线粒体基因组数据的分析方法和软件

ChineseJournalofAppliedEntomology2013501298－304．DOI10．7679/j．issn．2095－1353．2013．040*＊＊710062。StadenPackageContigExpress、DNAMAN、DNASTAＲ、BioEditSequencherDOGMA、MOSAS、MITOS、GOBASE、OGＲe、MitoZoa、tＲNAscan-SE、AＲWEN、BLASTMiTFi、rＲNA、tＲNAA+TMEGA5、SequinCGview、MTvizOGDＲAW。MethodsandsoftwaretoolsformitochondrialgenomeassemblyandannotationLIXue-JuanYANGJingWANGJun-HongＲENQian-LiLIXiaHUANGYuan＊＊SchoolofLifeSciencesShaanxiNormalUniversityXi’an710062ChinaAbstractWiththeincreasingpopularityofmitochondrialgenomestudiesthecorrectassemblyandannotationofgenomesarethebasisofallsubsequentresearchintoaspecies．HerewedescribetheprotocolsusingStadenPackagesoftwaretoassembleandannotatethemitochondrialgenomealongwithothercommonlyusedsoftwaresuchasContigExpressDNAMANDNASTAＲBioEditandSequencher．InadditionmethodsfortheuseofdifferentsoftwarepackagesincludingDOGMA、MOSAS、MITOS、GOBASE、OGＲe、MitoZoa、tＲNAscan-SE、AＲWEN、BLASTandMiTFitoannotatemitochondrialgenomicprotein-codinggenesrＲNAtＲNAandtheA+Tregionarebrieflyintroduced．FinallyapplicationofMEGA5softwaretoanalyzethecompositionofmitochondrialgenomesSequinsoftwaretosubmitsequencestoGenBankandmitochondrialgenomedatavisualizationtoolsCGview、MTvizandOGDＲAWarealsobrieflyintroduced．Keywordsmitochondrialgenomeassemblyannotation*3117207630970346。＊＊[e-mail]2012-12-212012-12-261、。。、、。。StadenPackageBonfieldetal．1995Pregap4、Trev、Gap4Spin、、。Pregap4Gap4Gap4。Pregap4Gap41·299·。*．seqSpin。ContigExpress、DNAMAN、DNASTAＲ、BioEditSequencher、rＲNA、tＲNAA+TSequin。2contig。DNA、、。Sanger28。ContigExpress、DNAMAN、DNASTAＲ、BioEdit、SequencherStadenPackage。、、SOAPdenovo。。ContigExpressVectorNTI。。DNASTAＲSeqManII64000。Sequencher、。StadenPackage1Pregap4*．abiPregap4。2ConfigureModules*．0．aux。3Gap4*．0．aux。Gap4ContigSelector。ContigSelectorContigComparator。4DNA。11。。tＲNA-Ile13'。ClustalX。5。。313、22tＲNA、2rＲNA1D-looptＲNAD-loop。NCBIＲefSeq。、tＲNA、rＲNA·300·ChineseJournalofAppliedEntomology50D-loop。、、、tＲNA、NJ、。。DOGMAhttp//dogma．ccbb．utexas．edu/、MOSAShttp//mosas．byu．eduMITOShttp//mitos．bioinf．uni-leipzig．de/3。GOBASEO’Brienetal．2009NCBIOGＲeJamesonetal．2003NCBI。MitoZoaLupietal．2010tＲNAscan-SE、AＲWENBLAST。Jex2010、SequinGenBank。DOGMAWeb。DOGMAFASTA。BLASTtＲNAs。GenBank。DOGMABLAST。BLAST。。tＲNArＲNA。SequinGenBank。DOGMA。MITOSＲNAsBerntetal．2012。MITOS、tＲNAMITOS。MITOSDenovo。METAMiGAFeijoetal．2006AMiGA。DOGMA、MOSASMITOSBLASTXBLASTrＲNA。DOGMAMITOSMOSAS。DOGMAMOSAStＲNAscan-SEtＲNAMITOSMiTFitＲNA。MITOS。3SequinGenBank。StandenPackageSpin。3.113、、NJ。BLAST、CLUSTALX、SPIN、OＲFFinderDOGMA。StandenPackageSPIN1。