Comparative transcriptome analysis revealed the genotype specific cold response mechanism in tobacco
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- 英文论文题名：Comparative transcriptome analysis revealed the genotype specific cold response mechanism in tobacco
- 论文作者：胡日生 ; Xianxin Zhu ; Shipeng Xiang ; Youguo Zhan ; Mingdong Zhu ; Hanqi Yin ; Qingming Zhou ; Lieshu Zhu ; Xianwen Zhang ; Zhi Liu
- 英文论文作者：Risheng Hu ; Xianxin Zhu ; Shipeng Xiang ; Youguo Zhan ; Mingdong Zhu ; Hanqi Yin ; Qingming Zhou ; Lieshu Zhu ; Xianwen Zhang ; Zhi Liu ; Central-South Agricultural Experiment Station of China Tobacco ; College of Agronomy ; Hunan Agricultural University ; Kunming Municipal Tobacco Company ; Hunan Rice Research Institute ; Shanghai Biotechnology Corporation ; College of Bioscience and Biotechnology ; Hunan Agricultural University
- 年：2016
- 作者机构：湖南省烟草公司;College of Agronomy, Hunan Agricultural University;Central-South Agricultural Experiment Station of China Tobacco;Kunming Municipal Tobacco Company;Hunan Rice Research Institute;Shanghai Biotechnology Corporation;College of Bioscience and Biotechnology, Hunan Agricultural University;
- 英文论文关键词：cold stress ; transcriptome ; tobacco ; circadian clock
- 会议召开时间：2016-12-01
- 会议录名称：中国烟草学会2016年度优秀论文汇编——烟草农业主题
- 语种：英文
- 分类号：S572
- 学会代码：ZGYG
- 学会名称：中国烟草学会
- 页数：13
- 文件大小：867k
- 原文格式：D
摘要
Cold stress is a major adverse environmental factor that affects plant growth, development, productivity and quality. In the present study, comparative genome-wide transcriptome analysis on two tobacco(Nicotiana tobacum L.) cultivars, cold-tolerant NC567 and cold-sensitive Taiyan8, was performed using RNA-seq technology. After the first assembly, total length of unigenes is from 101,308,644 to 123,781,795 bp, the N50 length is from 1357 to 1475 bp, and 152,688 unigenes in NC567 and 144,160 unigenes in Taiyan8 were identified, respectively. Functional classification of cold-responsive(COR) genes showed that the genes involved in cell wall metabolism, transcription factors, ubiquitin-proteasome system(UPS) and signaling are over-represented, and the COR genes are specifically induced during cold stress in NC567. Pathway analysis revealed the significant enrichment of the COR genes in plant circadian clock. Taken together, the present study suggested the positive roles of the highly induced expression of the COR genes and the conserved mechanism of circadian clock related genes in tobacco response to cold stress, and provided some valuable genes for crop improvement to cope with cold stress.
Cold stress is a major adverse environmental factor that affects plant growth, development, productivity and quality. In the present study, comparative genome-wide transcriptome analysis on two tobacco(Nicotiana tobacum L.) cultivars, cold-tolerant NC567 and cold-sensitive Taiyan8, was performed using RNA-seq technology. After the first assembly, total length of unigenes is from 101,308,644 to 123,781,795 bp, the N50 length is from 1357 to 1475 bp, and 152,688 unigenes in NC567 and 144,160 unigenes in Taiyan8 were identified, respectively. Functional classification of cold-responsive(COR) genes showed that the genes involved in cell wall metabolism, transcription factors, ubiquitin-proteasome system(UPS) and signaling are over-represented, and the COR genes are specifically induced during cold stress in NC567. Pathway analysis revealed the significant enrichment of the COR genes in plant circadian clock. Taken together, the present study suggested the positive roles of the highly induced expression of the COR genes and the conserved mechanism of circadian clock related genes in tobacco response to cold stress, and provided some valuable genes for crop improvement to cope with cold stress.
