Genome size - Wikipedia

coli (643 kb compared to 4.6 Mb) and can be view as a subset of the enteric bacteria gene inventory. From the confrontation of the two genomes emerged that some ... Genomesize FromWikipedia,thefreeencyclopedia Jumptonavigation Jumptosearch Genomesizeranges(inbasepairs)ofvariouslifeforms GenomesizeisthetotalamountofDNAcontainedwithinonecopyofasinglecompletegenome.Itistypicallymeasuredintermsofmassinpicograms(trillionths(10−12)ofagram,abbreviatedpg)orlessfrequentlyindaltons,orasthetotalnumberofnucleotidebasepairs,usuallyinmegabases(millionsofbasepairs,abbreviatedMborMbp).Onepicogramisequalto978megabases.[1]Indiploidorganisms,genomesizeisoftenusedinterchangeablywiththetermC-value. Anorganism'scomplexityisnotdirectlyproportionaltoitsgenomesize;totalDNAcontentiswidelyvariablebetweenbiologicaltaxa.Somesingle-celledorganismshavemuchmoreDNAthanhumans,forreasonsthatremainunclear(seenon-codingDNAandC-valueenigma). Contents 1Originoftheterm 2Variationingenomesizeandgenecontent 3Genomereduction 3.1Inobligateendosymbioticspecies 4Conversionfrompicograms(pg)tobasepairs(bp) 5Drake'srule 6Genomeminiaturizationandoptimalsize 7Mechanismsofgenomeminiaturization 8Evidenceofgenomeminiaturization 9Seealso 10References 10.1Furtherreading 11Externallinks Originoftheterm[edit] Treeoflifewithgenomesizesasouterbars Theterm"genomesize"isoftenerroneouslyattributedtoa1976paperbyRalphHinegardner,[2]evenindiscussionsdealingspecificallywithterminologyinthisareaofresearch(e.g.,Greilhuber2005[3]).Notably,Hinegardner[2]usedthetermonlyonce:inthetitle.Thetermactuallyseemstohavefirstappearedin1968,whenHinegardnerwondered,inthelastparagraphofanotherarticle,whether"cellularDNAcontentdoes,infact,reflectgenomesize".[4]Inthiscontext,"genomesize"wasbeingusedinthesenseofgenotypetomeanthenumberofgenes. Inapapersubmittedonlytwomonthslater,Wolfetal.(1969)[5]usedtheterm"genomesize"throughoutandinitspresentusage;thereforetheseauthorsshouldprobablybecreditedwithoriginatingtheterminitsmodernsense.Bytheearly1970s,"genomesize"wasincommonusagewithitspresentdefinition,probablyasaresultofitsinclusioninSusumuOhno'sinfluentialbookEvolutionbyGeneDuplication,publishedin1970.[6] Variationingenomesizeandgenecontent[edit] Withtheemergenceofvariousmoleculartechniquesinthepast50years,thegenomesizesofthousandsofeukaryoteshavebeenanalyzed,andthesedataareavailableinonlinedatabasesforanimals,plants,andfungi(seeexternallinks).NucleargenomesizeistypicallymeasuredineukaryotesusingeitherdensitometricmeasurementsofFeulgen-stainednuclei(previouslyusingspecializeddensitometers,nowmorecommonlyusingcomputerizedimageanalysis[7])orflowcytometry.Inprokaryotes,pulsedfieldgelelectrophoresisandcompletegenomesequencingarethepredominantmethodsofgenomesizedetermination. Nucleargenomesizesarewellknowntovaryenormouslyamongeukaryoticspecies.Inanimalstheyrangemorethan3,300-fold,andinlandplantstheydifferbyafactorofabout1,000.[8][9]Protistgenomeshavebeenreportedtovarymorethan300,000-foldinsize,butthehighendofthisrange(Amoeba)hasbeencalledintoquestion.