Big Genomes Facilitate the Comparative Identification of Regulatory Elements 英文参考文献.docVIP

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Big Genomes Facilitate the Comparative Identification of Regulatory Elements 英文参考文献.doc

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Big Genomes Facilitate the Comparative Identification of Regulatory Elements 英文参考文献

BigGenomesFacilitatetheComparativeIdentificationof RegulatoryElements BrantK.Peterson1,2.,EmilyE.Hare1,2.,VenkyN.Iyer1,StevenStorage1,LauraConner3,DanielR.Papaj3, RickKurashima4,EricJang4,MichaelB.Eisen1,2,5,6,7* 1DepartmentofMolecularandCellBiology,UniversityofCalifornia,Berkeley,California,UnitedStatesofAmerica,2GenomicsDivision,ErnestOrlandoLawrenceBerkeley National Laboratory, Berkeley, California, United States of America, 3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United StatesofAmerica,4PacificBasinAgriculturalResearchCenter,UnitedStatesDepartmentofAgriculture,Hilo,Hawaii,UnitedStatesofAmerica,5HowardHughesMedical Institute, University of California, Berkeley, California, United States of America, 6California Institute of Quantitative Biosciences, University of California, Berkeley, California,UnitedStatesofAmerica,7CenterforIntegrativeGenomics,UniversityofCalifornia,Berkeley,California,UnitedStatesofAmerica Abstract The identification of regulatory sequences in animal genomes remains a significant challenge. Comparative genomic methodsthatusepatternsofevolutionaryconservationtoidentifynon-codingsequenceswithregulatoryfunctionhave yieldedmanynewvertebrateenhancers.However,thesemethodshavenotcontributedsignificantlytotheidentificationof regulatory sequences in sequenced invertebrate taxa. We demonstrate here that this differential success, which is often attributedtofundamentaldifferencesinthenatureofvertebrateandinvertebrateregulatorysequences,isinsteadprimarily aproductoftherelativelysmallsizeofsequencedinvertebrategenomes.Wesequencedandcomparedlociinvolvedin early embryonic patterning from four species of true fruit flies (family Tephritidae) that have genomes four to six times largerthanthoseofDrosophilamelanogaster.UnlikeinDrosophila,wherevirtuallyallnon-codingDNAishighlyconserved, blocksofconservednon-codingsequenceintephritidsareflankedbylargestretchesofpoorlyconservedsequence,similar towhatisobservedinver