慈竹ARF基因的鉴定及虫害胁迫下的表达
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摘要
植物生长素响应因子(ARF)参与调节了植物的向性运动、子叶发育、胚胎形成、叶片器官衰老、维管束形成等,在植物生长发育过程发挥重要调控作用。为研究慈竹ARF基因家族及虫害胁迫下的表达,通过查询慈竹竹笋转录组数据库,分离出24个ARF基因家族成员。利用生物信息学方法分析,发现慈竹ARF家族序列保守,与毛竹亲缘性较近。通过对慈竹竹笋转录组中ARF基因表达模式分析发现,大部分ARF基因在竹笋中表达,少数ARF基因表达量在受到虫害胁迫后表达量发生显著变化。qRT-PCR结果表明,ARF基因在竹笋的几个部位在虫害胁迫后表达量均显著变化,推测其可能参与了竹笋对虫害胁迫响应,且在笋毛中表达量均升高,推测笋毛在抵御虫害胁迫中发挥了重要作用。
Auxin response factors( ARFs) play important roles in the whole processes of plant growth and development,which involved in the regulations of plant tropism,cotyledon development,embryo formation,leaf organ senescence and vascular bundle formation. The 24 members of ARF gene family were isolated and identified from the annotation of transcriptomic data in Bambusa emeiensis by bioinformatics methods. These genes are conserved,and the phylogenetic tree shows B. emeiensis is close to Phyllostachys heterocycla. The expression pattern of ARF family is the same in differently unfed bamboo shoots,and it is a little difference in fed and unfed position in the same bamboo shoot. Through the analysis of transcriptomic data,there are many of the ARF genes expressing in the bamboo shoots,and the expression of a few ARF genes change significantly under herbivore stress. The results of qRT-PCR show that the expression of these genes varies significantly under herbivore stress in different parts of bamboo shoots,and they may be involved in the response to herbivore stress. All expression levels increase in shoot trichome,which may play an important role in the response to herbivore stres.
Auxin response factors( ARFs) play important roles in the whole processes of plant growth and development,which involved in the regulations of plant tropism,cotyledon development,embryo formation,leaf organ senescence and vascular bundle formation. The 24 members of ARF gene family were isolated and identified from the annotation of transcriptomic data in Bambusa emeiensis by bioinformatics methods. These genes are conserved,and the phylogenetic tree shows B. emeiensis is close to Phyllostachys heterocycla. The expression pattern of ARF family is the same in differently unfed bamboo shoots,and it is a little difference in fed and unfed position in the same bamboo shoot. Through the analysis of transcriptomic data,there are many of the ARF genes expressing in the bamboo shoots,and the expression of a few ARF genes change significantly under herbivore stress. The results of qRT-PCR show that the expression of these genes varies significantly under herbivore stress in different parts of bamboo shoots,and they may be involved in the response to herbivore stress. All expression levels increase in shoot trichome,which may play an important role in the response to herbivore stres.
引文
[1] TIWARI S B,HAGEN G,GUILFOYLE T. The roles of auxin response factor domains in auxin-responsive transcription[J]. Plant Cell,2003,15(2):533-543.
[2]刘振华,于延冲,向凤宁.生长素响应因子与植物的生长发育[J].遗传,2011,33(12):1335-1346.
[3] DONG J L,PARK J W,HAN W L,et al. Genome-wide analysis of the auxin-responsive transcriptome downstream of iaa1 and its expression analysis reveal the diversity and complexity of auxinregulated gene expression[J]. Journal of Experimental Botany,2009,60(13):3935-3957.
[4] KALLURI U C,DIFAZIO S P,BRUNNER A M,et al. Genomewide analysis of Aux/IAA and ARF gene families in Populus trichocarpa[J]. BMC Plant Biology,2007,7(1):59-67.
[5] OKUSHIMA Y,OVERVOORDE P J,ARIMA K,et al. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana:unique and overlapping functions of ARF7 and ARF19[J]. Plant Cell,2005,17(2):444-463.
[6]陈磊,李晨曦,江涛,等.毛竹生长素响应因子基因家族的鉴定及其在竹笋发育中的表达[J].福建农林大学学报(自然科学版),2016,45(6):662-667.
[7]程占超,侯丹,马艳军,等.毛竹生长素反应因子基因的生物信息学分析及差异表达[J].浙江农林大学学报,2017,34(4):574-580.
[8] WANG W,GU L,YE S,et al. Genome-wide analysis and transcriptomic profiling of the auxin biosynthesis,transport and signaling family genes in moso bamboo(Phyllostachys heterocycla)[J].BMC Genomics,2017,18(1):870-878.
[9]李静,崔继哲,弭晓菊.生长素与植物逆境胁迫关系的研究进展[J].生物技术通报,2012(6):13-17.