[bywhom?]Ineukaryotes(butnotprokaryotes),genomesizeisnotproportionaltothenumberofgenespresentinthegenome,anobservationthatwasdeemedwhollycounter-intuitivebeforethediscoveryofnon-codingDNAandwhichbecameknownasthe"C-valueparadox"asaresult.However,althoughthereisnolongeranyparadoxicalaspecttothediscrepancybetweengenomesizeandgenenumber,thetermremainsincommonusage.Forreasonsofconceptualclarification,thevariouspuzzlesthatremainwithregardtogenomesizevariationinsteadhavebeensuggestedbyoneauthortomoreaccuratelycompriseapuzzleoranenigma(theso-called"C-valueenigma"). Genomesizecorrelateswitharangeofmeasurablecharacteristicsatthecellandorganismlevels,includingcellsize,celldivisionrate,and,dependingonthetaxon,bodysize,metabolicrate,developmentalrate,organcomplexity,geographicaldistribution,orextinctionrisk.[8][9]Basedoncurrentlyavailablecompletelysequencedgenomedata(asofApril2009),log-transformedgenenumberformsalinearcorrelationwithlog-transformedgenomesizeinbacteria,archaea,viruses,andorganellescombined,whereasanonlinear(semi-naturallogarithm)correlationisseenforeukaryotes.[10]Althoughthelattercontrastswiththepreviousviewthatnocorrelationexistsfortheeukaryotes,theobservednonlinearcorrelationforeukaryotesmayreflectdisproportionatelyfast-increasingnon-codingDNAinincreasinglylargeeukaryoticgenomes.Althoughsequencedgenomedataarepracticallybiasedtowardsmallgenomes,whichmaycompromisetheaccuracyoftheempiricallyderivedcorrelation,andultimateproofofthecorrelationremainstobeobtainedbysequencingsomeofthelargesteukaryoticgenomes,currentdatadonotseemtoruleoutapossiblecorrelation. Genomereduction[edit] Genomesizecomparedtonumberofgenes.Log-logplotofthetotalnumberofannotatedproteinsingenomessubmittedtoGenBankasafunctionofgenomesize.BasedondatafromNCBIgenomereports. Genomereduction,alsoknownasgenomedegradation,istheprocessbywhichanorganism'sgenomeshrinksrelativetothatofitsancestors.Genomesfluctuateinsizeregularly,andgenomesizereductionismostsignificantinbacteria. Themostevolutionarilysignificantcasesofgenomereductionmaybeobservedintheeukaryoticorganellesknowntobederivedfrombacteria:mitochondriaandplastids.Theseorganellesaredescendedfromprimordialendosymbionts,whichwerecapableofsurvivingwithinthehostcellandwhichthehostcelllikewiseneededforsurvival.Manypresent-daymitochondriahavelessthan20genesintheirentiregenome,whereasamodernfree-livingbacteriumgenerallyhasatleast1,000genes.Manygeneshaveapparentlybeentransferredtothehostnucleus,whileothershavesimplybeenlostandtheirfunctionreplacedbyhostprocesses. Otherbacteriahavebecomeendosymbiontsorobligateintracellularpathogensandexperiencedextensivegenomereductionasaresult.Thisprocessseemstobedominatedbygeneticdriftresultingfromsmallpopulationsize,lowrecombinationrates,andhighmutationrates,asopposedtoselectionforsmallergenomes.[citationneeded]Somefree-livingmarinebacterioplanktonsalsoshowssignsofgenomereduction,whicharehypothesizedtobedrivenbynaturalselection.