龙眼ERF家族成员鉴定及其在体胚发生早期的表达
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摘要
为了解龙眼ERF家族的基本性质以及在体胚发生早期的表达规律,该研究对龙眼基因组鉴定出108个ERF家族成员进行基本理化性质分析与进化树构建,并结合龙眼转录组及miRNA、lncRNA数据库对DlERF家族成员与lncRNA、miRNA之间的关系预测与表达模式分析。结果显示:(1)理化性质及进化树分析表明,AP2/ERF结构域在龙眼中相对最为保守,DlERF对龙眼的抗胁迫能力以及对病菌的防御能力可能起着重要作用。(2)RNA-Seq中的表达量分析可知,95个ERF基因在转录组中检测到表达,在愈伤组织(EC)、不完全胚性紧实结构(ICpEC)与球形胚(GE)阶段中分别存在31、11与53个ERF基因高表达。(3)qRT-PCR结果显示,在龙眼体胚发生早期显著表达5个ERF基因中,Dlo_008317.1ERF15-2、Dlo_022310.1ERF1-1与Dlo_009939.1ERF98在GE阶段表达量显著高于EC与ICpEC阶段,Dlo_009070.1ERF106-3与Dlo_022634.1ERF22-1则分别在EC与ICpEC阶段高表达。(4)DlERF家族成员与相关lncRNA、miRNA表达量分析显示,LTCONS_00013739对靶基因Dlo_008317.1ERF15-2为正调控关系;Dlo_miR413与Dlo_miR1510a共同靶向Dlo_009070.1ERF106-3,从EC到GE阶段均表现出显著负调控关系,而Dlo_miR413与Dlo_008317.1ERF15-2的表达量表现出正相关,推测相比于Dlo_008317.1ERF15-2,Dlo_miR413更倾向于调控Dlo_009070.1ERF106-3;调控Dlo_009939.1ERF98相关的Dlo_miR408与Dlo_miR774b,从表达趋势来看,Dlo_miR774b在龙眼体胚发生早期过程能够负调控Dlo_009939.1ERF98;Dlo_miR399c与Dlo_022310.1ERF1-1在EC到GE阶段可能存在负调控关系。(5)不同梯度浓度的乙烯处理使得DlERF基因表达显著下调。这些发现提供了有关龙眼体胚发生早期DlERF的重要见解,从而为将来对龙眼体胚发生早期过程中DlERF的功能分析奠定了基础。
In order to understand the basic properties of the longan ERFfamily and the expression of early embryogenesis,this study identified 108 ERFfamily members for basic physicochemical properties and phylogenetic tree construction in the longan genome.The relationship between DlERFfamily membersand lncRNA and miRNA was predicted and expressed in combination with longan transcriptome,miRNA and lncRNA database.The results showed that:(1)the physicochemical properties and phylogenetic tree analysis of the family indicated that the AP2/ERF domain is relatively the most conservative in longan,and DlERF may play an important role in the long-term stress resistance and defense ability of the pathogen.(2)Analysis of expression levels in RNA-Seq revealed that 95 ERFgenes were detected in the transcriptome,and there were 31,11 and 53 ERFgenes highly expressed in the callus,incomplete embryonic compact structure and globular embryo stage,respectively.(3)qRT-PCR results showed that among the five ERFgenes that were significantly expressed early in the longan somatic embryo,the expression levels of Dlo_008317.1 ERF15-2,Dlo_022310.1 ERF1-1 and Dlo_009939.1 ERF98 in GE stage were significantly higher than those of EC and ICpEC,Dlo_009070.1 ERF106-3 and Dlo_022634.1 ERF22-1 were highly expressed in the EC and ICpEC phases,respectively.(4)Analysis of DlERFfamily members and related lncRNA and miRNA expression levels showed that LTCONS_00013739 has a positive regulatory relationship with the target gene Dlo_008317.1 ERF15-2;Dlo_miR413 and Dlo_miR1510 atarget Dlo_009070.1 ERF106-3 together,showing a significant negative regulatory relationship from EC to GE,while Dlo_miR413 and Dlo_008317.1 ERF15-2 expression were positively correlated,presumably compared to Dlo_008317.1 ERF15-2 Dlo_miR413 is more inclined to regulate Dlo_009070.1 ERF106-3;Dlo_miR408 and Dlo_miR774 bregulate Dlo_009939.1 ERF98.From the expression trend,Dlo_miR774 bcan negatively regulate Dlo_009939.1 ERF98 in the early stage of longan somatic embryogenesis;Dlo_miR399 cand Dlo_022310.1 ERF1-1 may have negative regulation relationship in EC to GE stage.(5)Ethylene treatment with different gradient concentrations significantly down-regulated DlERFgene expression.These findings provide important insights into DlERFduring somatic embryogenesis in longan,and lay a foundation for further functional analysis of DlERFduring somatic embryogenesis in longan.
