基于叶绿体全基因组序列中的物种特有变异位点的木樨科植物资源遗传多样性的分子鉴定新方法
A Novel Molecular Identification Method for Assessing Genetic Diversity of Oleaceae Plant Resources Based on Taxon-Specific Variable Nucleotide Sites in Chloroplast Genome Sequences
DOI: 10.12677/jocr.2026.141003, PDF,    国家自然科学基金支持
作者: 刘美辰：北京市食品检验研究院(北京市食品安全监控和风险评估中心)，北京；左云娟：中国科学院东南亚生物多样性研究中心，云南 勐腊；中国科学院西双版纳热带植物园综合保护中心，云南 勐腊；李 斌*：中国林业科学研究院林业研究所，北京；中国林业科学研究院林木遗传和育种国家重点实验室，北京；严志宏*：江西中医药大学实验室服务中心，江西 南昌；靳晓白：国家植物园，北京；杨志荣：中国科学院植物研究所国家植物标本馆，北京；韩宜彤：河北师范大学生命科学学院，河北 石家庄；郭明星：汉中市茶业发展中心，陕西 汉中；索志立*：中国科学院植物研究所系统与进化植物学国家重点实验室，北京
关键词: 木樨科；植物资源多样性；叶绿体基因组；物种特有的核苷酸变异位点；分子鉴定；Oleaceae； Plant Resources Diversity； Chloroplast Whole-Genome Sequence； Taxon-Specific Variable Nucleotide Sites； Molecular Identification
摘要: 准确鉴定植物的遗传多样性是资源保护与可持续利用的基础。木樨科植物具有极高的食用、药用、观赏价值，同时在经济与生态保护方面也发挥着重要作用。由于植物的表型特征会受到发育阶段和环境条件的影响，不同学者对表型特征的理解和判断存在差异，导致基于表型特征的木樨科植物鉴定存在困难。本研究利用木樨科17个样品的叶绿体全基因组序列，从中筛选出物种特有的1114个核苷酸变异位点作为分子性状，并以此编制分子鉴定检索表，成功鉴定了供试样品。研究发现，物种特有的变异位点数量以及核苷酸构成，在属/种/亚种之间存在明显差异。结果显示，叶绿体全基因组DNA序列中的单核苷酸变异位点信息，能够用于木樨科植物资源遗传多样性的分子鉴定。本研究对于推动木樨科植物的分类修订、资源保护和利用具有重要意义。
Abstract: Accurate identification of plant genetic diversity is the foundation for resource conservation and sustainable utilization. Oleaceae plants possess extremely high edible, medicinal, and ornamental values, while also playing significant roles in economic and ecological protection. As plant phenotypic traits are influenced by developmental stages and environmental conditions, differences in understanding and judgment among scholars regarding these traits lead to challenges in identifying Oleaceae plants based on phenotypic characteristics. This study utilized the chloroplast genome sequences of 17 Oleaceae samples to screen 1114 taxon-specific nucleotide variation sites as molecular characters, based on which a molecular identification key was developed, successfully identifying the tested samples. The study found that both the number of taxon-specific variation sites and nucleotide composition exhibited significant differences among genera, species, and subspecies. The results showed that single nucleotide variation site information in chloroplast whole-genome DNA sequences can be used for molecular identification of genetic diversity in Oleaceae plant resources. This study holds significant importance for advancing taxonomic revision, resource conservation, and utilization of Oleaceae plants.
文章引用：刘美辰, 左云娟, 李斌, 严志宏, 靳晓白, 杨志荣, 韩宜彤, 郭明星, 索志立. 基于叶绿体全基因组序列中的物种特有变异位点的木樨科植物资源遗传多样性的分子鉴定新方法[J]. 有机化学研究, 2026, 14(1): 28-41. https://doi.org/10.12677/jocr.2026.141003

参考文献

[1] 中国科学院中国植物志编辑委员会. 中国植物志第61卷: 木樨科[M]. 北京: 科学出版社, 1992.
https://www.iplant.cn/info/Oleaceae?t=z
[2] Wu, Z.Y., Hong, D.Y. and Raven, P.H. (1996) Oleaceae. Flora of China, 15, 272-319.
