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Implications and Utility of DNA Barcoding

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Book cover DNA Barcoding and Molecular Phylogeny

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Abstract

Classical way of practicing taxonomy is in endangered race in the era of genomics. In recent years, taxonomy became fashionable owing to the revolutionary approaches in taxonomy called DNA barcoding. It is a novel approach that has generated optimism in enhancing biodiversity assessments. In DNA barcoding, complete data can be retrieved from a single specimen regardless of life stage or morphological characters. The core idea behind DNA barcoding is the fact of the minor variation of highly conserved region of DNA during the evolution within the species. Sequences that have successfully been utilized for DNA barcoding include cytoplasmic mitochondrial DNA (cox1) and chloroplast DNA (trnL-F, matK, ndhF, atpB, and rbcL) and nuclear DNA (ITS and housekeeping genes). Now it has been used for diverse applications such as biodiversity assessment, life history and ecological studies, forensic analysis, and many more. In this chapter, we discuss the significance and utility of DNA barcoding in various fields.

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References

  • Ahmad I, Fatma Z, Yazdani SS (2013) DNA barcode and lipid analysis of new marine algae potential for biofuel. Algal Res 2:10–15

    Google Scholar 

  • Ajmal Ali M, Gyulai G, Hidvégi N, Kerti B, Al Hemaid FM, Pandey AK, Lee J (2014) The changing epitome of species identification – DNA barcoding. Saudi J Biol Sci 21:204–231

    CAS  PubMed  PubMed Central  Google Scholar 

  • Alfonsi E, Meheust E, Fuchs S (2013) The use of DNA barcoding to monitor the marine mammal biodiversity along the French Atlantic coast. In: Nagy ZT, Backeljau T, De Meyer M, Jordaens K (eds) DNA barcoding: a practical tool for fundamental and applied biodiversity research, vol 365. Pensoft ZooKeys, Moscow, pp 5–24

    Google Scholar 

  • An J, Lee M-Y, Min M-S, Lee M-H, Lee H (2007) A molecular genetic approach for species identification of mammals and sex determination of birds in a forensic case of poaching from South Korea. Foren Sci Int 167:59–61

    CAS  Google Scholar 

  • Ardura A, Planes S, Garcia-Vazquez E (2013) Applications of DNA barcoding to fish landings: authentication and diversity assessment. In: Nagy ZT, Backeljau T, De Meyer M, Jordaens K (eds) DNA barcoding: a practical tool for fundamental and applied biodiversity research, vol 365. Pensoft ZooKeys, Moscow, pp 49–65

    Google Scholar 

  • Armstrong KF, Ball SL (2005) DNA barcodes for biosecurity: invasive species identification. Philos Trans R Soc Lond Ser B Biol Sci 360(1462):1813–1823

    CAS  Google Scholar 

  • Ashfaq M, Hebert PDN, Mirza JH, Khan AM, Zafar Y, Mirza S (2014) Analyzing mosquito (Diptera: Culicidae) diversity in Pakistan by DNA barcoding. PLoS One 9:e97268

    PubMed  PubMed Central  Google Scholar 

  • Aylagas E, Borja A, Rodríguez-Ezpeleta N (2014) Environmental status assessment using DNA metabarcoding: towards a genetics based marine biotic index (gAMBI). PLoS One 9(3):e90529

    PubMed  PubMed Central  Google Scholar 

  • Baker CS, Steel D, Choi Y, Lee H, Kim KS, Choi SK et al (2010) Genetic evidence of illegal trade in protected whales links Japan with the US and South Korea. Biol Lett 6(5):647–650. https://doi.org/10.1098/rsbl.2010.0239

    Article  PubMed  PubMed Central  Google Scholar 

  • Balajee SA, Houbraken J, Verweij PE, Hong SB, Yaghuchi T, Varga J, Samson RA (2007) Aspergillus species identification in the clinical setting. Stud Mycol 59:39–46

    CAS  PubMed  PubMed Central  Google Scholar 

  • Baldo L, Hotopp JCD, Jolley KA et al (2006) Multilocus sequence typing system for the endosymbiont Wolbachia pipientis. Appl Environ Microbiol 72(11):7098–7110

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ball SL, Armstrong KF (2006) DNA barcodes for insect pest identification: a test case with tussock moths (Lepidoptera: Lymantriidae). Can J For Res 36:337–350

    CAS  Google Scholar 

  • Barbanera F, Guerrini M, Beccani C, Forcina G, Anayiotos P, Panayides P (2012) Case report. Conservation of endemic and threatened wildlife: molecular forensic DNA against poaching of the Cypriot mouflon (Ovis orientalis ophion, Bovidae). Foren Sci Int Genet 6:671–675

    CAS  Google Scholar 

  • Barbuto M, Galimberti A, Ferri E, Labra M, Malandra R, Galli P et al (2010) DNA barcoding reveals fraudulent substitutions in shark seafood products: the Italian case of “palombo” (Mustelus spp.). Food Res Int 43:376–381

    CAS  Google Scholar 

  • Barrett RDH, Hebert PDN (2005) Identifying spiders through DNA barcodes. Can J Zool 83:481–491

    CAS  Google Scholar 

  • Begerow D, Nilsson H, Unterseher M, Maier W (2010) Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl Microbiol Biotechnol 87(1):99–108

    CAS  PubMed  Google Scholar 

  • Besansky NJ, Severson DW, Ferdig MT (2003) DNA barcoding of parasites and invertebrate disease vectors: what you don’t know can hurt you. Trends Parasitol 19:545–546

