Introduction
Inthefieldsofmolecularbiologyandgenetics,genomereferstothesumofallgeneticmaterialofanorganism.ThesegeneticmaterialincludeDNAorRNA(viralRNA).
GenomicDNAincludescodingDNAandnon-codingDNA,mitochondrialDNAandchloroplastDNA.
Thetermgenomewascreatedin1920byHansWinkler,professorofbotanyattheUniversityofHamburg,Germany.
Thescienceofstudyingthegenomeiscalledgenomics.
Classification
Viralgenome
TheviralgenomecanbecomposedofRNAorDNA.ThegenomeofanRNAviruscontainssingle-strandedordouble-strandedRNA,aswellasoneormoreindividualRNAmolecules.TheDNAviralgenomecanbesingle-strandedordouble-strandedDNA.MostDNAviralgenomesarecomposedofasinglelinearDNAmolecule,butsomearecomposedofDNAviralgenomescomposedofcircularDNAmolecules.
Prokaryoticgenome
ThegenomesofprokaryotesandeukaryotesarecomposedofDNA.ArchaeahaveaDNAgenomecomposedofcircularchromosomes.Mostbacteriaalsohaveacircularchromosome,however,somebacterialspeciescontainlinearchromosomesormultiplechromosomes.ThegenomesofmostprokaryotesdonotcontainrepetitiveDNA.Somesymbioticbacterialgenomespeciescontainahighproportionofpseudogenes.Forexample,Serratiasymbioticagenomespecieshasonlyabout40%ofitsDNAencodingproteins.Somebacterialgenomesalsocontainauxiliarygeneticmaterial,whichispresentinplasmids.Forthisreason,thetermgenomeshouldnotbeusedasasynonymforchromosome.
Theeukaryoticgenome
TheeukaryoticgenomeconsistsofoneormorelinearDNAchromosomes.Thenumberofchromosomesthatmakeupthegenomeofeukaryotesvariesgreatly.Jackjumperantsandasexualnematodeshaveonlyonepairofchromosomeseach,whilefernspecieshave720pairsofchromosomes.Humancellshave22pairsofautosomesand1pairofsexchromosomes.
Inadditiontothechromosomesinthenucleus,eukaryoticorganellessuchaschloroplastsandmitochondriahavetheirownDNAandchromosomes.Therefore,therearealsotheterms"mitochondrialgenome"and"plastidgenome".Likethebacteriafromwhichtheyoriginate,bothmitochondriaandchloroplastscontaincircularchromosomes.
Differentfromprokaryotes,eukaryoteshaveexon-intronorganizationofprotein-codinggenesandacertainamountofrepetitiveDNA.ThemajorityofmammalianandplantgenomesarecomposedofrepetitiveDNA.
Codingsequence
TheDNAsequencethatcarriesthegeneticinformationofthesyntheticproteinisthecodingsequence.Theproportionofcodingsequencesinthegenomevariesgreatlyindifferentspecies.Largergenomesdonotnecessarilycontainmoregenes,andtheproportionofnon-repetitiveDNAincomplexeukaryotesdecreasesasthesizeofthegenomeincreases.SimpleeukaryotessuchasCaenorhabditiselegansandDrosophilahaveahigherproportionofcodingDNAthanrepetitiveDNA,whilethegenomesofmorecomplexeukaryotesareoftencomposedofrepetitiveDNA.TheproportionofrepeatedDNAinthegenomesofsomeplantsandamphibiansexceeds80%.Similarly,only2%ofthehumangenomeencodesDNA.
Non-codingsequences
Non-codingsequencesincludeintrons,non-codingRNAsequences,regulatoryDNAandrepetitiveDNA.98%ofthehumangenomebelongstonon-codingsequences.TherepetitiveDNAofthegenomehastandemrepetitivesequencesandscatteredrepetitivesequences.
Transposons
Transposons(TEs)areDNAsequenceswithaspecificstructure.Theycanmovearoundthegenomewithoutafixedposition.ClassITEjumpsthroughthecopyandpastemechanism,andClassIITEisexcisedfromthegenomeandinsertedintoanewposition.
ThemovementofTEisthedrivingforcefortheevolutionofeukaryoticgenomes,becausetheirinsertioncandestroygenefunction,homologousrecombinationbetweenTEscanleadtogeneduplication,andTEcanalsocombineexonswithTheadjustmentsequenceisreorganizedtoanewposition.
Retrotransposons
RetrotransposonscanbetranscribedintoRNAandthencopiedintothegenomeatanothersite.Retrotransposonscanbedividedintotwocategories:longterminalrepeats(LTR)andnon-longterminalrepeats(non-LTR).
Genomesize
GenomesizeisthetotalnumberofDNAbasepairsinacopyofthehaploidgenome.
Genomesizeispositivelycorrelatedwiththemorphologicalcomplexityofprokaryotesandlowereukaryotes.However,aftermollusksandallotherhighereukaryotesmentionedabove,thiscorrelationnolongerexists,mainlybecauseofrepeatedDNA.
Genomechanges
Allcellsoftheorganismarederivedfromthesamesinglecell,sotheyshouldhavethesamegenome.However,insomecases,differencescanoccurbetweencells.BothDNAreplicationduringcelldivisionandtheactionofenvironmentalmutagenscancausemutationsinsomaticcells.Insomecases,suchmutationscancausecancerbecausetheycausecellstodividefasterandinvadesurroundingtissues.Duringmeiosis,diploidcellsdividetwicetoproducehaploidgermcells.Inthisprocess,recombinationcausesthegeneticmaterialtobereshuffledfromhomologouschromosomes,soeachgametehasauniquegenome.
Genomeevolution
Thegenomeisnotonlythesumofthegenesoftheorganism,thegenomealsocontainsothercharacteristicsthatcanbeconsideredforspecificgenesandtheirproducts.
Replicationplaysanimportantroleintheshapingofthegenome.Thescopeofreplicationincludestheextensionofshorttandemrepeats,thereplicationofgeneclusters,thereplicationofentirechromosomesandeventheentiregenome.Thisduplicationmaybethebasisforthecreationofnewgenetictraits.