Cold stress is a major adverse environmental factor that affects plant growth, development, productivity and quality. In the present study, comparative genome-wide transcriptome analysis on two tobacco(Nicotiana tobacum L.) cultivars, cold-tolerant NC567 and cold-sensitive Taiyan8, was performed using RNA-seq technology. After the first assembly, total length of unigenes is from 101,308,644 to 123,781,795 bp, the N50 length is from 1357 to 1475 bp, and 152,688 unigenes in NC567 and 144,160 unigenes in Taiyan8 were identified, respectively. Functional classification of cold-responsive(COR) genes showed that the genes involved in cell wall metabolism, transcription factors, ubiquitin-proteasome system(UPS) and signaling are over-represented, and the COR genes are specifically induced during cold stress in NC567. Pathway analysis revealed the significant enrichment of the COR genes in plant circadian clock. Taken together, the present study suggested the positive roles of the highly induced expression of the COR genes and the conserved mechanism of circadian clock related genes in tobacco response to cold stress, and provided some valuable genes for crop improvement to cope with cold stress.
引文
[1]V.Chinnusamy,M.Ohta,S.Kanrar,B.H.Lee,X.Hong,M.Agarwal,J..K.Zhu,ICE1:a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis,Genes Dev 17(2003)1043-1054.
[2]V.Chinnusamy,K.Schumaker,J.-K.Zhu,Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants,J.Exp.Bot.55(2004)225-236.
[3]L.Wu,Z.Zhang,H.Zhang,X.C.Wang,R.Huang,Transcriptional modulation of ethylene response factor protein JERF3 in the oxidative stress response enhances tolerance of tobacco seedlings to salt,drought,and freezing,Plant Physiol 148(2008)1953-1963.
[4]D.Q.Tian,X.Y.Pan,Y.M.Yu,W.Y.Wang,F.Zhang,Y.Y Ge,X.L.Shen,F.Q.Shen,X.J.Liu,De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress,BMC Genomics 14(2013)827.
[5]S.Fowler,M.F.Thomashow,Arabidopsis Transcriptome Profiling Indicates That Multiple Regulatory Pathways Are Activated during Cold Acclimation in Addition to the CBF Cold Response Pathway,Plant Cell 14(2002)1675-1690.
[6]B.H.Lee,D.A.Henderson,J.K.Zhu,The Arabidopsis cold-responsive transcriptome and its regulation by ICE1,Plant Cell 17(2005)3155-3175.
[7]S.Ishiguro,K.Ogasawara,K.Fujino,Y.Sato,Y.Kishima,Low temperature-responsive changes in the anther transcriptome's repeat sequences are indicative of stress sensitivity and pollen sterility in rice strains,Plant Physiol 164(2014)671-682.
[8]R.Hu,Z.Zeng,R.Shi,Z.Liu,Q.Yang,X.Dai,L.He,L.Zhu,A new way for identification of cold tolerance in tobacco at seedling stage,Chin Agri Sci Bull 30(2014)124-127.
[9]M.G.Grabherr,B.J.Haas,M.Yassour,J.Z.Levin,D.A.Thompson,I.Amit,X.Adiconis,L.Fan,R.Raychowdhury,Q.Zeng,Z.Chen,E.Mauceli,N.Hacohen,A.Gnirke,N.Rhind,F.di Palma,B.W.Birren,C.Nusbaum,K.Lindblad-Toh,N.Friedman,A.Regev,Full-length transcriptome assembly from RNA-Seq data without a reference genome,Nat Biotechnol 29(2011)644-652.
[10]M.D.Robinson,D.J.McCarthy,G.K.Smyth,edgeR:a Bioconductor package for differential expression analysis of digital gene expression data,Bioinformatics 26(2010)139-140.
[11]B.Usadel,A.Nagel,O.Thimm,H.Redestig,O.E.Blaesing,N.Palacios-Rojas,J.Selbig,J.Hannemann,M.C.Piques,D.Steinhauser,W.R.Scheible,Y.Gibon,R.Morcuende,D.Weicht,S.Meyer,M.Stitt,Extension of the visualization tool MapMan to allow statistical analysis of arrays,display of corresponding genes,and comparison with known responses,Plant Physiol 138(2005)1195-1204.