In order to understand the basic properties of the longan ERFfamily and the expression of early embryogenesis,this study identified 108 ERFfamily members for basic physicochemical properties and phylogenetic tree construction in the longan genome.The relationship between DlERFfamily membersand lncRNA and miRNA was predicted and expressed in combination with longan transcriptome,miRNA and lncRNA database.The results showed that:(1)the physicochemical properties and phylogenetic tree analysis of the family indicated that the AP2/ERF domain is relatively the most conservative in longan,and DlERF may play an important role in the long-term stress resistance and defense ability of the pathogen.(2)Analysis of expression levels in RNA-Seq revealed that 95 ERFgenes were detected in the transcriptome,and there were 31,11 and 53 ERFgenes highly expressed in the callus,incomplete embryonic compact structure and globular embryo stage,respectively.(3)qRT-PCR results showed that among the five ERFgenes that were significantly expressed early in the longan somatic embryo,the expression levels of Dlo_008317.1 ERF15-2,Dlo_022310.1 ERF1-1 and Dlo_009939.1 ERF98 in GE stage were significantly higher than those of EC and ICpEC,Dlo_009070.1 ERF106-3 and Dlo_022634.1 ERF22-1 were highly expressed in the EC and ICpEC phases,respectively.(4)Analysis of DlERFfamily members and related lncRNA and miRNA expression levels showed that LTCONS_00013739 has a positive regulatory relationship with the target gene Dlo_008317.1 ERF15-2;Dlo_miR413 and Dlo_miR1510 atarget Dlo_009070.1 ERF106-3 together,showing a significant negative regulatory relationship from EC to GE,while Dlo_miR413 and Dlo_008317.1 ERF15-2 expression were positively correlated,presumably compared to Dlo_008317.1 ERF15-2 Dlo_miR413 is more inclined to regulate Dlo_009070.1 ERF106-3;Dlo_miR408 and Dlo_miR774 bregulate Dlo_009939.1 ERF98.From the expression trend,Dlo_miR774 bcan negatively regulate Dlo_009939.1 ERF98 in the early stage of longan somatic embryogenesis;Dlo_miR399 cand Dlo_022310.1 ERF1-1 may have negative regulation relationship in EC to GE stage.(5)Ethylene treatment with different gradient concentrations significantly down-regulated DlERFgene expression.These findings provide important insights into DlERFduring somatic embryogenesis in longan,and lay a foundation for further functional analysis of DlERFduring somatic embryogenesis in longan.
引文
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[3]JOFUKU K D,DEN BOER B G,VAN M M,et al.Control of Arabidopsis flower and seed development by the homeotic gene APETALA2[J].Plant Cell,1994,6(9):1 211.
[4]WU Y M,TANG Y X,ZHOU M L.Genome-wide analysis of AP2/ERFtranscription factor family in Zea mays[J].Current Bioinformatics,2012,7(3):324-332
[5]LATA C,MISHRA A K,MUTHAMILARASAN M,et al.Genome-wide investigation and expression profiling of AP2/ERFtranscription factor superfamily in foxtail millet(Setaria italica L.)[J].Plos One,2014,9(11):e113092.
[6]ITO T M,POLIDO P B,RAMPIM M C,et al.Genome-wide identification and phylogenetic analysis of the AP2/ERFgene superfamily in sweet orange(Citrus sinensis)[J].Genetics&Molecular Research,2014,13(3):7 839-7 851.
[7]JING Z,PENG R H,CHENG Z M,et al.Genome-wide analysis of the putative AP2/ERFfamily genes in Vitis vinifera[J].Scientia Horticulturae,2009,123(1):73-81.
[8]ZHU X,QI L,LIU X,et al.The wheat ethylene response factor transcription factor pathogen-induced ERF1 mediates host responses to both the necrotrophic pathogen rhizoctonia cerealis and freezing stresses[J].Plant Physiology,2014,164(3):1 499-1 514.
[9]YANG Y,DONG C,LI X,et al.A novel Ap2/ERFtranscription factor from Stipa purpurea leads to enhanced drought tolerance in Arabidopsis thaliana[J].Plant Cell Reports,2016,35(11):1-13.
[10]YANG R,LIU J,LIN Z,et al.ERFtranscription factors involved in salt response in tomato[J].Plant Growth Regulation,2018:1-10.