    CAS  PubMed  Google Scholar 

  • Bhattacharjee MJ, Ghosh SK (2014) Design of mini-barcode for catfishes for assessment of archival biodiversity. Mol Ecol Res 14:469–477

    CAS  Google Scholar 

  • Bhattacharyya P, Kumaria S, Tandon P (2015) Applicability of ISSR and DAMD markers for phyto-molecular characterization and association with some important biochemical traits of Dendrobium nobile, an endangered medicinal orchid. Phytochemistry 117:306–316

    CAS  PubMed  Google Scholar 

  • Blaxter M, Elsworth B, Daub J (2004) DNA taxonomy of a neglected animal phylum: an unexpected diversity of tardigrades. Proc R Soc B 271:189–192

    Google Scholar 

  • Bourke BP, Oliveira TP, Suesdek L, Bergo ES, Sallum MA (2013) A multi-locus approach to barcoding in the anopheles strodei subgroup (Diptera: Culicidae). Parasit Vectors 6:111

    CAS  PubMed  PubMed Central  Google Scholar 

  • Carreon-Martinez L, Johnson TB, Ludsin SA, Heath DD (2011) Utilization of stomach content DNA to determine diet diversity in piscivorous fishes. J Fish Biol 78:1170–1182

    CAS  PubMed  Google Scholar 

  • Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2014) The Aspergillus genome database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucl Acids Res 42:D705–D710

    CAS  PubMed  Google Scholar 

  • Chakraborty M, Ghosh SK (2014) An assessment of the DNA barcodes of Indian freshwater fishes. Gene 537:20–28

    CAS  PubMed  Google Scholar 

  • Chandramohan A, Divya SR, Dhanarajan MS (2013) Matk gene based molecular characterization of medicinal plant—Croton bonplandianum Baill. Int J Biosci Res 2:1–7

    Google Scholar 

  • Chang C-H, James S (2011) A critique of earthworm molecular phylogenetics. Pedobiologia 54S:S3–S9

    Google Scholar 

  • Chen J, Li Q, Kong L (2011) How DNA barcodes complement taxonomy and explore species diversity: the case study of a poorly understood marine fauna. PLoS One 6(6):e21326

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chin TC, Bakar AA, Abidin DHZ, Nor SAM (2016) Detection of mislabelled seafood products in Malaysia by DNA barcoding: improving transparency in food market. Food Control 64:247–256

    Google Scholar 

  • Clarkston BE, Saunders GW (2010) A comparison of two DNA barcode markers for species discrimination in the red algal family Kallymeniaceae (Gigartinales, Florideophyceae), with a description of Euthora timburtonii sp. Botany 88:119–131

    CAS  Google Scholar 

  • Cohen NJ, Deeds JR, Wong ES, Hanner RH, Yancy HF, White KD et al (2009) Public health response to puffer fish (Tetrodotoxin) poisoning from mislabeled product. J Food Prot 72:810–817

    CAS  PubMed  Google Scholar 

  • Corse E, Costedoat C, Chappaz R, Pech N, Martin J, Gilles A (2010) A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces. Mol Ecol Resour 10:96–108

    CAS  PubMed  Google Scholar 

  • Costa FO, de Waard JR, Boutillier J, Ratnasingham S, Dooh RT, Hajibabaei M, Hebert PDN (2007) Biological identifications through DNA barcodes: the case of the Crustacea. Can J Fish Aquat Sci 64:272–295

    CAS  Google Scholar 

  • Dalton DL, Kotze A (2011) DNA barcoding as a tool for species identification in three forensic wildlife cases in South Africa. Foren Sci Int 207:e51–e54

    CAS  Google Scholar 

  • Daru BH, Yessoufou K, Mankga LT, Davies TJ (2013) A global trend towards the loss of evolutionarily unique species in mangrove ecosystems. PLoS One 8(6):e66686

    CAS  PubMed  PubMed Central  Google Scholar 

  • De Pasquale PP, Galimberti A (2014) New records of the Alcathoe bat, Myotis alcathoe (Vespertilionidae) for Italy. Barbastella 7:1

    Google Scholar 

  • Decaëns T, Porco D, Rougerie R, Brown GG, James SW (2013) Potential of DNA barcoding for earthworm research in taxonomy and ecology. Appl Soil Ecol 65:35–42

    Google Scholar 

  • Dentinger BTM, Didukh MY, Moncalvo J-M (2011) Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina). PLoS One 6:e25081

    CAS  PubMed  PubMed Central  Google Scholar 

  • Dhananjeyan KJ, Paramasivan R, Tewari SC, Rajendran R, Thenmozhi V, Jerald V, Leo S et al (2010) Molecular identification of mosquito vectors using genomic DNA isolated from eggshells, larval and pupal exuvium. Trop Biomed 27:47–53

    CAS  PubMed  Google Scholar 

  • Dubey B, Meganathan PR, Haque I (2011) DNA mini-barcoding: an approach for forensic identification of some endangered Indian snake species. Foren Sci Int: Genet 5:181–184

    CAS  Google Scholar 

  • Dudgeon D, Arthigton AH, Gessner MO et al (2006) Freshwater biodiversity: importance, threats, status and conservation challenges. Biol Rev Camb Philos Soc 81:163–182

