转录组测序技术在植物水淹胁迫研究中的应用
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摘要
水淹胁迫是植物遭受的主要非生物胁迫之一,对作物生长发育、产量、品质等都会带来严重影响,全面解析植物的耐涝机制,对选育耐涝品种具有重要意义。高通量转录组测序技术以其数字化信息、高灵敏度、广泛的检测范围及重复性好等优点,已被广泛用于生物体的多种功能研究。目前在水稻、玉米、油菜、黄瓜、大豆等多个物种中,已有从转录水平分析植物对水淹胁迫的分子响应机制相关研究报道,这对于深度解析植物耐涝的分子响应机制和加快作物耐涝品种选育具有重要意义。但目前尚未有转录组测序技术在植物水淹胁迫应用方面的综述。因此,本研究着重综述了植物水淹胁迫测序组织及时间点选择、各阶段基因表达水平、GO功能富集、小RNA的功能特征几个方面,并展望了新一代测序技术在植物抗逆机理研究中的应用前景。
Flooding stress is one of the main abiotic stresses on plants, which has serious impact on crop growth,yield, quality, etc. Comprehensive analysis of plant tolerance to mites is of great significance for breeding sorghum-tolerant varieties. High-throughput transcriptome sequencing has been used widely in the study of different fields of life science with its digital information, high sensitivity, extensive detection range and good repeatability.At present, in many species such as rice, corn, rape, cucumber, soybean and so on, it has been reported that the molecular response mechanism of plants to waterlogging stress has been analyzed at the transcriptional level. It is of great significance to analyze the molecular response mechanism of plant waterlogging tolerance and to accelerate the breeding of crop waterlogging tolerant varieties. While, there has been no comprehensive report on transcriptome studies of different species of waterlogging stress. In this review, this study focused on the following aspects:sequencing of plants under waterflooding stress, selection of time points, level of gene expression at different stages, enrichment of GO function, functional characteristics of small RNA. The application prospect of new generation sequencing technology in the study of plant stress resistance mechanism is also prospected
Flooding stress is one of the main abiotic stresses on plants, which has serious impact on crop growth,yield, quality, etc. Comprehensive analysis of plant tolerance to mites is of great significance for breeding sorghum-tolerant varieties. High-throughput transcriptome sequencing has been used widely in the study of different fields of life science with its digital information, high sensitivity, extensive detection range and good repeatability.At present, in many species such as rice, corn, rape, cucumber, soybean and so on, it has been reported that the molecular response mechanism of plants to waterlogging stress has been analyzed at the transcriptional level. It is of great significance to analyze the molecular response mechanism of plant waterlogging tolerance and to accelerate the breeding of crop waterlogging tolerant varieties. While, there has been no comprehensive report on transcriptome studies of different species of waterlogging stress. In this review, this study focused on the following aspects:sequencing of plants under waterflooding stress, selection of time points, level of gene expression at different stages, enrichment of GO function, functional characteristics of small RNA. The application prospect of new generation sequencing technology in the study of plant stress resistance mechanism is also prospected
引文
Abiko T.,Kotula L.,Shiono K.,Malik A.,Colmer T.D.,and Nakazono M.,2012,Enhanced formation of aerenchyma and induction of a barrier to radial oxygen loss in adventitious roots of Zea nicaraguensis contribute to its waterlogging tolerance as compared with maize(Zea mays ssp.mays),Plant Cell Environ.,35(9):1618-1630
