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1、Chapter14PlantGenomeAnnotationMethodsShuOuyang,FrançoiseThibaud-Nissen,KevinL.Childs,WeiZhu,andC.RobinBuellSummaryAnnotationofplantgenomicsequencescanbeseparatedintostructuralandfunctionalannotation.Structuralannotationisthefoundationofallgenomicsaswithoutaccurategenemode
2、lsunderstandinggenefunctionorevolutionofgenesacrosstaxacanbeimpeded.Structuralannotationisdependentonsensitive,specificcomputationalprogramsanddeepexperimentalevidencetoidentifygenefeatureswithingenomicDNA.Functionalannotationishighlydependentonsequencesimilaritytootherkn
3、owngenesorproteinsasthemajorityofinitial“first-pass”functionalannotationonagenomicscaleistransi-tive.Couplingstructuralandfunctionalannotationacrossgenomesinacomparativemannerpromotesmoreaccurateannotationaswellasanunderstandingofgeneandgenomeevolution.Withtheincreasingav
4、ailabilityofplantgenomesequencedata,thevalueofcomparativeannotationwillincrease.Aswithanynewfield,methodologiesareevolvingforgenomeannotationandwillimproveinthefuture.Keywords:Geneprediction,Genomesequence,Genestructure,Genefunction.1.IntroductionWiththeadventofrapidandin
5、expensivesequencetechnolo-gies,itisnowpossibletoworkonawiderangeofplantspeciesandtohaveaccesstolargesequencedatasets.Whilethebulkofallsequencedataisstillintheformoftranscriptsderivedfromexpressedsequencetags(ESTs),whicharesingle-passsequencesfromcDNAclones,genomesequences
6、foranumberofspecieshavebeengeneratedorareinprogress.Thus,awiderangeofcladeswithinthePlantKingdomhaveenteredthe“genomicsera”ofbiologicalresearch.CoupledwithaccesstogenomicortranscriptomicdatasetsistheabilitytointerpretthesequenceDarylJ.Somersetal.(eds.),MethodsinMolecularB
7、iology,PlantGenomics,vol.513©HumanaPress,apartofSpringerScience+BusinessMedia,LLC2009DOI:10.1007/978-1-59745-427-8_14263264Ouyangetal.inabiologicalcontext.Theprocessofannotationor“addingnotes”tosequenceisacombinationofcomputationalandbio-logicalanalysesinwhichthefinaloutp
8、utisofusetoabiolo-gist.Genomeannotationcanberoughlydividedintostructuralandfunctionalannotation.
