|
|
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
|
Abstract:
准确鉴定物种遗传多样性是植物资源保护和可持续利用的基础。兰属Cymbidium Sw.是单子叶植物，具有极高的观赏、药用和科研价值。由于形态特征受到发育阶段和环境条件的影响，不同学者对形态特征的理解和判断也存在差异，基于形态特征的兰属植物的鉴定存在困难。我们利用兰属的3个种的叶绿体基因组序列中的物种特有的1285个核苷酸变异位点作为分子性状编制分子鉴定检索表，成功鉴定供试样品。物种特有变异位点的数量和核苷酸构成存在种间差异。西藏虎头兰Cymbidium tracyanum L. Castle (1185)的特有变异位点的数量最多，分别是秋墨兰Cymbidium haematodes Lindl. (53)和莲瓣兰Cymbidium tortisepalum Fukuy. (47)的特有变异位点的数量的22倍和25倍。西藏虎头兰的特有变异位点中，A (31.39%)或T (30.97%)的比例明显高于C (20.08%)或G (17.55%)。莲瓣兰的特有变异位点中，A (21.28%)的比例略低于T (25.53%)、C (27.66%)或G (25.53%)的比例，T、C或G的比例差异较小。秋墨兰的特有变异位点中，C (32.08%)的比例明显高于T (18.87%)的比例，A (26.42%)和G (22.64%)的比例间于C的比例和T的比例之间，差异不大。结果显示，叶绿体基因组的单核苷酸变异位点信息，可用于兰属植物资源遗传多样性的分子鉴定。调查了中国过去120多年来兰属植物标本的收集和馆藏现状，讨论了存在的问题与对策。本研究对于兰属植物的分类修订、种质资源的保护和利用具有重要价值。
Accurate identification of genetic diversity is essential for conservation and sustainable utilization of plant resources. Plants of Cymbidium Sw. are extremely valuable for ornamental and medicinal uses as well as for scientific research. Since morphological characteristics are subjected to influences of developmental stages and environmental conditions, and there are differences among researchers in understanding and judgement on the morphological features, difficulties may occur in identification of Cymbidium plants. In this paper, 1285 taxon-specific variable nucleotide characters in the complete plastome of 3 species of Cymbidium were used as molecular traits to identify the plant genetic resource diversity of this plant genus and to compile a molecular classification key for the first time. There are differences in aspects of the amount and the base composition of variable nucleotide characters among the species. The amount of taxon-specific variable nucleotide characters in Cymbidium tracyanum L. Castle (1185) is the highest, being 22 times that of C. haematodes Lindl. (53) and 25 times that of C. tortisepalum Fukuy. (47). In C. tracyanum, the proportion of A (31.39%) or T (30.97%) is significantly higher than that of C (20.08%) or G (17.55%). The proportion of A (21.28%) is lower than that of T, C or G (25.53%~27.66%) in C. tortisepalum. In C. haematodes, the proportion of C (32.08%) is higher than that of T (18.87%), the proportion of A (26.42%) or G (22.64%) is between those of C and T which have minor differences in value. Our results indicated that taxon-specific variable nucleotide characters from the plastomes could be used for distinguishing different species
| [1] | 中国科学院中国植物志编辑委员会. 中国植物志第17卷: 兰科[M]. 北京: 科学出版社, 1999. https://www.iplant.cn/ |
| [2] | Wu, Z.Y., Hong, D.Y. and Raven, P.H. (2009) Flora of China, Vol. 25. Orchidaceae. Science Press, Beijing and Missouri Botanical Garden Press, St. Louis. https://www.iplant.cn/info/Orchidaceae?t=foc |
| [3] | 卢思聪, 张毓, 石雷, 赵世伟, 等. 世界栽培兰花百科图鉴[M]. 北京: 中国农业大学出版社, 2014: 50-51. |
| [4] | Guo, Y.Y., Luo, Y.B., Liu, Z.J., et al. (2012) Evolution and Biogeography of the Slipper Orchids: Eocene Vicariance of the Conduplicate Genera in the Old and New World Tropics. PLOS ONE, 7, e38788. https://doi.org/10.1371/journal.pone.0038788 |
| [5] | 罗毅波, 贾建生, 王春玲. 中国兰科植物保育的现状和展望[J]. 生物多样性, 2003, 11(1): 70-77. |
| [6] | 景袭俊, 胡凤荣. 兰科植物分子生物学研究进展[J]. 分子植物育种, 2018, 16(15): 5835-5848. |
| [7] | 杨明志, 单玉莹, 陈晓梅, 张朝凤, 李振坚. 中国石斛产业发展现状分析与考量[J]. 中国现代中药, 2022, 24(8): 1395-1402. |
| [8] | 傅巧娟, 李春楠, 赵福康, 孙瑶. 7种兰属种质表型性状遗传多样性分析[J]. 分子植物育种, 2018, 16(10): 3381-3394. |
| [9] | 王慧中, 王玉东, 周晓云, 应奇才, 郑康乐. 兰属14种植物遗传多样性RAPD及AFLP分析[J]. 实验生物学报, 37(6): 482-486. |
| [10] | 吴振兴, 王慧中, 施农农, 赵艳. 兰属Cymbidium植物ISSR遗传多样性分析[J]. 遗传, 2008, 30(5): 627-632. |
| [11] | Sharma, S.K., Dkhar, J., Kumaria, S., et al. (2012) Assessment of Phylogenetic Inter-Relationships in the Genus Cymbidium (Orchidaceae) Based on Internal Transcribed Spacer Region of rDNA. Gene, 495, 10-15. https://doi.org/10.1016/j.gene.2011.12.052 |
| [12] | 巫伟峰, 陈孝丑, 陈发兴, 陈春, 张毅智. 基于ITS2序列探讨兰属的DNA条形码鉴定和系统发育关系[J]. 浙江农业学报, 2019, 31(8): 1295-1304. |
| [13] | Zhang, L., Huang, Y.W., Huang, J.L., et al. (2023) DNA Barcoding of Cymbidium by Genome Skimming: Call for Next-Generation Nuclear Barcodes. Molecular Ecology Resources, 23, 424-439. https://doi.org/10.1111/1755-0998.13719 |
| [14] | 李明河. 兰科分子系统重建与生物地理学研究[D]: [博士学位论文]. 福州: 福建农林大学, 2015. |
| [15] | 胡国家. 兰科兜兰属与兰属植物比较叶绿体基因组学与系统发育研究[D]: [硕士学位论文]. 西安: 西北大学, 2020. |
| [16] | Yang, J.B., Tang, M., Li, H.T., Zhang, Z.R. and Li, D.Z. (2013) Complete Chloroplast Genome of the Genus Cymbidium: Lights into the Species Identification, Phylogenetic Implications and Population Genetic Analyses. BMC Evolutionary Biology, 13, Article No. 84. https://doi.org/10.1186/1471-2148-13-84 |
| [17] | Chen, H.Y., Zhang, Z.R., Yao, X., Ya, J.D. Jin, X.H., Wang, L., Lu, L., Li, D.Z., Yang, J.B. and Yu, W.B. (2024) Plastid Phylogenomics Provides New Insights into the Systematics, Diversification, and Biogeography of Cymbidium (Orchidaceae). Plant Diversity. https://doi.org/10.1016/j.pld.2024.03.001 |
| [18] | Dong, W.P., Xu, C., Li, D.L., Jin, X.B., Li, R.L., Lu, Q. and Suo Z.L. (2016) Comparative Analysis of the Complete Chloroplast Genome Sequences in Psammophytic Haloxylon Species (Amaranthaceae). PeerJ, 4, e2699. https://doi.org/10.7717/peerj.2699 |
| [19] | Dong, W.P., Xu, C., Li, W.Q., Xie, X.M., Lu, Y.Z., Liu, Y.L., Jin, X.B. and Suo, Z.L. (2017) Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences. Frontiers in Plant Science, 8, Article No. 1148. https://doi.org/10.3389/fpls.2017.01148 |
| [20] | Xu, C., Dong, W.P., Li, W.Y., Lu, Y.Z., Xie, X.M., Jin, X.B., Shi, J.P., He, K.H. and Suo, Z.L. (2017) Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes. Frontiers in Plant Science, 8, Article No. 15. https://doi.org/10.3389/fpls.2017.00015 |
| [21] | Li, W.Q., Liu, Y.L., Yang, Y., Xie, X.M., Lu, Y.Z., Yang, Z.R., Jin, X.B., Dong, W.P. and Suo, Z.L. (2018) Interspecific Chloroplast Genome Sequence Diversity and Genomic Resources in Diospyros. BMC Plant Biology, 18, Article No. 210. https://doi.org/10.1186/s12870-018-1421-3 |
