nrDNA-ITS区序列在植物系统与进化研究中的应用
Application of nrDNA-ITS Sequences in Plant Phylogeny and Evolution

作者: 刘锡红 , 张 磊 , 李 刚 , 覃 瑞 , 刘 虹 :中南民族大学生命科学学院,南方少数民族地区生物资源保护与综合利用工程中心,武汉;

关键词: ITS序列系统发育裸子植物被子植物高级结构ITS Sequence Phylogenetic Development Angiosperm Gymnosperm Advanced Structure

摘要:
本文就核rDNA (nrDNA)ITS区序列在植物系统与进化研究中的应用进行了讨论。nrDNA是植物系统发育研究中广泛应用的重要核基因片段5.8S rDNAnrDNA的内转录间隔区分为ITS1ITS2两部分。被子植物中ITS1的长度为165~298 bpITS2的长度为177~266 bp;裸子植物中ITS片段较长,且其长度变化主要由ITS1的长度变异所致。由于ITS序列变异较快,能够提供较丰富的变异位点和信息位点,已成为被子植物较低分类阶元的系统发育和分类研究中的重要分子标记,为探讨多倍体复合体网状进化关系,异源多倍体的起源提供了重要的系统学信息。

Abstract:
The application of nuclear rDNA ITS sequences in plant phylogeny and evolution analysis was discussed in this paper. Nuclear rDNA is an important nuclear gene fragment, which had been widely used in phylogenetic studies. The internal transcribed spacer of nuclear rDNA was divided into ITS1 and ITS2 by 5.8S rDNA. The length of ITS1 ranges from 165 bp to 298 bp in angiosperms, and the length of ITS2 ranges from 177 bp to 266 bp. ITS sequence is relatively longer in gymnosperms. It much depends on the length of ITS1. As mutate quickly, ITS sequences are capable of providing many variable sites and informative sites, which has become an important molecular marker in plant systematic development and classification researches within low-order angiosperm categories. AT the same time, it can prove important systematic information for exploring polyploidy reticulate evolution and allopolyploid origins.

文章引用: 刘锡红 , 张 磊 , 李 刚 , 覃 瑞 , 刘 虹 (2014) nrDNA-ITS区序列在植物系统与进化研究中的应用。 植物学研究, 3, 32-40. doi: 10.12677/BR.2014.31007

参考文献

[1] 郑言, 覃瑞 (2008) 水稻与药用野生稻、宽叶野生稻、高杆野生稻的ITS序列分析. 生命科学仪器, 6, 30-40.

[2] White, T.J., Bruns, T.D., Lee, S. and Taylor, J. (1990) Analysis of phylogenetic relationships by amplification and direct sequencing of ribosomal RNA genes. InnisMA. PCR Protocols: A guide to methods and applications. Academic, New York, 15-22.

[3] 赵玥, 赵文军 (2005) 核rDNA ITS序列在植物种质资源鉴定中的应用. 辽宁农业科学, 5, 26-28.

[4] Venema, J. and Tollervey, D. (1999) Ribosome synthesis in Saccharomyces cerevisiae. Annual Review of Genetics, 33, 261-311.

[5] Hadjiolova, A. Normann, J., Cavaillé, et al. (1994) Processing of truncated mouse or human rRNA transcribed from ribosomal minigenes transfected into mouse cells. Molecular and Cellular Biology, 14, 4044-4056.

[6] Lalev, A.I. and Nazar, R.N. (1999) Structural equivalence in the transcribed spacer of pre-rRNA transcripts in Schizosaccharomyces pombe. Nucleic Acids Research, 27, 3071-3078.

[7] Joseph, N., Krauskopf, E., Vera1, M.I., et al. (1999) Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acids Research, 27, 4533-4540.

[8] Baldwin, B.G., Sanderson, M.J., Porter, J.M., et al. (1995) The its region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden, 82, 247-277.

[9] Suzuki, A., Tanifuji, S., Komeda Y., et al. (1996) Structural and functional characterization of the intergenic spacer region of the rDNA in Daucus carota. Plant and Cell Physiology, 37, 233238.

[10] Wang, J.B. and Zhang, W.J. (2000) Concerted evolution of nuclear rDNA in allopolyploid plants. Hereditas, 22, 54-56.

[11] Sang, T., Crawford, D.J., Stuessy, T.F., et al. (1995) Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: Implications for biogeography and concerted evolution. Proceedings of the National Academy of Sciences of the United States of America, 92, 6813-6817.