[12]X.Zhang,J.Li,A.Liu,J.Zou,X.Zhou,J.Xiang,W.Rerksiri,Y Peng,X.Xiong,X.Chen,Expression profile in rice panicle:insights into heat response mechanism at reproductive stage,PLoS One 7(2012)e49652.
[13]C.H.Wu,R.Apweiler,A.Bairoch,D.A.Natale,W.C.Barker,B.Boeckmann,S.Ferro,E.Gasteiger,H.Huang,R.Lopez,M.Magrane,M.J.Martin,R.Mazumder,C.O'Donovan,N.Redaschi,B.Suzek,The Universal Protein Resource(UniProt):an expanding universe of protein information,Nucleic Acids Res 34(2006)D187-191.
[14]L.Zheng,G.Liu,X.Meng,Y Liu,X.Ji,Y.Li,X.Nie,Y Wang,A WRKY gene from Tamarix hispida,ThWRKY4,mediates abiotic stress responses by modulating reactive oxygen species and expression of stress-responsive genes,Plant Mol Biol 82(2013)303-320.
[15]N.Yokotani,Y Sato,S.Tanabe,T.Chujo,T.Shimizu,K.Okada,H.Yamane,M.Shimono,S.Sugano,H.Takatsuji,H.Kaku,E.Minami,Y Nishizawa,WRKY76 is a rice transcriptional repressor playing opposite roles in blast disease resistance and cold stress tolerance,J Exp Bot 64(2013)5085-5097.
[16]S.D.Lim,H.Y Cho,YC.Park,D.J.Ham,J.K.Lee,C.S.Jang,The rice RING finger E3ligase,OsHCIl,drives nuclear export of multiple substrate proteins and its heterogeneous overexpression enhances acquired thermotolerance,J Exp Bot 64(2013)2899-2914.
[17]X.Hu,X.Kong,C.Wang,L.Ma,J.Zhao,J.Wei,X.Zhang,G.J.Loake,T.Zhang,J.Huang,Y Yang,Proteasome-mediated degradation of FRIGIDA modulates flowering time in Arabidopsis during vernalization,Plant Cell 26(2014)4763-4781.
[18]F.Chen,K.J.Bradford,Expression of an Expansin Is Associated with Endosperm Weakening during Tomato Seed Germination,Plant Physiol 124(2000)1265-1274.
[19]Y.Wu,D.J.Cosgrove,Adaptation of roots to low water potentials by changes in cell wall extensibility and cell wall proteins,J Exp Bot 51(2000)1543-1553.
[20]A.Harb,A.Krishnan,M.M.R.Ambavaram,A.Pereira,Molecular and Physiological Analysis of Drought Stress in Arabidopsis Reveals Early Responses Leading to Acclimation in Plant Growth,Plant Physiol 154(2010)1254-1271.
[21]B.Vanholme,R.Vanholme,H.Turumtay,G.Goeminne,I.Cesarino,F.Goubet,K.Morreel,J.Rencoret,V.Bulone,C.Hooijmaijers,R.De Rycke,G.Gheysen,J.Ralph,M.De Block,F.Meulewaeter,W.Boerjan,Accumulation of N-acetylglucosamine oligomers in the plant cell wall affects plant architecture in a dose-dependent and conditional manner,Plant Physiol 165(2014)290-308.
[22]D.Alabadi,T.Oyama,M.J.Yanovsky,F.G.Harmon,P.Mas,S.A.Kay,Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock,Science 293(2001)880-883.
[23]N.Nakamichi,T.Kiba,M.Kamioka,T.Suzuki,T.Yamashino,T.Higashiyama,H.Sakakibara,T.Mizuno,Transcriptional repressor PRR5 directly regulates clock-output pathways,Proc Natl Acad Sci U S A 109(2012)17123-17128.
