Skip to main content

DNA Sequencing Technologies and DNA Barcoding

  • Protocol
  • First Online:
DNA Barcoding

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2744))

Abstract

DNA barcodes are short, standardized DNA segments that geneticists can use to identify all living taxa. On the other hand, DNA barcoding identifies species by analyzing these specific regions against a DNA barcode reference library. In its initial years, DNA barcodes sequenced by Sanger’s method were extensively used by taxonomists for the characterization and identification of species. But in recent years, DNA barcoding by next-generation sequencing (NGS) has found broader applications, such as quality control, biomonitoring of protected species, and biodiversity assessment. Technological advancements have also paved the way to metabarcoding, which has enabled massive parallel sequ.encing of complex bulk samples using high-throughput sequencing techniques. In future, DNA barcoding along with high-throughput techniques will show stupendous progress in taxonomic classification with reference to available sequence data.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 279.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Arnot DE, Roper C, Bayoumi RA (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

    Article  CAS  PubMed  Google Scholar 

  2. Shokralla S, Gibson JF, Nikbakht H et al (2014) Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Mol Ecol Resour 14:892–901. https://doi.org/10.1111/1755-0998.12236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Hebert PD, Cywinska A, Ball SL et al (2003) Biological identifications through DNA barcodes. Proc Biol Sci 270:313–321. https://doi.org/10.1098/rspb.2002.2218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Antil S, Abraham JS, Sripoorna S et al (2022) DNA barcoding, an effective tool for species identification: a review. Mol Biol Rep 29:1–5. https://doi.org/10.1007/s11033-022-08015-7

    Article  CAS  Google Scholar 

  5. Pires AC, Marinoni L (2010) DNA barcoding and traditional taxonomy unified through integrative taxonomy: a view that challenges the debate questioning both methodologies. Biota Neotrop 10:339–346. https://doi.org/10.1590/S1676-06032010000200035

    Article  Google Scholar 

  6. Valentini A, Pompanon F, Taberlet P (2009) DNA barcoding for ecologists. Trends Ecol Evol 24:110–117. https://doi.org/10.1016/j.tree.2008.09.011

    Article  PubMed  Google Scholar 

  7. Waugh J (2007) DNA barcoding in animal species: progress, potential and pitfalls. BioEssays 29:188–197. https://doi.org/10.1002/bies.20529

    Article  CAS  PubMed  Google Scholar 

  8. DeSalle R, Goldstein PZ (2019) Review and interpretation of trends in DNA barcoding. Front Ecol Evol 7:302. https://doi.org/10.3389/fevo.2019.00302

    Article  Google Scholar 

  9. Fišer Pečnikar Ž, Buzan EV (2014) 20 years since the introduction of DNA barcoding: from theory to application. J Appl Genet 55:43–52. https://doi.org/10.1007/s13353-013-0180-y

    Article  CAS  PubMed  Google Scholar 

  10. International Barcode for life. https://ibol.org/about/our-vision

  11. CBOL Plant Working Group 1, Hollingsworth PM, Forrest LL et al (2009) A DNA barcode for land plants. Proc Natl Acad Sci U S A 106:12794–12797. https://doi.org/10.1073/pnas.0905845106

    Article  Google Scholar 

  12. Ratnasingham S, Hebert PDN (2007) BOLD: the barcode of life data system. Mol Ecol Notes 7:355–364. https://doi.org/10.1111/j.1471-8286.2007.01678.x. http://www.barcodinglife.org

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kress WJ, Erickson DL (2008) DNA barcodes: genes, genomics, and bioinformatics. Proc Natl Acad Sci U S A 105:2761–2762. https://doi.org/10.1073/pnas.0800476105

    Article  PubMed  PubMed Central  Google Scholar 

  14. Hebert PD, Ratnasingham S, deWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B Sci 270:S96–S99. https://doi.org/10.1098/rsbl.2003.0025

    Article  CAS  Google Scholar 

  15. Kress WJ (2017) Plant DNA barcodes: applications today and in the future. J Syst Evol 55:291–307. https://doi.org/10.1111/jse.12254

    Article  Google Scholar 

  16. Lücking R, Aime MC, Robbertse B et al (2020) Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 11:14. https://doi.org/10.1186/s43008-020-00033-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Pawlowski J, Audic S, Adl S et al (2012) CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol 10:e1001419. https://doi.org/10.1371/journal.pbio.1001419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Lebonah DE, Dileep A, Chandrasekhar K et al (2014) DNA barcoding on bacteria: a review. Adv Biol 2:1–9. https://doi.org/10.1155/2014/541787

    Article  CAS  Google Scholar 

  19. Lynch M, Jarrell PE (1993) A method for calibrating molecular clocks and its application to animal mitochondrial DNA. Genetics 135:1197–1208. https://doi.org/10.1093/genetics/135.4.1197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Guo M, Yuan C, Tao L et al (2022) Life barcoded by DNA barcodes. Conser Genet Resour 15:1–5. https://doi.org/10.1007/s12686-022-01291-2

