GlobalTranscripomeProfilingofSalicorniaeuropa

GlobalTranscriptomeProfilingofSalicorniaeuropaeaL.ShootsunderNaClTreatmentJinbiaoMa1,MeiruZhang1,2,XinlongXiao1,2,JinjinYou1,JunruWang1,2,TaoWang3,YinanYao1*,ChangyanTian1*1KeyLaboratoryofBiogeographyandBioresourceinAridLand,XinjiangInstituteofEcologyandGeography,ChineseAcademyofScience,Urumqi,China,2UniversityofChineseAcademyofSciences,Beijing,China,3CollegeofResourceandEnvironmentScience,XinjiangUniversity,Urumqi,ChinaAbstractBackground:Soilsalinityisamajorabioticstressthatlimitsagricultureproductivityworldwide.Salicorniaeuropaeaiswelladaptedtoextremesalineenvironmentswithmorethan1,000mMNaClinthesoil,soitcouldserveasanimportantmodelspeciesforstudyinghalophilicmechanismsineuhalophytes.Toobtaininsightsintothemolecularbasisofsalttolerance,wepresentherethefirstextensivetranscriptomeanalysisofthisspeciesusingtheIlluminaHiSeqTM2000.PrincipalFindings:Atotalof41and39millioncleanreadsfromthesalt-treated(Se200S)andsalt-free(SeCKS)tissuesofS.europaeashootswereobtained,anddenovoassemblyproduced97,865and101,751unigenes,respectively.UponfurtherassemblywithESTdatafrombothSe200SandSeCKS,109,712high-qualitynon-redundantunigenesweregeneratedwithameanunigenesizeof639bp.Additionally,atotalof3,979differentiallyexpressedgenes(DEGs)weredetectedbetweentheSe200SandSeCKSlibraries,with348unigenessolelyexpressedinSe200Sand460unigenessolelyexpressedinSeCKS.Furthermore,weidentifiedalargenumberofgenesthatareinvolvedinionhomeostasisandosmoticadjustment,includingcationtransportersandproteinsforthesynthesisoflow-molecularcompounds.AllunigeneswerefunctionallyannotatedwithintheCOG,GOandKEGGpathways,and10geneswerevalidatedbyqRT-PCR.Conclusion:Ourdatacontainstheextensivesequencingandgene-annotationanalysisofS.europaea.Thisgeneticknowledgewillbeveryusefulforfuturestudiesonthemolecularadaptationtoabioticstressineuhalophytesandwillfacilitatethegeneticmanipulationofothereconomicallyimportantcrops.Citation:MaJ,ZhangM,XiaoX,YouJ,WangJ,etal.(2013)GlobalTranscriptomeProfilingofSalicorniaeuropaeaL.ShootsunderNaClTreatment.PLoSONE8(6):e65877.doi:10.1371/journal.pone.0065877Editor:DongshengZhou,BeijingInstituteofMicrobiologyandEpidemiology,ChinaReceivedJanuary15,2013;AcceptedApril29,2013;PublishedJune25,2013Copyright:2013Maetal.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited.Funding:Thisworkwassupportedbytheprogrammeof100DistinguishedYoungScientistsintheChineseAcademyofSciences,NaturalScienceFoundationinChina(GrantNo.31270660),theYouthScienceFoundationofXinjiangUygurAutonomousRegionofChina(GrantNo.2011211B47),theOpenFundoftheStateKeyLaboratoryofCropStressBiologyforAridAreas(CSBAA2011-04),andtheDoctorWestern-fundedProjectsofChineseAcademyofSciences(XBBS201201).Thefundershadnoroleinstudydesign,datacollectionandanalysis,decisiontopublish,orpreparationofthemanuscript.CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexist.*E-mail:[e-mail](YY);[e-mail](CT)IntroductionAlongwithenvironmentaldeteriorationandanthropogenicinfluence,soilsalinityisoneofthemajorabioticstressesinplantandcropsystems,causingyieldlossesofprimarycropsworldwide[1,2].Mucheffortshavebeenmadetoenhancesalttoleranceofeconomicallyimportantplantsforfutureagriculturaldemand[3].Manysaltstress-inducedgenesarepartofacomplicatedcascadeofmolecularnetworksandarethoughttoplayimportantrolesinrespondingtoenvironmentstress[4,5].Thesegenesareinvolvedinmanycellularandphysiologicalprocessessuchassignalperceptionandtransduction[6,7],photosynthesis,energymetab-olism[8],membranetraffickingandproteinbiosynthesis,foldinganddecay[9,10].Theisolationandidentificationofthesefunctionalgenes,usingthetoolsofmolecularbiology,isnecessaryforunderstandingthemechanismsofsalttoleranceinplants[11–13].Severalessentialgenesinvolvedindifferentmolecularprocessesarereportedlyinvolvedintheplantresponsetosaltstress,includingAtHKT1;1[14,15],PutHKT2;1[16],AtSOS1[17,18],AtNHX1[19],Ca2+/calmodulin-dependentproteinphosphatase[20],flavoproteinAtHAL3[21],plasmamembrane(PM)H+-ATPaseandtranscriptionfactorAlfin1[22,23].Howev-er,onlyafewsalt-tolerancegeneshavebeenpreviouslyidentified,andmostofthestudiesonplantsalttolerancehavefocusedonmodelplantssuchasArabidopsis,riceandtobacco.Researchonsalt-tolerantgenesinhalophytesisscarce,eventhoughsomeeuhalophyteshavethespecificabilitytocopewithhighlevelsofsalinityusinguniquemechanisms[24–30].SalicorniaeuropaeaL.,oneofthemostsalt-accumulatingeuhalophytes,canwithstandconcentrationsofmorethan1,000mMNaClinthesoilandiswidelydistributedincoastalandinlandsaltmarshesaroundtheworld[24,31].Itisanimportantspeciesforsoildesalinationbecauseithyper-accumu-latessaltinweaklysalinesoil,withsaltreaching50%ofthedryweightofshoots.Incontrasttoglycophytes,whicharenegativelyaffectedbyincreasingsalinitybeyondathresholdofapproximately50mM,S.europaeasurvivesinahighsalinehabitat.Theoptimalsalinityformaximumgrowthisintherangeof100to200mM,anditsg