Genomics - Wikipedia

Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's ... Genomics FromWikipedia,thefreeencyclopedia Jumptonavigation Jumptosearch Disciplineingenetics Thisarticleisaboutthescientificfield.Forthejournal,seeGenomics(journal). "Genomebiology"redirectshere.Forthejournalwiththesamename,seeGenomeBiology. PartofaseriesonGenetics Keycomponents Chromosome DNA RNA Genome Heredity Mutation Nucleotide Variation Outline Index Historyandtopics Introduction History Evolution(molecular) Populationgenetics Mendelianinheritance Quantitativegenetics Moleculargenetics Research Geneticist DNAsequencing Geneticengineering Genomics(template) Medicalgenetics Branchesofgenetics Personalizedmedicine Personalizedmedicine  Categoryvte Genomicsisaninterdisciplinaryfieldofbiologyfocusingonthestructure,function,evolution,mapping,andeditingofgenomes.Agenomeisanorganism'scompletesetofDNA,includingallofitsgenesaswellasitshierarchical,three-dimensionalstructuralconfiguration.[1][2][3]Incontrasttogenetics,whichreferstothestudyofindividualgenesandtheirrolesininheritance,genomicsaimsatthecollectivecharacterizationandquantificationofallofanorganism'sgenes,theirinterrelationsandinfluenceontheorganism.[4]Genesmaydirecttheproductionofproteinswiththeassistanceofenzymesandmessengermolecules.Inturn,proteinsmakeupbodystructuressuchasorgansandtissuesaswellascontrolchemicalreactionsandcarrysignalsbetweencells.GenomicsalsoinvolvesthesequencingandanalysisofgenomesthroughusesofhighthroughputDNAsequencingandbioinformaticstoassembleandanalyzethefunctionandstructureofentiregenomes.[5][6]Advancesingenomicshavetriggeredarevolutionindiscovery-basedresearchandsystemsbiologytofacilitateunderstandingofeventhemostcomplexbiologicalsystemssuchasthebrain.[7] Thefieldalsoincludesstudiesofintragenomic(withinthegenome)phenomenasuchasepistasis(effectofonegeneonanother),pleiotropy(onegeneaffectingmorethanonetrait),heterosis(hybridvigour),andotherinteractionsbetweenlociandalleleswithinthegenome.[8] Contents 1History 1.1Etymology 1.2Earlysequencingefforts 1.3DNA-sequencingtechnologydeveloped 1.4Completegenomes 1.5The"omics"revolution 2Genomeanalysis 2.1Sequencing 2.1.1Shotgunsequencing 2.1.2High-throughputsequencing 2.2Assembly 2.2.1Assemblyapproaches 2.2.2Finishing 2.3Annotation 2.4Sequencingpipelinesanddatabases 3Researchareas 3.1Functionalgenomics 3.2Structuralgenomics 3.3Epigenomics 3.4Metagenomics 3.5Modelsystems 3.5.1Virusesandbacteriophages 3.5.2Cyanobacteria 4Applicationsofgenomics 4.1Genomicmedicine 4.2Syntheticbiologyandbioengineering 4.3Populationandconservationgenomics 5Seealso 6References 7Furtherreading 8Externallinks History[edit] Etymology[edit] FromtheGreekΓΕΝ[9]gen,"gene"(gamma,epsilon,nu,epsilon)meaning"become,create,creation,birth",andsubsequentvariants:genealogy,genesis,genetics,genic,genomere,genotype,genusetc. Whilethewordgenome(fromtheGermanGenom,attributedtoHansWinkler)wasinuseinEnglishasearlyas1926,[10]thetermgenomicswascoinedbyTomRoderick,ageneticistattheJacksonLaboratory(BarHarbor,Maine),overbeeratameetingheldinMarylandonthemappingofthehumangenomein1986.[11] Earlysequencingefforts[edit] FollowingRosalindFranklin'sconfirmationofthehelicalstructureofDNA,JamesD.WatsonandFrancisCrick'spublicationofthestructureofDNAin1953andFredSanger'spublicationoftheAminoacidsequenceofinsulinin1955,nucleicacidsequencingbecameamajortargetofearlymolecularbiologists.[12]In1964,RobertW.Holleyandcolleaguespublishedthefirstnucleicacidsequenceeverdetermined,theribonucleotidesequenceofalaninetransferRNA.[13][14]Extendingthiswork,MarshallNirenbergandPhilipLederrevealedthetripletnatureofthegeneticcodeandwereabletodeterminethesequencesof54outof64codonsintheirexperiments.