Advance Search
GAO Jian, MENG Wan-Heng, DU Fang, LI Jun-Qing. DNA Barcoding of Acer palmatum (Aceraceae)[J]. Plant Science Journal, 2015, 33(6): 734-743. DOI: 10.11913/PSJ.2095-0837.2015.60734
Citation: GAO Jian, MENG Wan-Heng, DU Fang, LI Jun-Qing. DNA Barcoding of Acer palmatum (Aceraceae)[J]. Plant Science Journal, 2015, 33(6): 734-743. DOI: 10.11913/PSJ.2095-0837.2015.60734
shu

DNA Barcoding of Acer palmatum (Aceraceae)

  • 1.

    College of Forestry of Beijing Forestry University, Beijing 100083, China

  • 2. The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China

More Information
  • Received Date: June 28, 2015
  • Published Date: December 27, 2015
    Graphical Abstract
    • Abstract
  • Acer palmatum Thunb. (Aceraceae) is an important garden ornamental tree species in northern temperate regions. It is relatively difficult to classify by traditional methods due to frequent intraspecific hybridization and introgression. However, the emergence and development of DNA barcoding methods has provided an alternative approach to this issue. In this study, five candidate DNA noncoding regions (rpl16, psbA-trnH, trnL-trnF, rbcL and matK) from the chloroplast genome and internal transcribed spacer (ITS) region from the nuclear genome were used to distinguish eight taxa of A. palmatum. The identification efficiency estimated by PWG-distance and Tree-Building methods showed that single chloroplast DNA fragment (0% - 25%) or ITS fragment (12.5%) always showed low levels of species discrimination, while the combination of chloroplast DNA fragments (0% - 62.5%) and chloroplast DNA fragments plus ITS fragments (12.5% - 50%) had higher resolution for identifying A. palmatum. The highest discrimination rate of rpl16 + psbA-trnH + trnL-trnF reached 62.5%. Thus, we concluded that rpl16 + psbA-trnH + trnL-trnF could be considered as a potential barcode for taxa identification in A. palmatum.
    • FullText(HTML)
    • References (59)
  • [1]
    吕运舟, 黄利斌, 何旭东, 窦全琴. 鸡爪槭园艺品种分类及栽培研究综述[J]. 江苏林业科技, 2014, 41(5): 41-45.
    [2]
    方文培. 中国植物志: 第46卷[M]. 北京: 科学出版社, 1981: 129.
    [3]
    Schindel DE, Miller SE. DNA barcoding a useful tool for taxonomists[J]. Nature, 2005, 435(7038): 17.
    [4]
    Hollingsworth PM, Graham SW, Little DP. Choosing and using a plant DNA barcode[J]. PLoS One, 2011, 6(5): e19254.
    [5]
    高连明. DNA条形码在生物多样性编目与评价中的应用[J]. 生物多样性, 2015, 23(3): 286-287.
    [6]
    马克平. DNA条形码:从物种到生物群区[J]. 生物多样性, 2015, 23(3): 279-280.
    [7]
    Hebert PD, Ratnasingham S, Dewaard JR. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species[J]. Proc Biol Sci, 2003, 270(Suppl 1): 96-99.
    [8]
    Ward RD, Hanner R, Hebert PD. The campaign to DNA barcode all fishes, FISH-BOL[J]. J Fish Biol, 2009, 74(2): 329-356.
    [9]
    彭居俐, 王绪祯, 王丁, 何舜平. 基于线粒体COI基因序列的DNA条形码在鲤科鲌属鱼类物种鉴定中的应用[J]. 水生生物学报, 2009, 33(2): 271-276.
    [10]
    柳淑芳, 陈亮亮, 戴芳群, 庄志猛. 基于线粒体COI基因的DNA条形码在石首鱼科(Sciaenidae)鱼类系统分类中的应用[J]. 海洋与湖沼, 2010, 41(2): 223-232.
    [11]
    Hebert PD, Stoeckle MY, Zemlak TS, Francis CM. Identification of birds through DNA barcodes[J]. PLoS Biol, 2004, 2(10): e312.
    [12]
    Kerr KCR, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PDN. Comprehensive DNA barcode coverage of North American birds[J]. Mol Ecol Notes, 2007, 7(4): 535-543.
    [13]