    Article  CAS  Google Scholar 

  21. Hajibabaei M, McKenna C (2012) DNA mini-barcodes. Methods Mol Biol 858:339–353. https://doi.org/10.1007/978-1-61779-591-6_15

    Article  CAS  PubMed  Google Scholar 

  22. Gao Z, Liu Y, Wang X et al (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

    Article  PubMed  PubMed Central  Google Scholar 

  23. Zahn RJ, Silva AJ, Hellberg RS (2020) Development of a DNA mini-barcoding protocol targeting COI for the identification of elasmobranch species in shark cartilage pills. Food Control 109:106918. https://doi.org/10.1016/j.foodcont.2019.106918

    Article  CAS  Google Scholar 

  24. Hajibabaei M (2012) The golden age of DNA metasystematics. Trends Genet 28:535–537. https://doi.org/10.1016/j.tig.2012.08.001

    Article  CAS  PubMed  Google Scholar 

  25. Ter Schure ATM, Bruch AA, Kandel AW et al (2022) Sedimentary ancient DNA metabarcoding as a tool for assessing prehistoric plant use at the Upper Paleolithic cave site Aghitu-3, Armenia. J Hum Evol 172:103258. https://doi.org/10.1016/j.jhevol.2022.103258

    Article  PubMed  Google Scholar 

  26. Bucklin A, Batta-Lona PG, Questel JM et al (2022) COI metabarcoding of zooplankton species diversity for time-series monitoring of the NW Atlantic Continental Shelf. Front Mar Sci 9:867893. https://doi.org/10.3389/fmars.2022.867893

    Article  Google Scholar 

  27. Hawke T, Bino G, Shackleton ME et al (2022) Using DNA metabarcoding as a novel approach for analysis of platypus diet. Sci Rep 12:2247. https://doi.org/10.1038/s41598-022-06023-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Creer S, Deiner K, Frey S et al (2016) The ecologist’s field guide to sequence-based identification of biodiversity. Methods Ecol Evol 7:1008–1018. https://doi.org/10.1111/2041-210X.12574

    Article  Google Scholar 

  29. Pawlowski J, Kelly-Quinn M, Altermatt F et al (2018) The future of biotic indices in the ecogenomic era: integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. Sci Total Environ 637:1295–1310. https://doi.org/10.1016/j.scitotenv.2018.05.002

    Article  CAS  PubMed  Google Scholar 

  30. Guo J, Cheng T, Xu H et al (2019) An efficient and cost-effective method for primer-induced nucleotide labeling for massive sequencing on next-generation sequencing platforms. Sci Rep 28:1–7. https://doi.org/10.1038/s41598-019-38996-8

    Article  CAS  Google Scholar 

  31. Gautam A (2022) Applications of DNA sequencing Technologies for Current Research. In: DNA and RNA isolation techniques for non-experts. Techniques in life science and biomedicine for the non-expert. Springer, Cham, pp 179–195. https://doi.org/10.1007/978-3-030-94230-4_23

    Chapter  Google Scholar 

  32. Wong KC, Zhang J, Yan S et al (2019) DNA sequencing technologies: sequencing data protocols and bioinformatics tools. ACM Comput Surv 52:1–30. https://doi.org/10.1145/3340286

    Article  Google Scholar 

  33. Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci U S A 74:560–564. https://doi.org/10.1073/pnas.74.2.560

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467. https://doi.org/10.1073/pnas.74.12.5463

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Smith LM, Fung S, Hunkapiller MW et al (1985) The synthesis of oligonucleotides containing an aliphatic amino group at the 5’ terminus: synthesis of fluorescent DNA primers for use in DNA sequence analysis. Nucleic Acids Res 13:2399–2412. https://doi.org/10.1093/nar/13.7.2399

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Abdelsalam NR, Hasan ME, Javed T et al (2022) Endorsement and phylogenetic analysis of some Fabaceae plants based on DNA barcoding. Mol Biol Rep 2:1–3. https://doi.org/10.1007/s11033-022-07574-z

    Article  CAS  Google Scholar 

  37. Bansal G, Narta K, Teltumbade MR (2018) Next-generation sequencing: technology, advancements, and applications. In: Bioinformatics: sequences, structures, phylogeny. Springer, Singapore, pp 15–46. https://doi.org/10.1007/978-981-13-1562-6_2

    Chapter  Google Scholar 

  38. Pervez MT, Abbas SH, Moustafa MF et al (2022) A comprehensive review of performance of next-generation sequencing platforms. Biomed Res Int:2022. https://doi.org/10.1155/2022/3457806

  39. Rabbani B, Nakaoka H, Akhondzadeh S et al (2016) Next generation sequencing: implications in personalized medicine and pharmacogenomics. Mol BioSyst 12:1818–1830. https://doi.org/10.1039/C6MB00115G

    Article  CAS  PubMed  Google Scholar 

  40. Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380. https://doi.org/10.1038/nature03959

