Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing 英文参考文献.docVIP

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Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing 英文参考文献.doc

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Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing 英文参考文献

Sunetal.BMCPlantBiology2012,12:53 /1471-2229/12/53 RESEARCH ARTICLE OpenAccess Transcriptomeanalysisofstemdevelopmentin thetumourousstemmustardBrassicajunceavar. tumidaTsenetLeebyRNAsequencing QuanSun1,GuanfanZhou2,YingfanCai1*,YonghongFan2,XiaoyanZhu1,3,YihuaLiu2,XiaohongHe1, JinjuanShen2,HuaizhongJiang1,DaiwenHu2,ZhengPan1,LiuxinXiang1,GuanghuaHe3,DaiwenDong2and JianpingYang1 Abstract Background:Tumourousstemmustard(Brassicajunceavar.tumidaTsenetLee)isaneconomicallyand nutritionallyimportantvegetablecropoftheCruciferaefamilythatalsoprovidestherawmaterialforFuling mustard.Thegeneticsbreeding,physiology,biochemistryandclassificationofmustardshavebeenextensively studied,butlittleinformationisavailableontumourousstemmustardatthemolecularlevel.Togaingreater insightintothemolecularmechanismsunderlyingstemswellinginthisvegetableandtoprovideadditional informationformolecularresearchandbreeding,wesequencedthetranscriptomeoftumourousstemmustardat variousstemdevelopmentalstagesandcompareditwiththatofamutantvarietylackingswollenstems. Results:UsingIlluminashort-readtechnologywithatag-baseddigitalgeneexpression(DGE)system,we performeddenovotranscriptomeassemblyandgeneexpressionanalysis.Inouranalysis,weassembledgenetic informationfortumourousstemmustardatvariousstemdevelopmentalstages.Inaddition,weconstructedfive DGElibraries,whichcoveredthestrainsYong’anandDayejieatvariousdevelopmentstages.Illuminasequencing identified146,265unigenes,including11,245clustersand135,020singletons.Theunigenesweresubjectedtoa BLASTsearchandannotatedusingtheGOandKOdatabases.Wealsocomparedthegeneexpressionprofilesof threeswollenstemsampleswiththoseoftwonon-swollenstemsamples.Atotalof1,042geneswithsignificantly differentexpressionlevelsoccurringsimultaneouslyinthesixcomparisongroupswerescreenedout.Finally,the alteredexpressionlevelsofanumberofrandomlyselectedgeneswereconfirmedbyquantitativereal-timePCR. Conclusions:Ourdataprovidecomprehensivegeneexpressioninformationatthetranscriptionallevelandthe fi