[10] BAO F,LI J Y. Evidence that the auxin signaling pathway interacts with plant stress response[J]. Acta Botanica Sinica,2002,44(5):532-536.
[11] PETEK M,ROTTER A,KOGOVSEK P,et al. Potato virus Y infection hinders potato defence response and renders plants more vulnerable to Colorado potato beetle attack[J]. Molecular Ecology,2014,23(21):5378-5391.
[12] PANDEY S P,SRIVASTAVA S,GOEL R,et al. Simulated herbivory in chickpea causes rapid changes in defense pathways and hormonal transcription networks of JA/ethylene/GA/auxin within minutes of wounding[J]. Scientific Reports,2017,16(7). DOI:10.138/srep44729.
[13]段春香,董文渊,刘时才,等.慈竹无性系种群生长与立地条件关系[J].林业科技开发,2008,22(3):42-44.
[14]陈封政,王维德,王雄清,等.长足大竹象的发生危害与防治[J].植物保护,2005,31(2):89-90.
[15]李涛,高志兴,邓光明.长足大竹象的危害特性及防治技术[J].四川林业科技,2005,26(6):43-46.
[16]杨瑶君,汪淑芳,弓加文,等.长足大竹象虫口密度与虫孔数、竹笋受害率的关系[J].应用生态学报,2009,20(8):1980-1985.
[17] GRABHERR M G,HAAS B J,YASSOUR M,et al. Trinity:reconstructing a full-length transcriptome without a genome from RNA-Seq data[J]. Nature Biotechnology,2011,29(7):644-652.
[18] ASHBURNER M,BALL C A,BLAKE J A,et al. Gene Ontology:tool for the unification of biology[J]. Nature Genetics,2000,25(1):25-29.
[19] KANEHISA M,GOTO S,KAWASHIMA S,et al. The KEGG resource for deciphering the genome[J]. Nucleic Acids Research,2004,32(Database issue):277-280.
[20] ARTIMO P,JONNALAGEDDA M,ARNOLD K,et al. ExPASy:SIB bioinformatics resource portal[J]. Nucleic Acids Research,2012,40(Web Server issue):597-603.
[21] KUMAR S,STECHER G,TAMURA K. MEGA7:Molecular evolutionary genetics analysis version 7. 0 for bigger datasets[J].Molecular Biology&Evolution,2016,33(7):1870-1874.
[22] FELSENSTEIN J. Confidence limits on phylogenies:an approach using the bootstrap[J]. Evolution; International Journal of Organic Evolut,1985,39(4):783-791.
[23] BAILEY T L,WILLIAMS N,MISLEH C,et al. MEME:discovering and analyzing DNA and protein sequence motifs[J]. Nucleic Acids Research,2006,34(Web Server issue):369-373.
[24] SAEED A I,SHAROV V,WHITE J,et al. TM4:a free,opensource system for microarray data management and analysis[J].Biotechniques,2003,34(2):374-378.
[25]刘红梅,胡尚连,曹颖,等.慈竹WRKY转录因子基因克隆及其胁迫诱导表达[J].竹子研究汇刊,2016,35(3):1-8.
[26]赵艳,瓮巧云,马海莲,等.谷子ARF基因家族的鉴定与生物信息学分析[J].植物遗传资源学报,2016,17(3):547-554.
[27] TIWARI S B,WANG X J,HAGEN G,et al. AUX/IAA proteins are active repressors,and their stability and activity are modulated by auxin[J]. Plant Cell,2001,13(12):2809-2822.
[28] ULMASOV T,HAGEN G,GUILFOYLE T J. Activation and repression of transcription by auxin-response factors[J]. Proceedings of the National Academy of Sciences,1999,96(10):5844-5849.
[29] LI S B,XIE Z Z,HU C G,et al. A review of auxin response factors(ARFs)in plants[J]. Front Plant SCI,2016,7:47.
[30] FARCOT E,LAVEDRINE C,VERNOUX T. Correction:a modular analysis of the auxin signalling network[J]. PLoS One,2015,10(6).DOI:10.1371/journal.pone.0129605.
[31] ULMASOV T,MURFETT J,HAGEN G,et al. Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements[J]. Plant Cell,1997,9(11):1963-1971.
[32] GUILFOYLE T J,HAGEN G. Auxin response factors[J]. Journal of Plant Growth Regulation,2007,10(5):453-460.
[33] HARDTKE C S,CKURSHUMOVA W,VIDAURRE D P,et al.Overlapping and non-redundant functions of the Arabidopsis auxinresponse factors MONOPTEROS and NONPHOTOTROPIC HYPOCOTYL4[J]. Development,2004,131(5):1089-1100.