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Ansorge W.J.,2009,Next-generation DNA sequencing techniques,N Biotechnol,25(4):195-203
Arismendi M.J.,Almada R.,Pimentel P.,Bastias A.,Salvatierra A.,Rojas P.,Hinrichsen P.,Pinto M.,Genova A.D.,Travisany D.,Maass A.,and Sagredo B.,2015,Transcriptome sequencing of Prunus sp.rootstocks roots to identify candidate genes involved in the response to root hypoxia,Tree Genetics&Genomes,11(1):11
Arora K.,Panda K.K.,Mittal S.,Mallikarjuna M.G.,Rao A.R.,Dash P.K.,and Thirunavukkarasu N.,2017,RNAseq revealed the important gene pathways controlling adaptive mechanisms under waterlogged stress in maize,Sci.Rep.,7(1):10950
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Christianson J.A.,Llewellyn D.J.,Dennis E.S.,and Wilson I.W.,2010,Global gene expression responses to waterlogging in roots and leaves of cotton(Gossypium hirsutum L.),Plant Cell Physiol.,51(1):21-37
Gao Y.Z.,Zong J.Q.,Chen J.B.,Zhao R.S.,and Liu J.X.,2015,Response of 15 different warm season turfgrass germplasms to long-term submergence and waterlogging stress,Caoye Kexue(Pratacultural Science),32(3):354-362(高艳芝,宗俊勤,陈静波,赵瑞霜,刘建秀,2015,15份不同暖季型草坪草生长量对长期水淹和水涝胁迫的响应,草业科学,32(3):354-362)
Hakkinen J.,Nordborg N.,Mansson O.,and Vallonchristersson J.,2016,Implementation of an open source software solution for laboratory information management and automated RNA-seq data analysis in a large-scale cancer genomics initiative using BASE with extension package Reggie,Genetics,199(2):573-579
Herzog M.,Striker G.G.,Colmer T.D.,and Pedersen O.,2016,Mechanisms of waterlogging tolerance in wheat-a review of root and shoot physiology,Plant Cell Environ.,39(5):1068-1086
Huo D.,Sun L.,Li X.,Ru X.,Liu S.,Zhang L.,Xing L.,and Yang H.,2017,Differential expression of mi RNAs in the respiratory tree of the sea cucumber Apostichopus japonicas under hypoxia stress,G3(Bethesda),7(11):3681-3692
Juntawong P.,Sirikhachornkit A.,Pimjan R.,Sonthirod C.,Sangsrakru D.,and Yoocha T.,2014,Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling,Front Plant Sci.,5:658
Komatsu S.,Yamamoto R.,Nanjo Y.,Mikami Y.,Yunokawa H.,and Sakata K.,2009,A comprehensive analysis of the soybean genes and proteins expressed under flooding stress using transcriptome and proteome techniques,J.Proteome Res.,8(10):4766
Kreuzwieser J.,Hauberg J.,Howell K.A.,Carroll A.,Rennenberg H.,Millar A.H.,and Whelan J.,2009,Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia,Plant Physiol.,149(1):461
Lee Y.H.,Kim K.S.,Jang Y.S.,Hwang J.H.,Lee D.H.,and Choi I.H.,2014,Global gene expression responses to waterlogging in leaves of rape seedlings,Plant Cell Rep.,33(2):289-299
Li B.,and Dewey C.N.,2011,Rsem:accurate transcript quantification from RNA-Seq data with or without a reference genome,BMC Bioinformatics,12(1):323
Licausi F.,Weits D.A.,Pant B.D.,Scheible W.R.,Geigenberger P.,and van Dongen J.T.,2011,Hypoxia responsive gene expression is mediated by various subsets of transcription factors and mi RNAs that are determined by the actual oxygen availability,New Phytol.,190(2):442-456