[15]In1972,WalterFiersandhisteamattheLaboratoryofMolecularBiologyoftheUniversityofGhent(Ghent,Belgium)werethefirsttodeterminethesequenceofagene:thegeneforBacteriophageMS2coatprotein.[16]Fiers'groupexpandedontheirMS2coatproteinwork,determiningthecompletenucleotide-sequenceofbacteriophageMS2-RNA(whosegenomeencodesjustfourgenesin3569basepairs[bp])andSimianvirus40in1976and1978,respectively.[17][18] DNA-sequencingtechnologydeveloped[edit] FrederickSangerWalterGilbertFrederickSangerandWalterGilbertsharedhalfofthe1980NobelPrizeinChemistryforIndependentlydevelopingmethodsforthesequencingofDNA. Inadditiontohisseminalworkontheaminoacidsequenceofinsulin,FrederickSangerandhiscolleaguesplayedakeyroleinthedevelopmentofDNAsequencingtechniquesthatenabledtheestablishmentofcomprehensivegenomesequencingprojects.[8]In1975,heandAlanCoulsonpublishedasequencingprocedureusingDNApolymerasewithradiolabellednucleotidesthathecalledthePlusandMinustechnique.[19][20]Thisinvolvedtwocloselyrelatedmethodsthatgeneratedshortoligonucleotideswithdefined3'termini.Thesecouldbefractionatedbyelectrophoresisonapolyacrylamidegel(calledpolyacrylamidegelelectrophoresis)andvisualisedusingautoradiography.Theprocedurecouldsequenceupto80nucleotidesinonegoandwasabigimprovement,butwasstillverylaborious.Nevertheless,in1977hisgroupwasabletosequencemostofthe5,386nucleotidesofthesingle-strandedbacteriophageφX174,completingthefirstfullysequencedDNA-basedgenome.[21]TherefinementofthePlusandMinusmethodresultedinthechain-termination,orSangermethod(seebelow),whichformedthebasisofthetechniquesofDNAsequencing,genomemapping,datastorage,andbioinformaticanalysismostwidelyusedinthefollowingquarter-centuryofresearch.[22][23]InthesameyearWalterGilbertandAllanMaxamofHarvardUniversityindependentlydevelopedtheMaxam-Gilbertmethod(alsoknownasthechemicalmethod)ofDNAsequencing,involvingthepreferentialcleavageofDNAatknownbases,alessefficientmethod.[24][25]Fortheirgroundbreakingworkinthesequencingofnucleicacids,GilbertandSangersharedhalfthe1980NobelPrizeinchemistrywithPaulBerg(recombinantDNA). Completegenomes[edit] Theadventofthesetechnologiesresultedinarapidintensificationinthescopeandspeedofcompletionofgenomesequencingprojects.Thefirstcompletegenomesequenceofaeukaryoticorganelle,thehumanmitochondrion(16,568bp,about16.6kb[kilobase]),wasreportedin1981,[26]andthefirstchloroplastgenomesfollowedin1986.[27][28]In1992,thefirsteukaryoticchromosome,chromosomeIIIofbrewer'syeastSaccharomycescerevisiae(315kb)wassequenced.[29]Thefirstfree-livingorganismtobesequencedwasthatofHaemophilusinfluenzae(1.8Mb[megabase])in1995.[30]ThefollowingyearaconsortiumofresearchersfromlaboratoriesacrossNorthAmerica,Europe,andJapanannouncedthecompletionofthefirstcompletegenomesequenceofaeukaryote,S.cerevisiae(12.1Mb),andsincethengenomeshavecontinuedbeingsequencedatanexponentiallygrowingpace.[31]AsofOctober 2011[update],thecompletesequencesareavailablefor:2,719viruses,1,115archaeaandbacteria,and36eukaryotes,ofwhichabouthalfarefungi.[32][33] Thenumberofgenomeprojectshasincreasedastechnologicalimprovementscontinuetolowerthecostofsequencing.(A)Exponentialgrowthofgenomesequencedatabasessince1995.(B)ThecostinUSDollars(USD)tosequenceonemillionbases.(C)ThecostinUSDtosequencea3,000Mb(human-sized)genomeonalog-transformedscale. Mostofthemicroorganismswhosegenomeshavebeencompletelysequencedareproblematicpathogens,suchasHaemophilusinfluenzae,whichhasresultedinapronouncedbiasintheirphylogeneticdistributioncomparedtothebreadthofmicrobialdiversity.