    PubMed  Google Scholar 

  • Dumbrell AJ, Ashton PD, Aziz N, Feng G, Nelson M, Dytham C, Fitter AH, Helgason T (2011) Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing. New Phytol 190:794–804

    CAS  PubMed  Google Scholar 

  • Eaton MJ, Meyers GL, Kolokotronis S-O, Leslie MS, Martin AP, Amato G (2010) Barcoding bushmeat: molecular identification of central African and south American harvested vertebrates. Conserv Genet 11:1389–1404

    Google Scholar 

  • Enan MR, Ahamed A (2014) DNA barcoding based on plastid matK and RNA polymerase for assessing the genetic identity of date (Phoenix dactylifera L.) cultivars. Genet Mol Res 13:3527–3536

    CAS  PubMed  Google Scholar 

  • Ermakov OA, Simonov E, Surin VL, Titov SV, Brandler OV, Ivanova NV, Borisenko AV (2015) Implications of hybridization, NUMTs, and overlooked diversity for DNA barcoding of Eurasian ground squirrels. PLoS One 10(1):e0117201

    PubMed  PubMed Central  Google Scholar 

  • Eva B, Harmony P, Thomas G, Francois G, Alice V, Claude M, Tonya D (2016) Trails of river monsters: detecting critically endangered Mekong giant catfish Pangasianodon gigas using environmental DNA. Glob Ecol Conser 7:148–156

    Google Scholar 

  • Evans KM, Wortley AH, Mann DG (2007) An assessment of potential diatom “barcode” genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). Protist 158:349–364

    CAS  PubMed  Google Scholar 

  • Filonzi L, Chiesa S, Vaghi M, Marzano FN (2010) Molecular barcoding reveals mislabeling of commercial fish products in Italy. Food Res Int 43:1383–1388

    CAS  Google Scholar 

  • Finn DS, Zamora-Muñoz C, Múrria C, Sáinz-Bariáin M, Alba-Tercedor J (2014) Evidence from recently deglaciated mountain ranges that Baetis alpinus (Ephemeroptera) could lose significant genetic diversity as alpine glaciers disappear. Freshw Sci 33(1):207–216

    Google Scholar 

  • Floyd R, Abebe E, Papert A, Blaxter M (2002) Molecular barcodes for soil nematode identification. Mol Ecol 11:839–850

    CAS  PubMed  Google Scholar 

  • Francis CM, Borisenk AV, Ivanova NV, Eger JL, Lim BK, Guillen-Servent A, Kruskop SV, Mackie I, Hebert PDN (2010) The role of DNA barcode in understanding and conservation of mammal diversity in Southeast Asia. PLoS One 5(9):e12575

    PubMed  PubMed Central  Google Scholar 

  • Galan M, Pagès M, Cosson JF (2012) Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples. PLoS One 7(11):e48374

    CAS  PubMed  PubMed Central  Google Scholar 

  • Galimberti A, De Mattia F, Losa A, Bruni I, Federici S, Casiraghi M, Martellos S, Labra M (2013) DNA barcoding as a new tool for food traceability. Food Res Int 50:55–63

    CAS  Google Scholar 

  • Geiser DM, Klich MA, Frisvad JC, Peterson SW, Varga J, Samson RA (2007) The current status of species recognition and identification in Aspergillus. Stud Mycol 59:1–10

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gilmore SR, Gräfenhan T, Louis-Seize G, Seifert KA (2009) Multiple copies of cytochrome oxidase 1 in species of the fungal genus Fusarium. Mol Ecol Resour 9(Suppl S1):90–98

    CAS  PubMed  Google Scholar 

  • Gray JS (1997) Marine biodiversity: patterns, threats and conservation needs. Biodivers Conserv 6:153–175

    Google Scholar 

  • Greenstone MH, Rowley DL, Heimbach U, Lundgren JG, Pfannenstiel RS, Rehner SA (2005) Barcoding generalist predators by polymerase chain reaction: carabids and spiders. Mol Ecol 14:3247–3266

    CAS  PubMed  Google Scholar 

  • Gupta SK, Bhagavatula J, Thangaraj K, Singh L (2011) Case report. Establishing the identity of the massacred tigress in a case of wildlife crime. Foren Sci Int: Genet 5:74–75

    CAS  Google Scholar 

  • Gupta SK, Verma SK, Singh L (2005) Molecular insight into a wildlife crime: the case of a peafowl slaughter. Foren Sci Int 154:214–217

    CAS  Google Scholar 

  • Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci U S A 103:968–971

    PubMed  PubMed Central  Google Scholar 

  • Hanner R, Becker S, Ivanova NV, Steinke D (2011) FISH-BOL and seafood identification: geographically dispersed case studies reveal systemic market substitution across Canada. Mitochondrial DNA 22(S1):106–122

    CAS  PubMed  Google Scholar 

  • Hebert PDN, Cywinska A, Ball SL, de Waard JR (2003) Biological identifications through DNA barcodes. Proc Biol Sci 270(1512):313–321

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hebert PDN, de Waard JR, Landry J-F (2010) DNA barcodes for 1/1,000 of the animal kingdom. Biol Lett 6:359–362

    CAS  PubMed  Google Scholar 

  • Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54:852–859

    PubMed  Google Scholar 

  • Hebert PDN, Ratnasingham S, Zakharov EV, Telfer AC, Levesque-Beaudin V, Milton MA, Pedersen S, Jannetta P, de Waard JR (2016) Counting animal species with DNA barcodes: canadian insects. Phil Trans R Soc B 371:20150333