[34] LI X,DUAN X,JIANG H,et al. Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and arabidopsis[J]. Plant Physiology,2006,141(4):1167-1184.
[35] WENZEL C L,SCHUETZ M,YU Q,et al. Dynamics of MONOPTEROS and PIN-FORMED1 expression during leaf vein pattern formation in Arabidopsis thaliana[J]. Plant Journal for Cell&Molecular Biology,2007,49(3):387-398.
[36] HARDTKE C S,BERLETH T. The arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development[J]. The Embo Journal,1998,17(5):1405-1411.
[37] TIAN C E,MUTO H,HIGUCHI K,et al. Disruption and overexpression of auxin response factor 8 gene of Arabidopsis affect hypocotyl elongation and root growth habit,indicating its possible involvement in auxin homeostasis in light condition[J]. Plant Journal,2004,40(3):333-343.
[38] BOUZROUD S,GOUIAA S,HU N,et al. Auxin response factors(ARFs)are potential mediators of auxin action in tomato response to biotic and abiotic stress(Solanum lycopersicum)[J].PLoS One,2018,13(2).DOI:10.1371/journal.pone.0173517.
[39] WU M F,TIAN Q,REED J W. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression,and regulates both female and male reproduction[J]. Development,2006,133(21):4211-4218.
[40] KUMAR R,AGARWAL P,PAREEK A,et al. Genomic survey,gene expression,and Interaction analysis suggest diverse roles of ARF and Aux/IAA proteins in solanaceae[J]. Plant Molecular Biology Reporter,2015,33(5):1552-1572.
[2]刘振华,于延冲,向凤宁.生长素响应因子与植物的生长发育[J].遗传,2011,33(12):1335-1346.
[3] DONG J L,PARK J W,HAN W L,et al. Genome-wide analysis of the auxin-responsive transcriptome downstream of iaa1 and its expression analysis reveal the diversity and complexity of auxinregulated gene expression[J]. Journal of Experimental Botany,2009,60(13):3935-3957.
[4] KALLURI U C,DIFAZIO S P,BRUNNER A M,et al. Genomewide analysis of Aux/IAA and ARF gene families in Populus trichocarpa[J]. BMC Plant Biology,2007,7(1):59-67.
[5] OKUSHIMA Y,OVERVOORDE P J,ARIMA K,et al. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana:unique and overlapping functions of ARF7 and ARF19[J]. Plant Cell,2005,17(2):444-463.
[6]陈磊,李晨曦,江涛,等.毛竹生长素响应因子基因家族的鉴定及其在竹笋发育中的表达[J].福建农林大学学报(自然科学版),2016,45(6):662-667.
[7]程占超,侯丹,马艳军,等.毛竹生长素反应因子基因的生物信息学分析及差异表达[J].浙江农林大学学报,2017,34(4):574-580.
[8] WANG W,GU L,YE S,et al. Genome-wide analysis and transcriptomic profiling of the auxin biosynthesis,transport and signaling family genes in moso bamboo(Phyllostachys heterocycla)[J].BMC Genomics,2017,18(1):870-878.
[9]李静,崔继哲,弭晓菊.生长素与植物逆境胁迫关系的研究进展[J].生物技术通报,2012(6):13-17.
[10] BAO F,LI J Y. Evidence that the auxin signaling pathway interacts with plant stress response[J]. Acta Botanica Sinica,2002,44(5):532-536.
[11] PETEK M,ROTTER A,KOGOVSEK P,et al. Potato virus Y infection hinders potato defence response and renders plants more vulnerable to Colorado potato beetle attack[J]. Molecular Ecology,2014,23(21):5378-5391.
[12] PANDEY S P,SRIVASTAVA S,GOEL R,et al. Simulated herbivory in chickpea causes rapid changes in defense pathways and hormonal transcription networks of JA/ethylene/GA/auxin within minutes of wounding[J]. Scientific Reports,2017,16(7). DOI:10.138/srep44729.
[13]段春香,董文渊,刘时才,等.慈竹无性系种群生长与立地条件关系[J].林业科技开发,2008,22(3):42-44.
[14]陈封政,王维德,王雄清,等.长足大竹象的发生危害与防治[J].植物保护,2005,31(2):89-90.
[15]李涛,高志兴,邓光明.长足大竹象的危害特性及防治技术[J].四川林业科技,2005,26(6):43-46.
[16]杨瑶君,汪淑芳,弓加文,等.长足大竹象虫口密度与虫孔数、竹笋受害率的关系[J].应用生态学报,2009,20(8):1980-1985.
[17] GRABHERR M G,HAAS B J,YASSOUR M,et al. Trinity:reconstructing a full-length transcriptome without a genome from RNA-Seq data[J]. Nature Biotechnology,2011,29(7):644-652.
