桐花树叶片的转录组分析
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摘要
为了进一步了解桐花树耐盐的分子机制,本研究采用Illumina HiSeq 2000高通量测序平台对桐花树叶片转录组进行测序,经de novo组装后获得73 721个Unigenes,进一步利用7个公共数据库(NR, NT,GO, COG, KEGG, SwissProt和InterPro)进行比对,注释了50 338个Unigenes。结果表明,有34 991个Unigenes参与到136条KEGG通路上,其中在花青素和类黄酮合成途径中的Unigenes分别有49个和176个,这些基因可能参与了桐花树应对逆境的调控过程;此外,从转录组序列中搜索到34 509个SSR位点,其中二碱基重复出现次数最多,出现频率为65.75%;从转录组的数据中预测到了2 255个转录因子,分属于58个家族。本研究结果为桐花树的基因功能分析、分子标记开发和遗传多样性研究提供一定的理论参考。
The aim of this study was to further understand the salt-resistance molecular mechanism of Aegiceras corniculatum(L.) Blanco. In this study, the transcriptome of A. corniculatum leaf have been sequenced by Illumina HiSeq 2000. Then all the clean reads were de novo assembled, 73 721 Unigenes were yielded. After assembly, 50338 Unigenes were annotated with 7 databases(NR, NT, GO, COG, KEGG, SwissProt and InterPro). A total of 34991 transcripts were involved in 136 KEGG pathways, the number of Unigenes participated in pathway:anthocyanin biosynthesis and flavonoid biosynthesis were 49 and 176, respectively. These genes may play an important role in stress-responding regulation of A. corniculatum. In addition, 34 509 SSR were detected from Unigenes, in which di-nucleotide repeats most with a frequency of 65.75%. Furthermore, 2 255 transcription factors were predicted and classified into 58 families. The results of this study should be value in A. corniculatum gene function analysis, molecular marker development and genetic diversity research.
The aim of this study was to further understand the salt-resistance molecular mechanism of Aegiceras corniculatum(L.) Blanco. In this study, the transcriptome of A. corniculatum leaf have been sequenced by Illumina HiSeq 2000. Then all the clean reads were de novo assembled, 73 721 Unigenes were yielded. After assembly, 50338 Unigenes were annotated with 7 databases(NR, NT, GO, COG, KEGG, SwissProt and InterPro). A total of 34991 transcripts were involved in 136 KEGG pathways, the number of Unigenes participated in pathway:anthocyanin biosynthesis and flavonoid biosynthesis were 49 and 176, respectively. These genes may play an important role in stress-responding regulation of A. corniculatum. In addition, 34 509 SSR were detected from Unigenes, in which di-nucleotide repeats most with a frequency of 65.75%. Furthermore, 2 255 transcription factors were predicted and classified into 58 families. The results of this study should be value in A. corniculatum gene function analysis, molecular marker development and genetic diversity research.
引文
Fang L.,Yang Y.C.,Guo W.X.,Li J.F.,Zhong C.R.,Huang Y.L.,Zhou R.C.,and Shi S.H.,2016,De novo assembly of the transcriptome of Aegiceras corniculatum,a mangrove species in the indo-west pacific region,Mar.Genomics,28:49-52
Liu G.,Zhao T.T.,Yang H.H.,Zhang D.Y.,Jiang J.B.,Li J.F.,and Xu X.Y.,2016,Research progress on transcriptomics in tomato,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(10):2802-2807(刘冠,赵婷婷,杨欢欢,张冬野,姜景彬,李景富,许向阳,2016,番茄转录组学研究进展,基因组学与应用生物学,35(10):2802-2807)
Liu L.,Du H.,Tang X.F.,Wu Y.M.,Huang Y.B.,and Tang Y.X.,2008,The roles of MYB transcription factors on plant defense responses and its molecular mechanism,Yichuan(Hereditas),30(10):1265-1271(刘蕾,杜海,唐晓凤,吴燕民,黄玉碧,唐益雄,2008,MYB转录因子在植物抗逆胁迫中的作用及其分子机理,遗传,30(10):1265-1271)
Octavio A.,Exequiel E.,Gustavo D.,Va C.V.,Jason M.,and Enric S.,2008,Mangroves in the gulf of California increase fishery yields,Proc.Natl.Acad.Sci.USA,105(30):10456-10459