https://www.iplant.cn/foc/pdf/Oleaceae.pdf
[3] The Angiosperm Phylogeny Group (2016) An Update of the Angiosperm Phylogeny Group Classification for the Orders and Families of Flowering Plants: APG Iv. Botanical Journal of the Linnean Society, 181, 1-20. [Google Scholar] [CrossRef] 
[4] Qian, Y., Shan, L., Zhao, R., Tang, J., Zhang, C., Chen, M., et al. (2023) Recent Advances in Flower Color and Fragrance of Osmanthus fragrans. Forests, 14, Article 1403. [Google Scholar] [CrossRef] 
[5] Yang, J., Gu, T., Lu, Y., Xu, Y., Gan, R., Ng, S.B., et al. (2023) Edible Osmanthus fragrans Flowers: Aroma and Functional Components, Beneficial Functions, and Applications. Critical Reviews in Food Science and Nutrition, 64, 10055-10068. [Google Scholar] [CrossRef] [PubMed]
[6] Chen, H., Ying, J., An, H., Chen, Y., Huang, Y., Jiang, Y., et al. (2025) Chinese Jasmine Tea: The Harmonious Intertwining of Tea and Jasmine Fragrance. Comprehensive Reviews in Food Science and Food Safety, 24, e70210. [Google Scholar] [CrossRef] [PubMed]
[7] 王昱. 油橄榄资源研究与综合开发利用[M]. 长春: 吉林大学出版社, 2024.
[8] 国家药典委员会. 中华人民共和国药典[M]. 北京: 中国医药科技出版社, 2020.
[9] Wang, J., Ding, Y., Li, Y., Gao, X., Kong, X., Long, F., et al. (2024) Allopolyploidization Events and Immense Paleogenome Reshuffling Underlying the Diversification of Plants and Secondary Metabolites in Oleaceae. Journal of Systematics and Evolution, 63, 208-228. [Google Scholar] [CrossRef] 
[10] Dupin, J., Hong-Wa, C., Gaudeul, M. and Besnard, G. (2024) Phylogenetics and Biogeography of the Olive Family (Oleaceae). Annals of Botany, 134, 577-592. [Google Scholar] [CrossRef] [PubMed]
[11] Stearn, W.T. (1976) Union of Chionanthus and Linociera (Oleaceae). Annals of the Missouri Botanical Garden, 63, 355-357. [Google Scholar] [CrossRef] 
[12] Banfi, E. (2014) Chrysojasminum, a New Genus for Jasminum Sect. Alternifolia (Oleaceae, Jasmineae). Natural History Sciences, 1, 3-6. [Google Scholar] [CrossRef] 
[13] Batool, T., Zafar, M., Elshikh, M.S., Mustafa, A.E.M.A., Ahmad, M., Makhkamov, T., et al. (2024) Foliar Epidermal Micromorphology: A Contribution to the Taxonomy of Family Oleaceae. Genetic Resources and Crop Evolution, 72, 1853-1880. [Google Scholar] [CrossRef] 
[14] Li, Y., Zhang, M., Wang, X., Sylvester, S.P., Xiang, Q., Li, X., et al. (2020) Revisiting the Phylogeny and Taxonomy of Osmanthus (Oleaceae) Including Description of the New Genus Chengiodendron. Phytotaxa, 436, 283-292. [Google Scholar] [CrossRef] 
[15] Dong, W., Li, E., Liu, Y., Xu, C., Wang, Y., Liu, K., et al. (2022) Phylogenomic Approaches Untangle Early Divergences and Complex Diversifications of the Olive Plant Family. BMC Biology, 20, Article No. 92. [Google Scholar] [CrossRef] [PubMed]
[16] Harborne, J.B. and Green, P.S. (1980) A Chemotaxonomic Survey of Flavonoids in Leaves of the Oleaceae. Botanical Journal of the Linnean Society, 81, 155-167. [Google Scholar] [CrossRef] 
[17] Wallander, E. and Albert, V.A. (2000) Phylogeny and Classification of Oleaceae Based on rps16 and trnL‐F Sequence Data. American Journal of Botany, 87, 1827-1841. [Google Scholar] [CrossRef] [PubMed]