    Article  PubMed  PubMed Central  Google Scholar 

  41. Prigigallo MI, Abdelfattah A, Cacciola SO et al (2016) Metabarcoding analysis of Phytophthora diversity using genus-specific primers and 454 pyrosequencing. Phytopathology 106:305–313. https://doi.org/10.1094/PHYTO-07-15-0167-R

    Article  CAS  PubMed  Google Scholar 

  42. Illumina Inc (2022). https://www.illumina.com/systems/sequencing-platforms.html

  43. Lahens NF, Ricciotti E, Smirnova O et al (2017) A comparison of Illumina and ion torrent sequencing platforms in the context of differential gene expression. BMC Genomics 18:1–3. https://doi.org/10.1186/s12864-017-4011-0

    Article  CAS  Google Scholar 

  44. Lanner J, Curto M, Pachinger B et al (2019) Illumina midi-barcodes: quality proof and applications. Mitochondrial DNA 30:490–499. https://doi.org/10.1080/24701394.2018.1551386

    Article  CAS  PubMed  Google Scholar 

  45. Adolfo LM, Rao X, Dixon RA (2022) Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics. BMC Plant Biol 22:1–8. https://doi.org/10.1186/s12870-021-03383-x

    Article  CAS  Google Scholar 

  46. Rothberg JM, Hinz W, Rearick TM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352. https://doi.org/10.1038/nature10242

    Article  CAS  PubMed  Google Scholar 

  47. Thermo Fisher Scientific (2021). https://www.thermofisher.com/pk/en/home/brands/ion-torrent.html

  48. Galindo-González L, Pinzón-Latorre D, Bergen EA et al (2015) Ion torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome. Plant Methods 11:1–4. https://doi.org/10.1186/s13007-015-0062-x

    Article  CAS  Google Scholar 

  49. Ballard D, Winkler-Galicki J, Wesoły J (2020) Massive parallel sequencing in forensics: advantages, issues, technicalities, and prospects. Int J Legal Med 134:1291–1303. https://doi.org/10.1007/s00414-020-02294-0

    Article  PubMed  PubMed Central  Google Scholar 

  50. Gut IG (2013) New sequencing technologies. Clin Transl Oncol 15:879–881. https://doi.org/10.1007/s12094-013-1073-6

    Article  CAS  PubMed  Google Scholar 

  51. Liao YC, Cheng HW, Wu HC et al (2019) Completing circular bacterial genomes with assembly complexity by using a sampling strategy from a single MinION run with barcoding. Front Microbiol 10:2068. https://doi.org/10.3389/fmicb.2019.02068

    Article  PubMed  PubMed Central  Google Scholar 

  52. Baker CCM, Bittleston LS, Sanders JG, Pierce NE (2016) Dissecting host-associated communities with DNA barcodes. Philos Trans R Soc B Biol Sci 371:20150328. https://doi.org/10.1098/rstb.2015.0328

    Article  Google Scholar 

  53. PacBio (2022). https://www.pacb.com/

  54. Tedersoo L, Tooming-Klunderud A, Anslan S (2018) PacBio metabarcoding of fungi and other eukaryotes: errors, biases and perspectives. New Phytol 217:1370–1385. https://doi.org/10.1111/nph.14776

    Article  CAS  PubMed  Google Scholar 

  55. Shen Y, Nie J, Kuang L et al (2021) DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 14:323–362. https://doi.org/10.1111/1751-7915.13560

    Article  CAS  PubMed  Google Scholar 

  56. Eisenstein M (2012) Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 30:295–296. https://doi.org/10.1038/nbt0412-295

    Article  CAS  PubMed  Google Scholar 

  57. Knot IE, Zouganelis GD, Weedall GD et al (2020) DNA barcoding of nematodes using the MinION. Front Ecol Evol 8:100. https://doi.org/10.3389/fevo.2020.00100

    Article  Google Scholar 

  58. Srivathsan A, Lee L, Katoh K et al (2021) ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biol 19:217. https://doi.org/10.1186/s12915-021-01141-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Wang Y, Zhao Y, Bollas A et al (2021) Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 39:1348–1365. https://doi.org/10.1038/s41587-021-01108-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Ji Y, Ashton L, Pedley SM et al (2013) Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol Lett 16:1245–1257. https://doi.org/10.1111/ele.12162

    Article  PubMed  Google Scholar 

  61. Comtet T, Sandionigi A, Viard F, Casiraghi M (2015) DNA (meta) barcoding of biological invasions: a powerful tool to elucidate invasion processes and help managing aliens. Biol Invasions 17:905–922. https://doi.org/10.1007/s10530-015-0854-y

    Article  Google Scholar 

  62. Piper AM, Batovska J, Cogan NOI et al (2019) Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. Gigascience 8. https://doi.org/10.1093/gigascience/giz092

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Akash Gautam .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

David, A., Deepa Arul Priya, J., Gautam, A. (2024). DNA Sequencing Technologies and DNA Barcoding. In: DeSalle, R. (eds) DNA Barcoding. Methods in Molecular Biology, vol 2744. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3581-0_8

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-3581-0_8

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3580-3

  • Online ISBN: 978-1-0716-3581-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics