DOC

Genome

By Kim Diaz,2014-07-18 02:28
7 views 0
Genome

    Genome

gynogenticfamily

    ;YanZhanga,bLiqunLiang

    ;,

    ;PengJianga,bDayuLi

    ;,

    ;CuiyunLua,XiaowenSuna,

    ;HeilongfiangRiverFisheriesResearchInstitute,ChineseAcademyofFisheriesSciences,Harbin150070,China

    ;CollegeofAqua-lifeScienceandTechnology,ShanghaiFisheriesUniversity,Shanghai200090,China

    ;LifeScienceandTechnologyInstitute.DalianFisheriesUniversity,Dalian116023,China

    ;Receivedforpublication19April2007;revised1August2007;accepted1August2007

    ;Abstract

    ;Genomeevolutionarisesfromtwomainwaysofduplicationandreduction.Fishspecificgenomeduplication(FSGD)mayhaveoc.

    ;cuffedbeforetheradiationoftheteleosts.Commoncarp(CyprinuscarpioL.)hasbeenconsideredtobeatetraploidspecies,becauseof

    ;itschromosomenumbers(2n=l00)anditshighDNAcontent.Using69microsatelliteprimerpairs.thevariationswerestudiedtobeuer

    ;understandthegenomeevolution(genomeduplicationanddiploidization)ofcommoncarpfromagynogeneticfamily.About48%of

    ;primerpairswereestimatedtoamplifyduplicatesbasedonthenumberofPCRamplificationperindividua1.Segregationpatternsinthe

    ;familysuggestedapartiallyduplicatedgenomestructureanddisomicinheritance.Thisindicatesthatthecommoncarpistetraploidand

    ;polyploidyoccurredbyallotetraploidyTwoprimetpairsfHUO21andHL

    32)wereestimatedtoamplifyreductionbasedonthenumber

    ;ofPCRamplificationperindividua1.OnealleleinHUoo2locusandHLJ332locuswasclearlylostinthegynogeneticfamilyandthe

    ;sameasinsixwildpopulations.Segregationpatternsinthefamilysuggestedapartiallydiplodizationgenomestructure.Ahypothesis

    ;transition(dynamic)andequilibrium(static)wereproposedtoexplainthecommoncarpgenomeevolutionbetweengenomeduplication

    ;anddiploidization.

    ;Keywords:commoncarp;genomeduplication;genomediploidization ;Introduction

    ;Genomeevolutionarisesfrommanyways,suchasdu.

    ;plicationsordeletionsofgeneticmaterials,transfer,or

    ;pointmutations.Inbacteria,recombinationplaysanim.

    ;portantroleinmanyevents,asitisrelatedtophageinte. ;gration(KingandRichardson,1986),horizontaltransfer ;(Rayssiguiereta1.,1989),majorchromosomalrearrange- ;ments(HillandGray,1988),fastadaptationofoutmere. ;braneproteininpathogens(Moxoneta1.,1994),andrepair ;ofstalledreplicationforks(Kuzminov,2001).Butinver. ;tebrates,theduplicationofgenesandgenomesaremore ;importantinshapingtheevolutionofnovelandcomplex ;naturalselection(aaseta1.,2004).

    ;ithasbeensuggestedthatoneortworoundsofgenome ;Correspondingauthor.Tel:+86.45184862646.

    ;E.mailaddress:sunxw2002@163.corn

    ;duplicationinvertebrateevolutionoccurredbeforethe ;divergenceofthelampreylineageandafterthisdivergence, ;about450millionyearsago(MYA)(Hollandeta1.,1994; ;Sidow.1996;SkrabanekandWo1fe,1998).Additionalge. ;nomeduplication,specifictoray.finnedfish,possiblyoc. ;curredatabout360Mprecedingthedivergenceofthe ;teleostsfTayloreta1.,20011.Thisduplicationcouldhave ;enabledthemajordiversificationoftheteleosts,themost ;species.richgroupofvertebrates(Amoreseta1.,1998; ;MeyerandMalaga.11o.1999).Polyploidyhasbeensig.