Lu Y.Y.,Fu S.X.,Chen S.,Zhang W.,and Qi C.K.,2015,RNA-sequencing analysis of differentially expressed genes in wild type and BnERF-transgenic Arabidopsis under submergence treatment,Zhiwu Xuebao(Botany Gazette),50(3):321-330(吕艳艳,付三雄,陈松,张唯,戚存扣,2015,利用RNA-seq技术分析淹水胁迫下转bnerf拟南芥差异表达基因,植物学报,50(3):321-330)
Luo F.L.,2007,Photosynthesis and growth responses of several terrestrial plants in Three Gorges reservoir region as affected by simulated flooding,Thesis for M.S.,Southwestern University,Supervisor:Zeng B.,pp.14-15(罗芳丽,2007,三峡库区几种陆生植物对水淹的光合及生长响应,硕士学位论文,西南大学,导师:曾波,pp.14-15)
Luo Z.H.,Yu X.F.,and Zou J.,2013,Regulation mechanism of non coded RNA on tumor,Guoji Xiaohuabing Zazhi(International Journal of Digestive Diseases),33(2):97-100(罗子华,于晓峰,邹健,2013,非编码RNA对肿瘤的调控机制,国际消化病杂志,33(2):97-100)
Moldovan D.,Spriggs A.,Yang J.,Pogson B.J.,Dennis E.S.,and Wilson I.W.,2010,Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis,J.Exp.Bot.,61(1):165
Mustroph A.,Stock J.,Hess N.,Aldous S.,Dreilich A.,and Grimm B.,2013,Characterization of the phosphofructokinase gene family in rice and its expression under oxygen deficiency stress,Front Plant Sci.,4(7):125
Nakayama T.J.,Rodrigues F.A.,Neumaier N.,MarcolinoGs J.,Molinari H.B.C.,Santiago T.R.,Formighieri E.F.,Basso M.F.,Farias J.R.B.,Emygdio B.M.,de Oliveira A.C.B.,Campos A.D.,Borem A.,Harmon F.G.,Mertz-Henning L.M.,and Nepomuceno A.L.,2017,Insights into soybean transcriptome reconfiguration under hypoxic stress:functional,regulatory,structural,and compositional characterization,PLoSOne,12(11):e0187920
Nanjo Y.,Maruyama K.,Yasue H.,Yamaguchi S.K.,Shinozaki K.,and Komatsu S.,2011,Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings,Plant Mol.Biol.,77(1-2):129-144
Peng Z.,Lyu D.G.,Jia L.T.,He J.L.,and Qin S.J.,2017,Physiological and de novo transcriptome analysis of the fermentation mechanism of Cerasus sachalinensis roots in response to short-term waterlogging,BMC Genomics,18(1):649
Puyang X.,An M.,Xu L.,Han L.,and Zhang X.,2015,Antioxidant responses to waterlogging stress and subsequent recov ery in two Kentucky bluegrass(Poa pratensis L.)cultivars,Acta Physiol.Plant.,37(10):197
Qi B.,Yang Y.,Yin Y.,Xu M.,and Li H.,2014,De novo sequencing,assembly,and analysis of the Taxodium'Zhongshansa'roots and shoots transcriptome in response to short-term waterlogging,BMC Plant Biol.,14(1):201
Qi X.H.,Xu X.W.,Lin X.J.,Zhang W.J.,and Chen X.H.,2012,Identification of differentially expressed genes in cucumber(Cucumis sativus L.)root under waterlogging stress by digital gene expression profile,Genomics,99(3):160-168
Qi Y.X.,Liu Y.B.,and Rong W.H.,2011,RNA-Seq and its applications:a new technology for transcriptomics,Yichuan(Hereditas),33(11):1191-1202(祁云霞,刘永斌,荣威恒,2011,转录组研究新技术:RNA-Seq及其应用,遗传,33(11):1191-1202)
Reeksting B.J.,Coetzer N.,Mahomed W.,Engelbrecht J.,and Berg N.V.D.,2014,De novo sequencing,assembly,and analysis of the root transcriptome of Persea americana(Mill.)in response to Phytophthora cinnamomi and flooding,PLo S One,9(2):e86399
Reeksting B.J.,Olivier N.A.,and Berg N.V.D.,2016,Transcriptome responses of an ungrafted phytophthora root rot tolerant avocado(Persea americana)rootstock to flooding and P-hytophthora cinnamomi,BMC Plant Biol.,16(1):205
Ren B.Z.,Zhang J.W.,Dong S.T.,Liu P.,and Zhao B.,2016,Root and shoot responses of summer maize to waterlogging at different stages,Agronomy Journal,108(3):1060-1069
