叶绿体基因组分析在植物系统发育中的应用
The Applications of Chloroplast Genome Analysis in Plant System Development
DOI: 10.12677/BR.2014.31001, PDF, HTML,  被引量    科研立项经费支持
作者: 周 会, 李 刚, 张 磊, 覃 瑞, 刘 虹：中南民族大学，南方少数民族地区生物资源保护及综合利用工程中心，武汉；荆胜利：武汉大学生命科学学院，杂交水稻国家重点实验室，武汉
关键词: 叶绿体基因组；植物系统发育；DNA分析技术；Chloroplast Genome; Plant System Development; DNA Analysis Technology
摘要: 叶绿体是所有绿色植物和藻类微生物特有的细胞器结构，其基因组信息被广泛运用于比较基因组学和植物系统发育研究。本文对叶绿体基因组的结构特征，包括编码区基因如rbcL、makt、rps4和Ndhhf等叶绿体基因，非编码区中的间隔序列trnF-L、rps4-trns和psbA-trnH等以及内含子rpl16、rps16等在内的叶绿体基因组应用于植物系统发育方面研究概况与进展进行了概述，探讨了叶绿体各种DNA分析技术的原理、方法、应用及其优缺点，并展望了叶绿体基因组分析在植物系统发育中的应用前景。
Abstract: Chloroplast is a specific organelle structure of green plants and algae microorganisms, which is widely used in comparative genomics and plant system development. In this paper, according to the characteristics of chloroplast genome, we analyzed the applications of chloroplast genes including encoding genes: rbcL, makt, rps4 and Ndhhf; non-coding region interval sequences: trnF-L, rps4-trns and psbA-trnH; non-coding introns: rpl16 and rps16. We also analyzed the principle, method, application, advantages and disadvantages of chloroplast DNA technologies in plant system development.
文章引用：周会, 荆胜利, 李刚, 张磊, 覃瑞, 刘虹. 叶绿体基因组分析在植物系统发育中的应用[J]. 植物学研究, 2014, 3(1): 1-9. http://dx.doi.org/10.12677/BR.2014.31001

参考文献

[1] 李健仔, 李思光, 罗玉萍, 万璐 (2002) 叶绿体DNA分析技术及其在植物系统学研究中的应用. 江西科学, 3, 183-189.
[2] 石开明 (2002) DNA序列在植物系统进化研究中的应用. 湖北民族学院学报(自然科学版), 4, 5-10.
[3] Kato, S., Yamagach, H., Shimaoto, Y. and Mikami, T. (2000) The chloroplast genomes of azukibean and its close relatives: A deletion mutation found in weed azukibean. Hereditas, 132, 4348.
[4] 彭隽敏, 孔清, 徐乃瑜 (1995) 云南小麦、西藏半野生小麦及普通小麦叶绿体DNA限制性内切酶图谱的研究. 遗传, 6, 4-6.
[5] Kim, K.J. and Jansen, R.K. (1994) Comparison of phylogenetic hypothesis among different data sets in dwarf dandelions (krigia): Additional in formation from interal transcribed spacer sequences of nuclear ribosomal DNA. Plant Systematics and Evolution, 190, 157-185.
[6] Palmer, J.D., Shield, C.R., Cohen, D.B. and Orton, T.J. (1983) Chloroplast DNA evolution and the origin of amphidiploid Brassica species. Theoretical and Applied Genetics, 65, 181-189.
[7] Poulsen, C.R. (1983) Comments on the structure and function of the large subunit of the enzyme ribulose bisphosphate carboxylase-oxygenase. Carlsberg Research Communications, 48, 4857.
[8] 俸宇星, 汪小全, 潘开玉 (1998) RbcL基因序列分析对连香树科和交让木科系统位置的重新评价兼论低等金镂梅类的关系. 植物分类学报, 5, 411-422.
[9] 张文蘅, 陈之端, 陈虎彪, 汤彦承 (2001) 从叶绿体DNA trnL序列论双参属的归属问题. 植物分类学报, 4, 337-344.
[10] Zhang, Y.J., Ma, P.F. and Li, D.Z. (2011) High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae ). Plosone, 6, Article ID: e20596.
[11] Zeng, C.X., Zhang, Y.X., Triplett, J.K., Jimmy, K., Yang, J.B. and Li, D.Z. (2010) Large multilocusplastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals ten major lineages and low rate of molecular divergence. Molecular Phylogenetics and Evolution, 56, 821-839.
[12] Remiaw, A.W., Alistair, L.D. and Barbara, A.W. (2001) CpDNARFLP in Ceramium(rhodophyta): Intraspecific polymorphism and species-level phylogeny. American Journal of Botany, 88, 1209-1213.
[13] Wattier, R.A., Davidson, A.L., Ward, B.A., Ward, B.A. and Maggs, C.A. (2001) cpDNA-RFLP in Ceramium (Rhodophyta): Interspecific polymorphism and species-level phylogeny. American Journal of Botany, 88, 1209-1203.
[14] Wang, X.-R., Yoshihiko, T, Hiroshi, Y., Kazutoshi, N. and Alfredb, E.S. (1999) Phylogenetic relationships of Eurasionpines (Pinus Pinaceae) based on chloroplast rbcl, matk, rp120-rps18 spacer, and trnv intron sequences. American Journal of Botany, 86, 1742-1753.
[15] Ciprini G,Testolin R, Garder R. (1998) Restrictionsite variation of PCR-amplified chloroplast DNA regions and its implication for the evolution and taxonomy of Actinidia. Theoretical and Applied Genetics, 96, 389-396.
[16] Kurt, W. and Richard, C.G. (1999) A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome, 40, 9-19.
[17] Provan, J., Corbett, G., Waugh, R., Mcnicol, J.W., Morgante, M. and Powell, W. (1996) DNA fingerprints of rice (Oryza sativa) obtained from hyperva-riable chloroplast simple sequence repeats. Proceedings of the Royal Society B: Biological Sciences, 1375, 1275-1281.
[18] Zuccarello, G.C., Bartlett, J. and Yeates, P.H. (2000) Differentiation of calogloss leprieurii (Rhoolophyta) populations in northern and eastern Australia using plastid haplotypes[P]. European Journal of Phycology, 35, 357-363.
[19] Isoda, K., Shiraishi, S., Watanabe, S. and kitamura, K. (2000) Molecular evidence of natural hybridization between Abies veitdhii and A, homolepis (Pinaceae) revealed by chlorplast, mitochondrial and nuclear DNA markers. Molecular Ecology, 9, 1965-1974.
[20] Sugiura, M. (1992) The chloroplast genome. Plant Molecular Biology, 19, 149-168.
[21] 王艇, 苏应娟, 朱建明 (1999) 叶绿体rbcL基因序列在植物系统学研究中的应用. 武汉植物学研究, 增刊, 8-14.
[22] Chase, M.W., Soltis, D.E., Olmstead, R.G. and Morgan, D. (1993) Phylogenetia of seed plants: ananalysis of nucleotide sequences from the plastid gene rbcl. Annals of the Missouri Botanical Garden, 80, 528-586.
[23] Johnsom, S.A. and Soltis, D.E. (1995) Phylogentic inference in Saxi fragaceae sensus and Gilia (polemoniaceae) using matK sequence. Annals of the Missouri Botanical Garden, 82, 149-175.
[24] 吴世安, 吕海亮, 杨继, 绕广远, 尤瑞麟, 葛颂, 钟阳 (2000) 叶绿体DNA片段的分析在黄精族系统学研究中的应用. 植物分类学报, 2, 97-110.
[25] 何兴金, 葛颂, 许介眉, 洪德元 (2000) 中国葱属系统发育的PCR-RFLP分析. 中国科学(C辑), 2, 183-191.
[26] Nadot, S., Bitter, G., Cater, L., Lacroix, R. and lejeune, B. (1995) A phylogenetic analysis of monotyledonsbsed on the chloroplast gene rps4 using parsimony and a new numerical phenetics method. Molecular Phylogenetics and Evolution, 4, 257-282.
[27] Sasa, S., Lori, K. and Richard, G. (2002) Monophyly of the convol vulaceae and circumscription of their major lineages based on DNA sequence of multiple chloroplastloci. American Journal of Botany, 89, 1510-1522.
[28] 崔杰, 徐德昌, 李滨胜, 杨谦, 孙璟晗 (2006) 甜菜ATP合酶β亚基基因atpB的克隆、序列分析及进化. 植物研究, 5, 583-588.
[29] 王化坤, 娄晓鸣, 章镇 (2006) 叶绿体微卫星在植物种质资源研究中的应用. 分子植物育种, 3, 92-98.
[30] 刘畅, 杨足君, 李光蓉, 冯娟, 邓科君, 黄健, 任正隆 (2006) 叶绿体基因infA-rpl36区域在小麦族物种中的序列变异分析. 遗传, 10, 1265-1272.
[31] 黄冲, 吴乃虎 (1990) 叶绿体生物分子生物学研究进展. 生物工程进展, 226, 140-150.
[32] Lehnebach CA, Cano A, Monsalve C, McLenachan P, Horandel E, Lockhart P. (2007) Phylogenetic relationships of the monotypic Peruvian genus Laccopetalum ( Ranunculaceae). Plant Systematics and Evolution, 46, 109-116.