    ;nificantintheevolutionhistoryofvertebrates. ;Genomeduplicationintheevolutionofcommoncarp ;(CyprinuscarpioL.)issupportedbythefollowingobser- ;vation:thechromosomenumberofcommoncarp=50)is ;twiceofotherCyprinidae,andtheDNAcontentishigh ;fDavideta1..2003).About52%oftIliscarpenzymesshow ;apatternconsistentwithduplication(Davideta1.,2003). ;Tetraploidizationofcarpwassuggestedtotakeplaceat ;

    ;

    ;YahZhangetal/JournalofGeneticsandGenomics35(2008)97_|03 ;about50MYA(Davideta1.,2003).Someduplicatedgenes ;ofthecarpsuggestamorerecentdivergencetaneofless ;than16MYA(LarhammarandRisinger,1994).Itwasas- ;sumedthatgenomeduplicationhadtakenplaceinthe ;evolutionofcommoncarporwasstillduplicating. ;Microsatelfitemarkersprovideacodominantinheri- ;tancetoolforstudyingmostregionsofagenome.Inafew ;studies,microsatelliteshavebeenusefulforthestudyof ;duplications(Ludwigeta1.,2001;Pyatskowiteta1.,2001; ;Angerseta1..2002).Davideta1.(20o3)usedmicrosatel

    ;liteasatooltosolvegenomeduplication.Inthisarticle,

    ;thegenomeduplicationeventsandreductionofploidy ;levelswereinvestigatedincommoncarpbyusing ;microsatellitemarkers.

    ;Genomereductionusuallytookplaceaftergenomedu- ;plication.Itishardtoresolvebymolecularmarkers,be. ;causetherewouldbetime.consumingseveralgenerations ;fromgenomeduplicationtoreductionanditwouldculti. ;vateexperimentfamilyforages.Thegynogenesishadan ;advantageinresearchinggenomereduction.Ahomology ;linecanberapidlydeveloped,theprocessofevolutioncan ;beadvanced,andsegregationofallelestransferredfrom ;parenttoprogenycouldbeeasilyexaminedinanextreme ;highinbreeding.Together,gynogensiscouldbeasuper

    ;modelforstudyingthegenomereductionbymicrosatellite. ;So,agynogenticfamilywasconstructedtodiscoverge

    ;nomereductionbymicrosatellitemarkers.

    ;Materialsandmethods

    ;Experimentalfamilies

    ;Gynogensiswasproducedbytheprotocolsdeveloped ;byGomelskveta1.(1988,1989.1992)andKomeneta1. ;(1991).Maternallyderivedgynogeneticfamilywasmade ;fromahybridfemale,whichwasproducedbycrossinga

    ;malecommoncarprCcarpiohaematopterusTemmincket ;Schlege1)withafemaleBarblesscarp(Cpellegrinipelle

    ;griniTchang).Successfulgynogensisresultedinadiploid ;organismthatcontainedtwosetsofmammalchromo. ;somes.Gynogenesiswasaccomplishedbyirradiatin2 ;colnlTlOncarpspermwithUv_irradiationatanintensityof ;175mJ?cm-(k=254nm)todestroythepatemalnuclear ;genome.Thirtyminutesafterfertilization,a2minheat ;shockwasadministeredbytransferringtheeggsfromthe ;incubationsystemtoawaterbatl1at40.C.Thistiming ;correspondstothemetaphaseofthefirstmitoticdivision ;ofthezygotes(Komeneta1.,1991).T}legynogensis ;progenygroupwasrearedfor12months.

    ;Ascontroltoinvestigategenomereduction,sixwild ;groupsofcommoncarp(30individualsseparately)were ;distributedindifferentlatitude.Thesedrainageareasarein ;HainanProvince.YangtzeRiver.HubeiProvince,Moon ;Lake.JilinProvince,AmurLake,HeiloniangProvince, ;HulanLakeandBeierLake,InnerMongolia,China. ;Microsatellitelocf

    ;GenomicDNAwasisolatedusingastandardphe-

    ;noYchloroformextractionprocedure.Eachindividualfish

    ;wasgenotyPedwitl169microsatellitemarkers.whichare ;detailedasfollows:11formarkerswithmicrosatellite ;cloneofXiaowenSun’s1aboratory;21formarkersofthe

    ;prefixMFW(Crooijmanseta1..1997);3)formarkersof ;theprefixKoi(Davideta1..2001).PCRamplifications ;werecardedoutina25uLreactionmixturecontaining50 ;nggenomicDNA.10pmoi/Leachprimer,0.45inmoI/L ;dNTP,2.5vL10×reactionbufFer’and1UTaqDNApo.

