Abstract
The DNA barcoding methodology, utilizing sequence analysis of standardized gene regions, enables rapid and reliable characterization of species diversity within complex biological communities. This method uses standardized short DNA sequences (~400 to 800 base pairs) as “barcodes” to identify known species and assess biodiversity. The DNA barcoding approach typically targets one marker gene region that shows variation between species but conservation within species, such as CO1 for animals, matK for plants, 16S rRNA for prokaryotes, and for fungi the ITS region. These DNA barcode regions can be easily amplified and sequenced even from minute or degraded samples. Comparison to reference databases enables matching unknown samples to known species’ barcodes, allowing fast taxonomic identification. Beyond species assignment, DNA barcoding aids discoveries of new species, phylogenetic analyses, and studies of evolutionary processes. The versatility of DNA barcoding has led to diverse applications across many fields. In environmental science, it facilitates biodiversity assessment, detection of invasive species, agricultural pests, disease vectors, and monitoring of ecosystems. For industry, DNA barcoding verifies the authenticity of ingredients in food, pharmaceuticals, and other products, along with quality control. Forensic investigators use barcoding to identify the origins of samples and wildlife trafficking. Thus, DNA barcoding provides an invaluable molecular toolkit advancing our understanding of the natural world with applications in taxonomy, systematics, ecology, conservation biology, and applied sectors. This chapter elucidates the standard DNA barcoding methodology from sample collection to data analysis. It also highlights and underscores how DNA barcoding has transitioned from a novel concept to an essential framework for streamlining workflows in species identification and biodiversity studies across multiple life science sectors.
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References
Antil S, Abraham JS, Sripoorna S, Maurya S, Dagar J, Makhija S, Bhagat P, Gupta R, Sood U, Lal R et al (2023) DNA barcoding, an effective tool for species identification: a review. Mol Biol Rep 50:761–775. https://doi.org/10.1007/s11033-022-08015-7
Arnot DE, Roper C, Bayoumi RAL (1993) Digital codes from hypervariable tandemly repeated DNA sequences in the Plasmodium falciparum circumsporozoite gene can genetically barcode isolates. Mol Biochem Parasitol 61:15–24. https://doi.org/10.1016/0166-6851(93)90154-P
Austerlitz F, David O, Schaeffer B, Bleakley K, Olteanu M, Leblois R, Veuille M, Laredo C (2009) DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. BMC Bioinformatics 10:S10. https://doi.org/10.1186/1471-2105-10-S14-S10
Bagley M, Pilgrim E, Knapp M, Yoder C, Domingo JS, Banerji A (2019) High-throughput environmental DNA analysis informs a biological assessment of an urban stream. Ecol Indic 104:378–389. https://doi.org/10.1016/j.ecolind.2019.04.088
Becker B, Pushkareva E (2023) Metagenomics provides a deeper assessment of the diversity of bacterial communities in polar soils than metabarcoding. Genes (Basel) 14(4):812. https://doi.org/10.3390/genes14040812. PMID: 37107570; PMCID: PMC10138292
Bennett R, Blagoev G, Copley C (2019) Araneae of Canada. ZooKeys:41–56. https://doi.org/10.3897/zookeys.819.26391
Besse P, Da Silva D, Grisoni M (2021) Plant DNA barcoding principles and limits: a case study in the Genus Vanilla. In: Besse P (ed) Molecular plant taxonomy: methods and protocols. Springer US, New York, NY, pp 131–148
Bickford D, Lohman DJ, Sodhi NS, Ng PK, Meier R, Winker K, Ingram KK, Das I (2007) Cryptic species as a window on diversity and conservation. 22:148–155. https://doi.org/10.1016/j.tree.2006.11.004
Blaxter M, Mann J, Chapman T, Thomas F, Whitton C, Floyd R, Abebe E (2005) Defining operational taxonomic units using DNA barcode data. Philos Trans R Soc Lond Ser B Biol Sci 360:1935–1943. https://doi.org/10.1098/rstb.2005.1725