Peng Y.L.,and Wang Y.S.,2014,Molecular characterization and expression analysis of elongation factor 1 A from mangrove Aegiceras corniculatum,Shengtai Kexue(Ecological Science),33(4):704-712(彭亚兰,王友绍,2014,红树植物桐花树EF1A基因的克隆与表达分析,生态科学,33(4):704-712)
Rao P.S.,Mishra B.,Gupta,S.R.,and Rathore A.,2010,Reproductive stage tolerance to salinity and alkalinity stresses in rice genotypes,Plant Breeding,127(3):256-261
Rodriguezuribe L.,Higbie S.M.,Stewart J.M.,Wilkins T.A.,Lindemann W.,Senguptagopalan C.,and Zhang J.,2011,Identification of salt responsive genes using comparative microarray analysis in upland cotton(Gossypium hirsutum L.),Plant Science,180(3):461-469
Saudamini D.,and Jeffrey R.,2009,Mangroves protected villages and reduced death toll during Indian super cyclone,Proc.Natl.Acad.Sci.USA,106(18):7357-7360
Song H.,and Wang Y.S.,2011,Analysis and improvement of high-quality RNA extraction in leaves of mangrove plants,Shengtai Kexue(Ecological Science),30(2):201-206(宋晖,王友绍,2011,红树植物叶片总RNA提取方法比较与优化,生态科学,30(2):201-206)
Tang M.,Li K.,Xiang H.Y.,Dong X.,Jin H.X.,Wang Y.,Yang H.J.,and Zheng Z.X.,2014,Research on ecological,physiological and morphological adaptability of two mangrove species to salt stress,Shengtai Kexue(Ecological Science),33(3):513-519(唐密,李昆,向洪勇,董雪,金会鑫,王悦,杨海军,张振兴,2014,盐胁迫对两种红树植物生态、生理及解剖结构的影响,生态科学,33(3):513-519)
Van Oosten M.J.,Sharkhuu A.,Batelli G.,Bressan R.A.,and Maggio A.,2013,The Arabidopsis thaliana mutant air1 implicates SOS3 in the regulation of anthocyanins under salt stress,Plant Mol.Biol.,83(4-5):405-415
Yang J.,Guo W.S.,Ye X.Z.,Xie W.F.,Zhang S.T.,and Huang A.Z.,2015,Comparison on methods for total RNA extraction from E.grandis leaves,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(6):1272-1276(杨婕,郭文硕,叶小真,谢婉凤,张思庭,黄爱珍,2015,巨桉叶片总RNA提取方法比较,基因组学与应用生物学,34(6):1272-1276)
Yuan C.C.,Mo J.X.,Yuan L.J.,Yu R.F.,Liu Q.,Zhong J.D.,and Liu K.D.,2017,Digital gene expression profiling analysis of Avicennia marina under heavy metal stress treatment,Linye Kexue Yanjiu(Forest Research),30(2):206-213(袁长春,莫健新,袁柳娇,余如凤,刘倩,钟军弟,刘锴栋,2017,重金属胁迫下白骨壤数字基因表达谱分析,林业科学研究,30(2):206-213)
Yuan L.J.,Fu M.N.,Yu R.F.,Li H.L.,Yuan C.C.,Chen Y.,and Liu K.D.,2017,Digital gene expression profiling analysis of Kandelia candel under heavy metal stress treatment,Dongbei Linye Daxue Xuebao(Journal of Northeast Forestry U-niversity),45(2):22-28(袁柳娇,傅梦妮,余如凤,黎海利,袁长春,陈燕,刘锴栋,2017,秋茄(Kandelia candel L.)响应重金属胁迫的数字基因表达谱,东北林业大学学报,45(2):22-28)
Zhang L.D.,and Tang K.X.,2010,Development of plant EST-SSR markers and its application,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),29(3):534-541(张利达,唐克轩,2010,植物EST-SSR标记开发及其应用,基因组学与应用生物学,29(3):534-541)
Zhao Y.C.,Liu X.W.,Li Y.,and Zhao D.G.,2016,Transcriptome data assembly and gene function annotation of Zanthoxylum piperitum DC var.inerme Makino,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(7):1805-1819(赵懿琛,刘雪微,李岩,赵德刚,2016,朝仓花椒幼芽转录组测序数据组装及基因功能注释,基因组学与应用生物学,35(7):1805-1819)
Zhu J.K.,2000,Genetic analysis of plant salt tolerance using Arabidopsis,Plant Physiol.,124(3):941-948
Liu G.,Zhao T.T.,Yang H.H.,Zhang D.Y.,Jiang J.B.,Li J.F.,and Xu X.Y.,2016,Research progress on transcriptomics in tomato,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(10):2802-2807(刘冠,赵婷婷,杨欢欢,张冬野,姜景彬,李景富,许向阳,2016,番茄转录组学研究进展,基因组学与应用生物学,35(10):2802-2807)