[12] Wendel, J.F., Schnabel, A. and Seelanan, T. (1995) Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences of the United States of America, 92, 280-284.

[13] Elder, J.R. and Turner, B.J. (1995) Concerted evolution of repetitive DNA sequence in eukaryotes. The Quarterly Review of Biology, 70, 297-319.

[14] Ainouche, M.L. and Bayer, R.J. (1997) On the origins of the tetraploid Bromus species (section Bromus, Poaceae): Insights from internal transcribed spacer sequences of nuclear ribosomal DNA. Genome, 40, 730-743.

[15] 汪小全, 洪德元 (1997) 植物分子系统学近五年的研究进展概况. 植物分类学报, 35, 465-480.

[16] Kollipara, K.P., Singh, R.J. and Hymowitz, T. (1997) Phylogenetic and genomic relationships in the genus Glycine Willd Based on sequences from the ITS region of nuclear rDNA. Genome, 40, 57-68.

[17] Sang, T., Crawford, D.J. and Stuessy, T.F. (1995) Documentation of reticulae evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: Implications forbiogeography and concerted evolution. Proceedings of the National Academy of Sciences of the United States of America, 92, 6813-6817.

[18] 张文驹 (1998) 应用rDNA的ITS区探讨多倍体小麦的基因组起源. 武汉大学, 武汉.

[19] 陈之端, 汪小全, 孙海英等 (1998) 马尾树科的系统位置:来自rbcL基因核苷酸序列的证据. 植物分类学报, 1, 407-416.

[20] 王建波, 张文驹 (1999) 核rDNA的ITS序列在被子植物系统与进化研究中的应用. 植物分类学报, 4, 407-416.

[21] 周毅, 邹喻苹, 洪德元等 (1996) 中国野生稻及栽培稻核糖体DNA第一转录间隔区序列分析及其系统学意义. 植物学报, 38, 785-791.

[22] 汪小全, 李振宇 (1998) rDNA片段的序列分析在苦苣苔亚科系统学研究中的应用. 植物分类学报, 2, 97-105.

[23] 章群, 施苏华, 黄椰林等 (1999) 金缕梅亚科ITS序列分析及其系统发育初探. 中山大学学报(自然科学版), 1, 107-110.

[24] 章群, 施苏华, 黄椰林等 (2000) 金缕梅族ITS序列分析及其系统学意义. 中山大学学报(自然科学版), 1, 72-76.

[25] 刘忠, 汪小全, 黄椰林等 (2000) 五味子科的系统发育:核糖体DNA ITS区序列证据. 植物学报, 7, 758-761.

[26] Allice, L.A. and Campbell, C.S. (1999) Phylogeny of rubus (Rosaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. American Journal of Botany, 1, 81-97.

[27] 保曙琳, 丁小余, 常俊等 (2004) 长江中下游地区菱属植物的DNA分子鉴别. 中草药, 8, 926-930.

[28] Ding, X.Y., Wang, Z.T., Xu, H., et al. (2000) Database establishment of the whole rDNA ITS region of Dendrobium species of “Fengdou” and authentication by analysis of their sequences. Acta Pharmacologica Sinica, 7, 567-573.

[29] Ma, X.J., Wang, X.Q., Xiao, P.G., et al. (2000) Comparison of sequences between wild ginseng DNA and garden ginseing DNA. China Journal of Chinese Material Medical, 4, 206-209.

[30] 赵志礼, 周开亚, 董辉等 (2001) 国产“水山姜”的分类学研究——来自核糖体DNAITS区序列的证据. 云南植物研究, 4, 439-443.

[31] Bao, Y. and Ge, S. (2003) Identification of oryza species with the CD genome based on RFLP analysis of nuclear ribosomal ITS sequences. Acta Pharmacologica Sinica, 7, 762-765.

[32] 宋葆华, 陈之端, 汪小全等 (2000) 中国苋属nrDNA的ITS序列分析及其系统学意义. 植物学报, 11, 1184-1189.

[33] Francisco, O.J, Santos, G.A, Hines, A., et al. (1997) Molecular evidence for a Mediterranean origin of the Macaronesian endemic genus Argyranthemum (Asteraceae). American Journal of Botany, 84, 1595-1613.

[34] Hsiao, C., Chatterton, N.J. and Assay, K.H. (1994) Phylogenetic relationships of 10 grass species: An assessment of phylogenetic utility of the internal transcribed spacer region in nuclear ribosomal DNA in monocots. Genome, 37, 112-120.