    梁刚, 张卫, 雷富民, 尹祚华, 黄原, 李天宪. 雀形目15种鸟类CoI与Cytb基因序列的比较[J]. 动物分类学报, 2007, 32(3): 613-620.
    [14]
    Vences M, Thomas M, Bonett RM, Vieites DR. Deciphering amphibian diversity through DNA barcoding: chances and challenges[J]. Philos T Roy Soc B, 2005, 360(1462): 1859-1868.
    [15]
    Smith MA, Poyarkov NA, Hebert PD. COI DNA barcoding amphibians: take the chance, meet the challenge[J]. Mol Ecol Resour, 2008, 8(2): 235-246.
    [16]
    张蓉, 刘春生, 黄璐琦, 王学勇, 崔光红, 董栗. 鹿茸饮片的DNA条形码鉴别研究[J]. 中国药学杂志, 2011, 46(4): 263-266.
    [17]
    诸立新, 吴孝兵, 晏鹏. 基于COI基因部分序列对尾凤蝶属(鳞翅目, 凤蝶科)四种蝴蝶分子系统关系及相关问题的探讨[J]. 动物分类学报, 2006, 31(1): 25-30.
    [18]
    陈庆, 白洁, 刘力, 林红斌, 唐晖, 赵伟, 周红章, 严江伟, 刘雅诚, 胡松年. 北京地区7种常见嗜尸性蝇类的COI基因序列分析及DNA条形码的建立[J]. 昆虫学报, 2009, 52(2): 202-209.
    [19]
    Kress WJ, Erickson DL. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region[J]. PLoS One, 2007, 2(6): e508.
    [20]
    CBOL Plant Working Group. A DNA barcode for land plants[J]. Proc Natl Acad Sci USA, 2009, 106(31): 12794-12797.
    [21]
    Li DZ, Gao LM, Li HT, Wang H, Ge XJ, Liu JQ, Chen ZD, Zhou SL, Chen SL, Yang JB, Fu CX, Zeng CX, Yan HF, Zhu YJ, Sun YS, Chen SY, Zhao L, Wang K, Yang T, Duan GW. 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.
    [22]
    于杰, 闫化学, 鲁振华, 周志钦. 基于柑橘及其近缘属植物DNA条形码的叶绿体编码序列筛选[J]. 中国农业科学, 2011, 44(2): 341-348.
    [23]
    Chase MW, Cowan RS, Hollingsworth PM, Cassio VDB, Madri Án S, Petersen G, Seberg O, Rgsensen TJ, Cameron KM, Carine M. A proposal for a standardised protocol to barcode all land plants[J]. Taxon, 2007, 56(2): 295-299.
    [24]
    姚领爱, 胡之璧, 郑志仁, 周吉燕, 王莉莉, 化海霞, 黎万奎. 铁皮石斛种质资源研究中的DNA条形码初探[J]. 上海农业学报, 2012(1): 49-54.
    [25]
    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.
    [26]
    程芳婷, 李忠虎, 刘春艳, 原超, 李雪童, 刘占林. 地黄属植物的DNA条形码研究[J]. 植物科学学报, 2015, 33(1): 25-32.
    [27]
    李丹丹, 郭水良, 于晶, 李莎, 曹同. 基于4个叶绿体基因识别蓑藓属(Macromitrium)植物的可行性研究[J]. 植物科学学报, 2013, 31(1): 23-33.
    [28]
    Dong WP, Xu C, Li CH, Sun JH, Zuo YJ, Shi S, Cheng T, Guo JJ, Zhou SL. ycf1, the most promising plastid DNA barcode of land plants[J]. Sci Rep, 2015, 5: 8348.
    [29]
    Hall TA. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT[J]. Nucl Acids Sympos Series, 1999, 41: 95-98.
    [30]
    Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics, 2009, 25(11): 1451-1452.
    [31]
    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0[J]. Mol Biol Evol, 2013, 30(12): 2725-2729.
    [32]
    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.
    [33]
    Jordan WC, Courtney MW, Neigel JE. Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in North American duckweeeds (Lemnaceae)[J]. Am J Bot, 1996, 83(4): 430-439.
    [34]
    Asmussen CB. Toward a chloroplast DNA phylo-geny of the tribe Geonomeae (Palmae)[J]. Mem New York Bot Gard, 1999, 83: 121-129.
    [35]
    Sang T, Crawford D, Stuessy T. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae)[J]. Am J Bot, 1997, 84(9): 1120-1136.
    [36]
    Tate JA, Simpson BB. Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species[J]. Syst Bot, 2003, 28(4): 723-737.
    [37]
    Fay MF, Swensen SM, Chase MW. Taxonomic affinities of Medusagyne oppositifolia (Medusagynaceae)[J]. Kew Bullet, 1997, 52(1): 11-120.
    [38]