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Agrawal R.,Pandey P.,Jha P.,Dwivedi V.,Sarkar C.,and Kulshreshtha R.,2014,Hypoxic signature of microRNAs in glioblastoma:insights from small RNA deep sequencing,BMCGenomics,15(1):686
Ansorge W.J.,2009,Next-generation DNA sequencing techniques,N Biotechnol,25(4):195-203
Arismendi M.J.,Almada R.,Pimentel P.,Bastias A.,Salvatierra A.,Rojas P.,Hinrichsen P.,Pinto M.,Genova A.D.,Travisany D.,Maass A.,and Sagredo B.,2015,Transcriptome sequencing of Prunus sp.rootstocks roots to identify candidate genes involved in the response to root hypoxia,Tree Genetics&Genomes,11(1):11
Arora K.,Panda K.K.,Mittal S.,Mallikarjuna M.G.,Rao A.R.,Dash P.K.,and Thirunavukkarasu N.,2017,RNAseq revealed the important gene pathways controlling adaptive mechanisms under waterlogged stress in maize,Sci.Rep.,7(1):10950
Chen W.,Yao Q.M.,Patil G.B.,Gaurav A.,Deshmukh R.K.,Lin L.,Wang B.,Wang Y.Q.,Prince S.J.,Song L.,Xu D.,An Y.Q.C.,Valliyodan B.B.,Varshney R.K.,and Nguyen H.T.,2016,Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq,Front.Plant Sci.,7(244):1044
Christianson J.A.,Llewellyn D.J.,Dennis E.S.,and Wilson I.W.,2010,Global gene expression responses to waterlogging in roots and leaves of cotton(Gossypium hirsutum L.),Plant Cell Physiol.,51(1):21-37
Gao Y.Z.,Zong J.Q.,Chen J.B.,Zhao R.S.,and Liu J.X.,2015,Response of 15 different warm season turfgrass germplasms to long-term submergence and waterlogging stress,Caoye Kexue(Pratacultural Science),32(3):354-362(高艳芝,宗俊勤,陈静波,赵瑞霜,刘建秀,2015,15份不同暖季型草坪草生长量对长期水淹和水涝胁迫的响应,草业科学,32(3):354-362)
Hakkinen J.,Nordborg N.,Mansson O.,and Vallonchristersson J.,2016,Implementation of an open source software solution for laboratory information management and automated RNA-seq data analysis in a large-scale cancer genomics initiative using BASE with extension package Reggie,Genetics,199(2):573-579
Herzog M.,Striker G.G.,Colmer T.D.,and Pedersen O.,2016,Mechanisms of waterlogging tolerance in wheat-a review of root and shoot physiology,Plant Cell Environ.,39(5):1068-1086
Huo D.,Sun L.,Li X.,Ru X.,Liu S.,Zhang L.,Xing L.,and Yang H.,2017,Differential expression of mi RNAs in the respiratory tree of the sea cucumber Apostichopus japonicas under hypoxia stress,G3(Bethesda),7(11):3681-3692
Juntawong P.,Sirikhachornkit A.,Pimjan R.,Sonthirod C.,Sangsrakru D.,and Yoocha T.,2014,Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling,Front Plant Sci.,5:658
Komatsu S.,Yamamoto R.,Nanjo Y.,Mikami Y.,Yunokawa H.,and Sakata K.,2009,A comprehensive analysis of the soybean genes and proteins expressed under flooding stress using transcriptome and proteome techniques,J.Proteome Res.,8(10):4766
Kreuzwieser J.,Hauberg J.,Howell K.A.,Carroll A.,Rennenberg H.,Millar A.H.,and Whelan J.,2009,Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia,Plant Physiol.,149(1):461
Lee Y.H.,Kim K.S.,Jang Y.S.,Hwang J.H.,Lee D.H.,and Choi I.H.,2014,Global gene expression responses to waterlogging in leaves of rape seedlings,Plant Cell Rep.,33(2):289-299
Li B.,and Dewey C.N.,2011,Rsem:accurate transcript quantification from RNA-Seq data with or without a reference genome,BMC Bioinformatics,12(1):323
