Plant DNA barcoding and framework for biodiversity data sharing platform

doi:10.3724/SP.J.1003.2014.13268

Abstract

Abstract:

DNA barcoding technology provides an opportunity for rapid, accurate, and standardized species-level identification using short DNA sequences. This method speeds up species identification and classification, and presents a new tool for the management, conservation and sustainable development of biodiversity at a global level. Due to improvements in plant barcode database availability and functionality, it is becoming feasible to meet increasing demands for biodiversity information. A framework is needed for a barcoding server platform that utilizes, integrates, and shares among different data types. Such a platform would be an important step towards enabling the public to rapidly identify species and acquire species-related digital information. In this paper, we review current progress on plant DNA barcoding. Secondly, we summarize the current status of, and identify bottlenecks for, plant DNA barcode reference libraries specifically. Thirdly, in the Big Data era, it is indispensable to manage and make good use of massive amounts of plant information. We provide the following suggestions for the framework of server platform: (1) metadata should be substantial, accurate and correlative; (2) data should be normalized; (3) query entrance is convenient, efficient, easy to manage, and available for large-scale data sharing and global communication.

Key words: plant DNA barcoding, iFlora, biodiversity, server platform

Chunxia Zeng, Yanan Wang, Yuhua Wang, Hong Wang. Plant DNA barcoding and framework for biodiversity data sharing platform[J]. Biodiv Sci, 2014, 22(3): 285-292.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2014.13268