[34][35]Oftheothersequencedspecies,mostwerechosenbecausetheywerewell-studiedmodelorganismsorpromisedtobecomegoodmodels.Yeast(Saccharomycescerevisiae)haslongbeenanimportantmodelorganismfortheeukaryoticcell,whilethefruitflyDrosophilamelanogasterhasbeenaveryimportanttool(notablyinearlypre-moleculargenetics).ThewormCaenorhabditiselegansisanoftenusedsimplemodelformulticellularorganisms.ThezebrafishBrachydaniorerioisusedformanydevelopmentalstudiesonthemolecularlevel,andtheplantArabidopsisthalianaisamodelorganismforfloweringplants.TheJapanesepufferfish(Takifugurubripes)andthespottedgreenpufferfish(Tetraodonnigroviridis)areinterestingbecauseoftheirsmallandcompactgenomes,whichcontainverylittlenoncodingDNAcomparedtomostspecies.[36][37]Themammalsdog(Canisfamiliaris),[38]brownrat(Rattusnorvegicus),mouse(Musmusculus),andchimpanzee(Pantroglodytes)areallimportantmodelanimalsinmedicalresearch.[25] AroughdraftofthehumangenomewascompletedbytheHumanGenomeProjectinearly2001,creatingmuchfanfare.[39]Thisproject,completedin2003,sequencedtheentiregenomeforonespecificperson,andby2007thissequencewasdeclared"finished"(lessthanoneerrorin20,000basesandallchromosomesassembled).[39]Intheyearssincethen,thegenomesofmanyotherindividualshavebeensequenced,partlyundertheauspicesofthe1000GenomesProject,whichannouncedthesequencingof1,092genomesinOctober2012.[40]Completionofthisprojectwasmadepossiblebythedevelopmentofdramaticallymoreefficientsequencingtechnologiesandrequiredthecommitmentofsignificantbioinformaticsresourcesfromalargeinternationalcollaboration.[41]Thecontinuedanalysisofhumangenomicdatahasprofoundpoliticalandsocialrepercussionsforhumansocieties.[42] The"omics"revolution[edit] Generalschemashowingtherelationshipsofthegenome,transcriptome,proteome,andmetabolome(lipidome). Mainarticles:OmicsandHumanproteomeproject TheEnglish-languageneologismomicsinformallyreferstoafieldofstudyinbiologyendingin-omics,suchasgenomics,proteomicsormetabolomics.Therelatedsuffix-omeisusedtoaddresstheobjectsofstudyofsuchfields,suchasthegenome,proteomeormetabolomerespectively.Thesuffix-omeasusedinmolecularbiologyreferstoatotalityofsomesort;similarlyomicshascometorefergenerallytothestudyoflarge,comprehensivebiologicaldatasets.Whilethegrowthintheuseofthetermhasledsomescientists(JonathanEisen,amongothers[43])toclaimthatithasbeenoversold,[44]itreflectsthechangeinorientationtowardsthequantitativeanalysisofcompleteornear-completeassortmentofalltheconstituentsofasystem.[45]Inthestudyofsymbioses,forexample,researcherswhichwereoncelimitedtothestudyofasinglegeneproductcannowsimultaneouslycomparethetotalcomplementofseveraltypesofbiologicalmolecules.[46][47] Genomeanalysis[edit] Mainarticle:Genomeproject Afteranorganismhasbeenselected,genomeprojectsinvolvethreecomponents:thesequencingofDNA,theassemblyofthatsequencetocreatearepresentationoftheoriginalchromosome,andtheannotationandanalysisofthatrepresentation.[8] Overviewofagenomeproject.First,thegenomemustbeselected,whichinvolvesseveralfactorsincludingcostandrelevance.Second,thesequenceisgeneratedandassembledatagivensequencingcenter(suchasBGIorDOEJGI).Third,thegenomesequenceisannotatedatseverallevels:DNA,protein,genepathways,orcomparatively. Sequencing[edit] Mainarticle:DNASequencing Historically,sequencingwasdoneinsequencingcenters,centralizedfacilities(rangingfromlargeindependentinstitutionssuchasJointGenomeInstitutewhichsequencedozensofterabasesayear,tolocalmolecularbiologycorefacilities)whichcontainresearchlaboratorieswiththecostlyinstrumentationandtechnicalsupportnecessary.Assequencingtechnologycontinuestoimprove,however,anewgenerationofeffectivefastturnaroundbenchtopsequencershascomewithinreachoftheaverageacademiclaboratory.[48][49]Onthewhole,genomesequencingapproachesfallintotwobroadcategories,shotgunandhigh-throughput(ornext-generation)sequencing.[8] Shotgunsequencing[edit] AnABIPRISM3100GeneticAnalyzer.Suchcapillarysequencersautomatedearlylarge-scalegenomesequencingefforts. Mainarticle:Shotgunsequencing ShotgunsequencingisasequencingmethoddesignedforanalysisofDNAsequenceslongerthan1000basepairs,uptoandincludingentirechromosomes.