DNA Barcoding of the Genus Rehmannia (Scrophulariaceae)
-
摘要: 地黄属(Rehmannia)为玄参科(Scrophulariaceae)药用植物,广泛分布于中国中东部及北部地区。由于地黄属植物经历了快速成种,导致其属内物种间形态性状差异较小,运用传统的形态学分类方法已难以准确地鉴定物种,近年来迅速发展起来的DNA条形码技术为快速、准确地鉴别物种提供了新思路。本研究选用3个叶绿体DNA非编码区片段(trnL-trnF、trnM-trnV和trnS-trnG)及核基因ITS片段,运用PWG-distance和Tree-Building两种方法对地黄属5个物种75个个体进行了DNA条形码分析。结果表明:单个叶绿体DNA片段或核基因ITS片段对地黄属物种的鉴别率较低(0%～20%),组合的叶绿体DNA片段分辨能力虽然高于单个DNA片段,但并不能将地黄属5个物种完全区分开;trnS-trnG+ITS片段组合的分辨率可达100%,能够将地黄属5个物种准确区分,与所有叶绿体DNA片段和核基因ITS片段组合(trnL-trnF+trnM-trnV+trnS-trnG+ITS)的辨别率相同,因此推荐trnS-trnG+ITS作为地黄属植物的标准条形码。此外,利用DNA条形码鉴别物种时,可采用叶绿体DNA片段和核DNA片段组合的方法来提高物种鉴定的成功率。Abstract: Rehmannia, a genus of Scrophulariaceae, is widely distributed in central, eastern and northern China. However, it is relatively difficult to distinguish species by traditional morphological methods due to rapid speciation of the genus. Recently developed DNA barcoding provides a new approach to identify species quickly and accurately. In this study, three candidate DNA noncoding regions (trnL-trnF, trnM-trnV and trnS-trnG) from the chloroplast genome and internal transcribed spacer (ITS) region from the nuclear genome were evaluated among 75 individuals of five species of Rehmannia, and identification efficiency was assessed using PWG-distance and Tree-Building methods. Results indicated that the five Rehmannia species could not be accurately distinguished by single or the combination of chloroplast DNA fragments with low species discrimination rates (0%-20%), but could by the combination of chloroplasts and nuclear DNA regions (trnS-trnG+ITS) with 100% discrimination rates. Thus, trnS-trnG+ITS can be considered as a potential barcode for species identification in Rehmannia. The combination of chloroplasts and nuclear fragments can be widely adopted for the discrimination of plant species when a single DNA barcode fails.
-
Keywords:
- DNA barcoding /
- Rehmannia /
- Chloroplast DNA /
- nrDNA ITS /
- Discrimination rate
-
-
[1] 闰坤,赵楠,李宏庆.地黄属种间亲缘关系研究[J]. 西北植物学报,2007,27(6):1112-1120. [2] 肖玲,赵先贵,常思明. 地黄块根的发育解剖学研究[J].西北植物学报, 1996,16(5):44-47. [3] Sun P, Guo YH,Qi JJ,Zhou LL,Li XN. Isolation and expression analysis of tuberous root development related genes in Rehmannia glutinosa[J].Mol Biol Rep,2010,37(2):1069-1079.
[4] Albach DC,Li HQ,Zhao N. Molecular systematics and phytochemistry of Rehmannia (Scrophularia-ceae)[J].Biochem Syst Ecol,2007,35:293-300.
[5] 李宏庆.地黄属分类学与系统学研究[D].上海:华东师范大学,2005:42. [6] Xia Z,Wang YZ,Smith JF. Familial placement and relations of Rehmannia and Triaenophora (Scrophulariaceae) inferred from five gene regions[J].Am J Bot,2009,96(2):519-30.
[7] Hebert PD,Cywinska A,Ball SL,Jeremy R. Biological identifications through DNA barcodes[J].Proc Biol Sci,2003,1512(270):313-321.
[8] 夏至,高志明,张红瑞,李贺敏.黄芩及其同属近缘种的DNA条形码鉴定研究[J].中草药,2013,45(1):107-112. [9] Kerr KC,Stoeckle MY,Dove CJ. Comprehensive DNA Barcode coverage of North American birds[J].Mol Ecol Notes,2007,7(4):535-543.