[18] Hong-Wa, C. and Besnard, G. (2013) Intricate Patterns of Phylogenetic Relationships in the Olive Family as Inferred from Multi-Locus Plastid and Nuclear DNA Sequence Analyses: A Close-Up on Chionanthus and Noronhia (Oleaceae). Molecular Phylogenetics and Evolution, 67, 367-378. [Google Scholar] [CrossRef] [PubMed]
[19] Hong-Wa, C, Dupin, J., Frasier, C., Schatz, G.E. and Besnard, G. (2023) Systematics and Biogeography of Oleaceae Subtribe Schreberinae, with Recircumscription and Revision of the Malagasy Members. Botanical Journal of the Linnean Society, 202, 476-509. [Google Scholar] [CrossRef] 
[20] Liu, Y., Shen, F., Wang, L., Dou, J., Dong, T., Li, M., et al. (2025) Accelerating Moss Identification through the Development of Specific DNA Barcodes Based on the Whole Chloroplast Genome. Molecular Ecology Resources, 25, e70004. [Google Scholar] [CrossRef] [PubMed]
[21] Dong, W., Xu, C., Li, D., Jin, X., Li, R., Lu, Q., et al. (2016) Comparative Analysis of the Complete Chloroplast Genome Sequences in Psammophytic Haloxylon Species (Amaranthaceae). PeerJ, 4, e2699. [Google Scholar] [CrossRef] [PubMed]
[22] Dong, W., Xu, C., Li, W., Xie, X., Lu, Y., Liu, Y., et al. (2017) Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences. Frontiers in Plant Science, 8, Article 1148. [Google Scholar] [CrossRef] [PubMed]
[23] Xu, C., Dong, W., Li, W., Lu, Y., Xie, X., Jin, X., et al. (2017) Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes. Frontiers in Plant Science, 8, Article 15. [Google Scholar] [CrossRef] [PubMed]
[24] Li, W., Liu, Y., Yang, Y., Xie, X., Lu, Y., Yang, Z., et al. (2018) Interspecific Chloroplast Genome Sequence Diversity and Genomic Resources in Diospyros. BMC Plant Biology, 18, Article No. 210. [Google Scholar] [CrossRef] [PubMed]
[25] Dong, W., Xu, C., Liu, Y., Shi, J., Li, W. and Suo, Z. (2021) Chloroplast Phylogenomics and Divergence Times of Lagerstroemia (Lythraceae). BMC Genomics, 22, Article No. 434. [Google Scholar] [CrossRef] [PubMed]
[26] Guo, C., Liu, K., Li, E., Chen, Y., He, J., Li, W., et al. (2023) Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars. International Journal of Molecular Sciences, 24, Article 3606. [Google Scholar] [CrossRef] [PubMed]
[27] Suo, Z., Zhang, C., Zheng, Y., He, L., Jin, X., Hou, B., et al. (2012) Revealing Genetic Diversity of Tree Peonies at Micro-Evolution Level with Hyper-Variable Chloroplast Markers and Floral Traits. Plant Cell Reports, 31, 2199-2213. [Google Scholar] [CrossRef] [PubMed]
[28] Suo, Z., Chen, L., Pei, D., Jin, X. and Zhang, H. (2015) A New Nuclear DNA Marker from Ubiquitin Ligase Gene Region for Genetic Diversity Detection of Walnut Germplasm Resources. Biotechnology Reports, 5, 40-45. [Google Scholar] [CrossRef] [PubMed]
[29] 索志立, 顾翠花, 左云娟, 杨志荣, 孙忠民, 杨强发, 靳晓白. 利用叶绿体基因组大单拷贝区的单核苷酸多态位点鉴定紫薇属和马尾藻属植物[J]. 植物学研究, 2022, 11(2): 218-228. [Google Scholar] [CrossRef] 
[30] 李斌, 左云娟, 刘艳磊, 杨志荣, 靳晓白, 潘伯荣, 常青, 索志立. 基于叶绿体基因组的单核苷酸多态位点的落叶松属(Larix Mill.)植物的分子鉴定新方法[J]. 植物学研究, 2023, 12(4): 227-239. [Google Scholar] [CrossRef] 
[31] 刘美辰, 左云娟, 刘艳磊, 杨志荣, 靳晓白, 索志立. 基于叶绿体全基因组核苷酸变异位点的大豆属(Glycine Willd.)植物的分子鉴定新方法[J]. 植物学研究, 2024, 13(2): 124-142. [Google Scholar] [CrossRef] 