[18] ASHBURNER M,BALL C A,BLAKE J A,et al. Gene Ontology:tool for the unification of biology[J]. Nature Genetics,2000,25(1):25-29.
[19] KANEHISA M,GOTO S,KAWASHIMA S,et al. The KEGG resource for deciphering the genome[J]. Nucleic Acids Research,2004,32(Database issue):277-280.
[20] ARTIMO P,JONNALAGEDDA M,ARNOLD K,et al. ExPASy:SIB bioinformatics resource portal[J]. Nucleic Acids Research,2012,40(Web Server issue):597-603.
[21] KUMAR S,STECHER G,TAMURA K. MEGA7:Molecular evolutionary genetics analysis version 7. 0 for bigger datasets[J].Molecular Biology&Evolution,2016,33(7):1870-1874.
[22] FELSENSTEIN J. Confidence limits on phylogenies:an approach using the bootstrap[J]. Evolution; International Journal of Organic Evolut,1985,39(4):783-791.
[23] BAILEY T L,WILLIAMS N,MISLEH C,et al. MEME:discovering and analyzing DNA and protein sequence motifs[J]. Nucleic Acids Research,2006,34(Web Server issue):369-373.
[24] SAEED A I,SHAROV V,WHITE J,et al. TM4:a free,opensource system for microarray data management and analysis[J].Biotechniques,2003,34(2):374-378.
[25]刘红梅,胡尚连,曹颖,等.慈竹WRKY转录因子基因克隆及其胁迫诱导表达[J].竹子研究汇刊,2016,35(3):1-8.
[26]赵艳,瓮巧云,马海莲,等.谷子ARF基因家族的鉴定与生物信息学分析[J].植物遗传资源学报,2016,17(3):547-554.
[27] TIWARI S B,WANG X J,HAGEN G,et al. AUX/IAA proteins are active repressors,and their stability and activity are modulated by auxin[J]. Plant Cell,2001,13(12):2809-2822.
[28] ULMASOV T,HAGEN G,GUILFOYLE T J. Activation and repression of transcription by auxin-response factors[J]. Proceedings of the National Academy of Sciences,1999,96(10):5844-5849.
[29] LI S B,XIE Z Z,HU C G,et al. A review of auxin response factors(ARFs)in plants[J]. Front Plant SCI,2016,7:47.
[30] FARCOT E,LAVEDRINE C,VERNOUX T. Correction:a modular analysis of the auxin signalling network[J]. PLoS One,2015,10(6).DOI:10.1371/journal.pone.0129605.
[31] ULMASOV T,MURFETT J,HAGEN G,et al. Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements[J]. Plant Cell,1997,9(11):1963-1971.
[32] GUILFOYLE T J,HAGEN G. Auxin response factors[J]. Journal of Plant Growth Regulation,2007,10(5):453-460.
[33] HARDTKE C S,CKURSHUMOVA W,VIDAURRE D P,et al.Overlapping and non-redundant functions of the Arabidopsis auxinresponse factors MONOPTEROS and NONPHOTOTROPIC HYPOCOTYL4[J]. Development,2004,131(5):1089-1100.
[34] LI X,DUAN X,JIANG H,et al. Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and arabidopsis[J]. Plant Physiology,2006,141(4):1167-1184.
[35] WENZEL C L,SCHUETZ M,YU Q,et al. Dynamics of MONOPTEROS and PIN-FORMED1 expression during leaf vein pattern formation in Arabidopsis thaliana[J]. Plant Journal for Cell&Molecular Biology,2007,49(3):387-398.
[36] HARDTKE C S,BERLETH T. The arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development[J]. The Embo Journal,1998,17(5):1405-1411.
[37] TIAN C E,MUTO H,HIGUCHI K,et al. Disruption and overexpression of auxin response factor 8 gene of Arabidopsis affect hypocotyl elongation and root growth habit,indicating its possible involvement in auxin homeostasis in light condition[J]. Plant Journal,2004,40(3):333-343.
[38] BOUZROUD S,GOUIAA S,HU N,et al. Auxin response factors(ARFs)are potential mediators of auxin action in tomato response to biotic and abiotic stress(Solanum lycopersicum)[J].PLoS One,2018,13(2).DOI:10.1371/journal.pone.0173517.
[39] WU M F,TIAN Q,REED J W. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression,and regulates both female and male reproduction[J]. Development,2006,133(21):4211-4218.
[40] KUMAR R,AGARWAL P,PAREEK A,et al. Genomic survey,gene expression,and Interaction analysis suggest diverse roles of ARF and Aux/IAA proteins in solanaceae[J]. Plant Molecular Biology Reporter,2015,33(5):1552-1572.