[11]SHI Q,DONG Y,ZHOU Q,et al.Characterization of a maize ERFgene,ZmERF1,in hormone and stress responses[J].Acta Physiologiae Plantarum,2016,38(5):126.
[12]MANTIRI F R,KURDYUKOV S,LOHAR D P,et al.The transcription factor MtSERF1of the ERFsubfamily identified by transcriptional profiling is required for somatic embryogenesis induced by auxin plus cytokinin in Medicago truncatula[J].Plant Physiology,2008,146(4):1 622.
[13]PIYATRAKUL P,PUTRANTO R A,MARTIN F,et al.Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis[J].BMC Plant Biology,2012,12(1):244-244.
[14]张晓卫,曹蔚,王玉琨,等.龙眼的化学成分及药理作用研究进展[J].西北药学杂志,2012,27(5):493-496.ZHANG X W,CAO W,WANG Y K,et al.Study of the progress on chemical constituents and pharmacological activities of longan[J].Northwest Pharmaceutical Journal,2012,27(5):493-496.
[15]梁文裕,陈伟,宋瑞峰,等.龙眼胚胎发育研究进展[J].亚热带植物科学,2004,33(4):65-68.LIANG W Y,CHEN W,SONG R F,et al.Advances in embryo development of longan[J].Subtropical Plant Science,2004,33(4):65-68.
[16]赖钟雄.龙眼生物技术研究[M].福州:福建科学技术出版社,2003.
[17]LIN Y,MIN J,LAI R,et al.Genome-wide sequencing of longan(Dimocarpus longan Lour.)provides insights into molecular basis of its polyphenol-rich characteristics[J].Gigascience,2017,6(5):1-14.
[18]李惠华,赖钟雄,林玉玲,等.龙眼胚性愈伤组织ACC氧化酶基因的克隆及其在龙眼体胚发生过程中的表达分析[J].中国农业科学,2010,43(18):3 798-3 808.LI H H,LAI Z X,LIN Y L,et al.Cloning of ACOgene from embryogenic calli of Longan(Dimocarpus longan Lour.)and its expression during Longan somatic embryogenesis.[J].Scientia Agricultura Sinica,2010,43(18):3 798-3 808.
[19]李惠华,赖钟雄,苏明华,等.龙眼体胚发生过程中两个乙烯受体基因的定量表达分析[J].热带作物学报,2011,32(7):1 314-1 319.LI H H,LAI Z X,SU M H,et al.Quantitative expression analysis of two ethylene receptor genes from embryogenic callus in Dimocarpus longan Lour[J].Chinese Journal of Tropical Crops,2011,32(7):1 314-1 319.
[20]陈秋金.转录因子Dl-ASR1和Dl-ERF1与龙眼果实生长发育的关系[D].广州:华南农业大学,2009.
[21]QIN T,ZHAO H,CUI P,et al.A nucleus-localized long non-coding RNA enhances drought and salt stress tolerance[J].Plant Physiology,2017,175(3):1 321.
[22]GAO S,YANG L,ZENG H Q,et al.A cotton miRNA is involved in regulation of plant response to salt stress[J].Scientific Reports,2016,6:19 736.
[23]韩素芬.玉米纹枯病胁迫响应相关miRNA的功能研究[D].成都:四川农业大学,2012.
[24]LIN Y,LAI Z.Comparative analysis reveals dynamic changes in mirnas and their targets and expression during somatic embryogenesis in longan(Dimocarpus longan Lour.)[J].Plos One,2013,8(4):e60337.
[25]赖钟雄,潘良镇.龙眼胚性细胞系的建立与保持[J].福建农林大学学报(自然版),1997,(2):160-167.LAI Z X,PAN L Z.Establishment and maintenance of longan embryogenic cell lines[J].Journal of Fujian Agricultural University(Nat.Sci.Edi.),1997,(2):160-167.
[26]王亚婷.龙眼胚性愈伤组织中若干microRNA的初级体克隆及其功能分析[D].福州:福建农林大学,2013.
[27]OVERNAS E.Characterisation of members of the HD-Zip Iand DREB/ERF transcription factor families and their functions in plant stress responses[D].Uppsala:Uppsala University,2010.
[28]LASSERRE E,JOBET E,LLAURO C,et al.AtERF38(At2g35700),an AP2/ERFfamily transcription factor gene fromArabidopsis thaliana,is expressed in specific cell types of roots,stems and seeds that undergo suberization[J].Plant Physiology&Biochemistry,2008,46(12):1 051-1 061.
[29]CHIA K F.The Arabidopsis transcription factor ERF13negatively regulates defense against Pseudomonas syringae[D].San Diego:University of California,2013.
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