DNA Barcoding and Molecular Phylogeny

431 Pages·2018·7.88 MB·English

by  Subrata Trivedi

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
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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.