农业科学, 2020, 59(11): 76-80.
[7]	张洁, 龙主多杰, 亢俊铧, 拉本. 青海班玛地区藏族药用民族植物学研究[J]. 湖北农业科学, 2020, 59(1): 91-94.
[8]	郝爱平, 国会艳, 齐虹凌, 魏继承. 15种药用植物的GGPPS蛋白生物信息学分析[J]. 湖北农业科学, 2019, 58(2): 131-136.
[9]	马跃灵, 张娇, 杨欣平, 丁子安, 朱帆, 张绍鹏, 徐燃. 鄂西地区药用植物食用价值调查[J]. 湖北农业科学, 2018, 57(21): 80-82.
[10]	张宇, 张美德, 程天周. 恩施富硒区十种常见药用植物聚硒能力调查[J]. 湖北农业科学, 2018, 57(16): 14-15.