    Olmstead RG, Michaels HJ, Scott KM, Palmers JD. Monophyly of the Asteridae and identification of their major linages inferred from DNA sequences of rbcL[J]. Ann Mo Bot Gard, 1992, 79(2): 249-265.
    [39]
    Hilu KW, Borsch T, Müller K, Soltis DE, Soltis PS, Savolainen V, Chase MW, Powell MP, Alice LA, Evans R, Sauquet H, Neinhuis C, Slotta TA, Rohwer JG, Campbell CS, Chatrou LW. Angiosperm phylogeny based on matK sequence information[J]. Am J Bot, 2003, 90(12): 1758-1776.
    [40]
    Baum DA, Small RL, Wendel JF. Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets[J]. Syst Biol, 1998, 47(2): 181-207.
    [41]
    Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC, Percy DM, Hajibabaei M, Barrett SC. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well[J]. PLoS One, 2008, 3(7): e2802.
    [42]
    Lahaye R, Van DBM, 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.
    [43]
    陈士林, 姚辉, 韩建萍, 辛天怡, 庞晓慧, 石林春, 罗焜, 宋经元, 侯典云, 石上梅, 钱忠直. 中药材DNA条形码分子鉴定指导原则[J]. 中国中药杂志, 2013, 38(2): 54-61.
    [44]
    王晓玥, 陈晓辰, 廖保生, 王丽丽, 韩建萍. 基于DNA条形码鉴定豆蔻类中药材[J]. 中国现代中药, 2014, 16(11): 888-894.
    [45]
    Skepner AP, Krane DE. RAPD reveals genetic similarity of Acer saccharum and Acer nigrum[J]. Heredity, 1997, 80(4): 422-428.
    [46]
    Pfosser MF, Guzy-Wróbelska J, Sun BY, Stuessy TF, Sugawara T, Fuji N. The origin of species of Acer (Sapindaceae) endemic to Ullung Island, Korea[J]. Syst Bot, 2002, 27(2): 351-367.
    [47]
    张毅, 刘伟, 李桂祥. 世界各国的日本枫树垂枝型园艺品种资源[J]. 中国农学通报, 2014, 30(10): 73-82.
    [48]
    Renner SS,Grimm GW,Schneeweiss GM, Stuessy TF, Ricklefs RE. Rooting and dating maples (Acer) with an uncorrelated-rates molecular clock: implications for North American/Asian disjunctions[J]. Syst Biol, 2008, 57(5): 795-808.
    [49]
    宁淑萍, 颜海飞, 郝刚, 葛学军. 植物DNA条形码研究进展[J]. 生物多样性, 2008, 16(5): 417-425.
    [50]
    Starr JR, Naczi RF, Chouinard BN. Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae)[J]. Mol Ecol Resour, 2009, 9(Suppl 1): 151-163.
    [51]
    赵丽嘉, 贾渝, 周世良, 杜桂森. 藓类植物DNA条码的初步研究--以蔓藓科部分属为例[J]. 云南植物研究, 2010, 32(3): 239-249.
    [52]
    Du FK, Xiao LP, Jian QL, Lascoux M, Feng SH, Petit RJ. Direction and extent of organelle DNA introgression between two spruce species in the Qinghai-Tibetan Plateau[J]. New Phytol, 2011, 192(4): 1024-1033.
    [53]
    Du FK, Petit RJ, Liu JQ. More introgression with less gene flow: chloroplast vs. mitochondrial DNA in the Picea asperata complex in China, and comparison with other Conifers[J]. Mol Ecol, 2009, 18(7): 1396-1407.
    [54]
    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.
    [55]
    Hollingsworth PM. Refining the DNA barcode for land plants[J]. Proc Natl Acad Sci USA, 2011, 108(49): 19451-19452.
    [56]
    葛颂, Schaal BA, 洪德元. 用核糖体DNA的ITS序列探讨裂叶沙参的系统位置--兼论ITS片段在沙参属系统学研究中的价值[J]. 植物分类学报, 1997, 35(5): 385-395.
    [57]
    Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. Use of DNA barcodes to identify flo-wering plants[J]. Proc Natl Acad Sci USA, 2005, 102(23): 8369-8374.
    [58]
    Ren BQ, Xiang XG, Chen ZD. Species identification of Alnus (Betulaceae) using nrDNA and cpDNA genetic markers[J]. Mol Ecol Resour, 2010, 10(4): 594-605.
    [59]
    Xiang XG, Hu H, Wang W, Jin XH. DNA barco-ding of the recently evolved genus Holcoglossum (Orchidaceae: Aeridinae): a test of DNA barcode candidates[J]. Mol Ecol Resour, 2011, 11(6): 1012-1021.
    • Related Articles

