DNA Barcoding for Plant Specimen Identification*

doi:10.7677/ynzwyj201313186

Abstract

Abstract:

DNA barcoding comprises two distinct aims: specimen identification and species discovery. To achieve these goals, a DNA barcode reference library is indispensable and is currently under construction for Chinese plants. In this paper, we used the existing public database, NCBI, and also our DNA barcode reference library, which is under construction, to identify plant specimens. By combining DNA barcode sequences with scientific names determined by taxonomists, we first attempted to find incorrectly identified specimens and also to check specimens whose DNA sequences were wrongly labeled. Secondly, we attempted the identification of unknown specimens in some groups for which DNA barcodes are available. Thirdly, we make some suggestions for the development of a plant DNA barcode reference library.

Key words: Plants, Specimen identification, DNA barcoding, Reference library

CLC Number:

Q 949
Q 78.1

ZENG Chun-Xia, HE Zheng-Shan, YANG Jun-Bei. DNA Barcoding for Plant Specimen Identification*[J]. Plant Diversity, 2013, 35(6): 693-700.

References

Agnarsson I, Kuntner M, 2007. Taxonomy in a changing world: seeking solutions for a science in crisis［J］. Systematic Biology, 56: 531—539
Blaxter M, 2003. Molecular systematicscounting angels with DNA［J］. Nature, 421: 122—124
CBOL Plant Working Group, 2009. A DNA barcode for land plants［J］. Proceedings of the National Academy of Sciences of the United States of America, 106: 12794—12797
Chase MW, Fay F, 2009. Barcoding of plants and fungi［J］. Science, 325: 682—683
Che J, Huang DW, Li DZ et al., 2010. DNA barcoding and the international barcode of life project in China［J］. Bulletin of Chinese Academy of Sciences (中国科学院院刊), 24: 257—560
Dayrat B, 2005. Towards integrative taxonomy［J］. Biological Journal of the Linnean Society, 85: 407—415
DeSalle R, 2006. Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff［J］. Conservation Biology, 20: 1545—1457
DeSalle R, Egan MG, Siddall M, 2005. The unholy trinity: taxonomy, species delimitation and DNA barcoding［J］. Philosophical Transactions of the Royal Society of London-Series B: Biological Sciences, 360: 1905—1916
Fang W (方伟), Liu ED (刘恩德), 2012. The development of classical plant taxonomy and iFlora［J］. Plant Divesity and Resources (植物分类与资源学报), 34 (6): 525—531
Fitzhugh K, 2006. DNA barcoding: an instance of technologydriven science?［J］. Bioscience, 56 (6): 462—463
Gao LM (高连明), Liu J (刘杰), Cai J (蔡杰) et al., 2012. A synopsis of technical notes on the standards for plant DNA barcoding［J］. Plant Divesity and Resources (植物分类与资源学报), 34 (6): 592—606
Godfray HCJ, 2002. Towards taxonomy’s ‘glorious revolution’ ［J］. Nature, 420: 461
Haase M, Wilke T, Mildner P, 2007. Identifying species of Bythinella (Caenogastropoda: Rissooidea): a plea for an integrative approach［J］. Zootaxa, 1563: 1—16
Hajibabaei M, Singer GAC, Hebert PDN et al., 2007. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics［J］. Trends in Genetics, 23: 167—172
Hawksworth DL, 1995. Challenges in mycology［J］. Mycological Research, 99: 127—128
Hebert PDN, Cywinska A, Ball SL et al., 2003. Biological identifications through DNA barcodes［J］. Proceedings of the Royal Society of London-Series B, Biological Sciences, 270: 313—321
Hebert PDN, Gregory TR, 2005. The promise of DNA barcoding for taxonomy［J］. Systematic Biology, 54 (5): 852—859
Hollingsworth PM, Graham SW, Little DP, 2011. Choosing and using a plant DNA Barcode［J］. PLoS ONE, 6 (5): e19254
Kristiansen KA, Cilieborg M, Drabkova L et al., 2005. DNA taxonomythe riddle of Oxychloe (Juncaceae) ［J］. Systematic Botany, 30 (2): 284—289
Li DZ, Gao LM, Li HT et al., 2011a. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants［J］. Proceedings of the National Academy of Sciences of the United States of America, 108: 19641—19646
Li DZ, Liu JQ, Chen ZD et al., 2011b. Plant DNA barcoding in China［J］. Journal of Systematics and Evolution, 49: 165—168
Liu J, Michael Mller, Gao LM et al., 2011. DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species［J］. Molecular Ecology Resources, 11 (1): 89—100
Mallet J, Willmott K, 2003. Taxonomy: renaissance or tower of Babel? ［J］. Trends in Ecology and Evolution, 18: 57—59
Matz MV, Nielsen R, 2005. A likelihood ratio rest test for species membership based on DNA sequence data［J］. Philosophical Transactions of the Royal Society of London-Series B: Biological Sciences, 360: 1969—1974
Meier R, Shiyang K, Vaidya G et al., 2006. DNA barcoding and taxonomy in diptera: a tale of high intraspecific variability and low identification success［J］. Systematic Biology, 55 (5): 715—728
Meyer CP, Paulay G, 2005. DNA barcoding: error rates based on comprehensive sampling［J］. PLoS Biology, 3 (12): e422
Mora C, Tittensor DP, Adl S et al., 2011. How many species are there on earth and in the ocean? ［J］. PLoS Biology, 9 (8): e1001127Nielsen R, Matz M, 2006. Statistical approaches for DNA barcoding［J］. Systematic Biology, 55 (1): 162—169Ren BQ (任保青), Chen ZD (陈之端), 2010. DNA barcoding plant life［J］. Chinese Bulletin of Botany (植物学报), 45 (1): 1—12
Schindel DE, Miller SE, 2005. DNA barcoding a useful tool for taxonomists［J］. Nature, 435: 17Tautz D, Arctander P, Minelli A et al., 2003. A plea for DNA taxonomy［J］. Trends in Ecology & Evolution, 18 (2): 70—74Vogler AP, Monaghan MT, 2007. Recent advances in DNA taxonomy［J］. Journal of Zoological Systematics and Evolutionary Research, 45: 1—10Will KW, Mishler BD, Wheeler QD, 2005. The perils of DNA barcoding and the need for integrative taxonomy［J］. Systematic Biology, 54 (5): 844—851