Licausi F.,Weits D.A.,Pant B.D.,Scheible W.R.,Geigenberger P.,and van Dongen J.T.,2011,Hypoxia responsive gene expression is mediated by various subsets of transcription factors and mi RNAs that are determined by the actual oxygen availability,New Phytol.,190(2):442-456
Lu Y.Y.,Fu S.X.,Chen S.,Zhang W.,and Qi C.K.,2015,RNA-sequencing analysis of differentially expressed genes in wild type and BnERF-transgenic Arabidopsis under submergence treatment,Zhiwu Xuebao(Botany Gazette),50(3):321-330(吕艳艳,付三雄,陈松,张唯,戚存扣,2015,利用RNA-seq技术分析淹水胁迫下转bnerf拟南芥差异表达基因,植物学报,50(3):321-330)
Luo F.L.,2007,Photosynthesis and growth responses of several terrestrial plants in Three Gorges reservoir region as affected by simulated flooding,Thesis for M.S.,Southwestern University,Supervisor:Zeng B.,pp.14-15(罗芳丽,2007,三峡库区几种陆生植物对水淹的光合及生长响应,硕士学位论文,西南大学,导师:曾波,pp.14-15)
Luo Z.H.,Yu X.F.,and Zou J.,2013,Regulation mechanism of non coded RNA on tumor,Guoji Xiaohuabing Zazhi(International Journal of Digestive Diseases),33(2):97-100(罗子华,于晓峰,邹健,2013,非编码RNA对肿瘤的调控机制,国际消化病杂志,33(2):97-100)
Moldovan D.,Spriggs A.,Yang J.,Pogson B.J.,Dennis E.S.,and Wilson I.W.,2010,Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis,J.Exp.Bot.,61(1):165
Mustroph A.,Stock J.,Hess N.,Aldous S.,Dreilich A.,and Grimm B.,2013,Characterization of the phosphofructokinase gene family in rice and its expression under oxygen deficiency stress,Front Plant Sci.,4(7):125
Nakayama T.J.,Rodrigues F.A.,Neumaier N.,MarcolinoGs J.,Molinari H.B.C.,Santiago T.R.,Formighieri E.F.,Basso M.F.,Farias J.R.B.,Emygdio B.M.,de Oliveira A.C.B.,Campos A.D.,Borem A.,Harmon F.G.,Mertz-Henning L.M.,and Nepomuceno A.L.,2017,Insights into soybean transcriptome reconfiguration under hypoxic stress:functional,regulatory,structural,and compositional characterization,PLoSOne,12(11):e0187920
Nanjo Y.,Maruyama K.,Yasue H.,Yamaguchi S.K.,Shinozaki K.,and Komatsu S.,2011,Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings,Plant Mol.Biol.,77(1-2):129-144
Peng Z.,Lyu D.G.,Jia L.T.,He J.L.,and Qin S.J.,2017,Physiological and de novo transcriptome analysis of the fermentation mechanism of Cerasus sachalinensis roots in response to short-term waterlogging,BMC Genomics,18(1):649
Puyang X.,An M.,Xu L.,Han L.,and Zhang X.,2015,Antioxidant responses to waterlogging stress and subsequent recov ery in two Kentucky bluegrass(Poa pratensis L.)cultivars,Acta Physiol.Plant.,37(10):197
Qi B.,Yang Y.,Yin Y.,Xu M.,and Li H.,2014,De novo sequencing,assembly,and analysis of the Taxodium'Zhongshansa'roots and shoots transcriptome in response to short-term waterlogging,BMC Plant Biol.,14(1):201
Qi X.H.,Xu X.W.,Lin X.J.,Zhang W.J.,and Chen X.H.,2012,Identification of differentially expressed genes in cucumber(Cucumis sativus L.)root under waterlogging stress by digital gene expression profile,Genomics,99(3):160-168
Qi Y.X.,Liu Y.B.,and Rong W.H.,2011,RNA-Seq and its applications:a new technology for transcriptomics,Yichuan(Hereditas),33(11):1191-1202(祁云霞,刘永斌,荣威恒,2011,转录组研究新技术:RNA-Seq及其应用,遗传,33(11):1191-1202)
Reeksting B.J.,Coetzer N.,Mahomed W.,Engelbrecht J.,and Berg N.V.D.,2014,De novo sequencing,assembly,and analysis of the root transcriptome of Persea americana(Mill.)in response to Phytophthora cinnamomi and flooding,PLo S One,9(2):e86399
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