[24]W.Y Kim,Z.Ali,H.J.Park,S.J.Park,J.Y Cha,J.Perez-Hormaeche,F.J.Quintero,G.Shin,M.R.Kim,Z.Qiang,L.Ning,H.C.Park,S.Y.Lee,R.A.Bressan,J.M.Pardo,H.J.Bohnert,D.J.Yun,Release of SOS2 kinase from sequestration with GIGANTEA determines salt tolerance in Arabidopsis,Nat Commun 4(2013)1352.
[25]B.Strasser,M.J.Alvarez,A.Califano,P.D.Cerdan,A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature,Plant J 58(2009)629-640.
[26]F.Yon,P.J.Seo,J.Y.Ryu,CM.Park,I.T.Baldwin,S.G.Kim,Identification and characterization of circadian clock genes in a native tobacco,Nicotiana attenuata,BMC Plant Biol 12(2012)172.
[27]C.Li,Y.Zhang,K.Zhang,D.Guo,B.Cui,X.Wang,X.Huang,Promoting flowering,lateral shoot outgrowth,leaf development,and flower abscission in tobacco plants overexpressing cotton FLOWERING LOCUS T(FT)-like gene GhFT1,Front Plant Sci 6(2015)454.
[28]B.Lei,K.Lu,F.Ding,K.Zhang,Y Chen,H.Zhao,L.Zhang,Z.Ren,C.Qu,W.Guo,J.Wang,W.Pan,RNA sequencing analysis reveals transcriptomic variations in tobacco(Nicotiana tabacum)leaves affected by climate,soil,and tillage factors,Int J Mol Sci 15(2014)6137-6160.
[29]YH.Song,S.Ito,T.Imaizumi,Flowering time regulation:photoperiod-and temperature-sensing in leaves,Trends Plant Sci 18(2013)575-583.
[30]S.G.Fowler,D.Cook,M.F.Thomashow,Low temperature induction of Arabidopsis CBF1,2,and 3 is gated by the circadian clock,Plant Physiol 137(2005)961-968.
[31]B.Y Chow,S.E.Sanchez,G.Breton,J.L.Pruneda-Paz,N.T.Krogan,S.A.Kay,Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis,Curr Biol 24(2014)1518-1524.
[32]E.Seo,H.Lee,J.Jeon,H.Park,J.Kim,YS.Noh,I.Lee,Crosstalk between cold response and flowering in Arabidopsis is mediated through the flowering-time gene SOC1 and its upstream negative regulator FLC,Plant Cell 21(2009)3185-3197.
[33]C.H.Dong,M.Agarwal,Y.Zhang,Q.Xie,J.K.Zhu,The negative regulator of plant cold responses,HOS1,is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1,Proc Natl Acad Sci U S A 103(2006)8281-8286.
[2]V.Chinnusamy,K.Schumaker,J.-K.Zhu,Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants,J.Exp.Bot.55(2004)225-236.
[3]L.Wu,Z.Zhang,H.Zhang,X.C.Wang,R.Huang,Transcriptional modulation of ethylene response factor protein JERF3 in the oxidative stress response enhances tolerance of tobacco seedlings to salt,drought,and freezing,Plant Physiol 148(2008)1953-1963.
[4]D.Q.Tian,X.Y.Pan,Y.M.Yu,W.Y.Wang,F.Zhang,Y.Y Ge,X.L.Shen,F.Q.Shen,X.J.Liu,De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress,BMC Genomics 14(2013)827.
[5]S.Fowler,M.F.Thomashow,Arabidopsis Transcriptome Profiling Indicates That Multiple Regulatory Pathways Are Activated during Cold Acclimation in Addition to the CBF Cold Response Pathway,Plant Cell 14(2002)1675-1690.
[6]B.H.Lee,D.A.Henderson,J.K.Zhu,The Arabidopsis cold-responsive transcriptome and its regulation by ICE1,Plant Cell 17(2005)3155-3175.
[7]S.Ishiguro,K.Ogasawara,K.Fujino,Y.Sato,Y.Kishima,Low temperature-responsive changes in the anther transcriptome's repeat sequences are indicative of stress sensitivity and pollen sterility in rice strains,Plant Physiol 164(2014)671-682.