[1]	Hai-Su Hu, Jiu-Yang Mao, Xue Wang, Yu-Ze Liang, Bei Jiang, De-Quan Zhang. Plastid phylogenomics and species discrimination in the “Chinese” clade of Roscoea (Zingiberaceae) [J]. Plant Diversity, 2023, 45(05): 523-534.
[2]	Yan Ke, Feng-Ping Zhang, Yun-Bing Zhang, Wei Li, Qin Wang, Da Yang, Jiao-Lin Zhang, Kun-Fang Cao. Convergent relationships between flower economics and hydraulic traits across aquatic and terrestrial herbaceous plants [J]. Plant Diversity, 2023, 45(05): 601-610.
[3]	Thant Sin Aung, Alice C. Hughes, Phyo Kay Khine, Bo Liu, Xiao-Li Shen, Ke-Ping Ma. Patterns of floristic inventory and plant collections in Myanmar [J]. Plant Diversity, 2023, 45(03): 302-308.
[4]	Yi Jin, Hong Qian. U.PhyloMaker:An R package that can generate large phylogenetic trees for plants and animals [J]. Plant Diversity, 2023, 45(03): 347-352.
[5]	Shi-Yu Lv, Xia-Ying Ye, Zhong-Hu Li, Peng-Fei Ma, De-Zhu Li. Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia [J]. Plant Diversity, 2023, 45(02): 147-155.
[6]	Ya-Dong Zhou, Hong Qian, Yi Jin, Ke-Yan Xiao, Xue Yan, Qing-Feng Wang. Geographic patterns of taxonomic and phylogenetic β-diversity of aquatic angiosperms in China [J]. Plant Diversity, 2023, 45(02): 177-184.
[7]	Li-Guo Zhang, Xiao-Qian Li, Wei-Tao Jin, Yu-Juan Liu, Yao Zhao, Jun Rong, Xiao-Guo Xiang. Asymmetric migration dynamics of the tropical Asian and Australasian floras [J]. Plant Diversity, 2023, 45(01): 20-26.
[8]	Yi Jin, Hong Qian. V.PhyloMaker2：An updated and enlarged R package that can generate very large phylogenies for vascular plants [J]. Plant Diversity, 2022, 44(04): 335-339.
[9]	Wei-Bo Du, Peng Jia, Guo-Zhen Du. Current patterns of plant diversity and phylogenetic structure on the Kunlun Mountains [J]. Plant Diversity, 2022, 44(01): 30-38.
[10]	Zhihua Zhou, Ronghong Shi, Yu Zhang, Xiaoke Xing, Xiaohua Jin. Orchid conservation in China from 2000 to 2020: Achievements and perspectives [J]. Plant Diversity, 2021, 43(05): 343-349.
[11]	Jun Yang, Jifeng Luo, Qiliang Gan, Leiyu Ke, Fengming Zhang, Hairu Guo, Fuwei Zhao, Yuehu Wang. An ethnobotanical study of forage plants in Zhuxi County in the Qinba mountainous area of central China [J]. Plant Diversity, 2021, 43(03): 239-247.
[12]	Juan Yue, Rong Li. Phylogenetic relatedness of woody angiosperm assemblages and its environmental determinants along a subtropical elevational gradient in China [J]. Plant Diversity, 2021, 43(02): 111-116.
[13]	Huifu Zhuang, Chen Wang, Yanan Wang, Tao Jin, Rong Huang, Zihong Lin, Yuhua Wang. Native useful vascular plants of China: A checklist and use patterns [J]. Plant Diversity, 2021, 43(02): 134-141.
[14]	Yong Xiong, Xueyi Sui, Selena Ahmed, Zhi Wang, Chunlin Long. Ethnobotany and diversity of medicinal plants used by the Buyi in eastern Yunnan, China [J]. Plant Diversity, 2020, 42(06): 401-414.
[15]	Seyran Palabaş Uzun, Cennet Koca. Ethnobotanical survey of medicinal plants traded in herbal markets of Kahramanmaraş [J]. Plant Diversity, 2020, 42(06): 443-454.