Selection in Coastal Synechococcus (Cyanobacteria) Populations Evaluated from Environmental Metagenomes 英文参考文献.docVIP

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Selection in Coastal Synechococcus (Cyanobacteria) Populations Evaluated from Environmental Metagenomes 英文参考文献.doc

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Selection in Coastal Synechococcus (Cyanobacteria) Populations Evaluated from Environmental Metagenomes 英文参考文献

SelectioninCoastalSynechococcus(Cyanobacteria) PopulationsEvaluatedfromEnvironmental Metagenomes VeraTai1¤,ArtF.Y.Poon2,IanT.Paulsen3,BrianPalenik1* 1ScrippsInstitutionofOceanography,UniversityofCaliforniaSanDiego,LaJolla,California,UnitedStatesofAmerica,2BritishColumbiaCentreforExcellenceinHIV/ AIDS,Vancouver,BritishColumbia,Canada,3DepartmentofChemistryandBiomolecularSciences,MacquarieUniversity,Sydney,NewSouthWales,Australia Abstract Environmentalmetagenomicsprovidessnippetsofgenomicsequencesfromallorganismsinanenvironmentalsampleand areanunprecedentedresourceofinformationforinvestigatingmicrobialpopulationgenetics.Currentanalyticalmethods, however,arepoorlyequippedtohandlemetagenomicdata,particularlyofshort,unlinkedsequences.Acustomanalytical pipelinewasdevelopedtocalculatedN/dSratios,acommonmetrictoevaluatetheroleofselectionintheevolutionofa gene, from environmental metagenomes sequenced using 454 technology of flow-sorted populations of marine Synechococcus,thedominantcyanobacteriaincoastalenvironments.Thelargemajorityofgenes(98%)haveevolvedunder purifyingselection(dN/dS,1).Themetagenomesequencecoverageofthereferencegenomeswasnotuniformandgenes thatwerehighlyrepresentedintheenvironment(i.e.highreadcoverage)tendedtobemoreevolutionarilyconserved.Of thegenesthatmayhaveevolvedunderpositiveselection(dN/dS.1),77outof83(93%)werehypothetical.Notableamong annotated genes, ribosomal protein L35 appears to be under positive selection in one Synechococcus population. Other annotatedgenes,inparticularapossibleporin,alarge-conductancemechanosensitivechannel,anATPbindingcomponent ofanABCtransporter,andahomologueofapilusretractionproteinhadregionsofthegenewithelevateddN/dS.Withthe increasinguseofnext-generationsequencinginmetagenomicinvestigationsofmicrobialdiversityandecology,analytical methods need to accommodate the peculiarities of these data streams. By developing a means to analyze population diversitydatafromtheseenvironmentalmetagenomes,wehaveprovidedthefirstinsigh