[50]Itisnamedbyanalogywiththerapidlyexpanding,quasi-randomfiringpatternofashotgun.Sincegelelectrophoresissequencingcanonlybeusedforfairlyshortsequences(100to1000basepairs),longerDNAsequencesmustbebrokenintorandomsmallsegmentswhicharethensequencedtoobtainreads.MultipleoverlappingreadsforthetargetDNAareobtainedbyperformingseveralroundsofthisfragmentationandsequencing.Computerprogramsthenusetheoverlappingendsofdifferentreadstoassemblethemintoacontinuoussequence.[50][51]Shotgunsequencingisarandomsamplingprocess,requiringover-samplingtoensureagivennucleotideisrepresentedinthereconstructedsequence;theaveragenumberofreadsbywhichagenomeisover-sampledisreferredtoascoverage.[52] Formuchofitshistory,thetechnologyunderlyingshotgunsequencingwastheclassicalchain-terminationmethodor'Sangermethod',whichisbasedontheselectiveincorporationofchain-terminatingdideoxynucleotidesbyDNApolymeraseduringinvitroDNAreplication.[21][53]Recently,shotgunsequencinghasbeensupplantedbyhigh-throughputsequencingmethods,especiallyforlarge-scale,automatedgenomeanalyses.However,theSangermethodremainsinwideuse,primarilyforsmaller-scaleprojectsandforobtainingespeciallylongcontiguousDNAsequencereads(>500nucleotides).[54]Chain-terminationmethodsrequireasingle-strandedDNAtemplate,aDNAprimer,aDNApolymerase,normaldeoxynucleosidetriphosphates(dNTPs),andmodifiednucleotides(dideoxyNTPs)thatterminateDNAstrandelongation.Thesechain-terminatingnucleotideslacka3'-OHgrouprequiredfortheformationofaphosphodiesterbondbetweentwonucleotides,causingDNApolymerasetoceaseextensionofDNAwhenaddNTPisincorporated.TheddNTPsmayberadioactivelyorfluorescentlylabelledfordetectioninDNAsequencers.[8]Typically,thesemachinescansequenceupto96DNAsamplesinasinglebatch(run)inupto48runsaday.[55] High-throughputsequencing[edit] Seealso:IlluminadyesequencingandIonsemiconductorsequencing Thehighdemandforlow-costsequencinghasdriventhedevelopmentofhigh-throughputsequencingtechnologiesthatparallelizethesequencingprocess,producingthousandsormillionsofsequencesatonce.[56][57]High-throughputsequencingisintendedtolowerthecostofDNAsequencingbeyondwhatispossiblewithstandarddye-terminatormethods.Inultra-high-throughputsequencing,asmanyas500,000sequencing-by-synthesisoperationsmayberuninparallel.[58][59] IlluminaGenomeAnalyzerIISystem.Illuminatechnologieshavesetthestandardforhigh-throughputmassivelyparallelsequencing.[48] TheIlluminadyesequencingmethodisbasedonreversibledye-terminatorsandwasdevelopedin1996attheGenevaBiomedicalResearchInstitute,byPascalMayer [fr]andLaurentFarinelli.[60]Inthismethod,DNAmoleculesandprimersarefirstattachedonaslideandamplifiedwithpolymerasesothatlocalclonalcolonies,initiallycoined"DNAcolonies",areformed.Todeterminethesequence,fourtypesofreversibleterminatorbases(RT-bases)areaddedandnon-incorporatednucleotidesarewashedaway.Unlikepyrosequencing,theDNAchainsareextendedonenucleotideatatimeandimageacquisitioncanbeperformedatadelayedmoment,allowingforverylargearraysofDNAcoloniestobecapturedbysequentialimagestakenfromasinglecamera.Decouplingtheenzymaticreactionandtheimagecaptureallowsforoptimalthroughputandtheoreticallyunlimitedsequencingcapacity;withanoptimalconfiguration,theultimatethroughputoftheinstrumentdependsonlyontheA/Dconversionrateofthecamera.Thecameratakesimagesofthefluorescentlylabelednucleotides,thenthedyealongwiththeterminal3'blockerischemicallyremovedfromtheDNA,allowingthenextcycle.