牡丹(Paeonia suffruticosa Andr.)根组织差异表达基因分析
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摘要
本研究通过冰山雪莲(Paeonia rockii'Bing Shan Xue Lian')和牡丹主栽品种凤丹(Paeonia ostii'Phoenix White')根组织转录组测序进行差异表达基因分析,结果显示,冰山雪莲和凤丹基因表达量相近,差异表达基因487条,其中228条上调,259条下调;冰山雪莲特有表达基因数113 558,凤丹58 114,共有表达基因数55491;两品种4 228条低表达量基因聚集成2个子集,6 259条高表达量基因聚集成2个子集;GO富集注释差异基因1 487条,其中上调基因数1 137,下调基因数1 200,上调差异基因的主要功能与氧化还原和营养库活性有关;差异基因KEGG显著富集的代谢通路73条,富集前20的代谢通路中参与核糖体通路的基因最多,富集因子最高的代谢通路为硫胺素代谢、其次为C5-分支二元酸代谢和二萜类生物合成,参与植物病原体互作、谷胱甘肽代谢和RNA降解的上调差异基因数目相对较多,其次为异喹啉、托烷、哌啶、吡啶生物碱和萜类骨架合成、苯丙氨酸、酪氨酸、甘氨酸、丝氨酸和苏氨酸、肌醇磷酸和戊糖磷酸代谢、DNA复制和核苷酸剪切修复。通过转录组测序全面分析了冰山雪莲和凤丹根组织差异基因表达状况,为牡丹功能基因的研究提供了理论依据。
Through root tissue transcriptome sequencing of Paeonia rockii 'Bing Shan Xue Lian'(abbreviated BSXL) and the principal cultivated variety of Paeonia ostii 'Phoenix White'(abbreviated FD), this study analyzed the differentially expressed genes(DEG), and the results indicated as followings: the gene expression content of the two varieties were close, there were 487 differentially expressed genes, among them 228 were up-regulated and259 down-regulated, the number of BSXL specific expressed genes was 113 558, and the number of FD specific expressed genes was 58 114, and the number of common expressed genes between them was 55 491; 4 228 lower expression genes of the two peony cultivars clustered into 2 subsets, 6 259 higher expression genes clustered into 2 subsets; the differentially gene expression of GO enrichment and annotation was 1 487, of which the number of up-regulated genes was 1 137, and down-regulated genes was 1 200, the function of up-re gulated genes were mainly concerned with oxidation-reduction and nutrient reservoir activities. The DEG annotated in KEGG pathway enrichment terms were 73, in the KEGG pathway enriched top 20 the number of unigenes partic ipating in ribosome pathway was the most, in the KEGG pathway with the highest rich factor was thiamine metabolism, the next was C5-branched dibasic acid metabolism and diterpenoid biosynthesis, the number of up-regulated DEG participating in plant-pathogen interaction, glutathione metabolism and RNA degradation was relatively higher,and the next was isoquinoline alkaloid, tropane, piperidine and pyridine alkaloid biosynthesis, terpenoid backbone biosynthesis, phenylalanine, tyrosine, glycine, serine and threonine, and inositol phosphate metabolism and pentose phosphate pathway, DNA replication and nucleotide excision repair. This study comprehensive analyzed the DEG of BSXL and FD by transcriptome sequencing, it might provide the theoretical basis on the research of function gene in Paeonia suffruticosa.
Through root tissue transcriptome sequencing of Paeonia rockii 'Bing Shan Xue Lian'(abbreviated BSXL) and the principal cultivated variety of Paeonia ostii 'Phoenix White'(abbreviated FD), this study analyzed the differentially expressed genes(DEG), and the results indicated as followings: the gene expression content of the two varieties were close, there were 487 differentially expressed genes, among them 228 were up-regulated and259 down-regulated, the number of BSXL specific expressed genes was 113 558, and the number of FD specific expressed genes was 58 114, and the number of common expressed genes between them was 55 491; 4 228 lower expression genes of the two peony cultivars clustered into 2 subsets, 6 259 higher expression genes clustered into 2 subsets; the differentially gene expression of GO enrichment and annotation was 1 487, of which the number of up-regulated genes was 1 137, and down-regulated genes was 1 200, the function of up-re gulated genes were mainly concerned with oxidation-reduction and nutrient reservoir activities. The DEG annotated in KEGG pathway enrichment terms were 73, in the KEGG pathway enriched top 20 the number of unigenes partic ipating in ribosome pathway was the most, in the KEGG pathway with the highest rich factor was thiamine metabolism, the next was C5-branched dibasic acid metabolism and diterpenoid biosynthesis, the number of up-regulated DEG participating in plant-pathogen interaction, glutathione metabolism and RNA degradation was relatively higher,and the next was isoquinoline alkaloid, tropane, piperidine and pyridine alkaloid biosynthesis, terpenoid backbone biosynthesis, phenylalanine, tyrosine, glycine, serine and threonine, and inositol phosphate metabolism and pentose phosphate pathway, DNA replication and nucleotide excision repair. This study comprehensive analyzed the DEG of BSXL and FD by transcriptome sequencing, it might provide the theoretical basis on the research of function gene in Paeonia suffruticosa.
引文
Anders S.,and Huber W.,2010,Differential expression analysis for sequence count data,Genome Biology,11(10):R106
Cui H.L.,Huang N.Z.,Yan H.C.,and Liu J.X.,2017,Correlation between yield per plant and main phenotypic traits of Paeonia suffruticosa for oil production,Huanan Nongye Daxue Xuebao(Journal of South China Agricultural University),38(2):86-91(崔虎亮,黄弄璋,闫海川,刘建鑫,2017,油用牡丹单株产量和主要表型性状的相关性,华南农业大学学报,38(2):86-91)
Datta S.,and Datta S.,2006,Evaluation of clustering algorithms for gene expression data,BMC Bioinformatics,7(S4):S17
Davidson N.M.,and Oshlack A.,2014,Corset:enabling differential gene expression analysis for de novo assembled transcriptomes,Genome Biology,15(7):410-416
Grabher M.G.,Haas B.J.,Yassour M.,Levin J.Z.,Thompson D.A.,Amit I.,Adiconis X.,Fan L.,Raychowdhury R.,Zeng Q.D.,Chen Z.H.,Mauceli E.,Hacohen N.,Gnirke A.,Rhind N.,Palma F.D.,Birren B.W.,Nusbaum C.,Lindblad-Toh K.,Friedman N.,and Regev A.,2011,Full-lengthtranscriptome assembly from RNA-Seq data without a reference genome,Nat.Biotech.,29(7):644-652
Han J.G.,Li X.Q.,Liu Z.,and Hu Y.H.,2014,Potential applications of tree peony as an oil plant,Liangshi Yu Youzhi(Cereals and Oils),27(5):21-25(韩继刚,李晓青,刘炤,胡永红,2014,牡丹油用价值及其应用前景,粮食与油脂,27(5):21-25)
Han X.Y.,Zhang Y.L.,Niu L.X.,and Luo J.R.,2014a,Fatty acid composition of'Fengdan'peony seed oils from different growing regions,Shipin Kexue(Food Science),35(22):181-184(韩雪源,张延龙,牛立新,罗建让,2014a,不同产地‘凤丹’牡丹籽油主要脂肪酸成分分析,食品科学,35(22):181-184)
Han X.Y.,Zhang Y.L.,and Niu L.X.,2014b,Morphological traits based taxonomy of 39 tree peony cultivars,Xibei Nonglin Keji Daxue(Journal of Northwest A&F University),42(9):128-136(韩雪源,张延龙,牛立新,2014b,39个牡丹品种的形态学分类研究,西北农林科技大学学报,42(9):128-136)
Hao D.C.,Ma P.,Mu J.,Chen S.L.,Xiao P.G.,Peng Y.,Huo L.,Xu L.J.,and Sun C.,2012,De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum,Zhongguo Kexue(Scientia Sinica(Vitae)),42(5):398-412,431-433(郝大程,马培,穆军,陈士林,肖培根,彭勇,霍利,徐利嘉,孙超,2012,中药植物虎杖根的高通量转录组测序及转录组特征分析,中国科学:生命科学,42(5):398-412,431-433)
Hong D.Y.,and Pan K.Y.,1999,Taxonomical history and revision of Paeonia sect.Moutan(Paeoniaceae),Zhiwu Fenlei Xuebao(Acta Phytotaxonomica Sinica),37(4):351-368(洪德元,潘开玉,1999,芍药属牡丹组的分类历史和分类处理,植物分类学报,37(4):351-368)
Huang Q.L.,He R.,and Zhan R.T.,2017,Analysis on differential expressed genes from Nervilia fordii based on transcriptome Sequencing,Zhongyao Xinyao Yu Linchuang Yaoli(Traditional Chinese Drug Research and Clinical Pharmacology),28(5):687-691(黄琼林,何瑞,詹若挺,2017,基于转录组测序的青天葵差异表达基因分析,中药新药与临床药理,28(5):687-691)
Kanehisa M.,Araki M.,Goto S.,Hattori M.,Hirakawa M.,Itoh M.,Katayama T.,Kawashima S.,Okuda S.,Tokimatsu T.,and Yamanishi Y.,2008,KEGG for linking genomes to life and the environment,Nucleic Acids Res.,36(1):D480-484
Kanehisa M.,Sato Y.,Kawashima M.,Furumichi M.,and Tanabe M.,2016,KEGG as a reference resource for gene and protein annotation,Nucleic Acids Res.,44(1):457-462
Li C.F.,Zhu Y.J.,Guo X.,Sun C.,Luo H.M.,Song J.Y.,Li Y.,Wang L.Z.,Qian J.,and Chen S.L.,2013,Tanscriptome analysis reveals ginsenosides biosynthetic genes,microRNSs and simple repeats in Panax gensen CA Meyer,BMC Genomics,14:245
Li Y.,Sun C.,Luo H.M.,Li X.W.,Niu Y.Y.,and Chen S.L.,2010,Transcriptome characterization for Salvia miltiorrhiza using 454 GS FLX,Yaoxue Xuebao(Acta Pharmaceutica),45(4):524-529(李滢,孙超,罗红梅,李西文,牛云云,陈士林,2010,基于高通量测序454GS FLX的丹参转录组学研究,药学学报,45(4):524-529)
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)
Mao S.Q.,and Li X.J.,2017,Progress in peony seed oil and comprehensive utilization value of oil peony,Zhongguo Youzhi(China Oils and Fats),42(5):123-126(毛善巧,李西俊,2017,牡丹籽油的研究进展及油用牡丹综合利用价值分析,中国油脂,42(5):123-126)
Mao X.Z.,Cai T.,Olyarchuk J.G.,and Wei L.P.,2005,Automated genome annotation and pathway identification using the KEGG Orthology(KO)as a controlled vocabulary,Bioinformatics,21(19):3787-3793
Peng H.S.,Wang D.Q.,Peng D.Y.,and Huang L.Q.,2017,Research and investigation on original plants of medicinal Moutan,Zhongguo Zhongyao Zazhi(China Journal of Chinese Materia Medica),42(9):1632-1636(彭华胜,王德群,彭代银,黄璐琦,2017,药用牡丹基原的考证和调查,中国中药杂志,42(9):1632-1636)
Song J.,Guo H.Y.,Li Z.D.,You P.S.,Long Y.H.,and Xing C.B.,2016,Analysis of transicriptomes and differentially expressed genes in Eleutherococcus senticosus,Zhongcaoyao(Chinese Traditional and Herbal Drugs),47(22):4049-4053(宋菊,国红玉,李志栋,尤鹏升,龙月红,邢朝斌,2016,刺五加转录组和差异性表达分析,中草药,47(22):4049-4053)
Trapnell C.,Williams B.A.,Pertea G.,Mortazavi A.,Kwan G.,van Baren M.J.,Salzberg S.L.,Wold B.J.,and Pachter L.,2010,Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms,Nat.Biotechnol.,28(5):511-515
Wu J.,Chen F.Y.,and Zhong Y.,2016,The numerical classification of flower color phenotype in flare tree peony,Yuanyi Xuebao(Acta Horticulturae Sinica),43(5):947-956(吴静,成仿云,钟原,2016,紫斑牡丹花色表型数量分类研究,园艺学报,43(5):947-956)
Xie D.M.,Yu N.J.,Huang L.Q.,Peng D.Y.,Liu C.B.,Zhu Y.J.,and Huang H.,2017,Next generation sequencing and transcriptome analysis of root bark from Paeonia suffruticosa cv.Feng Dan,Zhongguo Zhongyao Zazhi(China Journal of Chinese Materia Medica),42(15):2954-2961(谢冬梅,俞年军,黄璐琦,彭代银,刘丛彬,朱月健,黄浩,2017,基于高通量测序的药用植物“凤丹”根皮的转录组分析,中国中药杂志,42(15):2954-2961)
Xiu Y.,Wu G.D.,Chen D.Z.,Zhao X.Q.,Tang W.S.,and Wang H.F.,2017,Propagation and afforestation techniques of tree peonies for greening and seed oil production,Beijing Linye Daxue Xuebao(Journal of Beijing Forestry University),39(1):112-118(修宇,吴国栋,陈德忠,赵孝庆,唐文思,王华芳,2017,牡丹绿化油用品种繁殖栽培技术,北京林业大学学报,39(1):112-118)
