蒲儿根基因组大小评估与特征分析

doi:10.14088/j.cnki.issn0439-8114.2026.05.032

湖北农业科学 ›› 2026, Vol. 65 ›› Issue (5): 214-220.doi: 10.14088/j.cnki.issn0439-8114.2026.05.032

蒲儿根基因组大小评估与特征分析

张鹏^1a, 张泽志², 游磊^1a,b,c,d, 郑兰兰^1a,b,c,d, 张勇洪^1a,b,c,d

1.湖北医药学院,a.基础医学院;b.药用植物及进化遗传学十堰市重点实验室;c.生物医药研究院;d.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:2026-01-12 出版日期:2026-05-25 发布日期:2026-05-26
通讯作者: 张勇洪(1986-),男,湖北襄阳人,教授,博士,主要从事中药基原研究与表观药理研究,(电子信箱)zhangyh@hbmu.edu.com。
作者简介:张鹏(2000-),男,湖北十堰人,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)zpe0701@163.com。
基金资助:
国家自然科学基金项目(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)

Genome size estimation and characterization of Sinosenecio oldhamianus

ZHANG Peng^1a, ZHANG Ze-zhi², YOU Lei^1a,b,c,d, ZHENG Lan-lan^1a,b,c,d, ZHANG Yong-hong^1a,b,c,d

1a. School of Basic Medical Sciences; 1b. Shiyan Key Laboratory of Medicinal Plants and Evolutionary Genetics; 1c. Institute of Biomedical Sciences; 1d. 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:2026-01-12 Published:2026-05-25 Online:2026-05-26

摘要/Abstract

摘要： 为明确药用植物蒲儿根（Sinosenecio oldhamianus）的基因组规模与序列组成特征,推动其基因组遗传资源的开发与利用,采用流式细胞术,以本氏烟草(Nicotiana benthamiana)为内参,估算蒲儿根基因组大小;基于Illumina NovaSeq 6000平台开展基因组survey测序,对测序数据进行K-mer分析,评估基因组杂合度、GC含量及重复序列占比,并通过NCBI NT数据库进行序列相似性比对。流式细胞术测算结果显示,蒲儿根基因组大小约为1 620 Mb。基于Illumina平台测序,共获得122.10 Gb高质量数据,平均测序深度65×。对蒲儿根基因组19-mer频率分布进行统计分析,其基因组大小约为1 725 Mb,GC含量为38.66%,整体分布均匀,未表现出明显偏向性,表明测序数据质量可靠且不存在显著外源污染。蒲儿根基因组的杂合度高达12.10%,重复序列占比49.20%,属于典型的高杂合度、高重复序列复杂基因组类型。NCBI NT数据库比对结果显示,蒲儿根序列与止痢蚤草（Pulicaria dysenterica）参考序列的匹配率最高,其次为Gynoxys mandonii、蒲儿根（Sinosenecio oldhamianus）及长叶铁线莲（Morina longifolia）。

关键词: 蒲儿根（Sinosenecio oldhamianus）, 本氏烟草(Nicotiana benthamiana), 流式细胞术, K-mer分析, 基因组大小, 药用植物, 特征分析

Abstract: To determine the genome size and sequence composition characteristics of the medicinal plant Sinosenecio oldhamianus and to promote the development and utilization of its genome genetic resources, flow cytometry was used with Nicotiana benthamiana as a reference to estimate the genome size of Sinosenecio oldhamianus. Based on the Illumina NovaSeq 6000 platform, genome survey sequencing was conducted, K-mer analysis was performed on the sequencing data to evaluate genome heterozygosity, GC content, and repetitive sequence proportion, and sequence similarity comparison was carried out through the NCBI NT database. Flow cytometry measurement results showed that the genome size of Sinosenecio oldhamianus was approximately 1 620 Mb. Based on Illumina platform sequencing, a total of 122.10 Gb of high-quality data was obtained, with an average sequencing depth of 65×. Statistical analysis of the 19-mer frequency distribution of the Sinosenecio oldhamianus genome showed that its genome size was approximately 1 725 Mb, GC content was 38.66%, and the overall distribution was uniform without obvious bias, indicating that the sequencing data quality was reliable and there was no significant exogenous contamination. The heterozygosity of the Sinosenecio oldhamianus genome was as high as 12.10%, and the repetitive sequence proportion was 49.20%, indicating that it belonged to a typical complex genome type with high heterozygosity and high repetitive sequence content. The NCBI NT database comparison results showed that the sequences of Sinosenecio oldhamianus had the highest matching rate with the reference sequence of Pulicaria dysenterica, followed by Gynoxys mandonii, Sinosenecio oldhamianus, and Morina longifolia.