    PubMed  Google Scholar 

  • Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:1657–1663

    CAS  Google Scholar 

  • Hendrich L, Moriniere J, Haszprunar G, Hebert PDN, Hausmann A, Kohler F, Balke M (2015) A comprehensive DNA barcode database for central European beetles with a focus on Germany: adding more than 3500 identified species to BOLD. Mol Ecol Resour 15:795–818

    CAS  PubMed  Google Scholar 

  • Hogg ID, Hebert PDN (2004) Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes. Can J Zool 82:749–754

    Google Scholar 

  • Holmes BH, Steinke D, Ward RD (2009) Identification of shark and ray fins using DNA barcoding. Fish Res 95:280–288

    Google Scholar 

  • Hou DY, Song JY, Shi LC, Ma XC, Xin TY, Han JP (2013) Stability and accuracy assessment of identification of traditional Chinese materia medica using DNA barcoding: a case study on Flos Lonicerae japonicae. Biomed Res Int 2013:549037

    PubMed  PubMed Central  Google Scholar 

  • Hubert N, Hanner RH, Holm E, Mandrak NE, Taylor EB, Burridge M et al (2008) Identifying Canadian freshwater fishes through DNA barcodes. PLoS One 3:e2490

    PubMed  PubMed Central  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180(18):4765–4774

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hurwood DA, Dammannagoda S, Krosch MN, Jung H, Salin KR, Youssef MA-BH, de Bruyn M, Mather PB (2014) Impacts of climatic factors on evolution of molecular diversity and the natural distribution of wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii). Freshw Sci 33(1):217–231

    Google Scholar 

  • Jo H, Gim J-A, Jeong K-S, Kim H-S, Joo G-J (2014) Application of DNA barcoding for identification of freshwater carnivorous fish diets: is number of prey items dependent on size class for Micropterus salmoides? Ecol Evol 4(2):219–229

    PubMed  Google Scholar 

  • Johnsen A, Rindal E, Ericson PGP et al (2010) DNA barcoding of Scandinavian birds reveals divergent lineages in trans-Atlantic species. J Ornithol 151:565–578

    Google Scholar 

  • Jose D, Nidhin B, Anil Kumar KP, Pradeep PJ, Harikrishnan M (2016) A molecular approach towards the taxonomy of fresh water prawns Macrobrachium striatum and M. equidens (Decapoda, Palaemonidae) using mitochondrial markers. Mitochondrial DNA 27(4):2585–2593

    CAS  PubMed  Google Scholar 

  • Kermarrec L, Franc A, Rimet F, Chaumeil P, Frigerio J-M, Humbert J-F, Bouchez A (2014) A next-generation sequencing approach to river biomonitoring using benthic diatoms. Freshw Sci 33(1):349–363

    Google Scholar 

  • Kerr KCR, Lijtmaer DA, Barreira AS et al (2009) Probing evolutionary patterns in Neotropical birds through DNA barcodes. PLoS One 4:e4379

    PubMed  PubMed Central  Google Scholar 

  • Kerr KCR, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PDN (2007) Comprehensive DNA barcode coverage of north American birds. Mol Ecol Notes 7:535–543

    CAS  PubMed  PubMed Central  Google Scholar 

  • Keskin E, Atar HH (2013) DNA barcoding commercially important fish species of Turkey. Mol Ecol Resour 13(5):788–797

    CAS  PubMed  Google Scholar 

  • Kim MS, Yang MY, Cho GY (2010) Applying DNA barcoding to Korean Gracilariaceae (Rhodophyta) Cryptogamie. Algologie 31(4):387–401

    Google Scholar 

  • Kondo T, Gullan PJ, Williams DJ (2008) Coccidolog. The study of scale insects (Hemiptera: Sternorrhyncha: Coccoidea). Revista Corpoica – Ciencia Y Tecnologia Agropecuaria 9:55–61

    Google Scholar 

  • Kruger A, Obermayr U, Czajka C, Bueno-Mari R, Jost A, Rose A (2014) COI sequencing for invasive mosquito surveillance in Germany reveals genetically divergent specimens near Aedes geniculatus (Diptera: Culicidae). J Eur Mosq Control Assoc 32:22–26

    Google Scholar 

  • Kumar NP, Krishnamoorthy N, Sahu SS, Rajavel AR, Sabesan S, Jambulingam P (2013) DNA barcodes indicate members of the Anopheles fluviatilis (Diptera: Culicidae) species complex to be conspecific in India. Mol Ecol Resour 13:354–361

    Google Scholar 

  • Kumar NP, Rajavel AR, Natarajan R, Jambulingam P (2007) DNA barcodes can distinguish species of Indian mosquitoes (Diptera: Culicidae). J Med Entomol 44:1–7

    CAS  PubMed  Google Scholar 

  • Lakra WS, Singh M, Goswami M, Gopalakrishnan A, Lal KK, Mohindra V, Sarkar UK, Punia PP, Singh KV, Bhatt JP, Ayyappan S (2016) DNA barcoding Indian freshwater fishes. Mitochondrial DNA 27(6):4510–4517

    CAS  PubMed  Google Scholar 

  • Lambert DM, Baker A, Huynen L, Haddrath O, Hebert PDN, Millar CD (2005) Is a large-scale DNA-based inventory of ancient life possible? J Hered 96:279–284

    CAS  PubMed  Google Scholar 

  • Laramie MB, Pilliod DS, Goldberg CS (2015) Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biol Conserv 183:29–37

    Google Scholar 

  • Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N (2010) Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett 307:80–86

    CAS  PubMed  PubMed Central  Google Scholar 

  • Layton KKS, Martel AL, Hebert PDN (2014) Patterns of DNA barcode variation in Canadian marine molluscs. PLoS One 9(4):e95003

    PubMed  PubMed Central  Google Scholar 

  • Les DH, Moody ML, Jacobs SWL, Bayer RJ (2002) Systematics of seagrasses (Zosteraceae) in Australia and New Zealand. Syst Bot 27:468–484

    Google Scholar 

  • Li J, Han H, Gao Q, Jin Q, Chi M, Wu C, Zhang A (2012) Species identification of Noctuidae (Insecta: Lepidoptera) with DNA barcoding of support vector machine and neighbor-joining method. J Biosafety 21:308–314

    Google Scholar 

  • Lim NKM, Tay YC, Srivathsan A, Tan JWT, Kwik JTB, Baloğlu B, Meier R, Yeo DCJ (2016) Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities. R Soc Open Sci 3:160635

    PubMed  PubMed Central  Google Scholar 

  • Links MG, Dumonceaux TJ, Hemmingsen SM, Hill JE (2012) The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS One 7(11):e49755

    CAS  PubMed  PubMed Central  Google Scholar 

  • Little DP (2014) Authentication of Ginkgo biloba herbal dietary supplements using DNA barcoding. Genome 57:513–516

    CAS  PubMed  Google Scholar 

  • Lohman DJ, Ingram KK, Prawiradilaga DM et al (2010) Cryptic genetic diversity in “widespread” southeast Asian bird species suggests that Philippine avian endemism is gravely underestimated. Biol Conserv 143:1885–1890

    Google Scholar 

  • Lorenz JG, Jackson WE, Beck JC, Hanner R (2005) The problems and promise of DNA barcodes for species diagnosis of primate biomaterials. Philos Trans R Soc B 360:1869–1877

    CAS  Google Scholar 

  • Lowenstein JH, Amato G, Kolokotronis S-O (2009) The real maccoyii: identifying tuna sushi with DNA barcodes – contrasting characteristic attributes and genetic distances. PLoS One 4(11):e7866

    PubMed  PubMed Central  Google Scholar 

  • Lu L, Chesters D, Zhang W, Li G, Ma Y, Ma H, Song X, Wu H, Meng F, Zhu C, Liu Q (2012) Small mammal investigation in spotted fever focus with DNA-barcoding and taxonomic implications on rodents species from Hainan of China. PLoS One 7(8):e43479

    CAS  PubMed  PubMed Central  Google Scholar 

  • Luo AR, Zhang AB, Ho SYW, Xu WJ, Zhang YZ, Shi WF et al (2011) Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals. BMC Genomics 12:84

    CAS  PubMed  PubMed Central  Google Scholar 

  • Maas AE, Blanco-Bercial L, Lawson GL (2013) Reexamination of the species assignment of Diacavolinia pteropods using DNA barcoding. PLoS One 8(1):e53889

    CAS  PubMed  PubMed Central  Google Scholar 

  • Makarova O, Contaldo N, Paltrinieri S, Kawube G, Bertaccini A, Nicolaisen M (2012) DNA barcoding for identification of “Candidatus phytoplasmas” using a fragment of the elongation factor Tu gene. PLoS One 7(12):e52092

    CAS  PubMed  PubMed Central  Google Scholar 

  • Marie-Stephane T, Mireille O, Serge K (2012) An integrative morphological and molecular diagnostics for Typhlodromus pyri (Acari: Phytoseiidae). Zool Scr 41:68–78

    Google Scholar 

  • Marín JC, Saucedo CE, Corti P, González BA (2009) Application of DNA forensic techniques for identifying poached guanacos (Lama guanicoe) in Chilean Patagonia. J Foren Sci 54(5):1073–1076

    Google Scholar 

  • Markmann M, Tautz D (2005) Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Philos Trans R Soc B 360:1917–1924

    CAS  Google Scholar 

  • Molnar JL, Gamboa RL, Revenga C (2008) Assessing the global threat of invasive species to marine biodiversity. Front Ecol Environ 6:485–492

    Google Scholar 

  • Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B (2011) How many species are there on earth and in the ocean? PLoS Biol 9:e1001127

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mouquet N, Devictor V, Meynard CN et al (2012) Ecophylogenetics: advances and perspectives. Biol Rev 87(4):769–785

    PubMed  Google Scholar 

  • Naddaf SR, Oshaghi MA, Vatandoost H (2012) Confirmation of two sibling species among Anopheles fluviatilis mosquitoes in south and southeastern Iran by analysis of cytochrome oxidase I gene. J Arthropod-Borne Dis 6:144–150

    PubMed  PubMed Central  Google Scholar 

  • Nagoshi RN, Meagher RL, Brambila J (2011) Use of DNA barcodes to identify invasive armyworm Spodoptera species in Florida. J Insect Sci 11:154

    PubMed  PubMed Central  Google Scholar 

  • Nagy ZT, Sonet G, Glaw F (2012) First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoS One 7(3):e34506

    CAS  PubMed  PubMed Central  Google Scholar 

  • Naro-Maciel E, Reid B, Fitzsimmons NN, Le M, Desalle R, Amato G (2010) DNA barcodes for globally threatened marine turtles: a registry approach to documenting biodiversity. Mol Ecol Resour 10:252–263

    CAS  PubMed  Google Scholar 

  • Natalie JWW (2013) Determining the microbial diversity in chaparral soils before and after wildfires through DNA barcoding. Project Number-S1119, California State Science Fair, Project Summary

    Google Scholar 

  • Neigel J, Domingo A, Stake J (2007) DNA barcoding as a tool for coral reef conservation. Coral Reefs 26:487–499

    Google Scholar 

  • Newmaster SG, Grguric M, Shanmughanandhan D, Ramalingam S, Ragupathy S (2013) DNA barcoding detects contamination and substitution in north American herbal products. BMC Med 11:222

    PubMed  PubMed Central  Google Scholar 

  • Ngamskulrungroj P, Gilgado F, Faganello J, Litvintseva AP, Leal AL, Tsui KM, Mitchell TG, Vainstein MH, Meyer W (2009) Genetic diversity of the Cryptococcus species complex suggests that Cryptococcus gattii deserves to have varieties. PLoS One 4:e5862

    PubMed  PubMed Central  Google Scholar 

  • Nieukerken EJV, Doorenweerd C, Stokvis FR, Dick SJ, Groenenberg DSJ (2012) DNA barcoding of the leaf-mining moth subgenus Ectoedemias. Str. (Lepidoptera: Nepticulidae) with COI and EF1-a: two are better than one in recognizing cryptic species. Contr Zool 81:1–24

    Google Scholar 

  • Nwani CD, Becker S, Braid HE, Ude EF, Okogwu OI, Hanner R (2011) DNA barcoding discriminates freshwater fishes from southeastern Nigeria and provides river system-level phylogeographic resolution within some species. Mitochondrial DNA 22(Suppl 1):43–51

    CAS  PubMed  Google Scholar 

  • Panprommin D, Panprommin N (2017) Assessment of the DNA barcoding for identification of Trigonostigma somphongsi, a critically endangered species in Thailand. Biochem Systemat Ecol 70:200–204

    CAS  Google Scholar 

  • Parvathy VA, Swetha VP, Sheeja TE, Leela NK, Chempakam B, Sasikumar B (2014) DNA barcoding to detect chilli adulteration in traded black pepper powder. Food Biotechnol 28:25–40

    CAS  Google Scholar 

  • Parvathy VA, Swetha VP, Sheeja TE, Sasikumar B (2015) Detection of plant-based adulterants in turmeric powder using DNA barcoding. Pharm Biol 53:1774–1779

    CAS  PubMed  Google Scholar 

  • Patel S, Waugh J, Millar CD, Lambert DM (2010) Conserved primers for DNA barcoding historical and modern samples from New Zealand and Antarctic birds. Mol Ecol Res 10:431–438

    CAS  Google Scholar 

  • Pauls SU, Blahnik RJ, Zhou X, Wardwell CT, Holzenthal RW (2010) DNA barcode data confirm new species and reveal cryptic diversity in Chilean Smicridea (Smicridea) (trichoptera:hydropsychidae). J N Am Benthol Soc 29:1058–1074

    Google Scholar 

  • Prendini L (2005) Comment on “identifying spiders through DNA barcodes”. Can J Zool 83:498–504

    CAS  Google Scholar 

  • Rai PS, Bellampalli R, Dobriyal RM, Agarwal A, Satyamoorthy K, Narayana DBA (2012) DNA barcoding of authentic and substitute samples of herb of the family Asparagaceae and Asclepiadaceae based on the ITS2 region. J Ayurveda Integr Med 3:136–140

    PubMed  PubMed Central  Google Scholar 

  • Rainer J, de Hoog GS (2006) Molecular taxonomy and ecology of Pseudallescheria, Petriella and Scedosporium prolificans (Microascaceae) containing opportunistic agents on humans. Mycol Res 110:151–160

    CAS  PubMed  Google Scholar 

  • Raja HA, Baker TR, Little JG, Oberlies NH (2017) DNA barcoding for identification of consumer-relevant mushrooms: a partial solution for product certification? Food Chem 214:383–392

    CAS  PubMed  Google Scholar 

  • Rastogi G, Dharne MS, Walujkar S, Kumar A, Patole MS, Shouche YS (2007) Species identification and authentication of tissues of animal origin using mitochondrial and nuclear markers. Meat Sci 76:666–674

    CAS  PubMed  Google Scholar 

  • Rebijith KB, Asokan R, Kumar NKK, Krishna V, Chaitanya BN, Ramamurthy VV (2013) DNA barcoding and elucidation of cryptic aphid species (Hemiptera: Aphididae) in India. Bull Entomol Res 3:601–610

    Google Scholar 

  • Remigio EA, Hebert PDN (2003) Testing the utility of partial COI sequences for phylogenetic estimates of gastropod relationships. Mol Phylogenet Evol 29:641–647

    CAS  PubMed  Google Scholar 

  • Renaud AK, Savage J, Adamowicz SJ (2012) DNA barcoding of northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits. BMC Ecol 12:24

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roe AD, Rice AV, Bromilow SE, Cooke JE, Sperling FA (2010) Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle. Mol Ecol Resour 10:946–959

    CAS  PubMed  Google Scholar 

  • Rossi N, Mantelatto FL (2013) Molecular analysis of the freshwater prawn Macrobrachium olfersii (Decapoda, Palaemonidae) supports the existence of a single species throughout its distribution. PLoS One 8(1):e54698

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ruiz-García M, Pinedo-Castro M, Shostell JM (2014) How many genera and species of woolly monkeys (Atelidae, Platyrrhine, primates) are there? The first molecular analysis of Lagothrix flavicauda, an endemic Peruvian primate species. Mol Phylogenet Evol 79:179–198

    PubMed  Google Scholar 

  • Sanches A, Perez WAM, Figueiredo MG, Rossini BC, Cervini M, Galetti PM Jr et al (2011) Wildlife forensic DNA and lowland tapir (Tapirus terrestris) poaching. Conserv Genet Resour 3:189–193

    Google Scholar 

  • Schneider KL, Marrero G, Alvarez AM, Presting GG (2011) Classification of plant associated bacteria using RIF, a computationally derived DNA marker. PLoS One 6(4):e18496

    CAS  PubMed  PubMed Central  Google Scholar 

  • Scorzetti G, Fell JW, Fonseca A, Statzell-Tallman A (2002) Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions. FEMS Yeast Res 2:495–517

    CAS  PubMed  Google Scholar 

  • Seifert KA, Samson RA, Dewaard JR, Houbraken J, Lévesque CA, Moncalvo JM, Louis-Seize G, Hebert PD (2007) Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proc Natl Acad Sci U S A 104:3901–3906

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shander C, Willassen E (2005) What can biological barcoding do for marine biology. Mar Biol Resour 1:79–83

    Google Scholar 

  • Shivji MS, Chapman DD, Pikitch EK, Raymond PW (2005) Genetic profiling reveals illegal international trade in fins of the great white shark Carcharodon carcharias. Conser Genet 6(6):1035–1039

    Google Scholar 

  • Smith MA, Fernandez-Triana JL, Eveleigh E, Gomez J, Guclu C, Hallwachs W, Hebert PDN et al (2013) DNA barcoding and the taxonomy of Microgastrinae wasps (hymenoptera, Braconidae): impacts after 8 years and nearly 20000 sequences. Mol Ecol Res 13:168–176

    Google Scholar 

  • Smith MA, Fisher BL, Hebert PDN (2005) DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Philos Trans R Soc B 360:1825–1834

    CAS  Google Scholar 

  • Smith PJ, McVeagh SM, Steinke D (2008) DNA barcoding for the identification of smoked fish products. J Fish Biol 72:464–471

    CAS  Google Scholar 

  • Smith MA, Poyarkov NA, Hebert PDN (2008) CO1 DNA barcoding amphibians: take the chance, meet the challenge. Mol Ecol Resour 8:235–246

    CAS  PubMed  Google Scholar 

  • Steinke D, Zemlak TS, Hebert PDN (2009) Barcoding Nemo: DNA-based identifications for the ornamental fish trade. PLoS One 4(7):e6300

    PubMed  PubMed Central  Google Scholar 

  • Stoeckle MY (2008) Blog: DNA identifies invasive parasitic wasp’ in the barcode of life blog. http://phe.rockefeller.edu/barcode/blog/2008/07/07/dna-identifies-invasive-parasitic-wasps/. Accessed 26 Feb 2011

  • Stoeckle MY, Gamble CC, Kirpekar R, Yung G, Ahmed S, Little DP (2011) Commercial teas highlight plant DNA barcode identification successes and obstacles. Nat Sci Rep 1:42

    Google Scholar 

  • Stoeckle MY, Hebert PDN (2008) Barcode of life: DNA tags help classify animals. Sci Am 298(10):39–43

    Google Scholar 

  • Swartz ER, Mwale M, Hanner R (2008) A role for barcoding in the study of African fish diversity and conservation. South Afr J Sci 104(4):293–298

    Google Scholar 

  • Sweeney BW, Battle JM, Jackson JK (2011) Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? J North Am Benthol Soc 30(1):195–216

    Google Scholar 

  • 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(3):e14

    PubMed  Google Scholar 

  • Tack JF, Berghe E, Polk PH (1992) Ecomorphology of Crassostrea cucullata (born, 1778) (Ostreidae) in a mangrove creek (Gazi, Kenya). Hydrobiologia 247:109–117

    Google Scholar 

  • Thao L, James T, Alexandra B et al (2013) Bar-coded Enterobacteria: an undergraduate microbial ecology laboratory module. Am J Educ Res 1(1):26–30

    Google Scholar 

  • Trivedi S, Affan R, Alessa AHA et al (2014) DNA barcoding of Red Sea fishes from Saudi Arabia – the first approach. DNA Barcodes 2:17–20

    Google Scholar 

  • Trivedi S, Ghosh SK, Choudhury A (2013) DNA sequence of cytochrome c oxidase subunit 1 (COI) region of an oyster Saccostrea cucullata collected from Sunderbans. J Environ Sociobiol 10(1):77–81

    Google Scholar 

  • Uchimura M, Faye EJ, Shimada S, Inoue T, Nakamura Y (2008) A reassessment of Halophila species (Hydrocharitaceae) diversity with special reference to Japanese representatives. Bot Mar 51:258–268

    Google Scholar 

  • Udayasuriyan R, Saravana Bhavan P, Vadivalagan C, Rajkumar G (2015) Efficiency of different COI markers in DNA barcoding of freshwater prawn species. J Entomol Zool Stud 3(3):98–110

    Google Scholar 

  • Vargas SM, Araujo FCF, Santos FR (2009) DNA barcoding of Brazilian sea turtles (Testudines). Genet Mol Biol 32(3):608–612

