利用叶绿体基因组高变片段对7个软枣猕猴桃居群遗传多样性的研究
Study on Genetic Diversity of 7 Populations of Actinidia by Using Chloroplast Genome Fragment

DOI: 10.12677/BR.2014.36030, PP. 238-248

Keywords: 软枣猕猴桃，叶绿体基因组，高变片段，系统进化树
Actinidia arguta, Chloroplast Genome, Hypervariable Segment, Phylogenetic Tree

Full-Text   Cite this paper   Add to My Lib

Abstract:

软枣猕猴桃是猕猴桃属内倍性最复杂的物种之一，本研究针对分布在国内4个省份具有代表性的7个野生软枣猕猴桃居群，选用21对叶绿体基因组高变片段对7个居群的软枣猕猴桃进行序列比对、系统构建和多态性分析。研究发现，21对引物中有7对引物在7个软枣猕猴桃居群样本中均能扩增成功，第13号片段rpl32-trnL的分辨率最好。利用片段rpl32-trnL对7个软枣猕猴桃居群分别采用MP算法和NJ法构建的系统进化树表明，来自长白山的2个居群位于系统树最基部，来自大别山的3个居群并未处于同一支中，21个片段的平均多态位点数达到27.16。本研究为猕猴桃属叶绿体基因组的开发和应用奠定了基础。
Actinidia arguta is one of the most complex species in the genus of Actinidia with different ploidy. In this paper, we choose seven representative wild populations of A. arguta in four provinces of China. We use 21 pairs of chloroplast genome hypervariable segments to analyse genetic diversity of seven populations. The result shows that seven pairs within twenty one pairs of primer fragment can amplify samples successfully. The No. 13 fragments rpl32-trnL had the best resolution ratio. We used the fragment rpl32-trnL to build the phylogenetic tree of seven populations with MP algorithm and NJ method. The experimental results show that two populations from Changbai Mountain are located at the base of the tree. Three populations from the Dabie Mountains are not in the same branch. At last, the average polymorphic locus of 21 fragments is 27.16. This study provided basis for the development and application of chloroplast genome in Actinidia species.

References

[1]	王玲, 董文攀, 周世良 (2012) 被子植物叶绿体基因组的结构变异研究进展. 西北植物学报, 6, 1282-1288.
[2]	Shinozaki, K., Ohme, M., Tanaka, M., et al. (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. The EMBO Journal, 5, 2043-2049.
[3]	Ohyama, K., Kohchi, T., et al. (1986) Chloroplast gene organization deduced from complete sequence of Liverwort Marchantia polymorpha chloroplast DNA. Nature, 322, 572-574.
[4]	Wu, C.S., Lai, Y.T., Lin, C.P., Wang, Y.N. and Chaw, S.M. (2009) Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes; selection toward a lower-cost strategy. Molecular Phylogenetics and Evolution, 52, 115-124.
[5]	Leseberg, C.H. and Duvall, M.R. (2009) The complete chloroplast genome of Coix lacryma-Jobi and a comparative molecular evolutionary analysis of plastomes in cereals. Journal of Molecular Evolution, 69, 311-318.
[6]	Guisinger, M.M., Kuehl, J.V., Boore, J.L. and Jansen, R.K. (2011) Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: Rearrangements, repeats, and codon usage. Molecular Biology and Evolution, 28, 583-600.
[7]	Jansen, R.K., Raubeson, L.A., Boore, J.L., et al. (2005) Method for obbtaining and analyzing whole chloroplast genome sequences, methods in enzymology. Academic Press, 348-384.
[8]	曹家树, 秦岭 (2005) 园艺植物种质资源学. 中国农业出版社, 北京, 140.
[9]	李坤明, 胡忠荣, 陈伟 (2006) 昭通地区野生猕猴桃资源及其利用评价. 中国野生植物资源, 2, 39-41.
[10]	Kataoka, I., Mizugami, T., Kim, J.G., et al. (2006) Distribution and character of ploidy variance in Actinidia arguta. 园学杂志, 2, 121.
[11]	李作洲 (2006) 猕猴桃属植物的分子系统学研究. 中科院武汉植物园, 武汉.
[12]	邹游, 丁建, 申瑛, 赵建, 杨志荣, 吴成 (2007) 11个猕猴桃品种间的遗传多样性分析. 应用与环境生物学报, 2, 172-175.
[13]	刘磊, 姚小洪, 黄宏文 (2013) 猕猴桃EPIC标记开发及其在猕猴桃属植物系统发育分析中的应用. 园艺学报, 6, 1162-1168.
[14]	董文攀 (2012) 蜡梅科叶绿体基因组进化及被子植物高变叶绿体基因标记开发与应用. 东北林业大学, 哈尔滨, 43.
[15]	Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. and Higgins, D.G. (1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25, 4876-4882.
[16]	Tamura, K., Peterson, D., Stecher, G., Nei, M. and Kumar, S. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
[17]	Caicedo, A.L. and Schaal, B.A. (2004) Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Molecular Ecology, 13, 1871-1882.
[18]	Rozas, J., Sánchez-DelBarrio, J.C., Messeguer, X. and Rozas, R. (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496-2497.
[19]	刘阳, 杨世雄, 高立志 (2010) 云南古茶园栽培大叶茶和大理茶群体的叶绿体RPL32-TRNL核苷酸变异和遗传分化. 云南植物研究, 5, 427-434.
[20]	Chen, S.Y., Wu, G.L., Zhang, D.J., Gao, Q.B., Duan, Y.Z., Zhang, F.Q. and Chen, S.L. (2008) Molecular phylogeography of alpine plant Metagentiana striata (Gentianaceae). Journal of Systematics and Evolution, 46, 573-585.
[21]	黄岳, 朴一龙, 王琳 (2009) 长白山区野生软枣猕猴桃种质RAPD分析. 延边大学农学学报, 2, 119-123.
[22]	Shaw, J., Lickey, E.B., Schilling, E.E. and Small, R.L. (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III. American Journal of Botany, 94, 275-288.
[23]	Kress, W.J., Wurdack, K.J., Zimmer, E.A., Weigt, L.A. and Janzen, D.H. (2005) Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America, 102, 8369-8374.
[24]	Yue, J.P., Sun, H., Baum, D.A., Li, J.H., Al-Shehbaz, I.A. and Ree, R. (2009) Molecular phylogeny of Solms-laubachia (Brassicaceae) s.l., based on multiple nuclear and plastid DNA sequences, and its biogeographic implications. Journal of Systematics and Evolution, 47, 402-415.
[25]	Quan, X. and Zhou, S.L. (2011) Molecular identification of species in Primus sect. Persica (Rosaceae), with emphasis on evaluation of candidate barcodes for plants. Journal of Systematics and Evolution, 49, 138-145.

Full-Text