The Application of Metabarcoding Technology in Identification of Plant Species Diversity

doi:10.7677/ynzwyj201313198

Abstract

Abstract:

Botany has entered a postFlora era. Benefited from traditional plant taxonomy and related studies, the success of iFlora requires the integration of DNA barcoding through state of art highthroughputsequencing technologies and portable equipment for rapid taxonomic identification and information platform. Traditional plant identification relies mostly on morphological features, while DNA barcoding has been widely applied as a complementary molecular approach to facilitating fast species identification. However, issues remain in classic DNA barcoding, e.g., specieslevel resolution can only be achieved via multiple barcode markers; taxon identity cannot be revealed for pooled plant samples via Sanger sequencing. In this review, the authors introduce recent developments in metabarcoding, which is based on the nextgenerationsequencing technologies, and its applications in a few key aspects in plant diversity and its potential role in iFlora.

Key words: Flora, Plant diversity, DNA barcoding, iFlora, Metabarcoding techonology

CLC Number:

Q 949
Q 78

TANG Min-, YI Ting-Shuang-, WANG Xin-, TAN Mei-Hua-, ZHOU Xin. The Application of Metabarcoding Technology in Identification of Plant Species Diversity[J]. Plant Diversity, 2013, 35(6): 769-773.

References

Arnot DE, Roper C, Bayoumi RA, 1993. Digital codes from hypervariable tandemly repeated DNA sequences in the Plasmodium falciparum circumsporoz oite gene can genetically barcode isolates［J］. Molecular and Biochemical Parasitology, 61 (1): 15—24
Burgess KS, Fazekas AJ, Kursanakurti PR et al., 2011. Discriminating plant species in a local temperate flora using the rbc+matK DNA barcode［J］. Methods in Ecology and Evolution, 2 (4): 333—340
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 (31): 12794—12797
Chase MW, Cowan RS, Hollingsworth PM et al., 2007. A proposal for a standardised protocol to barcode all land plants［J］. Taxon, 56 (2): 295—299
Czernik M, Taberlet P, S′wisocka M et al., 2013. Fast and efficient DNAbased method for winter diet analysis from stools of three cervids: moose, red deer, and roe deer［J］. Acta Theriologica, 58 (4): 1—8
Enghoff H, Seberg O, 2006. A taxonomy of taxonomy and taxonomists［J］. The Systematist, Newsletter of the Systematics Association, 27: 13—15
Fang W (方伟), Liu ED (刘恩德), 2012. The development of classical plant taxonomy and iFlora［J］. Plant Diversity and Resources (植物分类与资源学报), 34 (6): 525—531
Floyd R, Abebe E, Papert A et al., 2002. Molecular barcodes for soil nematode identification［J］. Molecular Ecology, 11 (40): 839—850
Gugerli F, Alvarez N, Tinner W, 2013. A deep dig—hindsight on Holocene vegetation composition from ancient environmental DNA［J］. Molecular Ecology, 22 (13): 3433—3436
Hajibabaei M, 2012. The golden age of DNA metasystematics［J］. Trends in Genetics, 28 (11): 535—537
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 (1512): 313—321
Hibert F, Taberlet P, Chaves J et al., 2013. Unveiling the diet of elusive rainforest herbivores in next generation sequencing era? The Tapir as a Case Study［J］. PloS ONE, 8 (4): e60799
Hiiesalu I, Opik M, Metsis M et al., 2012. Plant species richness belowground: higher richness and new patterns revealed by nextgeneration sequencing［J］. Molecular Ecology, 21 (8): 2004—2016
Hollingsworth PM, Graham SW, Little DP, 2011. Choosing and using a plant DNA barcode［J］. PloS ONE, 6 (5): e19254
Jrgensen T, Kjaer KH, Haile J et al., 2012. Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA Metabarcoding［J］. Molecular Ecology, 21 (8): 1980—1988
Kress WJ, Erickson DL, 2007. A twolocus global DNA barcode for land plants: the coding rbcL gene complements the noncoding trnHpsbA spacer region［J］. PloS ONE, 2 (6): e508
Kress WJ, Wurdack KJ, Zimmer EA et al., 2005. Use of DNA barcodes to identify flowering plants［J］. Proceedings of the National Academy of Sciences of the United States of America, 102 (23): 8369—8374
Lahaye R, Savolainen V, Duthoit S et al., 2008a. A test of psbKpsbI and atpFatpH as potential plant DNA barcodes using the flora of the Kruger National Park as a model system (South Africa) ［J］. Nature Procedings: hdl: 10101/npre.2008.1896.1