[32] 刘美辰, 张建农, 左云娟, 杨志荣, 靳晓白, 潘伯荣, 常青, 索志立. 基于叶绿体全基因组序列变异位点的葫芦科植物资源遗传多样性的分子鉴定新方法[J]. 植物学研究, 2024, 13(3): 289-314. [Google Scholar] [CrossRef] 
[33] 刘美辰, 李斌, 左云娟, 靳晓白, 索志立. 基于质体基因组序列变异位点的松科油杉属和冷杉属植物资源遗传多样性的分子鉴定新方法[J]. 植物学研究, 2024, 13(4): 434-445. [Google Scholar] [CrossRef] 
[34] 刘美辰, 刘一心, 左云娟, 靳晓白, 杨志荣, 索志立. 基于叶绿体基因组变异位点的百合属(百合科)植物资源遗传多样性的分子鉴定新方法[J]. 植物学研究, 2024, 13(4): 469-486. [Google Scholar] [CrossRef] 
[35] 刘美辰, 左云娟, 靳晓白, 杨志荣, 索志立. 基于叶绿体基因组变异位点的兰属(兰科)植物资源遗传多样性的分子鉴定新方法[J]. 计算生物学, 2024, 14(2): 13-28. [Google Scholar] [CrossRef] 
[36] 刘美辰, 汪星辰, 李冬芳, 严志宏, 左云娟, 靳晓白, 杨志荣, 索志立. 基于叶绿体基因组变异位点的葛属(豆科)植物资源遗传多样性的分子鉴定新方法[J]. 分析化学进展, 2024, 14(3): 164-175. [Google Scholar] [CrossRef] 
[37] 刘美辰, 郑勇奇, 李斌, 左云娟, 靳晓白, 杨志荣, 田宏, 郭明星, 索志立. 基于叶绿体基因组的单核苷酸多态位点的松属(松科)植物资源遗传多样性的分子鉴定新方法[J]. 植物学研究, 2024, 13(6): 574-590. [Google Scholar] [CrossRef] 
[38] Katoh, K. and Standley, D.M. (2013) MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30, 772-780. [Google Scholar] [CrossRef] [PubMed]
[39] Kumar, S., Stecher, G. and Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution, 33, 1870-1874. [Google Scholar] [CrossRef] [PubMed]
[40] Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E., et al. (2017) Dnasp 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Biology and Evolution, 34, 3299-3302. [Google Scholar] [CrossRef] [PubMed]
[41] Goodwin, Z.A., Harris, D.J., Filer, D., Wood, J.R.I. and Scotland, R.W. (2015) Widespread Mistaken Identity in Tropical Plant Collections. Current Biology, 25, R1066-R1067. [Google Scholar] [CrossRef] [PubMed]
[42] Liu, M.C., Zuo, Y.J., Li, B., Jin, X.B., Yang, Z.R. and Suo, Z.L. (2025) Correct Names, Synonyms, and Specimen Composition of Oleaceae in Chinese Herbarium Collections. Journal on Communications, 20, 1-22.
https://jocs.review/volume-20-issue-11-2025/
[43] Turland, N.J., Wiersema, J.H., Barrie, F.R., Gandhi, K.N., Gravendyck, J., Greuter, W., et al. (2025) International Code of Nomenclature for algae, fungi, and plants (Madrid Code). University of Chicago Press.
[44] 白佩瑜. 西藏木犀科新植物[J]. 云南植物研究, 1979, 1(1): 151-156.
[45] 洪德元. 生物多样性事业需要科学、可操作的物种概念[J]. 生物多样性, 2016, 24(9): 979-999. [Google Scholar] [CrossRef] 
[46] 王文采, 等. 世界植物简志[M]. 北京: 北京出版集团北京出版社, 2021: 1-172.
[47] Lenton, T.M., Milkoreit, M., Willcock, S., Abrams, J.F., Armstrong McKay, D.I., Buxton, J.E., et al. (2025) The Global Tipping Points Report 2025. University of Exeter.
https://global-tipping-points.org/resources-gtp-2025
[48] Krämer, C., Boehm, C.R., Liu, J., Ting, M.K.Y., Hertle, A.P., Forner, J., et al. (2024) Removal of the Large Inverted Repeat from the Plastid Genome Reveals Gene Dosage Effects and Leads to Increased Genome Copy Number. Nature Plants, 10, 923-935. [Google Scholar] [CrossRef] [PubMed]
[49] Boyle, E.A., Li, Y.I. and Pritchard, J.K. (2017) An Expanded View of Complex Traits: From Polygenic to Omnigenic. Cell, 169, 1177-1186. [Google Scholar] [CrossRef] [PubMed]
[50] Duan, S., Zeng, Y., Wang, H. and Jin, H. (2024) Coordination of Genome Stability: Novel Communication Pathways between Chloroplasts and Other Compartments in Plant Cells. Fundamental Research. [Google Scholar] [CrossRef] 

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