Whole-GenomeandChromosomeEvolutionAssociatedwithHostAdaptationandSpeciationoftheWheatPathogenMycosphaerellagraminicolaEvaH.Stukenbrock1¤*,FrankG.Jørgensen1,MarcelloZala2,TroelsT.Hansen1,BruceA.McDonald2,MikkelH.Schierup11BioinformaticsResearchCenter,AarhusUniversity,Aarhus,Denmark,2PlantPathologyGroup,InstituteofIntegrativeBiology,SwissFederalInstituteofTechnology(ETH)Zurich,Zurich,SwitzerlandAbstractThefungusMycosphaerellagraminicolahasbeenapathogenofwheatsincehostdomestication10,000–12,000yearsagointheFertileCrescent.Thewheat-infectinglineageemergedfromcloselyrelatedMycosphaerellapathogensinfectingwildgrasses.WeuseacomparativegenomicsapproachtoassesshowtheprocessofhostspecializationaffectedthegenomestructureofM.graminicolasincedivergencefromtheclosestknownprogenitorspeciesnamedM.graminicolaS1.ThegenomeofS1wasobtainedbyIlluminasequencingresultingina35Mbdraftgenomesequenceof32X.AssembledcontigswerealignedtothepreviouslysequencedM.graminicolagenome.Thealignmentcovered.90%ofthenon-repetitiveportionoftheM.graminicolagenomewithanaveragedivergenceof7%.ThesequencedM.graminicolastrainisknowntoharborthirteenessentialchromosomespluseightdispensablechromosomes.Wefoundevidencethatstructuralrearrangementssignificantlyaffectedthedispensablechromosomeswhiletheessentialchromosomesweresyntenic.Atthenucleotidelevel,theessentialanddispensablechromosomeshaveevolveddifferently.Theaveragesynonymoussubstitutionrateindispensablechromosomesisconsiderablylowerthaninessentialchromosomes,whereastheaveragenon-synonymoussubstitutionrateisthreetimeshigher.Differencesinmolecularevolutioncanberelatedtodifferenttransmissionandrecombinationpatterns,aswellastodifferencesineffectivepopulationsizesofessentialanddispensablechromosomes.Inordertoidentifygenespotentiallyinvolvedinhostspecializationorspeciation,wecalculatedratiosofsynonymousandnon-synonymoussubstitutionratesinthe.9,500alignedproteincodinggenes.Thegenesaregenerallyunderstrongpurifyingselection.Weidentified43candidate