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凡纳滨对虾是世界养殖最广泛的甲壳动物,但是目前凡纳滨对虾的基因组及转录组数据还比较缺乏。为了获得凡纳滨对虾的转录组信息,本研究应用454高通量测序技术对凡纳滨对虾肝胰腺的转录组进行测序。获得了500177条凡纳滨对虾EST,平均长度363bp。拼接获得了20225条unigene,长度范围50~8980bp,平均长度507bp。所有unigene与NCBI的非冗余蛋白质数据库(Nr)进行相似搜索(E值<10-5),结果一共有13676条unigene(68%)与数据库中的已知基因同源。此外,还对unigene进行了GO、COG和KEGG的功能注释、分类或通路分析。我们通过高通量测序,获得了丰富的凡纳滨对虾转录组信息,为凡纳滨对虾的新基因克隆和基因组学研究提供了有价值的数据。
Abstract：Litopenaeus vannamei shrimp is the most extensively farmed crustacean species in the world. However, the genome and transcriptome data of Litopenaeus vannamei is still relatively lacking. To obtain transcriptome information of Litopenaeus vanname, the transcriptome of Litopenaeus vannamei hepatopancreas was sequenced by 454 high-throughput sequencing technology. A total of 500 177 ESTs were produced, with an average length of 363 bp. De novo assembly of ESTs data generated 20 225 unigenes between 50 and 8 980 bp in length, with an average length of 507 bp. Similarity searches against the NCBI-Nr database revealed that 13 676 (68%) of these unigenes have significant matches (E-value<10 -5 ). In addition, the unigenes were similarity search against the GO, COG and KEGG databases, and were annotated with gene functional descriptions, gene ontology terms, or pathways. By high-throughput sequencing, we obtained abundant transcriptome information that could contribute to novel gene identification and genome research in Litopenaeus vannamei.
Clavero-Salas A.,Sotelo-Mundo R.R.,Gollas-Galvan T.,Her-nandez-Lopez J.,Peregrino-Uriarte A.B.,Muhlia-AlmazanA.,and Yepiz-Plascencia G.,2007,Transcriptome analysisof gills from the white shrimp Litopenaeus vannamei infect-ed with white spot syndrome virus,Fish&Shellfish Im-munology,23(2):459-472
Conesa A.,and Gotz S.,2008,Blast2GO:A comprehensive suitefor functional analysis in plant genomics,International Jour-nal of Plant Genomics,2008:619832
De Gregoris T.B.,Rupp O.,Klages S.,Knaust F.,Bekel T.,KubeM.,Burgess J.G.,Arnone M.I.,Goesmann A.,Reinhardt R.,and Clare A.S.,2011,Deep sequencing of naupliar-,cyprid-and adult-specific normalised expressed sequence tag(EST)libraries of the acorn barnacle Balanus amphitrite,Biofoul-ing,27(4):367-374
Etebari K.,Palfreyman R.W.,Schlipalius D.,Nielsen L.K.,GlatzR.V.,and Asgari S.,2011,Deep sequencing-based tran-scriptome analysis of Plutella xylostella larvae parasitized byDiadegma semiclausum,BMC Genomics,12:446
Franssen S.U.,Shrestha R.P.,Brautigam A.,Bornberg-Bauer E.,and Weber A.P.,2011,Comprehensive transcriptome analy-sis of the highly complex Pisum sativum genome using nextgeneration sequencing,BMC Genomics,12:227
He L.,Wang Q.,Jin X.,Wang Y.,Chen L.,and Liu L.,2012,Transcriptome profiling of testis during sexual maturationstages in Eriocheir sinensis using illumina sequencing,PloSone,7(3):e33735
Jung H.,Lyons R.E.,Dinh H.,Hurwood D.A.,McWilliam S.,and Mather P.B.,2011,Transcriptomics of a giant freshwa-ter prawn(Macrobrachium rosenbergii):De novo assembly,annotation and marker discovery,PloS One,6(12):e27938