[8]R.Hu,Z.Zeng,R.Shi,Z.Liu,Q.Yang,X.Dai,L.He,L.Zhu,A new way for identification of cold tolerance in tobacco at seedling stage,Chin Agri Sci Bull 30(2014)124-127.
[9]M.G.Grabherr,B.J.Haas,M.Yassour,J.Z.Levin,D.A.Thompson,I.Amit,X.Adiconis,L.Fan,R.Raychowdhury,Q.Zeng,Z.Chen,E.Mauceli,N.Hacohen,A.Gnirke,N.Rhind,F.di Palma,B.W.Birren,C.Nusbaum,K.Lindblad-Toh,N.Friedman,A.Regev,Full-length transcriptome assembly from RNA-Seq data without a reference genome,Nat Biotechnol 29(2011)644-652.
[10]M.D.Robinson,D.J.McCarthy,G.K.Smyth,edgeR:a Bioconductor package for differential expression analysis of digital gene expression data,Bioinformatics 26(2010)139-140.
[11]B.Usadel,A.Nagel,O.Thimm,H.Redestig,O.E.Blaesing,N.Palacios-Rojas,J.Selbig,J.Hannemann,M.C.Piques,D.Steinhauser,W.R.Scheible,Y.Gibon,R.Morcuende,D.Weicht,S.Meyer,M.Stitt,Extension of the visualization tool MapMan to allow statistical analysis of arrays,display of corresponding genes,and comparison with known responses,Plant Physiol 138(2005)1195-1204.
[12]X.Zhang,J.Li,A.Liu,J.Zou,X.Zhou,J.Xiang,W.Rerksiri,Y Peng,X.Xiong,X.Chen,Expression profile in rice panicle:insights into heat response mechanism at reproductive stage,PLoS One 7(2012)e49652.
[13]C.H.Wu,R.Apweiler,A.Bairoch,D.A.Natale,W.C.Barker,B.Boeckmann,S.Ferro,E.Gasteiger,H.Huang,R.Lopez,M.Magrane,M.J.Martin,R.Mazumder,C.O'Donovan,N.Redaschi,B.Suzek,The Universal Protein Resource(UniProt):an expanding universe of protein information,Nucleic Acids Res 34(2006)D187-191.
[14]L.Zheng,G.Liu,X.Meng,Y Liu,X.Ji,Y.Li,X.Nie,Y Wang,A WRKY gene from Tamarix hispida,ThWRKY4,mediates abiotic stress responses by modulating reactive oxygen species and expression of stress-responsive genes,Plant Mol Biol 82(2013)303-320.
[15]N.Yokotani,Y Sato,S.Tanabe,T.Chujo,T.Shimizu,K.Okada,H.Yamane,M.Shimono,S.Sugano,H.Takatsuji,H.Kaku,E.Minami,Y Nishizawa,WRKY76 is a rice transcriptional repressor playing opposite roles in blast disease resistance and cold stress tolerance,J Exp Bot 64(2013)5085-5097.
[16]S.D.Lim,H.Y Cho,YC.Park,D.J.Ham,J.K.Lee,C.S.Jang,The rice RING finger E3ligase,OsHCIl,drives nuclear export of multiple substrate proteins and its heterogeneous overexpression enhances acquired thermotolerance,J Exp Bot 64(2013)2899-2914.
[17]X.Hu,X.Kong,C.Wang,L.Ma,J.Zhao,J.Wei,X.Zhang,G.J.Loake,T.Zhang,J.Huang,Y Yang,Proteasome-mediated degradation of FRIGIDA modulates flowering time in Arabidopsis during vernalization,Plant Cell 26(2014)4763-4781.
[18]F.Chen,K.J.Bradford,Expression of an Expansin Is Associated with Endosperm Weakening during Tomato Seed Germination,Plant Physiol 124(2000)1265-1274.
[19]Y.Wu,D.J.Cosgrove,Adaptation of roots to low water potentials by changes in cell wall extensibility and cell wall proteins,J Exp Bot 51(2000)1543-1553.