  • Related Articles

    [1]Long Bing-Hong, Jiang Xiang-Hui, Song Rong, Li Sheng-Hua, Xiao Long-Qian, Yi Zi-Li, She Chao-Wen. Application of DNA barcodes in identification and genetic diversity analysis of medicinal plants of the genus Polygonatum[J]. Plant Science Journal, 2022, 40(4): 533-543. DOI: 10.11913/PSJ.2095-0837.2022.40533
    [2]Lü Ding-Hao, Liu An-Li, Xu Wen-Fen, He Shun-Zhi. Study on the genus Aspidistra based on DNA barcoding[J]. Plant Science Journal, 2018, 36(6): 784-789. DOI: 10.11913/PSJ.2095-0837.2018.60784
    [3]Cai Jin-Long, Xie Shi-Qing, Zhang Guang-Hui, Liu Tao, Yang Sheng-Chao, Chen Jun-Wen. Current advances in DNA barcoding of medicinal plants[J]. Plant Science Journal, 2017, 35(3): 452-464. DOI: 10.11913/PSJ.2095-0837.2017.30452
    [4]Lei Mei-Yan, Zhang Na-Na, Zhang Jun, Xin Tian-Yi, Yi Si-Rong, Song Jing-Yuan. Identification of Dichroa febrifuga and its adulterants based on DNA barcoding technology[J]. Plant Science Journal, 2017, 35(3): 379-386. DOI: 10.11913/PSJ.2095-0837.2017.30379
    [5]Yang Peng, Shu Jian-Feng, Cai Sha-Sha, Zhao Cai. nrDNA ITS sequence analysis and genetic relationship of Allium macrostemon from different geographical regions in Guizhou[J]. Plant Science Journal, 2017, 35(2): 171-176. DOI: 10.11913/PSJ.2095-0837.2017.20171
    [6]CHENG Fang-Ting, LI Zhong-Hu, LIU Chun-Yan, YUAN Chao, LI Xue-Tong, LIU Zhan-Lin. DNA Barcoding of the Genus Rehmannia (Scrophulariaceae)[J]. Plant Science Journal, 2015, 33(1): 25-32. DOI: 10.11913/PSJ.2095-0837.2015.10025
    [7]YU Li-Xuan, LIU Mei-Yan, CAO Qing-He, YU Yi-Cheng, XIE Yi-Ping, LUO Yong-Hai, HAN Yong-Hua, LI Zong-Yun. Analysis of nrDNA ITS Sequences in Ipomoea batatas and its Relative Wild Species[J]. Plant Science Journal, 2014, 32(1): 40-49. DOI: 10.3724/SP.J.1142.2014.10040
    [8]ZHOU A-Tao, YUE Liang-Liang, LI Min, LIU Di-Qiu, DING Yuan-Ming. Intra-genomic Polymorphism in the nrDNA ITS Sequence of Camellia reticulata[J]. Plant Science Journal, 2013, 31(1): 1-10. DOI: 10.3724/SP.J.1142.2013.10001
    [9]TAO Li, WANG Yue-Jin, YOU Min, WANG You-Wei. Construction of AFLP Fingerprints and Seedling Sex Discrimination of Siraitia grosvenori (Swingle)[J]. Plant Science Journal, 2005, 23(1): 77-80.
    [10]Zhang Chi, Hu Hongjun, Li Zhongkui, Li Yeguang, Zhong Yang. PHYLOGENETIC ANALYSIS ON GENUS CHLAMYDOMONAS BASED ON MORPHOLOGICAL CHARACTERS AND nrDNA ITS SEQUENCE[J]. Plant Science Journal, 2000, 18(3): 189-194.

Catalog

    Get Citation
    PDF
    XML
    Article views (1333) PDF downloads (1699) Cited by()
    Turn off MathJax
    Article Contents
    Abstract
    References
    Related Articles
    Copyright © 2022 Plant Science Journal 鄂ICP备05004779号-3
    Address：No. 201, Jiufeng 1st Road, Donghu High tech Zone, WuhanPostal Code：430074

    Supported by: Beijing Renhe Information Technology Co., Ltd.  Baidu Analytics

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return