Key words: Sinosenecio oldhamianus, Nicotiana benthamiana, flow cytometry, K-mer analysis, genome size, medicinal plant, characterization

中图分类号:

S567.23

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.

ZHANG Peng, ZHANG Ze-zhi, YOU Lei, ZHENG Lan-lan, ZHANG Yong-hong. Genome size estimation and characterization of Sinosenecio oldhamianus[J]. HUBEI AGRICULTURAL SCIENCES, 2026, 65(5): 214-220.

参考文献

[1] SUN Y, ZHANG C, PENG J, et al.The plastid genome and phylogenetic status of Sinosenecio eriopodus C. Jeffrey & Y. L. Chen 1984 (Asteraceae)[J].Mitochondrial DNA part B-resources,2025,10(1):26-31.
[2] 杨茹, 曾献磊, 王彩芳. 2-甲基-6-(2-甲苯基)-2-庚烯的波谱学研究[J]. 波谱学杂志, 2014, 31(2): 262-267.
[3] 吴文武,吴立军. 千里光属植物的化学成分研究进展[J]. 中国中药杂志, 2003, 28(2): 97-100.
[4] 梁爱华,叶祖光. 千里光属植物的毒性研究进展[J]. 中国中药杂志, 2006, 31(2): 93-97.
[5] 石瑛,王瑞祥,胡变芳. 山西省野生菊科药用植物资源研究[J]. 安徽农业科学, 2010, 38(23): 12462-12466.
[6] WU M,WU Y,LI R,et al.Genus senecio in China: A review on its traditional uses, phytochemistry, pharmacology, and toxicity[J]. Journal of ethnopharmacology, 2025, 347: 119651.
[7] DOLEZEL J, BARTOS J.Plant DNA flow cytometry and estimation of nuclear genome size[J]. Ann Bot, 2005, 95(1): 99-110.
[8] HARDIE D C,GREGORY T R,HEBERT P D.From pixels to picograms: a beginners’ guide to genome quantification by Feulgen image analysis densitometry[J]. J Histochem Cytochem,2002,50(6):735-749.
[9] DOLEZEL J, GREILHUBER J, SUDA J.Estimation of nuclear DNA content in plants using flow cytometry[J]. Nat Protoc, 2007, 2(9): 2233-2244.
[10] 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.
[11] 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.
[12] 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.
[13] 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.
[14] 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-resources, 2024, 9(8): 1015-1019.
[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] 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.
[17] 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(2024-09-03).https://kns.cnki.net/kcms2/article/abstractv=Jz5IuRg0t00PPCreCX6_k88SW6DB-9Ee6VsaiFocorwiD6PohqYjvZ6yCCGDCQPZOTX0BGvGDZbNv5C44-CFrbXLeRGUlNLX4F51sDQaI1VcjHyFD_t7yXZMC6PmYtMR20MDoJ-cXfPDaUc9J-SMfc_JkeSIjKaiCwtAYnPrqzJubvg4QMoWEA==&uniplatform=NZKPT&language=CHS.
[18] 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.
[19] 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(2025-04-18).https://kns.cnki.net/kcms2/article/abstractv=Jz5IuRg0t00_RfzCpsS0-0rXt6Lv5MZUekpSuGFghmep5kjJAO7izI2v5IPRVP2dnUUSmRPI48X8SNlnwdJRCbSJVr45IC_HqDev3vfvK3JY6cw-lJ21z8p0ZhfbWzBruu2yBI85qZSs7opyhrzhZ9g9DTA4qKXskCNJg5GVwR1JeJOWxppOTg==&uniplatform=NZKPT&language=CHS.
[20] 蒲昕颖, 陈晓娇, 王欣格,等. 基于流式细胞术和基因组Survey的红大戟基因组大小测定和分析[J/OL]. 分子植物育种: 1-13(2022-10-28).https://kns.cnki.net/kcms2/article/abstractv=Jz5Iu Rg0t01jMVrkVQqp44XRozjFNRuEE2pEkjT9INEtTXybC2oMASf 0JMFUAzBLkxXyxo6-cOI14brZeClgSO_Jz9hg9wp94A3XCBer9S MGZbojJq-hXpKmwmBJqL-KY9FNe-Y46_GABzZv-uDZlfHAk JTZ80Wl3UHWzdKSLu2uTvsysw9lEQ==&uniplatform=NZKPT&
language=CHS.
[21] CHEN Y, CHEN Y, SHI C, et al.SOAPnuke: A MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data[J]. Gigascience, 2018, 7(1): 1-6.
[22] DE SENA BRANDINE G,SMITH A D. Falco: High-speed fastQC emulation for quality control of sequencing data[J]. F1000Res,2019, 8: 1874.
[23] 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.
[24] LIU B, SHI Y, YUAN J, 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.
[25] VURTURE G W, SEDLAZECK F J, NATTESTAD M, et al.GenomeScope: Fast reference-free genome profiling from short reads[J]. Bioinformatics, 2017, 33(14): 2202-2204.
[26] BOMBARELY A, ROSLI H G, VREBALOV J, et al.A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research[J]. Mol Plant Microbe Interact, 2012, 25(12): 1523-1530.
[27] ABOUL-MAATY N A F,ORABY H A S. Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method[J]. Bulletin of the national research centre, 2019, 43(1):25.
[28] 朱春染,徐江,杜梅丽,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.
[29] 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: 548.
[30] 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 (Basel),2022, 11(23):3322.
[31] PALAZZESI L, PELLICER J, BARREDA V D, et al.Asteraceae as a model system for evolutionary studies: From fossils to genomes[J]. Botanical journal of the linnean society, 2022, 200(2):143-164.
[32] STATON S E, BURKE J M.Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance[J]. BMC genomics, 2015, 16(1): 623.
[33] LIANG X Y, BAI T D, WANG J Z, et al.Genome survey and development of 13 SSR markers in Eucalyptus cloeziana by NGS[J]. J Genet, 2022, 101:39.
[34] ZHANG Z, ZHANG J, YANG Q, et al.Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers[J]. Molecular biology reports, 2021,48(1): 241-250.
[35] LU M, AN H, LI L.Genome survey sequencing for the characterization of the genetic background of Rosa roxburghii Tratt and leaf ascorbate metabolism genes[J].PLoS one,2016,11(2):e0147530.
[36] MCGINNIS S, MADDEN T L.BLAST: At the core of a powerful and diverse set of sequence analysis tools[J]. Nucleic acids research, 2004, 32: 20-25.
[37] HINCHLIFF C E, SMITH S A.Some limitations of public sequence data for phylogenetic inference (in plants)[J]. PLoS one, 2014, 9(7): e98986.

蒲儿根基因组大小评估与特征分析

Genome size estimation and characterization of Sinosenecio oldhamianus

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 12

编辑推荐

Metrics

本文评价

[1]	蔡阳光, 厉健康, 段龙飞, 覃剑锋, 吴峻琪. 花魔芋HSF基因家族全基因组鉴定与功能进化特征分析[J]. 湖北农业科学, 2026, 65(2): 215-222.
[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]	薛玉涵, 任助, 商雨, 唐国毅, 贾妙妙, 鲁岳峰, 李琼琼, 李慧敏, 罗青平, 温国元, 潘兹书, 赵宗正. 低致病性与高致病性H7N9亚型禽流感病毒分子特征及受体结合能力分析[J]. 湖北农业科学, 2020, 59(7): 212-217.
[7]	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.
[8]	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.
[9]	陈青, 唐佐阳, 吕校华, 唐娅琼, 杨科. 邵阳市多普勒雷达产品在人工防雹中的应用[J]. 湖北农业科学, 2019, 58(21): 97-103.
[10]	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.
[11]	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.
[12]	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.