[20]A.Harb,A.Krishnan,M.M.R.Ambavaram,A.Pereira,Molecular and Physiological Analysis of Drought Stress in Arabidopsis Reveals Early Responses Leading to Acclimation in Plant Growth,Plant Physiol 154(2010)1254-1271.
[21]B.Vanholme,R.Vanholme,H.Turumtay,G.Goeminne,I.Cesarino,F.Goubet,K.Morreel,J.Rencoret,V.Bulone,C.Hooijmaijers,R.De Rycke,G.Gheysen,J.Ralph,M.De Block,F.Meulewaeter,W.Boerjan,Accumulation of N-acetylglucosamine oligomers in the plant cell wall affects plant architecture in a dose-dependent and conditional manner,Plant Physiol 165(2014)290-308.
[22]D.Alabadi,T.Oyama,M.J.Yanovsky,F.G.Harmon,P.Mas,S.A.Kay,Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock,Science 293(2001)880-883.
[23]N.Nakamichi,T.Kiba,M.Kamioka,T.Suzuki,T.Yamashino,T.Higashiyama,H.Sakakibara,T.Mizuno,Transcriptional repressor PRR5 directly regulates clock-output pathways,Proc Natl Acad Sci U S A 109(2012)17123-17128.
[24]W.Y Kim,Z.Ali,H.J.Park,S.J.Park,J.Y Cha,J.Perez-Hormaeche,F.J.Quintero,G.Shin,M.R.Kim,Z.Qiang,L.Ning,H.C.Park,S.Y.Lee,R.A.Bressan,J.M.Pardo,H.J.Bohnert,D.J.Yun,Release of SOS2 kinase from sequestration with GIGANTEA determines salt tolerance in Arabidopsis,Nat Commun 4(2013)1352.
[25]B.Strasser,M.J.Alvarez,A.Califano,P.D.Cerdan,A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature,Plant J 58(2009)629-640.
[26]F.Yon,P.J.Seo,J.Y.Ryu,CM.Park,I.T.Baldwin,S.G.Kim,Identification and characterization of circadian clock genes in a native tobacco,Nicotiana attenuata,BMC Plant Biol 12(2012)172.
[27]C.Li,Y.Zhang,K.Zhang,D.Guo,B.Cui,X.Wang,X.Huang,Promoting flowering,lateral shoot outgrowth,leaf development,and flower abscission in tobacco plants overexpressing cotton FLOWERING LOCUS T(FT)-like gene GhFT1,Front Plant Sci 6(2015)454.
[28]B.Lei,K.Lu,F.Ding,K.Zhang,Y Chen,H.Zhao,L.Zhang,Z.Ren,C.Qu,W.Guo,J.Wang,W.Pan,RNA sequencing analysis reveals transcriptomic variations in tobacco(Nicotiana tabacum)leaves affected by climate,soil,and tillage factors,Int J Mol Sci 15(2014)6137-6160.
[29]YH.Song,S.Ito,T.Imaizumi,Flowering time regulation:photoperiod-and temperature-sensing in leaves,Trends Plant Sci 18(2013)575-583.
[30]S.G.Fowler,D.Cook,M.F.Thomashow,Low temperature induction of Arabidopsis CBF1,2,and 3 is gated by the circadian clock,Plant Physiol 137(2005)961-968.
[31]B.Y Chow,S.E.Sanchez,G.Breton,J.L.Pruneda-Paz,N.T.Krogan,S.A.Kay,Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis,Curr Biol 24(2014)1518-1524.
[32]E.Seo,H.Lee,J.Jeon,H.Park,J.Kim,YS.Noh,I.Lee,Crosstalk between cold response and flowering in Arabidopsis is mediated through the flowering-time gene SOC1 and its upstream negative regulator FLC,Plant Cell 21(2009)3185-3197.
[33]C.H.Dong,M.Agarwal,Y.Zhang,Q.Xie,J.K.Zhu,The negative regulator of plant cold responses,HOS1,is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1,Proc Natl Acad Sci U S A 103(2006)8281-8286.