https://www.biodiversity-science.net/EN/Y2014/V22/I3/285

Figures/Tables 1

References 40

[1]	Agnarsson I, Kuntner M (2007) Taxonomy in a changing world: seeking solutions for a science in crisis.Systematic Biology, 56, 531-539.
[2]	Bourlat SJ, Nakano H, Akerman M, Telford MJ, Thorndyke MC, Obst M (2008) Feeding ecology of Xenoturbella bocki (phylum Xenoturbellida) revealed by genetic barcoding.Molecular Ecology Resources, 8, 18-22.
[3]	CBOL Plant Working Group (2009) A DNA barcode for land plants.Proceedings of the National Academy of Sciences, USA, 106, 12794-12797.
[4]	Chase MW, Fay F (2009) Barcoding of plants and fungi.Science, 325, 682-683.
[5]	Chen ZD (陈之端), Li DZ (李德铢) (2013) On barcode of life and tree of life.Plant Diversity and Resources(植物分类与资源学报), 35, 675-681. (in Chinese with English abstract)
[6]	DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding.Philosophical Transactions of the Royal Society of London: Series B: Biological Sciences, 360, 1905-1916.
[7]	Gao LM (高连明), Liu J (刘杰), Cai J (蔡杰), Yang JB (杨俊波), Zhang T (张挺), Li DZ (李德铢) (2012) A synopsis of technical notes on the standards for plant DNA barcoding.Plant Diversity and Resources(植物分类与资源学报), 34, 592-606. (in Chinese with English abstract)
[8]	García-Robledo C, Erickson DL, Staines CL, Erwin TL, Kress WJ (2013) Tropical plant-herbivore networks: reconstructing species interactions using DNA barcodes.PLoS ONE, 8, e52967.
[9]	Hajibabaei M, Hanzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish species of tropical Lepodoptera.Proceedings of the National Academy of Sciences, USA, 103, 968-971.
[10]	Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics.Trends in Genetics, 23, 167-172.
[11]	Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes.Proceedings of the Royal Society of London: Series B, 270, 313-321.
[12]	Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator.Proceedings of the National Academy of Sciences, USA, 101, 14812-14817.
[13]	Hiiesalu I, Opik M, Metsis M, Lilje L, Davison J, Vasar M, Moora M, Zobel M, Wilson SD, Pärtel M (2012) Plant species richness belowground: higher richness and new patterns revealed by next-generation sequencing.Molecular Ecology, 21, 2004-2016.
[14]	Hollingsworth PM (2011) Refining the DNA barcode for land plants.Proceedings of the National Academy of Sciences, USA, 180, 19451-19452.
[15]	Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA Barcode.PLoS ONE, 6, e19254.
[16]	Huler J, Mogia M, Isua B, Novotny V (2007) Host specificity of ambrosia and bark beetles (Col., Curculionidae: Scolytinae and Platypodinae) in a New Guinea rain forest.Ecological Entomology, 32, 762-772.
[17]	Jørgensen T, Kjaer KH, Haile J, Rasmussen M, Boessenkool S, Andersen K, Coissac E, Taberlet P, Brochmann C, Orlando L, Gilbert MTP, Willerslve E (2012) Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding.Molecular Ecology, 21, 1980-1988.
[18]	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.PLoS ONE, 2, e508.
[19]	Kress WJ, Erickson DL, Jones FA, Swenson NG, Perez R, Sanjur O, Bermingham E (2009) Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama.Proceedings of the National Academy of Sciences, USA, 106, 18621-18626.
[20]	Li DZ, Gao LM, Li HT, Wang H, Ge XJ, Liu JQ, Chen ZD, Zhou SL, Chen SL, Yang JB (2011) Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants.Proceedings of the National Academy of Sciences, USA, 108, 19641-19646.
[21]	Li DZ (李德铢), Wang YH (王雨华), Yi TS (伊廷双), Wang H (王红), Gao LM (高连明), Yang JB (杨俊波) (2012) The next-generation flora: iFlora.Plant Diversity and Resources(植物分类与资源学报), 34, 525-531. (in Chinese with English abstract)
[22]	Liu J, Möller M, Gao LM, Zhang DQ, Li DZ (2011) DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species.Molecular Ecology Resources, 11, 89-100.
[23]	Liu J, Möller M, Provan J, Gao LM, Poudel RC, Li DZ (2013) Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot.New Phytologist, 199, 1093-1108.
[24]	Möller M, Gao LM, Robert RM, Liu J, Zhang DQ, Poudel RC, Li DZ (2013) A multidisciplinary approach reveals hidden diversity in the taxonomically challenging Taxus walliachiana complex.Taxon, 62, 1161-1177.
[25]	Murray DC, Pearson SG, Fulagar R, Chase BM, Houston J, Atchison J, White NE, Bellgard MI, Clarke E, Macphail M, Gilbert MTP, Haile J, Bunce M (2012) High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens.Quaternary Science Reviews, 58, 135-145.
[26]	Passmore AJ, Passmore AJ, Jarman S, Kawaguchi S, McMinn A, Nicol S (2006) DNA as a dietary biomarker in Antarctic krill, Euphausia superba.Marine Biotechnology, 8, 686-696.
[27]	Pei NC (裴男才) (2012) Identification of plant species based on DNA barcode technology.Chinese Journal of Applied Ecology(应用生态学报), 23, 1240-1246. (in Chinese with English abstract)
[28]	Pei NC, Lian JY, Erickson DL, Swenson NG, Kress WJ, Ye WH, Ge XJ (2011) Exploring tree habitat associations in a Chinese subtropical forest plot using a molecular phylogeny generated from DNA barcode loci.PLoS ONE, 6, e21273.
[29]	Pompanon F, Coissac E, Taberlet P (2011) Metabarcoding a new way to analyze biodiversity.Biofutur, 3, 30-32.
[30]	Ramírez SR, Eltz T, Fujiwara MK, Gerlach G, Goldman-Huertas B, Tsutsui ND, Pierce NE (2011) Asynchronous diversification in a specialized plant-pollinator mutualism.Science, 333, 1742-1746.
[31]	Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E (2011) ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis.Nucleic Acids Research, 39, e145.
[32]	Roy HE, Lawson Handley LG, Dunn A (2012) Networking: a community approach to invaders and their parasites.Functional Ecology, 26, 1238-1248.
[33]	Smith MA, Fisher BL, Hebert PDN (2005) DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar.Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1825-1834.
[34]	Vogler AP, Monaghan MT (2007) Recent advances in DNA taxonomy.Journal of Zoological Systematics and Evolutionary Research, 45, 1-10.
[35]	Wang H (王红), Wang YH (王雨华), Yang ZL (杨祝良), Li DZ (李德铢) (2013) iFlora: innovation and development. Plant Diversity and Resources (植物分类与资源学报), 35, I-III. (in Chinese with English abstract)
[36]	Will KW, Mishler BD, Wheeler QD (2005) The perils of DNA barcoding and the need for integrative taxonomy.Systematic Biology, 54, 844-851.
[37]	Yoccoz NG, Brathen KA, Gielly L, Haile J, Edwards ME, Goslar T, Von Stedingk H, Brysting AK, Coissac E, Pompanon F, Sønstebø JH, Miquel C, Valentini A, De Bello F, Chave J, Thuiller W, Wincker P, Cruaud C, Gavory F, Rasmussen M, Gilbert MT, Orlando L, Brochmann C, Willerslev E, Taberlet P (2012) DNA from soil mirrors plant taxonomic and growth from diversity.Molecular Ecology, 21, 3647-3655.
[38]	Yoo HS, Eah JY, Kim JS, Kim YJ, Min MS, Paek WK, Lee H, Kim CB (2006) DNA barcoding Korean birds.Molecules and Cells, 22, 323-327.
[39]	Zeng CX (曾春霞), Yang JB (杨俊波), Yang J (杨静), Yi TS (伊廷双), Lin CY (林春艳) (2012) A proposed framework for iFlora.Plant Diversity and Resources(植物分类与资源学报), 34, 555-561. (in Chinese with English abstract)
[40]	Zhuang HF (庄会富), Wang YH (王雨华) (2012) A framework of scientific-cloud for iFlora.Plant Diversity and Resources(植物分类与资源学报), 34, 623-630. (in Chinese with English abstract)