[61] Analternativeapproach,ionsemiconductorsequencing,isbasedonstandardDNAreplicationchemistry.Thistechnologymeasuresthereleaseofahydrogenioneachtimeabaseisincorporated.AmicrowellcontainingtemplateDNAisfloodedwithasinglenucleotide,ifthenucleotideiscomplementarytothetemplatestranditwillbeincorporatedandahydrogenionwillbereleased.ThisreleasetriggersanISFETionsensor.Ifahomopolymerispresentinthetemplatesequencemultiplenucleotideswillbeincorporatedinasinglefloodcycle,andthedetectedelectricalsignalwillbeproportionallyhigher.[62] Assembly[edit] Mainarticle:Sequenceassembly Overlappingreadsformcontigs;contigsandgapsofknownlengthformscaffolds.Pairedendreadsofnextgenerationsequencingdatamappedtoareferencegenome.Multiple,fragmentedsequencereadsmustbeassembledtogetheronthebasisoftheiroverlappingareas. SequenceassemblyreferstoaligningandmergingfragmentsofamuchlongerDNAsequenceinordertoreconstructtheoriginalsequence.[8]ThisisneededascurrentDNAsequencingtechnologycannotreadwholegenomesasacontinuoussequence,butratherreadssmallpiecesofbetween20and1000bases,dependingonthetechnologyused.ThirdgenerationsequencingtechnologiessuchasPacBioorOxfordNanoporeroutinelygeneratesequencingreads>10kbinlength;however,theyhaveahigherrorrateatapproximately15percent.[63][64]Typicallytheshortfragments,calledreads,resultfromshotgunsequencinggenomicDNA,orgenetranscripts(ESTs).[8] Assemblyapproaches[edit] Assemblycanbebroadlycategorizedintotwoapproaches:denovoassembly,forgenomeswhicharenotsimilartoanysequencedinthepast,andcomparativeassembly,whichusestheexistingsequenceofacloselyrelatedorganismasareferenceduringassembly.[52]Relativetocomparativeassembly,denovoassemblyiscomputationallydifficult(NP-hard),makingitlessfavourableforshort-readNGStechnologies.Withinthedenovoassemblyparadigmtherearetwoprimarystrategiesforassembly,Eulerianpathstrategies,andoverlap-layout-consensus(OLC)strategies.OLCstrategiesultimatelytrytocreateaHamiltonianpaththroughanoverlapgraphwhichisanNP-hardproblem.EulerianpathstrategiesarecomputationallymoretractablebecausetheytrytofindaEulerianpaththroughadeBruijngraph.[52] Finishing[edit] Finishedgenomesaredefinedashavingasinglecontiguoussequencewithnoambiguitiesrepresentingeachreplicon.[65] Annotation[edit] Mainarticle:Genomeannotation TheDNAsequenceassemblyaloneisoflittlevaluewithoutadditionalanalysis.[8]Genomeannotationistheprocessofattachingbiologicalinformationtosequences,andconsistsofthreemainsteps:[66] identifyingportionsofthegenomethatdonotcodeforproteins identifyingelementsonthegenome,aprocesscalledgeneprediction,and attachingbiologicalinformationtotheseelements. Automaticannotationtoolstrytoperformthesestepsinsilico,asopposedtomanualannotation(a.k.a.curation)whichinvolveshumanexpertiseandpotentialexperimentalverification.[67]Ideally,theseapproachesco-existandcomplementeachotherinthesameannotationpipeline(alsoseebelow). Traditionally,thebasiclevelofannotationisusingBLASTforfindingsimilarities,andthenannotatinggenomesbasedonhomologues.[8]Morerecently,additionalinformationisaddedtotheannotationplatform.Theadditionalinformationallowsmanualannotatorstodeconvolutediscrepanciesbetweengenesthataregiventhesameannotation.Somedatabasesusegenomecontextinformation,similarityscores,experimentaldata,andintegrationsofotherresourcestoprovidegenomeannotationsthroughtheirSubsystemsapproach.Otherdatabases(e.g.Ensembl)relyonbothcurateddatasourcesaswellasarangeofsoftwaretoolsintheirautomatedgenomeannotationpipeline.[68]Structuralannotationconsistsoftheidentificationofgenomicelements,primarilyORFsandtheirlocalisation,orgenestructure.Functionalannotationconsistsofattachingbiologicalinformationtogenomicelements. Sequencingpipelinesanddatabases[edit] Theneedforreproducibilityandefficientmanagementofthelargeamountofdataassociatedwithgenomeprojectsmeanthatcomputationalpipelineshaveimportantapplicationsingenomics.