    CAS  PubMed  PubMed Central  Google Scholar 

  • Vassou SL, Kusuma G, Parani M (2015) DNA barcoding for species identification from dried and powdered plant parts: a case study with authentication of the raw drug market samples of Sida cordifolia. Gene 559:86–93

    CAS  PubMed  Google Scholar 

  • Vialle A, Feau N, Allaire M, Didukh M, Martin F, Moncalvo JM, Hamelin RC (2009) Evaluation of mitochondrial genes as DNA barcode for Basidiomycota. Mol Ecol Resour 9(Suppl S1):99–113

    CAS  PubMed  Google Scholar 

  • Wang G, Li C, Guo X, Xing D, Dong Y (2012) Identifying the main mosquito species in China based on DNA barcoding. PLoS One 7:e47051

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang J, Soininen J, He J, Shen J (2012) Phylogenetic clustering increases with elevation for microbes. Environ Microbiol Rep 4(2):217–226

    PubMed  Google Scholar 

  • Ward RD, Holmes BH, White WT, Last PR (2008) DNA barcoding Australasian chondrichtyans: results and potential uses in conservation. Mar Freshw Res 59(1):57–71

    CAS  Google Scholar 

  • Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B 360:1847–1857

    CAS  Google Scholar 

  • Waycott M, Duarte CM, Carruthers TJB et al (2009) Accelerating loss of seagrasses across the globe threatens coastal ecosystems. Proc Natl Acad Sci U S A 106:12377–12381

    CAS  PubMed  PubMed Central  Google Scholar 

  • Weigt LA, Baldwin CC, Driskell A (2012) Using DNA barcoding to assess Caribbean reef fish biodiversity: expanding taxonomic and geographic coverage. PLoS One 7(7):e41059

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wilson EO (ed) (1994) Biodiversity. National Academy Press, Washington, DC

    Google Scholar 

  • Wilson EO (2003) The encyclopaedia of life. Trends Ecol Evol 18:77–80

    Google Scholar 

  • Wong KL, But PPH, Shaw PC (2013) Evaluation of seven DNA barcodes for differentiating closely related medicinal Gentiana species and their adulterants. Chin Med 8:16

    PubMed  PubMed Central  Google Scholar 

  • Wong EHK, Hanner RH (2008) DNA barcoding detects market substitution in north American seafood. Food Res Int 41:828–837

    CAS  Google Scholar 

  • Woodcock TS, Boyle EE, Roughley RE, Kevan PG, Labbee RN, Smith ABT, Goulet H et al (2013) The diversity and biogeography of the Coleoptera of Churchill: insights from DNA barcoding. BMC Ecol 13:40

    PubMed  PubMed Central  Google Scholar 

  • Wu H, Wan Q-H, Fang S-G, Zhang S-Y (2005) Application of mitochondrial DNA sequence analysis in the forensic identification of Chinese sika deer subspecies. Foren Sci Int 148:101–105

    CAS  Google Scholar 

  • Yang Q, Zhao S, Kucerova Z, Stejskal V, Opit G, Qin M, Cao Y, Li F et al (2013) Validation of the 16S rDNA and COI DNA barcoding technique for rapid molecular identification of stored product Psocids (Insecta: Psocodea: Liposcelididae). J Econ Entomol 106:419–425

    CAS  PubMed  Google Scholar 

  • Zhou J, Wang W, Liu M, Liu Z (2014) Molecular authentication of the traditional medicinal plant Peucedanum praeruptorum and its substitutes and adulterants by DNA – barcoding technique. Pharmacogn Mag 10:385–390

    PubMed  PubMed Central  Google Scholar 

  • Zimmermann J, Glöckner G, Jahn R, Enke N, Gemeinholzer B (2015) Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies. Mol Ecol Resour 15(3):526–542

    CAS  PubMed  Google Scholar 

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Acknowledgments

The authors are grateful to the University Grants Commission (UGC), New Delhi—Dr. D.S. Kothari Post-Doctoral Fellowship—for their financial support.

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Authors and Affiliations

  1. Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India

    J. Suriya & M. Krishnan

  2. Department of Biomedical Engineering, Nano-Biomedicine Lab, Pukyong National University, Busan, South Korea

    S. Bharathiraja

  3. National Centre for Sustainable Coastal Management, Ministry of Environment, Forests & Climate Change, Anna University Campus, Chennai, Tamil Nadu, India

    V. Sekar & V. Sachithanandam

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Editors and Affiliations

  1. Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia

    Subrata Trivedi

  2. Department of Urology, The University of Alabama at Birmingham (UAB), Birmingham, AL, USA

    Hasibur Rehman

  3. Department of Cell, Developmental and Integrative Biology (CDIB), The University of Alabama at Birmingham (UAB), Birmingham, AL, USA

    Shalini Saggu

  4. Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia

    Chellasamy Panneerselvam

  5. University of Kalyani, Kalyani, Nadia, West Bengal, India

    Sankar K. Ghosh

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Suriya, J., Krishnan, M., Bharathiraja, S., Sekar, V., Sachithanandam, V. (2020). Implications and Utility of DNA Barcoding. In: Trivedi, S., Rehman, H., Saggu, S., Panneerselvam, C., Ghosh, S. (eds) DNA Barcoding and Molecular Phylogeny. Springer, Cham. https://doi.org/10.1007/978-3-030-50075-7_1

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