    ;1ymerase.Amplificationwasconductedfollowingthepro. ;gramof94~Cfor5min.20cyclesof94.Cfor30s.48-59.C ;for30s.72~Cfor30s.andthen72.Cfor10sasafinalex. ;tension.Twopercentagarosegelswereusedtoseparate ;PCRproductsand8%polyacrylamidegelswereusedto ;verifvdiploidizationloci.Gelswereinterpretedusingthe ;softwarepackagesGelPro(http://www.mediacy.corn). ;Results

    ;ScreeningofF1

    ;The69primerpairsstudiedwereclassifiedintothree ;categoriesaccordingtothenumberofPCRfragments ;foundinoneparentofthegynogeneticfamily:1)6primer ;pairs(8.7O%)hadonefragmentinparent,2)30primer ;pairs(43.48%)amplifiedtwofragmentsinparent,and3)

    ;33primerpairs(47.83%,thatexhibitedmorethantwo ;fragmentsintheparent.

    ;Geneduplication

    ;Intotal,69segregationpatternsofpolymorphicprimers ;wereanalyzed(Table11.Someprimersindicatedgene ;duplication.Forexample.primerpairHJ117wasstudied

    ;inthefamilywherebothgrandparentshadtwofragments ;andshareda325bpfragment.However,thedamhadthree ;fragmentsincludingallthefragmentsofgrandparentsand ;88%oftheoffspringhadthe325bpfragment(Fig.1).The ;325bpfragmentwasobservedinallprogeniesexceptfor3 ;individuals.whereastheothertwofragmentssegregated. ;Fragments240bpand221bpwerepresentinapproxi

    ;matelyhalfofthefishpopulation.Theproportionsofthe ;genotypesinprogenyexhibiteda1:1:1:1ratio.Fromsuch ;segregationpatternse..frequenciesofallelesandgeno- ;typesinprogeny)andgenotypesoftheparents,thefrag- ;mentswhichhaveaUelicrelationshipsandwhichfrag. ;mentsarenotallelesbutduplicatescanbedetermined.The ;segregationofratiof1:1:1:11indicatedtl1atprimerPairs ;tl1atfittedatetrasomicmodealsofittedadisomicmode1. ;

    ;YanZhangeta1./JournalofGeneticsandGenomics35(2008)97-103 ;Theobservedproportionsofgenotypesfittedthispostu. ;1atedratio(test,P=0.92).Fiveof33(15.2%)patterns ;deviatedsignificantlyfromtheexpectedratio(test,P< ;0.05,Tab1e1).A11primerpairsofduplicatedlocithatfitted ;atetrasomicmodeofinheritancealsofittedadisomic ;mode1.Ontheotherhand,someofthepatternsthatfitteda ;disomicmodeofinhefitancecouldnotbeexplainedbv ;tetrasomicinheritance.Locithatweredefinedasdiploid ;fT{1e1)andmainlythosewhoseallelessegregatedina ;1:1:1:1ratiocouldfitatetrasomicmodelaswel1.However, ;disomicinheritancewasusedtoexplainsegregationpat. ;Table1

    ;Summaryofsegregationpatternsofmicrosatellitelociinfamilies ;terns,sinceitismoreconservativeandexplainsmoreseg

    ;regationratiosatbothsingleandduplicatedloci. ;Theduplicatednatureoflociwasinferredbasedonthe ;numberoffragmentsperindividua1.Segregationpatterns ;infamiliessupportedthisassessmentin47.83%ofthe ;cases.Thesegregationpatternsofthe33duplicatedloci ;werecategorizedintotwotypes:128lociwerefoundto ;beduplicatedandtofitadisomicmodeofinheritance;and

;2,5lociwerefoundtobeduplicatedbutwithsegregation

    ;patternsthatdidnotfiteitherdisomicorduplicationmode

    ;ofinheritance(Table2).

    ;NumberTypePrimerpairFamily(n----2,4fish)NumberTypePrimerpairFa

    mily(n--44fish)

    ;11HLJ021Diploid362HLJ332Diploid ;21HLJ035Diploid373HLJ05ODuplicate ;31HLJ036Diploid383HLJ052Duplicate ;41HLJ038Diploid393HLJ053Duplicate ;51HLJ044Diploid403HLJ058Duplicate ;61HLJO46Diploid413HLJ064Duplicate ;71HLJ060Diploid423HLJ091Duplicate ;81HU063Diploid433HL04Duplicate

    ;91HLJ084Diploid443HLJl11Duplicate ;1O1HLJ108Diploid453HLJl14Duplicate ;l11HLJ119Diploid463HLJ117Duplicate ;121HLJ122Diploid473HLJ302Duplicate ;131HLJ124Diploid483HLJ319Duplicate ;141HJ125DirIloid493HLJ330Duplicate ;151HLJ129Diploid503HLJ370Duplicate ;161HLJ133Diploid513HLJ380Duplicate ;171HLJ138DiD1oid523HLJ437Duplicate

Report this document

For any questions or suggestions please email
cust-service@docsford.com