[69] Researchareas[edit] Functionalgenomics[edit] Mainarticle:Functionalgenomics Functionalgenomicsisafieldofmolecularbiologythatattemptstomakeuseofthevastwealthofdataproducedbygenomicprojects(suchasgenomesequencingprojects)todescribegene(andprotein)functionsandinteractions.Functionalgenomicsfocusesonthedynamicaspectssuchasgenetranscription,translation,andprotein–proteininteractions,asopposedtothestaticaspectsofthegenomicinformationsuchasDNAsequenceorstructures.FunctionalgenomicsattemptstoanswerquestionsaboutthefunctionofDNAatthelevelsofgenes,RNAtranscripts,andproteinproducts.Akeycharacteristicoffunctionalgenomicsstudiesistheirgenome-wideapproachtothesequestions,generallyinvolvinghigh-throughputmethodsratherthanamoretraditional“gene-by-gene”approach. Amajorbranchofgenomicsisstillconcernedwithsequencingthegenomesofvariousorganisms,buttheknowledgeoffullgenomeshascreatedthepossibilityforthefieldoffunctionalgenomics,mainlyconcernedwithpatternsofgeneexpressionduringvariousconditions.Themostimportanttoolsherearemicroarraysandbioinformatics. Structuralgenomics[edit] Mainarticle:Structuralgenomics AnexampleofaproteinstructuredeterminedbytheMidwestCenterforStructuralGenomics. Structuralgenomicsseekstodescribethe3-dimensionalstructureofeveryproteinencodedbyagivengenome.[70][71]Thisgenome-basedapproachallowsforahigh-throughputmethodofstructuredeterminationbyacombinationofexperimentalandmodelingapproaches.Theprincipaldifferencebetweenstructuralgenomicsandtraditionalstructuralpredictionisthatstructuralgenomicsattemptstodeterminethestructureofeveryproteinencodedbythegenome,ratherthanfocusingononeparticularprotein.Withfull-genomesequencesavailable,structurepredictioncanbedonemorequicklythroughacombinationofexperimentalandmodelingapproaches,especiallybecausetheavailabilityoflargenumbersofsequencedgenomesandpreviouslysolvedproteinstructuresallowscientiststomodelproteinstructureonthestructuresofpreviouslysolvedhomologs.Structuralgenomicsinvolvestakingalargenumberofapproachestostructuredetermination,includingexperimentalmethodsusinggenomicsequencesormodeling-basedapproachesbasedonsequenceorstructuralhomologytoaproteinofknownstructureorbasedonchemicalandphysicalprinciplesforaproteinwithnohomologytoanyknownstructure.Asopposedtotraditionalstructuralbiology,thedeterminationofaproteinstructurethroughastructuralgenomicseffortoften(butnotalways)comesbeforeanythingisknownregardingtheproteinfunction.Thisraisesnewchallengesinstructuralbioinformatics,i.e.determiningproteinfunctionfromits3Dstructure.[72] Epigenomics[edit] Mainarticle:Epigenomics Epigenomicsisthestudyofthecompletesetofepigeneticmodificationsonthegeneticmaterialofacell,knownastheepigenome.[73]Epigeneticmodificationsarereversiblemodificationsonacell'sDNAorhistonesthataffectgeneexpressionwithoutalteringtheDNAsequence(Russell2010p. 475).TwoofthemostcharacterizedepigeneticmodificationsareDNAmethylationandhistonemodification.Epigeneticmodificationsplayanimportantroleingeneexpressionandregulation,andareinvolvedinnumerouscellularprocessessuchasindifferentiation/developmentandtumorigenesis.[73]Thestudyofepigeneticsonagloballevelhasbeenmadepossibleonlyrecentlythroughtheadaptationofgenomichigh-throughputassays.[74] Metagenomics[edit] EnvironmentalShotgunSequencing(ESS)isakeytechniqueinmetagenomics.(A)Samplingfromhabitat;(B)filteringparticles,typicallybysize;(C)LysisandDNAextraction;(D)cloningandlibraryconstruction;(E)sequencingtheclones;(F)sequenceassemblyintocontigsandscaffolds. Mainarticle:Metagenomics Metagenomicsisthestudyofmetagenomes,geneticmaterialrecovereddirectlyfromenvironmentalsamples.Thebroadfieldmayalsobereferredtoasenvironmentalgenomics,ecogenomicsorcommunitygenomics.Whiletraditionalmicrobiologyandmicrobialgenomesequencingrelyuponcultivatedclonalcultures,earlyenvironmentalgenesequencingclonedspecificgenes(oftenthe16SrRNAgene)toproduceaprofileofdiversityinanaturalsample.Suchworkrevealedthatthevastmajorityofmicrobialbiodiversityhadbeenmissedbycultivation-basedmethods.