Breton G, Johansson ACV, Sjödin P, Schlebusch CM, Jakobsson M (2021) Comparison of sequencing data processing pipelines and application to underrepresented African human populations. BMC Bioinformatics 22:488. https://doi.org/10.1186/s12859-021-04407-x
Buglione M, Maselli V, Rippa D, de Filippo G, Trapanese M, Fulgione D (2018) A pilot study on the application of DNA metabarcoding for non-invasive diet analysis in the Italian hare. Mamm Biol 88:31–42. https://doi.org/10.1016/j.mambio.2017.10.010
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421. https://doi.org/10.1186/1471-2105-10-421
Chimeno C, Morinière J, Podhorna J, Hardulak L, Hausmann A, Reckel F, Grunwald JE, Penning R, Haszprunar G (2019) DNA barcoding in forensic entomology—establishing a DNA reference library of potentially forensic relevant arthropod species. J Forensic Sci 64:593–601. https://doi.org/10.1111/1556-4029.13869
Coissac E, Hollingsworth PM, Lavergne S, Taberlet P (2016) From barcodes to genomes: extending the concept of DNA barcoding. Mol Ecol 25:1423–1428. https://doi.org/10.1111/mec.13549
Costa J, Campos B, Amaral JS, Nunes ME, Oliveira MBPP, Mafra I (2016) HRM analysis targeting ITS1 and matK loci as potential DNA mini-barcodes for the authentication of Hypericum perforatum and Hypericum androsaemum in herbal infusions. Food Control 61:105–114. https://doi.org/10.1016/j.foodcont.2015.09.035
Darling JA, Mahon AR (2011) From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environ Res 111:978–988. https://doi.org/10.1016/j.envres.2011.02.001
Dawan J, Ahn J (2022) Application of DNA barcoding for ensuring food safety and quality. Food Sci Biotechnol 31:1355–1364. https://doi.org/10.1007/s10068-022-01143-7
de Boer HJ, Ichim MC, Newmaster SG (2021) Correction to: DNA barcoding and pharmacovigilance of herbal medicines. Drug Saf 44:397. https://doi.org/10.1007/s40264-020-01029-9
de Vere N, Jones LE, Gilmore T, Moscrop J, Lowe A, Smith D, Hegarty MJ, Creer S, Ford CR (2017) Using DNA metabarcoding to investigate honey bee foraging reveals limited flower use despite high floral availability. Sci Rep 7:42838. https://doi.org/10.1038/srep42838
DeSalle R, Goldstein P (2019) Review and interpretation of trends in DNA barcoding. 7. https://doi.org/10.3389/fevo.2019.00302
Erickson DL, Reed E, Ramachandran P, Bourg NA, McShea WJ, Ottesen A (2017) Reconstructing a herbivore’s diet using a novel rbcL DNA mini-barcode for plants. AoB Plants 9:plx015. https://doi.org/10.1093/aobpla/plx015
Fadiji AE, Babalola OO (2020) Metagenomics methods for the study of plant-associated microbial communities: a review. J Microbiol Methods 170:105860. https://doi.org/10.1016/j.mimet.2020.105860
Fernandes TJR, Amaral JS, Mafra I (2021) DNA barcode markers applied to seafood authentication: an updated review. Crit Rev Food Sci Nutr 61:3904–3935. https://doi.org/10.1080/10408398.2020.1811200
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3:294–299
Galan M, Pagès M, Cosson J-F (2012) Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples. Plos One 7:e48374. https://doi.org/10.1371/journal.pone.0048374
Galimberti A, Labra M, Sandionigi A, Bruno A, Mezzasalma V, De Mattia F (2014) DNA barcoding for minor crops and food traceability. Adv Agric 2014:831875. https://doi.org/10.1155/2014/831875
Gao Z, Liu Y, Wang X, Wei X, Han J (2019) DNA mini-barcoding: a derived barcoding method for herbal molecular identification. Front Plant Sci 10:987. https://doi.org/10.3389/fpls.2019.00987
Guo M, Yuan C, Tao L, Cai Y, Zhang W (2022) Life barcoded by DNA barcodes. Conserv Genet Resour 14:351–365. https://doi.org/10.1007/s12686-022-01291-2
Hajibabaei M, Smith MA, Janzen DH, Rodriguez JJ, Whitfield JB, Hebert PDN (2006) A minimalist barcode can identify a specimen whose DNA is degraded. 6:959–964. https://doi.org/10.1111/j.1471-8286.2006.01470.x
Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54:852–859. https://doi.org/10.1080/10635150500354886