Stadenspinfile。2file。3sequenceHorizonalVerticalXY。1·301·4ComparisonLocalsequences。tＲNA-Ile1。5TranslationSetgeneticcodeInvertebratemitochondrial。6。TranslationFindopenreadingframesWriteproteinasfastafile。、。。①TTA②TTA、SPIN。Spin2。7NCBIBlast。DOGMA。BLASTX6BLASTE。DOGMA。DOGMABLASThit。3.2rＲNArＲNA2rＲNA、。BLAST、CLUSTALX、DOGMAInfernal。StandenpackageSPINrＲNAComparisonAlignsequencesＲNA。ＲNA。①。②NCBIBlastrＲNABLAST。③rＲNA。rＲNAＲNAStructurerＲNA。ViennaＲNAPackageHofackeretal．1994ＲNAＲNA。3.3tＲNAtＲNA、、、、·302·ChineseJournalofAppliedEntomology50、NJ。22tＲNA2tＲNAtＲNA。tＲNA2tＲNAtＲNAtＲNA。tＲNAtＲNAscan-SE、CLUSTALX、AＲWENMiTFi。tＲNAscan-SELoweandEddy1997tＲNAtＲNAscanEufindtＲNA2tＲNA。tＲNAscan-SEtＲNA1fastatＲNAscan-SEhttp//lowelab．ucsc．edu/tＲNAscan-SE/。2searchmodeDefault。tＲNA。。Source“Mito/Chloroplast”Format“ＲawSequence”FASTA“Showresultsinthisbrowser”“Ｒeceiveresultsbye-mailinstead”“GeneticCodefortＲNAIsotypePrediction”“InvertebrateMito”。“Covescorecutoff”20tＲNA20181323tＲNA。。3“runtＲNAscan-SE”tＲNA。4。tＲNA“ViewtＲNA”tＲNA“S”*．gif“---tＲNA-tＲNA”。tＲNA①“Covescorecutoff”tＲNAscan-SE20。tＲNACystＲNASer②tＲNAtＲNAtＲNA。③tＲNAscantＲNA。MiTFiInfernalNawrockietal．200922tＲNAtＲNA。MiTFiNCBI。MiTFi。tＲNAMiTFi。AＲWENLaslettandCanbck2008tＲNAscan-SE。tＲNAscan-SEAＲWEND-T-。AＲWEN。3.4D-loopA+TD-loopA+T、CLUSTALXSPIN。1·303·D-loopA+TStandenPackageSPIN。D-loopA+TTandemＲepeatsFinderBenson1999。4、、。MEGA5、DAMBE、BioEditDNASTAＲ。、。MEGA5DNA1MEGA“*．meg”“*．meg”。2DNA“ViewSequenceData”“Satistics→DesplayＲesultsinTextEditor”“TextFileEditorandFormatConvertor”“Excel”“Comma-delimitedformat”“Satistics→NucleotideComposition”built-intexteditor“TextFileEditorandFormatConvertor”。3“Satistics→CodonUsage”“TextFileEditorandFormatConvertor”1、2、3。5SequinNCBIGenBank、Email。SequinFASTA。Sequin、、PHYLIPNEXUSMACAWFASTA+GAP。Sequin。SequinNCBIENTＲEZBLASTNCBI。MiscENTＲEZGenBankMEDLINE、、、。Sequin1GenBank、EMBL＆DDBJStartNewSubmission。2。3、。4。5。67、、、、、。。7。“LocationofSequence”Genomic。“GenomicCodeforTranslation”。8。genomicDNAgenomicＲNAmＲNAcDNAcircularlinear。9“Annotate”·304·ChineseJournalofAppliedEntomology50GenesandNamedＲegionGeneCodingＲegionandTranscripsCDSStructuralＲNAtＲNArＲNAtＲNArＲNAtＲNA、、。10。。“Done”。11Sequin*[e-mail]。2*．sqn*．sqn。6、rＲNAtＲNA。CorelDrawIllustrator。CGviewhttp//stothard．afns．ualberta．ca/cgview_server/MTvizhttp//pacosy．informatik．uni-leipzig．de/mtviz/mtvizOGDＲAWOrganellarGenomeDＲAWhttp//ogdraw．mpimp-golm．mpg．de/GenBank。7。。、、、。ＲeferencesBensonG1999．TandemrepeatsfinderaprogramtoanalyzeDNAsequences．NucleicAcidsＲes．272573－580．BerntMDonathAJühlingFExternbrinkFFlorent