[33] Sousa, L.O.F., Wendt, T., Brown, G.K., Tuthill, D.E. and Evans, T.M. (2007) Mmonophyly and phylogenetic ralationships in Lymania(Bromeliaceae: Bromelioideae)based on morphology and chloroplast DNA Sequences. Systematic Botany, 32, 264270.
[34] 周奕华, 侯丙凯, 石东乔, 肖宇红, 石锐, 胡赞民, 陈正华 (2001) 杨树叶绿体3′rps12基因、rps7基因和ndhB基因片段的克隆及序列分析. 中国生物化学与分子生物学报, 5, 606-616.
[35] 刘志文, 韩旭, 李莉, 李宪臻, 陈温福 (2008) 叶绿体和线粒体DNA在植物系统发育中的应用进展. 河南农业科学, 7, 59.
[36] Elspeth, M.H., Gwilym, P.L. and Julie, A.H. (2005) A phylogenetic reappraisal of the peltophorum group (Caesal pinieae: Leguminosae) based on the chloroplast trnL-F, rbcLand rps16 sequence data. American Journal of Botany, 92, 1359-1371.
[37] 王玉金, 刘建全 (2004) 利用叶绿体DNA trnL-F序列初步探讨菊科风毛菊属的系统发育. 植物分类学报, 2, 136-153.
[38] 侯鑫, 刘俊娥, 赵一之, 赵利清 (2006) 基于ITS序列和trnL-F序列探讨小叶锦鸡儿、中间锦鸡儿和柠条锦鸡儿的种间关系. 植物分类学报, 2, 126-134.
[39] 陆树刚, 李春香 (2006) 用叶绿体 rbcL和rps4-trnS区序列确定亚洲特有单型属-篦齿蕨属的系统位置. 植物分类学报, 5 494-502.
[40] Charles, A. and Robert, S. (2004) phylogenetic studies of mammillaria(cactaceae) insight from chloroplast sequence variation and hypothesis testing using the parametricboot strap. American Journal of Botany, 91, 1086-1098.
[41] 孙华钦, 罗科, 邹文俊, 邓思杨 (2006) 穿龙薯蓣、黄山药和盾叶薯蓣psbA-trnH片段序列分析. 应用与环境生物学报, 6, 792-797.
[42] Su, Y., Wang, T., Zheng, B., Jiang, Y., Chen, G. and Gu, H.Y. (2004) Population genetic structure and phylogeographical pattern of a relict tree fern, Alsophila spinulosa(Cyatheaceae), inferredfrom cpDNA atpB-rbcL intergenic spacers. Theoretical and Applied Genetics, 109, 1459-1467.
[43] 刘明珍, 周忠泽, 邱英雄, 孙伟, 董翔 (2007) 分子证据支持蓝药蓼和大铜钱叶蓼归入冰岛蓼属. 植物分类学报, 2, 227233.
[44] Goremykin V, Hirsch KI, Wolfl S, Hellwing FH. (2003) The chloroplast genome of the ‘basal’ angiosperm Caly-canthus fertilis-structural and phylogenetic analyses. Plant Systematics and Evolution, 242, 119-135.
[45] Charles, A. and Robert, S. (2004) Phylogenetic studies of mammillaria(cactaceae) insight from chloroplast sequence variation and hypothesis testing using the parametric bootstrap. merican Journal of Botany, 91, 1086-1098.
[46] Joey, S. and Randall, L. (2005) Chloroplast DNA phylogeny and phylogeography of the north american plums (Prunus subgenus prunussection prunuocerasus, rosaceae). American Journal of Botany, 92, 2011-2030.
[47] 杨俊波, 李洪涛, 杨世雄, 李德铢, 杨莹燕 (2006) 四个DNA片段在山茶属分子系统学研究中的应用. 云南植物研究, 2, 108-114.
[48] Elspeth, M.H., Gwilym, P.L. and Julie, A.H. (2005)A phylogenetic reappraisal of the peltophorum group (Caesalpinieae: leguminosae) based on the chloroplast trnL-F, rbcL and rps16 sequence data. American Journal of Botany, 92, 1359-1371.
[49] Dong, W.P., Liu, J., Yu, J., Wang, L. and Zhou, S.L. (2012) Highly variable chlo-roplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. Plose One, 7, Article ID: e35071.
[50] 田欣, 李德株 (2002) DNA序列在植物系统学研究中的应用. 云南植物研究, 2, 50-53.
[51] 徐宏发, 王静波 (2001) 分子系统学研究进展. 生态学杂志, 3, 41-46.