Hebert PD, Cywinska A, Ball SL, deWaard JR (2003a) Biological identifications through DNA barcodes. Proc Biol Sci 270:313–321. https://doi.org/10.1098/rspb.2002.2218
Hebert PD, Ratnasingham S, deWaard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci 270(Suppl 1):S96–S99. https://doi.org/10.1098/rsbl.2003.0025
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. 101:14812–14817. https://doi.org/10.1073/pnas.0406166101
Hering D, Borja A, Jones JI, Pont D, Boets P, Bouchez A, Bruce K, Drakare S, Hänfling B, Kahlert M et al (2018) Implementation options for DNA-based identification into ecological status assessment under the European water framework directive. Water Res 138:192–205. https://doi.org/10.1016/j.watres.2018.03.003
Hubby JL, Lewontin RC (1966) A molecular approach to the study of genic heterozygosity in natural populations. I. The number of alleles at different loci in Drosophila pseudoobscura. Genetics 54:577–594. https://doi.org/10.1093/genetics/54.2.577
Ibrahim M, Liang TC, Scott K, Chakrabarty K, Karri R (2020) Molecular barcoding as a defense against benchtop biochemical attacks on DNA fingerprinting and information forensics. IEEE Trans Inf Forensics Secur 15:3595–3609. https://doi.org/10.1109/TIFS.2020.2994742
Imtiaz A, Nor SAM, Naim DM (2017) Progress and potential of DNA barcoding for species identification of fish species. Biodivers J Biol Divers 18:1394–1405. https://doi.org/10.13057/biodiv/d180415
Ivanova NV, Clare EL, Borisenko AV (2012) DNA barcoding in mammals. In: Methods in molecular biology, vol 858, Clifton, N.J, pp 153–182. https://doi.org/10.1007/978-1-61779-591-6_8
Jin S, Kim KY, Kim M-S, Park C, Jin S, Kim KY, Kim M-S, Park C (2020) An assessment of the taxonomic reliability of DNA barcode sequences in publicly available databases. Algae 35:293–301. https://doi.org/10.4490/algae.2020.35.9.4
Joly S, Davies TJ, Archambault A, Bruneau A, Derry A, Kembel SW, Peres-Neto P, Vamosi J, Wheeler TA (2014) Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead. Mol Ecol Resour 14:221–232. https://doi.org/10.1111/1755-0998.12173
Kennedy SR, Prost S, Overcast I, Rominger AJ, Gillespie RG, Krehenwinkel H (2020) High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities. Dev Genes Evol 230:185–201. https://doi.org/10.1007/s00427-020-00652-x
Kim HM, Jo J, Park C, Choi B-J, Lee H-G, Kim KY, Kim HM, Jo J, Park C, Choi B-JJA (2019) Epibionts associated with floating Sargassum horneri in the Korea Strait. 34:303–313
Kotrba M (2019) Commentary on: Chimeno C, Morinière J, Podhorna J, Hardulak, L, Hausmann a, Reckel F, et al. DNA barcoding in forensic entomology-establishing a DNA reference library of potentially forensic relevant arthropod species. J Forensic Sci 2019;64(2):593–601. J Forensic Sci 64:1285–1286. https://doi.org/10.1111/1556-4029.14094
Kress WJ, Erickson DL (2008) DNA barcodes: Genes, genomics, and bioinformatics. 105:2761–2762. https://doi.org/10.1073/pnas.0800476105
Kress WJ, García-Robledo C, Uriarte M, Erickson DL (2015) DNA barcodes for ecology, evolution, and conservation. Trends Ecol Evol 30:25–35. https://doi.org/10.1016/j.tree.2014.10.008
Krishna Krishnamurthy P, Francis RAA (2012) Critical review on the utility of DNA barcoding in biodiversity conservation. Biodivers Conserv 21:1901–1919. https://doi.org/10.1007/s10531-012-0306-2
Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V (2008) DNA barcoding the floras of biodiversity hotspots. 105:2923–2928. https://doi.org/10.1073/pnas.0709936105
Larsen BB, Miller EC, Rhodes MK, Wiens JJ (2017) Inordinate fondness multiplied and redistributed: the number of species on earth and the new pie of life. 92:229–265. https://doi.org/10.1086/693564
Lebonah DE, Dileep A, Chandrasekhar K, Sreevani S, Sreedevi B, Pramoda Kumari J (2014) DNA barcoding on bacteria: a review. Adv Biol 2014:541787. https://doi.org/10.1155/2014/541787
Lee TR, Alemseged Y, Mitchell A (2018) Dropping hints: estimating the diets of livestock in rangelands using DNA metabarcoding of faeces. Metabarcoding Metagenomics 2:e22467