[75]Recentstudiesuse"shotgun"Sangersequencingormassivelyparallelpyrosequencingtogetlargelyunbiasedsamplesofallgenesfromallthemembersofthesampledcommunities.[76]Becauseofitspowertorevealthepreviouslyhiddendiversityofmicroscopiclife,metagenomicsoffersapowerfullensforviewingthemicrobialworldthathasthepotentialtorevolutionizeunderstandingoftheentirelivingworld.[77][78] Modelsystems[edit] Virusesandbacteriophages[edit] Bacteriophageshaveplayedandcontinuetoplayakeyroleinbacterialgeneticsandmolecularbiology.Historically,theywereusedtodefinegenestructureandgeneregulation.Alsothefirstgenometobesequencedwasabacteriophage.However,bacteriophageresearchdidnotleadthegenomicsrevolution,whichisclearlydominatedbybacterialgenomics.Onlyveryrecentlyhasthestudyofbacteriophagegenomesbecomeprominent,therebyenablingresearcherstounderstandthemechanismsunderlyingphageevolution.Bacteriophagegenomesequencescanbeobtainedthroughdirectsequencingofisolatedbacteriophages,butcanalsobederivedaspartofmicrobialgenomes.AnalysisofbacterialgenomeshasshownthatasubstantialamountofmicrobialDNAconsistsofprophagesequencesandprophage-likeelements.[79]Adetaileddatabaseminingofthesesequencesoffersinsightsintotheroleofprophagesinshapingthebacterialgenome:Overall,thismethodverifiedmanyknownbacteriophagegroups,makingthisausefultoolforpredictingtherelationshipsofprophagesfrombacterialgenomes.[80][81] Cyanobacteria[edit] Atpresentthereare24cyanobacteriaforwhichatotalgenomesequenceisavailable.15ofthesecyanobacteriacomefromthemarineenvironment.ThesearesixProchlorococcusstrains,sevenmarineSynechococcusstrains,TrichodesmiumerythraeumIMS101andCrocosphaerawatsoniiWH8501.Severalstudieshavedemonstratedhowthesesequencescouldbeusedverysuccessfullytoinferimportantecologicalandphysiologicalcharacteristicsofmarinecyanobacteria.However,therearemanymoregenomeprojectscurrentlyinprogress,amongstthosetherearefurtherProchlorococcusandmarineSynechococcusisolates,AcaryochlorisandProchloron,theN2-fixingfilamentouscyanobacteriaNodulariaspumigena,LyngbyaaestuariiandLyngbyamajuscula,aswellasbacteriophagesinfectingmarinecyanobaceria.Thus,thegrowingbodyofgenomeinformationcanalsobetappedinamoregeneralwaytoaddressglobalproblemsbyapplyingacomparativeapproach.SomenewandexcitingexamplesofprogressinthisfieldaretheidentificationofgenesforregulatoryRNAs,insightsintotheevolutionaryoriginofphotosynthesis,orestimationofthecontributionofhorizontalgenetransfertothegenomesthathavebeenanalyzed.[82] Applicationsofgenomics[edit] Genomicshasprovidedapplicationsinmanyfields,includingmedicine,biotechnology,anthropologyandothersocialsciences.[42] Genomicmedicine[edit] Next-generationgenomictechnologiesallowcliniciansandbiomedicalresearcherstodrasticallyincreasetheamountofgenomicdatacollectedonlargestudypopulations.[83]Whencombinedwithnewinformaticsapproachesthatintegratemanykindsofdatawithgenomicdataindiseaseresearch,thisallowsresearcherstobetterunderstandthegeneticbasesofdrugresponseanddisease.[84][85]EarlyeffortstoapplythegenometomedicineincludedthosebyaStanfordteamledbyEuanAshleywhodevelopedthefirsttoolsforthemedicalinterpretationofahumangenome.[86][87][88]TheGenomes2PeopleresearchprogramatBrighamandWomen’sHospital,BroadInstituteandHarvardMedicalSchoolwasestablishedin2012toconductempiricalresearchintranslatinggenomicsintohealth.BrighamandWomen'sHospitalopenedaPreventiveGenomicsClinicinAugust2019,withMassachusettsGeneralHospitalfollowingamonthlater.[89][90]TheAllofUsresearchprogramaimstocollectgenomesequencedatafrom1millionparticipantstobecomeacriticalcomponentoftheprecisionmedicineresearchplatform.