[10] Palmer JD,Herbon LA. Plant mitochondrial DNA evolves rapidly in structure,but slowly in sequence[J].J Mol Evolution,1988-1989(1-2):87-97.
[11] CBOL Plant Working Group. A DNA barcode for landplant[J].Proc Natl Acad Sci USA,2009,106(31):12794-12797.
[12] Hollingsworth PM. Refining the DNA barcode for landplants[J].Proc Natl Acad Sci USA,2011,108(49):19451-19452.
[13] Hollingsworth PM,Graham SW,Little DP. Choosing and using a plant DNA barcode [J].PLoS ONE,2011,6(5): e19254.
[14] China Plant BOL Group,Li DZ,Gao LM,Li HT, Wang H,Ge XJ,Liu JQ,et al. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants[J].Proc Natl Acad Sci USA,2011,108(49):19641-19646.
[15] Taberlet P,Gielly L,Pautou G,Bouvet J. Universal primers for amplification of three non-coding regions of chloroplast DNA[J]. Plant Mol Biol,1991,17(5): 1105-1109.
[16] Cheng YP,Hwang SY,Lin TP. Potential refugia in Taiwan revealed by the phylogeographical study of Castanopsis carlesii Hayata (Fagaceae)[J].Mol Ecol,2005,14(7):2075-2085.
[17] Dong W,Liu J,Yu J,Zhou S. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding[J].PLoS One,2012,7(4): e35071.
[18] Kang SM,Schneider DB,Lin Z,Hanahan D,Dichek DA,Stock PG,Baekkeskov S.Fas ligand expression in islets of Langerhans does not confer immune privilege and instead targets them for rapid destruction[J].Nat Med,1997,3(7):738-743.
[19] Tate JA,Simpson BB.Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploidy species[J]. Syst Bot,2003,28(4):723-737.
[20] Hilu KW,Borsch T,Müller K,Soltis DE,Savo-lainen V,Chatrou LW,et al. Angiosperm phylo-geny based on matK sequence information[J].Am J Bot,2003,90(12):1758-1776.
[21] Ivanova NV,Fazekas AJ,Hebert PDN. Semi-automated,membrane-based protocol for DNA isolation from plants[J].Plant Mol Biol Rep,2008,26(3):186-198.
[22] Hall TA. BioEdit:a user-friendly biological sequence alignment editor and analysis program or windows 95/98/NT[C]//Nucleic acids symposium series.Oxford University Press, 1999,41:95-98.
[23] Sudhir K,Masatoshi N,Joel D,Koichiro T.MEGA:Abiologist-centric software for evolutionary analysis of DNA and protein sequence[J].Brief Bioinform,2008,9(4):299-306.
[24] Librado P,Rozas J.DnaSPv5:A software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11): 1451-1452.
[25] CBOL Plant Working Group. A DNA barcode for land plants[J]. Proc Natl Acad Sci USA,2009,106(31): 12794-12797.
[26] Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V.DNA barcoding the floras of biodiversity hotspots[J]. Proc Natl Acad Sci USA,2008,105(8):2923-2928.
[27] 刘占林,李建芳. 地黄属分子系统学分析[J].西北植物学报,2014,34(1):77-82. [28] 杜芳,徐放.基因流介导的种间渐渗与物种界定[J].植物分类与资源学报,2012,34(3):257-262. [29] 丁铭,曾丽萍,马红,张宁.初探低拷贝核基因在低等分类阶元系统发育重建中的适用性[J]. 植物分类与资源学报,2012,34(3):211-221. [30] 邹嘉宾,王茜,李丽丽,刘建全. 结合叶绿体和核DNA序列变异可提高云杉属物种的分子鉴别率[J]. 植物分类与资源学报,2013,35(3):375-385. [31] Ren BQ,Xiang XG,Chen ZD. Species identification of Alnus (Betulaceae) using nrDNA and cp-DNA genetic markers[J].Mol Ecol Resour,2010,10(4):594-605.
[32] Xiang XG,Hu H,Wang W,Jin XH. DNA barcoding of the recently evolved genus Holcoglossum (Orchidaceae:Aeridinae):a test of DNA barcode candidates[J].Mol Ecol Resour,2011,11(6): 1012-1021.
计量
- 文章访问数: 1337
- HTML全文浏览量: 0
- PDF下载量: 2208
下载:
