combining bioinformatics and phylogenetics to identify large sets of single copy orthologous genes (cosii) for comparative, evolutionary外语英文电子书

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1、CopyrightÓ2006bytheGeneticsSocietyofAmericaDOI:10.1534/genetics.106.062455CombiningBioinformaticsandPhylogeneticstoIdentifyLargeSetsofSingle-CopyOrthologousGenes(COSII)forComparative,EvolutionaryandSystematicStudies:ATestCaseintheEuasteridPlantCladeFeinanWu,*,†LukasA.Mueller,*,†DominiqueCrouz

2、illat,‡VincentPe´tiard‡andStevenD.Tanksley*,†,1*DepartmentofPlantBreedingandGenetics,CornellUniversity,Ithaca,NewYork14853,DepartmentofPlantBiology,CornellUniversity,Ithaca,NewYork14853andNestle´ResearchCenter,37097ToursCedex2,FranceManuscriptreceivedJune23,2006AcceptedforpublicationAugust8,2

3、006ABSTRACTWereporthereintheapplicationofasetofalgorithmstoidentifyalargenumber(2869)ofsingle-copyorthologs(COSII),whicharesharedbymost,ifnotall,euasteridplantspeciesaswellasthemodelspeciesArabidopsis.AlignmentsoftheorthologoussequencesacrossmultiplespeciesenabledthedesignofuniversalPCRprimer

4、s,whichcanbeusedtoamplifythecorrespondingorthologsfromabroadrangeoftaxa,includingthoselackinganysequencedatabases.Functionalannotationrevealedthattheseconserved,single-copyorthologsencodeahigher-than-expectedfrequencyofproteinstransportedandutilizedinorganellesandapaucityofproteinsassociatedw

5、ithcellwalls,proteinkinases,transcriptionfactors,andsignaltransduction.Theenablingpowerofthisneworthologresourcewasdemonstratedinphylogeneticstudies,aswellasincomparativemappingacrosstheplantfamiliestomato(familySolanaceae)andcoffee(familyRubiaceae).Thecombinedresultsofthesestudiesprovidecomp

6、ellingevidencethat(1)theancestralspeciesthatgaverisetothecoreeuasteridfamiliesSolanaceaeandRubiaceaehadabasicchro-mosomenumberofx¼11or12.2)Nowhole-genomeduplicationevent(i.e.,polyploidization)occurredimmediatelypriortooraftertheradiationofeitherSolanaceaeorRubiaceaeashasbeenrecentlysuggested.

7、RTHOLOGSaredefinedasgenessharingacom-etal.2002),dependontheavailabilityofvalidatedsetsofOmonancestorbyspeciation.Bycontrast,paralogsorthologousgenes.areduplicatedcopieswithinagenomeandariseTherecentdevelopmentofsequencedatasetsforthroughsuchph