[91] Syntheticbiologyandbioengineering[edit] Thegrowthofgenomicknowledgehasenabledincreasinglysophisticatedapplicationsofsyntheticbiology.[92]In2010researchersattheJ.CraigVenterInstituteannouncedthecreationofapartiallysyntheticspeciesofbacterium,Mycoplasmalaboratorium,derivedfromthegenomeofMycoplasmagenitalium.[93] Populationandconservationgenomics[edit] Populationgenomicshasdevelopedasapopularfieldofresearch,wheregenomicsequencingmethodsareusedtoconductlarge-scalecomparisonsofDNAsequencesamongpopulations-beyondthelimitsofgeneticmarkerssuchasshort-rangePCRproductsormicrosatellitestraditionallyusedinpopulationgenetics.Populationgenomicsstudiesgenome-wideeffectstoimproveourunderstandingofmicroevolutionsothatwemaylearnthephylogenetichistoryanddemographyofapopulation.[94]Populationgenomicmethodsareusedformanydifferentfieldsincludingevolutionarybiology,ecology,biogeography,conservationbiologyandfisheriesmanagement.Similarly,landscapegenomicshasdevelopedfromlandscapegeneticstousegenomicmethodstoidentifyrelationshipsbetweenpatternsofenvironmentalandgeneticvariation. Conservationistscanusetheinformationgatheredbygenomicsequencinginordertobetterevaluategeneticfactorskeytospeciesconservation,suchasthegeneticdiversityofapopulationorwhetheranindividualisheterozygousforarecessiveinheritedgeneticdisorder.[95]Byusinggenomicdatatoevaluatetheeffectsofevolutionaryprocessesandtodetectpatternsinvariationthroughoutagivenpopulation,conservationistscanformulateplanstoaidagivenspecieswithoutasmanyvariablesleftunknownasthoseunaddressedbystandardgeneticapproaches.[96] Seealso[edit] Biologyportal Cognitivegenomics Computationalgenomics Epigenomics Functionalgenomics GeneCalling,anmRNAprofilingtechnology Genomicsofdomestication Geneticsinfiction Glycomics Immunomics Metagenomics Pathogenomics Personalgenomics Proteomics Transcriptomics Venomics Psychogenomics Wholegenomesequencing ThomasRoderick References[edit] ^""Molecularstructureofnucleicacids.Molecularconfigurationinsodiumthymonucleate.1953"". 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Furtherreading[edit] LeskAM(2017).IntroductiontoGenomics(3rd ed.).NewYork:OxfordUniversityPress.p. 544.ISBN 978-0-19-107085-3.ASIN 0198754833. StunnenbergHG,HubnerNC(2014)."Genomicsmeetsproteomics:identifyingtheculpritsindisease".HumanGenetics.133(6):689–700.doi:10.1007/s00439-013-1376-2.PMC 4021166.PMID 24135908. ShibataT(2012)."Cancergenomicsandpathology:alltogethernow".PathologyInternational.62(10):647–59.doi:10.1111/j.1440-1827.2012.02855.x.PMID 23005591.S2CID 27886018. RoychowdhuryS,ChinnaiyanAM(2016)."Translatingcancergenomesandtranscriptomesforprecisiononcology".CA:ACancerJournalforClinicians.66(1):75–88.doi:10.3322/caac.21329.PMC 4713245.PMID 26528881. VadimNG,ZhangY(2013)."Chapter16ComparativeGenomicsAnalysisoftheMetallomes".InBanciL(ed.).MetallomicsandtheCell.MetalIonsinLifeSciences.12.Springer.doi:10.1007/978-94-007-5561-10_16(inactive31October2021).ISBN 978-94-007-5560-4.CS1maint:DOIinactiveasofOctober2021(link)electronic-bookISBN 978-94-007-5561-1ISSN 1559-0836electronic-ISSN 1868-0402 Externallinks[edit] AnnualReviewofGenomicsandHumanGenetics BMCGenomics:ABMCjournalonGenomics Genomicsjournal Genomics.org:Anopenfreegenomicsportal. NHGRI:USgovernment'sgenomeinstitute JCVIComprehensiveMicrobialResource KoreaGenome.org:ThefirstKoreanGenomepublishedandthesequenceisavailablefreely. GenomicsNetwork:Looksatthedevelopmentanduseofthescienceandtechnologiesofgenomics. InstituteforGenomeSciences:Genomicsresearch. MITOpenCourseWareHST.512GenomicMedicineAfree,self-studycourseingenomicmedicine.Resourcesincludeaudiolecturesandselectedlecturenotes. 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