Lahaye R, van der Bank M, Bogarin D et al., 2008b. DNA barcoding the floras of biodiversity hotspots［J］. Proceedings of the National Academy of Sciences of the United States of America, 105 (8): 2923—2928
Li DZ, Liu JQ, Chen ZD et al., 2011. Plant DNA barcoding in China［J］. Journal of Systematics and Evolution, 49 (3): 165—168
Li DZ (李德铢), Wang YH (王雨华), Yi TS (伊廷双) et al., 2012. The nextgeneration Flora iFlora［J］. Plant Diversity and Resources (植物分类与资源学报), 34 (6): 525—531
Li HT (李洪涛), Zeng CX (曾春霞), Gao LM (高连明) et al., 2012. Genetic Information and Technologies Related to iFlora［J］. Plant Diversity and Resources (植物分类与资源学报), 34 (6): 585—591
Murray DC, Pearson SG, Fulagar R et al., 2012. Highthroughput sequencing of ancient plant and mammal DNA preserved in herbivore middens［J］. Quaternary Science Reviews, 58 (14): 135—145
Newmaster SG, Fazekas AJ, Steeve RA et al., 2008. Testing candidate plant barcode regions in the Myristicaceae［J］. Molecular Ecology Resources, 8 (3): 480—490
Nock CJ, Waters DL, Edwards MA et al., 2011. Chloroplast genome sequences from total DNA for plant identification［J］. Plant Biotechnology Journal, 9 (3): 328—333
Parducci L, Matetovici I, Fontana SL et al., 2013. Molecular and pollenbased vegetation analysis in lake sediments from central Scandinavia［J］. Molecular Ecology, 22 (13): 3511—3524
Parks M, Cronn R, Liston A, 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes［J］. BMC Biology, 7 (1): 84
Pompanon F, Coissac E, Taberlet P, 2011. Metabarcoding a new way to analyze biodiversity［J］. Biofuture, 319: 30—32
Pompanon F, Deagle BE, Symondson WOC et al., 2012. Who is eating what: diet assessment using next generation sequencing［J］. Molecular Ecology, 21 (8): 1931—1950
Quéméré E, Hibert F, Miquel C et al., 2013. A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range［J］. PloS ONE, 8 (3): e58971
Roy S, Tyagi A, Shukla V et al., 2010. Universal plant DNA barcode loci may not work in complex groups: a case study with Indian Berberis species［J］. PloS ONE, 5 (10): e13674
Shehzad W, Raiz T, Miquel C et al., 2012. Carnivore diet analysis based on nextgeneration sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan［J］. Molecular Ecology, 21 (8): 1951—1965
Soininen EM, Ravolainen VT, Brthen KA et al., 2013. Arctic small Rodents have diverse diets and flexible food selection［J］. PloS ONE, 8 (6): e68128
Starr JR, Naczi RF, Chouinard BN, 2009. Chouinard, Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae) ［J］. Molecular Ecology Resources, 9 (s1): 151—163
Stoeckle MY, Gamble CC, Kirpekar R et al., 2011. Commercial teas highlight plant DNA barcode identification successes and obstacles［J］. Scientific Reports, 1: 42
Taberlet P, Coissac E, Pompanon F et al., 2007. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding［J］. Nucleic Acids Research, 35 (3): e14—e14
Taberlet P, Coissac E, Pompanon F et al., 2012. Towards nextgeneration biodiversity assessment using DNA metabarcoding［J］. Molecular Ecology, 21 (8): 2045—2050
Valentini A, Miquel C, Nawaz MA et al., 2009. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach［J］. Molecular Ecology Resources, 9 (1): 51—60
Whitlock BA, Hale AM, Groff PA, 2010. Intraspecific inversions pose a challenge for the trnHpsbA plant DNA barcode［J］. PloS ONE, 5 (7): e11533
Yang JB, Wang YP, Mller M et al., 2012. Applying plant DNA barcodes to identify species of Parnassia (Parnassiaceae) ［J］. Molecular Ecology Resources, 12 (2): 267—275
Yoccoz NG, 2012. The future of environmental DNA in ecology［J］. Molecular Ecology, 21 (8): 2031—2038
Yoccoz N, Brthen KA, Gielly L et al., 2012. DNA from soil mirrors plant taxonomic and growth form diversity［J］. Molecular Ecology, 21 (15): 3647—3655
Yu DW, Ji YQ, Emerson BC et al., 2012. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring［J］. Methods in Ecology and Evolution, 3 (4): 613—623
Zeng CX (曾春霞), Yang JB (杨俊波), Yang J (杨静) et al., 2012. A Proposed Framework for iFlora［J］. Plant Diversity and Resources (植物分类与资源学报), 34 (6): 555—561
Zhou X, Li YY, Liu SL et al., 2013. Ultradeep sequencing enables highfidelity recovery of biodiversity for bulk arthropod samples without PCR amplification［J］. GigaScience, 2: 4