Liu L.,Du H.,Tang X.F.,Wu Y.M.,Huang Y.B.,and Tang Y.X.,2008,The roles of MYB transcription factors on plant defense responses and its molecular mechanism,Yichuan(Hereditas),30(10):1265-1271(刘蕾,杜海,唐晓凤,吴燕民,黄玉碧,唐益雄,2008,MYB转录因子在植物抗逆胁迫中的作用及其分子机理,遗传,30(10):1265-1271)
Octavio A.,Exequiel E.,Gustavo D.,Va C.V.,Jason M.,and Enric S.,2008,Mangroves in the gulf of California increase fishery yields,Proc.Natl.Acad.Sci.USA,105(30):10456-10459
Peng Y.L.,and Wang Y.S.,2014,Molecular characterization and expression analysis of elongation factor 1 A from mangrove Aegiceras corniculatum,Shengtai Kexue(Ecological Science),33(4):704-712(彭亚兰,王友绍,2014,红树植物桐花树EF1A基因的克隆与表达分析,生态科学,33(4):704-712)
Rao P.S.,Mishra B.,Gupta,S.R.,and Rathore A.,2010,Reproductive stage tolerance to salinity and alkalinity stresses in rice genotypes,Plant Breeding,127(3):256-261
Rodriguezuribe L.,Higbie S.M.,Stewart J.M.,Wilkins T.A.,Lindemann W.,Senguptagopalan C.,and Zhang J.,2011,Identification of salt responsive genes using comparative microarray analysis in upland cotton(Gossypium hirsutum L.),Plant Science,180(3):461-469
Saudamini D.,and Jeffrey R.,2009,Mangroves protected villages and reduced death toll during Indian super cyclone,Proc.Natl.Acad.Sci.USA,106(18):7357-7360
Song H.,and Wang Y.S.,2011,Analysis and improvement of high-quality RNA extraction in leaves of mangrove plants,Shengtai Kexue(Ecological Science),30(2):201-206(宋晖,王友绍,2011,红树植物叶片总RNA提取方法比较与优化,生态科学,30(2):201-206)
Tang M.,Li K.,Xiang H.Y.,Dong X.,Jin H.X.,Wang Y.,Yang H.J.,and Zheng Z.X.,2014,Research on ecological,physiological and morphological adaptability of two mangrove species to salt stress,Shengtai Kexue(Ecological Science),33(3):513-519(唐密,李昆,向洪勇,董雪,金会鑫,王悦,杨海军,张振兴,2014,盐胁迫对两种红树植物生态、生理及解剖结构的影响,生态科学,33(3):513-519)
Van Oosten M.J.,Sharkhuu A.,Batelli G.,Bressan R.A.,and Maggio A.,2013,The Arabidopsis thaliana mutant air1 implicates SOS3 in the regulation of anthocyanins under salt stress,Plant Mol.Biol.,83(4-5):405-415
Yang J.,Guo W.S.,Ye X.Z.,Xie W.F.,Zhang S.T.,and Huang A.Z.,2015,Comparison on methods for total RNA extraction from E.grandis leaves,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(6):1272-1276(杨婕,郭文硕,叶小真,谢婉凤,张思庭,黄爱珍,2015,巨桉叶片总RNA提取方法比较,基因组学与应用生物学,34(6):1272-1276)
Yuan C.C.,Mo J.X.,Yuan L.J.,Yu R.F.,Liu Q.,Zhong J.D.,and Liu K.D.,2017,Digital gene expression profiling analysis of Avicennia marina under heavy metal stress treatment,Linye Kexue Yanjiu(Forest Research),30(2):206-213(袁长春,莫健新,袁柳娇,余如凤,刘倩,钟军弟,刘锴栋,2017,重金属胁迫下白骨壤数字基因表达谱分析,林业科学研究,30(2):206-213)
Yuan L.J.,Fu M.N.,Yu R.F.,Li H.L.,Yuan C.C.,Chen Y.,and Liu K.D.,2017,Digital gene expression profiling analysis of Kandelia candel under heavy metal stress treatment,Dongbei Linye Daxue Xuebao(Journal of Northeast Forestry U-niversity),45(2):22-28(袁柳娇,傅梦妮,余如凤,黎海利,袁长春,陈燕,刘锴栋,2017,秋茄(Kandelia candel L.)响应重金属胁迫的数字基因表达谱,东北林业大学学报,45(2):22-28)
Zhang L.D.,and Tang K.X.,2010,Development of plant EST-SSR markers and its application,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),29(3):534-541(张利达,唐克轩,2010,植物EST-SSR标记开发及其应用,基因组学与应用生物学,29(3):534-541)
Zhao Y.C.,Liu X.W.,Li Y.,and Zhao D.G.,2016,Transcriptome data assembly and gene function annotation of Zanthoxylum piperitum DC var.inerme Makino,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(7):1805-1819(赵懿琛,刘雪微,李岩,赵德刚,2016,朝仓花椒幼芽转录组测序数据组装及基因功能注释,基因组学与应用生物学,35(7):1805-1819)
Zhu J.K.,2000,Genetic analysis of plant salt tolerance using Arabidopsis,Plant Physiol.,124(3):941-948