Subrata Trivedi · Hasibur Rehman  Shalini Saggu · Chellasamy Panneerselvam  Sankar K. Ghosh Editors DNA Barcoding and Molecular Phylogeny DNA Barcoding and Molecular Phylogeny (cid:129) (cid:129) Subrata Trivedi Hasibur Rehman (cid:129) (cid:129) Shalini Saggu Chellasamy Panneerselvam Sankar K. Ghosh Editors DNA Barcoding and Molecular Phylogeny Editors SubrataTrivedi HasiburRehman FacultyofScience,DepartmentofBiology FacultyofScience,DepartmentofBiology UniversityofTabuk UniversityofTabuk Tabuk,SaudiArabia Tabuk,SaudiArabia DepartmentsofPathology SchoolofMedicine,TheUniversityofAlabama atBirmingham(UAB) Birmingham,AL,USA ShaliniSaggu ChellasamyPanneerselvam FacultyofScience,DepartmentofBiology FacultyofScience,DepartmentofBiology UniversityofTabuk UniversityofTabuk Tabuk,SaudiArabia Tabuk,SaudiArabia DepartmentsofDermatology SchoolofMedicine,TheUniversityof AlabamaatBirmingham(UAB) Birmingham,AL,USA SankarK.Ghosh UniversityofKalyani Kalyani,WestBengal,India ISBN978-3-319-90679-9 ISBN978-3-319-90680-5 (eBook) https://doi.org/10.1007/978-3-319-90680-5 LibraryofCongressControlNumber: 2018947792 ©SpringerInternationalPublishingAG,partofSpringerNature2018 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe materialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped. 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Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Contents PartI DNABarcoding:AdvantagesandSignificance DNABarcodingSignificanceandUtilities. . . . . . . . . . . . . . . . . . . . . . . . 3 SambashivaDaravath,ReddyaNaikBannoth,ManickamTamilSelvi, andSrinivasAnkanagari RinDNABarcoding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 AsimKumarMahadani,PradoshMahadani,andGoutamSanyal ImplicationsandUtilityofDNABarcoding. . . . . . . . . . . . . . . . . . . . . . 45 J.Suriya,M.Krishnan,S.Bharathiraja,V.Sekar,andVSachithanandam “SignificanceofDNABarcodinginAvianSpecies:Tracing theHistoryandBuildingtheFuture”. . . . . . . . . . . . . . . . . . . . . . . . . . . 65 FarhinaPasha DNABarcoding:APotentialToolforInvasiveSpeciesIdentification. . . 73 MuniyandiNagarajan,AkashNambidiParambath,andVandanaR.Prabhu PartII DNABarcodingofMicrobes MicrobialDNABarcoding:ProspectsforDiscovery andIdentification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 AnandMohan,BableenFlora,MadhuriGirdhar,andS.M.Bhatt DNABarcodingonBacteriaandItsApplicationinInfection Management.. . . . . . . . . .. . . . . . . . . . .. . . . . . . . . .. . . . . . . . . . .. . . 103 MohammadZubair,FarhaFatima,ShaminaBegum, andZahidHameedSiddiqui v vi Contents PartIII DNABarcodinginPlants DNABarcoding:ImplicationsinPlant-AnimalInteractions. . . . . . . . . . 123 MuniyandiNagarajan,VandanaR.Prabhu,RanganathanKamalakkannan, andPalattyAlleshSinu DNABarcodinginForensicBotany. . . . . . . . . . . . . . . . . . . . . . . . . . . . 143 MohamedRizkEnan AMolecularAssessmentofRedAlgaewithReferencetotheUtility ofDNABarcoding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 ZahidHameedSiddiqui,ZahidKhorshidAbbas,KhalidRehmanHakeem, MatherAliKhan,andAbdulIlah DNADatabases:PromisesandLimitationsforPlantDNA Barcoding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179 SelvarajDhivya,MohanasundaramSaravanan, andRamalingamSathishkumar AquaticPlantBiodiversityandDNABarcoding. . . . . . . . . . . . . . . . . . . 197 SufiaIrfanandAishahAlatawi PartIV DNABarcodinginAnimals DNABarcodingofMosquitoSpecies. . . . . . . . . . . . . . . . . . . . . . . . . . . 217 LalitaGupta,SanjeevKumar,andKuldeepGupta DNABarcodingofRaysfromtheSouthChinaSea. . . . . . . . . . . . . . . . 229 B.AkbarJohn,M.A.MuhamadAsrul,WahidahMohdArshaad, K.C.A.Jalal,andHassanI.Sheikh MolecularPhylogenyofElasmobranchs. . . . . . . . . . . . . . . . . . . . . . . . . 245 A.Pavan-Kumar,P.Gireesh-Babu,A.K.Jaiswar,S.G.Raje, A.Chaudhari,andG.Krishna AReviewonDNABarcodingonFishTaxonomyinIndia. . . . . . . . . . . 259 V.SachithanandamandP.M.Mohan ApplicationsofDNABarcodinginFisheries. . . . . . . . . . . . . . . . . . . . . . 281 A.Pavan-Kumar,A.K.Jaiswar,P.Gireesh-Babu,A.Chaudhari, andG.Krishna IdentificationandConservationofReptilesThroughDNA Barcoding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293 SubrataTrivedi,HasiburRehman,ShaliniSaggu,AlThabianiAziz, ChellasamyPanneerselvam,andSankarK.Ghosh DNABarcodinginAvianSpecieswithSpecialReference toTaxonomicallyWideBiogeographicStudies. . . . . . . . . . . . . . . . . . . . 305 FarhinaPasha Contents vii MolecularCharacterizationofRuminantMammalsUsing DNABarcodes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317 MuniyandiNagarajan,KoodaliNimisha,andSubhashThomas PartV CaseStudies PhylogeneticDiversityofCulturableMarineActinobacteriaIsolated fromtheHavelockIsland,theAndamans,India. . . . . . . . . . . . . . . . . . . 333 GobalakrishnanRajagopalandSivakumarKannan DNABarcodingandMolecularPhylogenyofIndigenousBacteria inFishesfromaTropicalTidalRiverinMalaysia. . . . . . . . . . . . . . . . . 351 MohammadMustafizurRahman,MohdHaikalIzzuddin, NajmusSakibKhan,AkbarJohn,andMohdAzrulNaim DNABarcodingofIchthyoplanktonandJuvenileFishesofaTropical RiverinMalaysia. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367 B.AkbarJohn,HassanI.Sheikh,K.C.A.Jalal,B.Y.Kamaruzzaman, H.Sanower,M.NurHanisah,M.H.Rahman,andM.Rozihan GeneticVariationofWildandHatcheryPopulationsofClimbing Perch,Anabastestudineus(Bloch,1792),inPeninsularMalaysia. . . . . . 383 AhmadAzfarMohamed,SitiWaznahAbdurahman,andAkbarJohn MolecularIdentificationofReptilesfromTabukRegion ofSaudiArabiaThroughDNABarcoding:ACaseStudy. . . . . . . . . . . 397 BishalDhar,MohuaChakraborty,N.NeelimaDevi, SorokhaibamMalvika,MadhurimaChakraborty,SubrataTrivedi, AbdulhadiA.Aloufi,andSankarK.Ghosh Hippophaerhamnoides(SeaBuckthorn):AHigh-AltitudeMedicinal andAdaptogenicPlant—MolecularCharacterization andBar-Coding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413 ShwetaSaxena,OmPrakashChaurasia,andRatanKumar ClosingShots:DNABarcodingandMolecularPhylogeny. . . . . . . . . . . 439 SubrataTrivedi,HasiburRehman,ShaliniSaggu, ChellasamyPanneerselvam,andSankarK.Ghosh Part I DNA Barcoding: Advantages fi and Signi cance fi DNA Barcoding Signi cance and Utilities SambashivaDaravath,ReddyaNaikBannoth,ManickamTamilSelvi, andSrinivasAnkanagari Abstract DNA barcoding is a genetic-based tool and used as an integrated approach with taxonomy for species identification and authentication. In recent years, different genetic and genomic approaches are taken in identifying gene markers for universal applicable DNA barcode in different taxonomic groups and samples. In the postgenomics era, combination of molecular biology techniques, bioinformatics, DNA barcoding, and metabarcoding is giving an opportunity to change the existing use of biodiversity information for basic and practical applica- tions.DNAbarcodingprojectsindifferentorganismsareestablishingthereference libraries with known sequences available for open access databases to identify unknownspecimens.SOPs inDNA barcodingareimportantfor eachspeciesfrom sampling to analysis by the researchers. DNA barcoding is aiding to catalogue the listofspeciesbiodiversityandanswerfundamentalquestionsinecology,evolution, andconservationbiology.DNAbarcodingcanbeusedbyregulatoryauthoritiesand have advantages as quality control test. DNA barcoding can also improve quality assurance of industrial products. There is also emerging significance in implementingDNAbarcodinginconsumer,environmental,health,andagricultural protection. Keywords DNAbarcoding·DNAmetabarcoding·Informatics·SOP·Quality control·Biodiversityassessment S.Daravath DepartmentofBiotechnology,NizamCollege,Hyderabad,Telangana,India R.NaikBannoth DepartmentofZoology,OsmaniaUniversity,Hyderabad,Telangana,India M.T.Selvi ValueAddedCorporateServicesPvtLtd,Chennai,TamilNadu,India S.Ankanagari(*) DepartmentofGenetics,OsmaniaUniversity,Hyderabad,Telangana,India ©SpringerInternationalPublishingAG,partofSpringerNature2018 3 S.Trivedietal.(eds.),DNABarcodingandMolecularPhylogeny, https://doi.org/10.1007/978-3-319-90680-5_1 4 S.Daravathetal. 1 DNA Barcoding: A Genetic Approach-Based Tool for Species Identification Developments in molecular genetics and genomic technologies help in easy and reliableidentificationofspecies.ResearchersareusingshortDNAsequences,called as DNA barcode, from the specified region of genome. The concept of DNA barcoding was proposed by Hebert et al. (2003a). A DNA barcode is a part of the genome ofthe organism that stands for standardizedtarget regions of genic and/or intergenicinanybiologicalspecies.DNAbarcodinginvolvesamplifying,sequenc- ing, and querying of information from extranuclear genomes, both chloroplast and mitochondrial. Once the DNA barcoding sequence has been retrieved from an unknown sample, an algorithm is used to compare with unknown sequence to reference database containing known barcodes from identified samples that makes easy to identify the unknown samples. When identification of biological species based on morphological characters is not possible, DNA sequences of highly conserved genes are used. DNA barcoding helps to differentiate similar-looking speciesandidentifyingimmatureordamagedspecimens.DNAbarcodecarriesboth specific and systematic data. DNA barcode development established an error-free andfastmethodofspeciesidentificationandcanfunctionasmolecularidentifierfor everyspecies. 1.1 Significance: Biodiversity Assessment BiodiversityisthevariabilityoflifeonEarth,includingthegeneswhichtheycarry and complex ecosystems that create the environment (Primack et al. 2001). The degree of biodiversity is constantly changing; the rate of extinction is 100–1000 timeshigher,almostexclusivelyasaconsequenceofhumanactivity.Inrecentyears, theefforttomapandtoprotectglobalbiodiversityhasbeeneverincreasing.Thusthe global project aimed at the mapping and protection of biodiversity using a new taxonomicmethodcalled“DNAbarcoding”wasstarted.DNAbarcodingassistsin cataloging the list of species biodiversity and answers fundamental questions in ecology, evolution, and conservation biology. Many authors have proposed DNA barcodingasanintegratedapproachwithclassicaltaxonomyforspeciesidentifica- tionandauthenticationinthepostgenomicsera(KaneandCronk2008;Newmaster etal.2009;SahareandSrinivasu2012;VohraandKhera2013).Sinceithasenough nucleotide diversity,DNA barcodesare usedtodiscover, describe, andunderstand biodiversity of unknown species. The universal coded labels found by the researchers are used as unique identification marker for the species on the planet (Kress et al. 2015). Combination of molecular biology techniques, bioinformatics, and DNA barcoding is giving an opportunity to change the existing use of biodi- versityinformationforbasicandpracticalapplications.