Leray M, Knowlton N (2015) DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proc Natl Acad Sci USA 112:2076–2081. https://doi.org/10.1073/pnas.1424997112
Liu M, Li XW, Liao BS, Luo L, Ren YY (2019) Species identification of poisonous medicinal plant using DNA barcoding. Chin J Nat Med 17:585–590. https://doi.org/10.1016/s1875-5364(19)30060-3
Lopez-Vaamonde C, Kirichenko N, Cama A, Doorenweerd C, Godfray HCJ, Guiguet A, Gomboc S, Huemer P, Landry J-F, Laštůvka A et al (2021) Evaluating DNA barcoding for species identification and discovery in European gracillariid moths. 9. https://doi.org/10.3389/fevo.2021.626752
McCord BR, Gauthier Q, Cho S, Roig MN, Gibson-Daw GC, Young B, Taglia F, Zapico SC, Mariot RF, Lee SB et al (2019) Forensic DNA analysis. Anal Chem 91:673–688. https://doi.org/10.1021/acs.analchem.8b05318
Meiklejohn KA, Damaso N, Robertson JM (2019) Assessment of BOLD and GenBank—their accuracy and reliability for the identification of biological materials. PLoS One 14:e0217084. https://doi.org/10.1371/journal.pone.0217084
Meusnier I, Singer GAC, Landry J-F, Hickey DA, Hebert PDN, Hajibabaei M (2008) A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9:214. https://doi.org/10.1186/1471-2164-9-214
Mohammed Abubakar B, Mohd Salleh F, Shamsir Omar MS, Wagiran A (2017) Review: DNA barcoding and chromatography fingerprints for the authentication of botanicals in herbal medicinal products. Evid Based Complement Alternat Med 2017:1352948. https://doi.org/10.1155/2017/1352948
Nakazato T, Jinbo U (2022) Cross-sectional use of barcode of life data system and GenBank as DNA barcoding databases for the advancement of museomics. 10. https://doi.org/10.3389/fevo.2022.966605
Nathulal D, Acharya R (2022) DNA bar-coding, pharmacognostical, and phytochemical analysis of Atalantia monophylla DC. leaves. J Drug Res Ayurvedic Sci 7:119–132. https://doi.org/10.4103/jdras.jdras_18_21
Nehal N, Choudhary B, Nagpure A, Gupta RK (2021) DNA barcoding: a modern age tool for detection of adulteration in food. Crit Rev Biotechnol 41:767–791. https://doi.org/10.1080/07388551.2021.1874279
Palhares RM, Gonçalves Drummond M, Brasil BDSAF, Pereira Cosenza G, das Graças Lins Brandão M, Oliveira G (2015) Medicinal plants recommended by the world health organization: DNA barcode identification associated with chemical analyses guarantees their quality. PLoS One 10:e0127866. https://doi.org/10.1371/journal.pone.0127866
Paranaiba R, Carvalho C, Freitas J, Fassio L, Botelho É, Neves D, Silva R, Aguiar S (2019) Forensic botany and forensic chemistry working together: application of plant DNA barcoding as a complement to forensic chemistry—a case study in Brazil. Genome 62:11–18. https://doi.org/10.1139/gen-2018-0066
Parveen I, Gafner S, Techen N, Murch SJ, Khan IA (2016) DNA barcoding for the identification of botanicals in herbal medicine and dietary supplements: strengths and limitations. Planta Med 82:1225–1235. https://doi.org/10.1055/s-0042-111208
Pompanon F, Deagle BE, Symondson WOC, Brown DS, Jarman SN, Taberlet P (2012) Who is eating what: diet assessment using next generation sequencing. 21:1931–1950. https://doi.org/10.1111/j.1365-294X.2011.05403.x
Purty RS, Chatterjee S (2016) DNA barcoding: an effective technique in molecular taxonomy. Austin J Biotechnol Bioeng 3(1):1059
Raclariu AC, Heinrich M, Ichim MC, de Boer H (2018) Benefits and limitations of DNA barcoding and metabarcoding in herbal product authentication. Phytochem Anal 29:123–128. https://doi.org/10.1002/pca.2732
Rashmi KV, Sathyanarayana N, Vidya SM (2017) Validation of DNA barcoding markers in common Mucuna species of India for taxonomy and pharmacognosy applications. Plant Gene 12:98–104. https://doi.org/10.1016/j.plgene.2017.09.001
Robeson MS II, Khanipov K, Golovko G, Wisely SM, White MD, Bodenchuck M, Smyser TJ, Fofanov Y, Fierer N, Piaggio AJ (2018) Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa). 8:185–196. https://doi.org/10.1002/ece3.3638