[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]	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.
[4]	Yao-Ke Li, Julian Harber, Chuan Peng, Zhi-Qiang Du, Yao-Wu Xing, Chih-Chieh Yu. Taxonomic synopsis of Berberis (Berberidaceae) from the northern Hengduan mountains region in China, with descriptions of seven new species [J]. Plant Diversity, 2022, 44(05): 505-517.
[5]	Aysajan Abdusalam, Reyilamu Maimaitituerxun, Halibinuer Hashan, Gulzar Abdukirim. Pollination adaptations of group-by-group stamen movement in a meadow plant with temporal floral closure [J]. Plant Diversity, 2021, 43(04): 308-316.
[6]	Yazhou Zhang, Lishen Qian, Daniel Spalink, Lu Sun, Jianguo Chen, Hang Sun. Spatial phylogenetics of two topographic extremes of the Hengduan Mountains in southwestern China and its implications for biodiversity conservation [J]. Plant Diversity, 2021, 43(03): 181-191.
[7]	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.
[8]	Kai-Wen Jiang, Rong Zhang, Zhong-Fu Zhang, Bo Pan, Bin Tian. DNA barcoding and molecular phylogeny of Dumasia (Fabaceae: Phaseoleae) reveals a cryptic lineage [J]. Plant Diversity, 2020, 42(05): 376-385.
[9]	Bin Yang, Min Deng, Ming-Xia Zhang, Aung Zaw Moe, Hong-Bo Ding, Mya Bhone Maw, Pyae Pyae Win, Richard T. Corlett, Yun-Hong Tan. Contributions to the flora of Myanmar from 2000 to 2019 [J]. Plant Diversity, 2020, 42(04): 292-301.
[10]	Jian-Fei Ye, Yun Liu, Zhi-Duan Chen. Dramatic impact of metric choice on biogeographical regionalization [J]. Plant Diversity, 2020, 42(02): 67-73.
[11]	Gulnara T. Sitpayeva, Gulmira M. Kudabayevа, Liliya A. Dimeyeva, Nadezhda G. Gemejiyeva, Polina V. Vesselova. Crop wild relatives of Kazakhstani Tien Shan: Flora, vegetation, resources [J]. Plant Diversity, 2020, 42(01): 19-32.
[12]	Zhi-Li Zhou, Yuan-Wen Duan, Yan Luo, Yong-Ping Yang, Zhi-Qiang Zhang. Cell number explains the intraspecific spur-length variation in an Aquilegia species [J]. Plant Diversity, 2019, 41(05): 307-314.
[13]	Hong-Bo Ding, Bin Yang, Shi-Shun Zhou, Mya Bhone Maw, Kyaw Win Maung, Yun-Hong Tan. New contributions to the flora of Myanmar I [J]. Plant Diversity, 2019, 41(03): 135-152.
[14]	Pratikshya Kandel, Nakul Chettri, Ram P. Chaudhary, Hemant Kumar Badola, Kailash S. Gaira, Sonam Wangchuk, Namgay Bidha, Yadav Uprety, Eklabya Sharma. Plant diversity of the Kangchenjunga Landscape, Eastern Himalayas [J]. Plant Diversity, 2019, 41(03): 153-165.
[15]	Popova Svetlana, Utescher Torsten, Averyanova Anna, Tarasevich Valentina, Tropina Polina, Xing Yaowu. Early Miocene flora of central Kazakhstan (Turgai Plateau) and its paleoenvironmental implications [J]. Plant Diversity, 2019, 41(03): 183-197.