[35] Wojciechowski, M.F., Sanderson, M.J., Baldwin, B.G., et al. (1993) Monophyly of aneuploid astragalus (fabaceae): Evidence from nuclear ribosomal dna internal transcribed spacer sequences. American Journal of Botany, 80, 711-722.

[36] Downie, S., Ramanath, S., Katz-Downie, D. and Llanas, E (1996) A molecular phylogeny of apiaceae subfamily apioideae: Evidence from nuclear ribosomal dna internal transcribed spacer sequences. American Journal of Botany, 83, 234-251.

[37] Buckler, E.S. and Holtsford, T.P. (1996) Zea systematics: Ribosomal ITS evidence. Molecular Biology and Evolution, 13, 612622.

[38] Suh, W.C., Ross, W. and Record, Jr., M.T. (1993) Two open complexes and a requirement for Mg2+ to open the lambda PR transcription start site. Science, 259, 358-361.

[39] Ainouche, M.L. and Bayer, R.J. (1997) On the origins of the tetraploid Bromus species (section Bromus, Poaceae): Insights from internal transcribed spacer sequences of nuclear ribosomal. DNA Genome, 40, 730-743.

[40] Karvonen, P. (1995) Genetic variation and structure of ribosomal DNA (rDNA) in Scots pine and Norway spruce. Acta University Ovluensis Series A Scientiae Rerum Naturalium, 10, 1-68.

[41] 向巧萍, 向秋云 (2000) ITS (nrDNA)片段在冷杉属植物中的长度多态性及其在松科的系统与演化研究中的应用. 植物学报, 9, 946-951.

[42] Qu, L.H., Xi, B.Q., Shi, S.H., et al. (1993) A characteristic size of the ITS in gymnosperm rDNA. 15th International Botanical Congress, Tokyo, 28 August-3 September 1993, 201.

[43] Gernandt, D.S. and Liston, A. (1999) Internal transcribed spacer region evolution in Lanx and Pseudotsuga (Pinaceae). American Journal of Botany, 86, 711-723.

[44] Gething, M.J. and Sambrook, J. (1992) Protein folding in the cell. Nature, 355, 33-45.

[45] Gernandt, D.S. and Liston, A. (1999) Internal transcribed spacer region evolution in Larix and Pseudotsuga (Pinaceae). American Journal of Botany, 5, 711-723.46.

[46] 张文驹, 瞿礼嘉 (1998) 普通小麦基因组最可能的4个供体的ITS1和ITS2序列及其亲缘关系. 植物学报:英文版, 11, 994-1000.

[47] Chen, S.L., Yao, H., Han, J.P., et al. (2010) Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One, 5, 370-375.

[48] 高婷, 姚辉, 马新业等 (2010) 中国黄芪属药用植物DNA条形码(ITS2)鉴定. 世界科学技术(中医药现代化), 2, 222-227.

[49] Coleman, A.W. (2003) ITS2 is a doble-edged tool for eukayote evolutionary comparisons. Trends in Genetics, 19, 370-375.

[50] Chiou, S.J., Yen, J.H., Fang, C.L., et al. (2007) Authentication of medicinal herbs using PCR-Amplified ITS2 with specific primers. Plant Medica, 73, 1421-1426.

[51] Coleman, A.W. (2007) Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Research, 35, 33223329.

[52] Prasad, P.K., Tandon, V., Biswal, D.K., et al. (2009) Phylogenetic reconstrucion using secondary structures and sequence motifs of ITS2 rDNA of Paragonimus westermani (Kerbert,1878) Braun,1899 (Digenea: Paragonimidae) and related species. BMC Genomics, 10, S25.

[53] Wolf, M., Achtziger, M., Schultz, J., et al. (2005) Homology modeling revealed more than 20000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA, 11, 1616-1623.

[54] Meier, C.P. and Paulay, G. (2005) DNA barcoding: Error rates based on comprehensive sampling. PLoS Biology, 3, Article ID: e422.

[55] Meier, R., Zhang, G. and Ali, F. (2008) The use of mean instead of smallest interspecific distances exaggerates the size of the “Barcoding Gap” and leads to misidentification. Systematic Biology, 57, 809-813.

[56] Lahaye, R., Van der Bank, M., Bogarin, D., et al. (2008) DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences of the United States of America, 105, 2923-2928.

[57] Kress, W.J. and Erickson, D.L. (2007) A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS One, 2, Article ID: e508.

[58] Ross, H.A., Murgan, S. and Li, W.L. (2008) Testing the reliability of genetic methods of species identification via simulation. Systematic Biology, 57, 216-230.

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