Rubinoff D (2006) Utility of mitochondrial DNA barcodes in species conservation. Conserv Biol 20:1026–1033. https://doi.org/10.1111/j.1523-1739.2006.00372.x
Ruppert K, Kline R, Rahman M (2019) Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: a systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 17:e00547. https://doi.org/10.1016/j.gecco.2019.e00547
Särkinen T, Staats M, Richardson JE, Cowan RS, Bakker FT (2012) How to open the treasure chest? Optimising DNA extraction from herbarium specimens. PLoS One 7:e43808. https://doi.org/10.1371/journal.pone.0043808
Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R (2005) Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philos Trans R Soc Lond Ser B Biol Sci 360:1805–1811. https://doi.org/10.1098/rstb.2005.1730
Seah A, Lim MCW, McAloose D, Prost S, Seimon TA (2020) MinION-based DNA barcoding of preserved and non-invasively collected wildlife samples. Genes 11. https://doi.org/10.3390/genes11040445
Seena S, Pascoal C, Marvanová L, Cássio F (2010) DNA barcoding of fungi: a case study using ITS sequences for identifying aquatic hyphomycete species. Fungal Divers 44:77–87
Sigwart JD, Garbett A (2018) Biodiversity assessment, DNA barcoding, and the minority majority. Integr Comp Biol 58:1146–1156. https://doi.org/10.1093/icb/icy076
Singh M, Singh N (2020) DNA barcoding for species identification in genetically engineered fungi. In: Hesham AE-L, Upadhyay RS, Sharma GD, Manoharachary C, Gupta VK (eds) Fungal biotechnology and bioengineering. Springer International Publishing, Cham, pp 371–396
Song M, Dong GQ, Zhang YQ, Liu X, Sun W (2017) Identification of processed Chinese medicinal materials using DNA mini-barcoding. Chin J Nat Med 15:481–486. https://doi.org/10.1016/s1875-5364(17)30073-0
Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res 35:e14. https://doi.org/10.1093/nar/gkl938
Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E (2012) Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol 21:2045–2050. https://doi.org/10.1111/j.1365-294X.2012.05470.x
Tedersoo L, Albertsen M, Anslan S, Callahan B (2021) Perspectives and benefits of high-throughput long-read sequencing in microbial ecology. Appl Environ Microbiol 87:e0062621. https://doi.org/10.1128/aem.00626-21
Toju H (2015) High-throughput DNA barcoding for ecological network studies. Popul Ecol 57:37–51. https://doi.org/10.1007/s10144-014-0472-z
Trivedi S, Aloufi AA, Ansari AA, Ghosh SK (2016) Role of DNA barcoding in marine biodiversity assessment and conservation: an update. Saudi J Biol Sci 23:161–171. https://doi.org/10.1016/j.sjbs.2015.01.001
Wells JD, Stevens JR (2008) Application of DNA-based methods in forensic entomology. Annu Rev Entomol 53:103–120. https://doi.org/10.1146/annurev.ento.52.110405.091423
Yang J, Dong L-l, Wei G-F, Hu H-Y, Zhu G-W, Zhang J, Chen S-l (2018) Identification and quality analysis of Panax notoginseng and Panax vietnamensis var. fuscidicus through integrated DNA barcoding and HPLC. Chin Herb Med 10:177–183. https://doi.org/10.1016/j.chmed.2018.03.008
Zhang Z-L, Song M-F, Guan Y-H, Li H-T, Niu Y-F, Zhang L-X, Ma X-J (2015) DNA barcoding in medicinal plants: Testing the potential of a proposed barcoding marker for identification of Uncaria species from China. 60:8–14. https://doi.org/10.1016/j.bse.2015.02.017
Zhou Y, Du X-L, Zheng X, Huang M, Li Y, Wang X-M (2017) ITS2 barcode for identifying the officinal rhubarb source plants from its adulterants. 70:177–185. https://doi.org/10.1016/j.bse.2016.12.004
Zhou H, Ma S, Song J, Lin Y, Wu Z, Han Z, Yao H (2018) QR code labeling system for Xueteng-related herbs based on DNA barcode. Chin Herb Med 11:52. https://doi.org/10.1016/j.chmed.2018.09.006
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Abdi, G. et al. (2024). DNA Barcoding and its Applications. In: Singh, V. (eds) Advances in Genomics. Springer, Singapore. https://doi.org/10.1007/978-981-97-3169-5_5
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