Liu K.F.,Chiu C.H.,Shiu Y.L.,Cheng W.,and Liu C.H.,2010,Effects of the probiotic,Bacillus subtilis E20,on the sur-vival,development,stress tolerance,and immune status ofwhite shrimp,Litopenaeus vannamei larvae,Fish&ShellfishImmunology,28(5-6):837-844
Liu L.,Li Y.,Li S.,Hu N.,He Y.,Pong R.,Lin D.,Lu L.,andLaw M.,2012,Comparison of next-generation sequencingsystems,J.Biomed.Biotechnol.,2012:251364
Ma N.,Chen X.H.,Zeng D.G.,Peng M.,and Li Y.M.,2008,SNPanalysis of the Cathepsin L gene in Litopenaeus vannamei,Wuhan Daxue Xuebao(Lixueban)(Journal of Wuhan Unive-rsity:Natural Science Edition),54(4):503-506(马宁,陈晓汉,曾地刚,彭敏,李咏梅,2008,凡纳滨对虾组织蛋白酶L基因的单核苷酸多态性分析,武汉大学学报(理学版),54(04):503-506)
Margulies M.,Egholm M.,Altman W.E.,Attiya S.,Bader J.S.,Bemben L.A.,Berka J.,Braverman M.S.,Chen Y.J.,ChenZ.,Dewell S.B.,Du L.,Fierro J.M.,Gomes X.V.,GodwinB.C.,He W.,Helgesen S.,Ho C.H.,Irzyk G.P.,Jando S.C.,Alenquer M.L.,Jarvie T.P.,Jirage K.B.,Kim J.B.,Knight J.R.,Lanza J.R.,Leamon J.H.,Lefkowitz S.M.,Lei M.,Li J.,Lohman K.L.,Lu H.,Makhijani V.B.,McDade K.E.,McK-enna M.P.,Myers E.W.,Nickerson E.,Nobile J.R.,Plant R.,Puc B.P.,Ronan M.T.,Roth G.T.,Sarkis G.J.,Simons J.F.,Simpson J.W.,Srinivasan M.,Tartaro K.R.,Tomasz A.,VogtK.A.,Volkmer G.A.,Wang S.H.,Wang Y.,Weiner M.P.,Yu P.,Begley R.F.,and Rothberg J.M.,2005,Genome se-quencing in microfabricated high-density picolitre reactors,Nature,437(7057):376-380
Ogata H.,Goto S.,Sato K.,Fujibuchi W.,Bono H.,and KanehisaM.,1999,KEGG:Kyoto encyclopedia of genes and geno-mes,Nucleic Acids Research,27(1):29-34
Robalino J.,Almeida J.S.,McKillen D.,Colglazier J.,Trent H.F.,Chen Y.A.,Peck M.E.,Browdy C.L.,Chapman R.W.,WarrG.W.,and Gross P.S.,2007,Insights into the immune tran-scriptome of the shrimp Litopenaeus vannamei:Tissue-spe-cific expression profiles and transcriptomic responses to im-mune challenge,Physiological Genomics,29(1):44-56
Tatusov R.L.,Galperin M.Y.,Natale D.A.,and Koonin E.V.,2000,The COG database:A tool for genome-scale analysisof protein functions and evolution,Nucleic Acids Research,28(1):33-36
You F.M.,Huo N.,Deal K.R.,Gu Y.Q.,Luo M.C.,McGuire P.E.,Dvorak J.,and Anderson O.D.,2011,Annotation-basedgenome-wide SNP discovery in the large and complex Aegi-lops tauschii genome using next-generation sequencing with-out a reference genome sequence,BMC Genomics,12:59
Zhang F.,Guo H.,Zheng H.,Zhou T.,Zhou Y.,Wang S.,Fang R.,Qian W.,and Chen X.,2010,Massively parallel pyrose-quencing-based transcriptome analyses of small brown plan-thopper(Laodelphax striatellus),a vector insect transmittingrice stripe virus(RSV),BMC Genomics,11:303
Zheng Y.,Zhao L.,Gao J.and Fei Z.,2011,iAssembler:A pack-age for de novo assembly of Roche-454/Sanger transcrip-tome sequences,BMC Bioinformatics,12:453
Zhou J.,Fang W.,Yang X.,Zhou S.,Hu L.,Li X.,Qi X.,Su H.,andXie L.,2012,A nonluminescent and highly virulent Vibrioharveyi strain is associated with“bacterial white tail disease”of Litopenaeus vannamei shrimp,PloS One,7(2):e29961
基本信息:
中图分类号:S917.4
引用信息:
[1]曾地刚,陈秀荔,谢达祥,等.基于高通量测序的凡纳滨对虾的转录组分析[J].基因组学与应用生物学,2013,32(03):308-313.
基金信息:
国家自然科学基金项目(31160531)资助
2013-06-28
2013-06-28