| [22] | Dong, W.P., Xu, C., Liu, Y.L., Shi, J.P., Li, W.Y. and Suo, Z.L. (2021) Chloroplast Phylogenomics and Divergence Times of Lagerstroemia (Lythraceae). BMC Genomics, 22, Article No. 434. https://doi.org/10.1186/s12864-021-07769-x |
| [23] | Guo, C., Liu, K.J., Li, E.Z., Chen, Y.F., He, J.Y., Li, W.Y., Dong, W.P. and Suo, Z.L. (2023) Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars. International Journal of Molecular Sciences, 24, Article No. 3606. https://doi.org/10.3390/ijms24043606 |
| [24] | Suo, Z.L., Zhang, C.H., Zheng, Y.Q., He, L.X., Jin, X.B., Hou, B.X. and Li, J.J. (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. https://doi.org/10.1007/s00299-012-1330-0 |
| [25] | Suo, Z.L., Chen, L.N., Pei, D., Jin, X.B. and Zhang, H.J. (2015) A New Nuclear DNA Marker from Ubiquitin Ligase Gene Region for Genetic Diversity Detection of Walnut Germplasm Resources. Biotechnology Reports, 5, 40-45. https://doi.org/10.1016/j.btre.2014.11.003 |
| [26] | Suo, Z.L., Li, W.Y., Jin, X.B. and Zhang, H.J. (2016) A New Nuclear DNA Marker Revealing both Microsatellite Variations and Single Nucleotide Polymorphic Loci: A Case Study on Classification of Cultivars in Lagerstroemia indica L. Journal of Microbial & Biochemical Technology, 8, 266-271. https://doi.org/10.4172/1948-5948.1000296 |
| [27] | 李文清, 杨勇, 解孝满, 鲁仪增, 常青, 靳晓白, 索志立. E3泛素-蛋白连接酶UPL3 DNA序列揭示德阳柿和油柿为栽培柿的最近缘物种[J]. 农业科学, 2018, 8(6): 657-673. |
| [28] | 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. |
| [29] | 刘儒, 潘文婷, 李斌, 靳晓白, 李锐丽, 索志立. 利用叶绿体全基因组的单核苷酸多态位点对鹅掌楸和北美鹅掌楸的分子鉴定[J]. 农业科学, 2022, 12(11): 1098-1108. |
| [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. |
| [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. |
| [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. https://www.hanspub.org/journal/PaperInformation?paperID=87157 |
| [33] | 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. https://doi.org/10.1093/molbev/mst010 |
| [34] | 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. https://doi.org/10.1093/molbev/msw054 |
| [35] | Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado P., Ramos-Onsins, S.E. and Sán chez-Gracia, A. (2017) DnaSP6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Biology and Evolution, 34, 3299-3302. https://doi.org/10.1093/molbev/msx248 |
| [36] | Tan, K., Pastor, L.M. and Ren, M.X. (2020) Origin and Evolution of Biodiversity Hotspots in Southeast Asia. Acta Ecologica Sinica, 40, 3866-3877. |
| [37] | Goodwin, Z.A., Harris, D.J., Filer, D., Wood, J.R.I. and Scotland, R.W. (2015) Wide Spread Mistaken Identity in Tropical Plant Collections. Current Biology, 25, R1057-R1069. https://doi.org/10.1016/j.cub.2015.10.002 |
| [38] | 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. |
| [39] | 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. |
| [40] | Karbstein, K., K？sters, L., Hoda？, L., et al. (2024) Species Delimitation 4.0: Integrative Taxonomy Meets Artificial Intelligence. Trends in Ecology & Evolution. https://doi.org/10.1016/j.tree.2023.11.002 |