[11][12][13] Inobligateendosymbioticspecies[edit] Obligateendosymbioticspeciesarecharacterizedbyacompleteinabilitytosurviveexternaltotheirhostenvironment.Thesespecieshavebecomeaconsiderablethreattohumanhealth,astheyareoftencapableofevadinghumanimmunesystemsandmanipulatingthehostenvironmenttoacquirenutrients.Acommonexplanationforthesemanipulativeabilitiesistheirconsistentlycompactandefficientgenomicstructure.ThesesmallgenomesaretheresultofmassivelossesofextraneousDNA,anoccurrencethatisexclusivelyassociatedwiththelossofafree-livingstage.Asmuchas90%ofthegeneticmaterialcanbelostwhenaspeciesmakestheevolutionarytransitionfromafree-livingtoanobligateintracellularlifestyle.Duringthisprocessthefutureparasitesubjectedtoanenvironmentrichofmetabolitewheresomehowneedstohidewithinthehostcell,thosefactorsreducetheretentionandincreasethegeneticdriftleadingtoanaccelerationofthelossofnon-essentialgenes.[14][15][16]CommonexamplesofspecieswithreducedgenomesincludeBuchneraaphidicola,Rickettsiaprowazekii,andMycobacteriumleprae.Oneobligateendosymbiontofleafhoppers,Nasuiadeltocephalinicola,hasthesmallestgenomecurrentlyknownamongcellularorganismsat112kb.[17]Despitethepathogenicityofmostendosymbionts,someobligateintracellularspecieshavepositivefitnesseffectsontheirhosts. Thereductiveevolutionmodelhasbeenproposedasanefforttodefinethegenomiccommonalitiesseeninallobligateendosymbionts.[18]Thismodelillustratesfourgeneralfeaturesofreducedgenomesandobligateintracellularspecies: "genomestreamlining"resultingfromrelaxedselectionongenesthataresuperfluousintheintracellularenvironment; abiastowardsdeletions(ratherthaninsertions),whichheavilyaffectsgenesthathavebeendisruptedbyaccumulationofmutations(pseudogenes);[19] verylittleornocapabilityforacquiringnewDNA;and considerablereductionofeffectivepopulationsizeinendosymbioticpopulations,particularlyinspeciesthatrelyonverticaltransmissionofgeneticmaterial. Basedonthismodel,itisclearthatendosymbiontsfacedifferentadaptivechallengesthanfree-livingspeciesand,asemergedfromtheanalysisbetweendifferentparasites,theirgenesinventoriesareextremelydifferent,leadingustotheconclusionthatthegenomeminiaturizationfollowsadifferentpatternforthedifferentsymbionts.[20][21][22] Conversionfrompicograms(pg)tobasepairs(bp)[edit] Mainarticle:C-value numberofbasepairs = massinpg × 9.78 × 10 8 {\displaystyle{\text{numberofbasepairs}}={\text{massinpg}}\times9.78\times10^{8}} orsimply: 1 pg = 978  Mbp {\displaystyle1{\text{pg}}=978{\text{Mbp}}} [1] Drake'srule[edit] In1991,JohnW.Drakeproposedageneralrule:thatthemutationratewithinagenomeanditssizeareinverselycorrelated.[23]ThisrulehasbeenfoundtobeapproximatelycorrectforsimplegenomessuchasthoseinDNAvirusesandunicellularorganisms.Itsbasisisunknown. IthasbeenproposedthatthesmallsizeofRNAvirusesislockedintoathree-partrelationbetweenreplicationfidelity,genomesize,andgeneticcomplexity.ThemajorityofRNAviruseslackanRNAproofreadingfacility,whichlimitstheirreplicationfidelityandhencetheirgenomesize.Thishasalsobeendescribedasthe"Eigenparadox".[24]AnexceptiontotheruleofsmallgenomesizesinRNAvirusesisfoundintheNidoviruses.Thesevirusesappeartohaveacquireda3′-to-5′exoribonuclease(ExoN)whichhasallowedforanincreaseingenomesize.[25] Genomeminiaturizationandoptimalsize[edit] In1972MichaelDavidBennett[26]hypothesizedthattherewasacorrelationwiththeDNAcontentandthenuclearvolumewhileCommonerandvan’tHofandSparrowbeforehimpostulatedthatevencellsizeandcell-cyclelengthwerecontrolledbytheamountofDNA.[27][28]Morerecenttheorieshavebroughtustodiscussaboutthepossibilityofthepresenceofamechanismthatconstrainsphysicallythedevelopmentofthegenometoanoptimalsize.[29] ThoseexplanationshavebeendisputedbyCavalier-Smith’sarticle[30] wheretheauthorpointedthatthewaytounderstandtherelationbetweengenomesizeandcellvolumewasrelatedtotheskeletaltheory.Thenucleusofthistheoryisrelatedtothecellvolume,determinedbyanadaptationbalancebetweenadvantagesanddisadvantagesofbiggercellsize,theoptimizationoftherationucleus:cytoplasm(karyoplasmaticratio)[31][32]andtheconceptthatlargergenomesprovidesaremorepronetotheaccumulationofduplicativetransposonsasconsequencesofhighercontentofnon-codingskeletalDNA.[30]Cavalier-Smithalsoproposedthat,asconsequentreactionofacellreduction,thenucleuswillbemorepronetoaselectioninfavorforthedeletioncomparedtotheduplication.[30] Fromtheeconomicwayofthinking,sincephosphorusandenergyarescarce,areductionintheDNAshouldbealwaysthefocusoftheevolution,unlessabenefitisacquired.Therandomdeletionwillbethenmainlydeleteriousandnotselectedduetothereductionofthegainedfitnessbutoccasionallytheeliminationwillbeadvantageousaswell.Thistrade-offbetweeneconomyandaccumulationofnon-codingDNAisthekeytothemaintenanceofthekaryoplasmaticratio. Mechanismsofgenomeminiaturization[edit] Thebasequestionbehindtheprocessofgenomeminiaturizationiswhetheritoccursthroughlargestepsorduetoaconstanterosionofthegenecontent.Inordertoassesstheevolutionofthisprocessisnecessarytocompareanancestralgenomewiththeonewheretheshrinkageissupposedtobeoccurred.ThankstothesimilarityamongthegenecontentofBuchneraaphidicolaandtheentericbacteriaEscherichiacoli,89%identityforthe16SrDNAand62%fororthologousgeneswaspossibletoshedlightonthemechanismofgenomeminiaturization.[33]ThegenomeoftheendosymbiontB.aphidicolaischaracterizedbyagenomesizethatisseventimessmallerthanE.coli(643kbcomparedto4.6Mb)[34][35]andcanbeviewasasubsetoftheentericbacteriageneinventory.[35]Fromtheconfrontationofthetwogenomesemergedthatsomegenespersistaspartiallydegraded.[35]indicatingthatthefunctionwaslostduringtheprocessandthatconsequenteventsoferosionshortenedthelengthasdocumentedinRickettsia.[36][37][38]ThishypothesisisconfirmedbytheanalysisofthepseudogenesofBuchnerawherethenumberofdeletionswasmorethantentimeshighercomparedtotheinsertion.[38] InRickettsiaprowazekii,aswithothersmallgenomebacteria,thismutualisticendosymbionthasexperiencedavastreductionoffunctionalactivitywithamajorexceptioncomparedtootherparasites stillretainthebio-syntheticabilityofproductionofaminoacidneededbyitshost.[39][40][35]Thecommoneffectsofthegenomeshrinkingbetweenthisendosymbiontandtheotherparasitesarethereductionoftheabilitytoproducephospholipids,repairandrecombinationandanoverallconversionofthecompositionofthegenetoaricherA-T[41]contentduetomutationandsubstitutions.[14][39]EvidenceofthedeletionofthefunctionofrepairandrecombinationisthelossofthegenerecA,geneinvolvedintherecombinasepathway.Thiseventhappenedduringtheremovalofalargerregioncontainingtengenesforatotalofalmost10kb.[35][39]SamefaithoccurreduvrA,uvrBanduvrC,genesencodingforexcisionenzymesinvolvedintherepairdamagedDNAduetoUVexposure.[33] Oneofthemostplausiblemechanismsfortheexplanationofthegenomeshrinkingisthechromosomalrearrangementbecauseinsertion/deletionoflargerportionofsequencearemoreeasilytobeseeninduringhomologousrecombinationcomparedtotheillegitimate,thereforethespreadofthetransposableelementswillpositivelyaffecttherateofdeletion.[30]Thelossofthosegenesintheearlystagesofminiaturizationnotonlythisfunctionbutmustplayedaroleintheevolutionoftheconsequentdeletions.EvidencesofthefactthatlargereventofremovaloccurredbeforesmallerdeletionemergedfromthecomparisonofthegenomeofBuckneraandareconstructedancestor,wherethegenethathavebeenlostareinfactnotrandomlydispersedintheancestorgenebutaggregatedandthenegativerelationbetweennumberoflostgenesandlengthofthespacers.[33]Theeventofsmalllocalindelsplaysamarginalroleonthegenomereduction[42]especiallyintheearlystageswherealargernumberofgenesbecamesuperfluous.[43][33] Singleeventsinsteadoccurredduetothelackofselectionpressurefortheretentionofgenesespeciallyifpartofapathwaythatlostitsfunctionduringapreviousdeletion.AnexampleforthisisthedeletionofrecF,generequiredforthefunctionofrecA,anditsflankinggenes.[44]Oneoftheconsequencesoftheeliminationofsuchamountofsequencesaffectedeventheregulationoftheremaininggenes.Thelossoflargesectionofgenomescouldinfactleadtoalossinpromotorsequences.Thiscouldinfactpushedtheselectionfortheevolutionofpolycistronicregionswithapositiveeffectforbothsizereduction[45]andtranscriptionefficiency.[46] Evidenceofgenomeminiaturization[edit] Oneexampleoftheminiaturizationofthegenomeoccurredinthemicrosporidia,ananaerobicintracellularparasiteofarthropodsevolvedfromaerobicfungi. Duringthisprocessthemitosomes[47]wasformedconsequenttothereductionofthemitochondriatoarelicvoidedofgenomesandmetabolicactivityexcepttotheproductionofironsulfurcentersandthecapacitytoenterintothehostcells.[48][49]Exceptfortheribosomes,miniaturizedaswell,manyotherorganelleshavebeenalmostlostduringtheprocessoftheformationofthesmallestgenomefoundintheeukaryotes.[30]Fromtheirpossibleancestor,azygomycotinefungi,themicrosporidiashrunkitsgenomeeliminatingalmost1000genesandreducedeventhesizeofproteinandprotein-codinggenes.[50]Thisextremeprocesswaspossiblethankstotheadvantageousselectionforasmallercellsizeimposedbytheparasitism. Anotherexampleofminiaturizationisrepresentedbythepresenceofnucleomorphs,enslavednuclei,insideofthecelloftwodifferentalgae,cryptophytesandchlorarachneans.[51] Nucleomorphsarecharacterizedbyoneofthesmallestgenomesknown(551and380kb)andasnoticedformicrosporidia,somegenomesarenoticeablereducedinlengthcomparedtoothereukaryotesduetoavirtuallackofnon-codingDNA.[30]Themostinterestingfactorisrepresentedbythecoexistenceofthosesmallnucleiinsideofacellthatcontainsanothernucleusthatneverexperiencedsuchgenomereduction.Moreover,evenifthehostcellshavedifferentvolumesfromspeciestospeciesandaconsequentvariabilityingenomesize,thenucleomorphremaininvariantdenotingadoubleeffectofselectionwithinthesamecell. 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Furtherreading[edit] EvolutionofChlamydiaceae AnderssonJOAnderssonSG;Andersson(1999)."GenomedegradationisanongoingprocessinRickettsia".MolecularBiologyandEvolution.16(9):1178–1191.doi:10.1093/oxfordjournals.molbev.a026208.PMID 10486973. 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