Yin L.,Huang C.H.,and Ni J.,2006,Custering of gene expressions data:performance and similarity analysis,BMC Bioinformatics,S4:S19
Yin L.Q.,Wang X.Q.,Hu Y.H.,Liu Z.,Li X.F.,and Zhang J.J.,2012,Several factors influencing tissue culture of Paeonia suffruticosa,Shanghai Nongye Xuebao(Acta Agriculturae Shanghai),28(1):17-21(殷丽青,王新其,胡永红,刘炤,李秀芬,张建军,2012,牡丹组织培养若干影响因子研究,上海农业学报,28(1):17-21)
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Zhang T.,Gao T.S.,Bai R.Y.,Huang X.L.,Guo N.,Lu J.X.,and Luo A.C.,2015,Utilization and research progress of oil tree peony,Chongqing Shifan Daxue Xuebao(Journal of Chongqing Normal University),32(2):143-149(张涛,高天姝,白瑞英,黄兴琳,郭楠,陆俊杏,罗安才,2015,油用牡丹利用与研究进展,重庆师范大学学报,32(2):143-149)
Zhao Z.Y.,Wang S.Y.,Guo F.G.,Yin D.M.,Zhu X.H.,and Du Y.X.,2017,RNA-sequencing and its application in medicinal plants,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),32(2):820-825(赵振宇,王仕玉,郭凤根,尹冬梅,朱旭海,杜玉霞,2017,转录组测序及其在药用植物上的应用,基因组学与应用生物学,32(2):820-825)
Cui H.L.,Huang N.Z.,Yan H.C.,and Liu J.X.,2017,Correlation between yield per plant and main phenotypic traits of Paeonia suffruticosa for oil production,Huanan Nongye Daxue Xuebao(Journal of South China Agricultural University),38(2):86-91(崔虎亮,黄弄璋,闫海川,刘建鑫,2017,油用牡丹单株产量和主要表型性状的相关性,华南农业大学学报,38(2):86-91)
Datta S.,and Datta S.,2006,Evaluation of clustering algorithms for gene expression data,BMC Bioinformatics,7(S4):S17
Davidson N.M.,and Oshlack A.,2014,Corset:enabling differential gene expression analysis for de novo assembled transcriptomes,Genome Biology,15(7):410-416
Grabher M.G.,Haas B.J.,Yassour M.,Levin J.Z.,Thompson D.A.,Amit I.,Adiconis X.,Fan L.,Raychowdhury R.,Zeng Q.D.,Chen Z.H.,Mauceli E.,Hacohen N.,Gnirke A.,Rhind N.,Palma F.D.,Birren B.W.,Nusbaum C.,Lindblad-Toh K.,Friedman N.,and Regev A.,2011,Full-lengthtranscriptome assembly from RNA-Seq data without a reference genome,Nat.Biotech.,29(7):644-652
Han J.G.,Li X.Q.,Liu Z.,and Hu Y.H.,2014,Potential applications of tree peony as an oil plant,Liangshi Yu Youzhi(Cereals and Oils),27(5):21-25(韩继刚,李晓青,刘炤,胡永红,2014,牡丹油用价值及其应用前景,粮食与油脂,27(5):21-25)
Han X.Y.,Zhang Y.L.,Niu L.X.,and Luo J.R.,2014a,Fatty acid composition of'Fengdan'peony seed oils from different growing regions,Shipin Kexue(Food Science),35(22):181-184(韩雪源,张延龙,牛立新,罗建让,2014a,不同产地‘凤丹’牡丹籽油主要脂肪酸成分分析,食品科学,35(22):181-184)
Han X.Y.,Zhang Y.L.,and Niu L.X.,2014b,Morphological traits based taxonomy of 39 tree peony cultivars,Xibei Nonglin Keji Daxue(Journal of Northwest A&F University),42(9):128-136(韩雪源,张延龙,牛立新,2014b,39个牡丹品种的形态学分类研究,西北农林科技大学学报,42(9):128-136)
Hao D.C.,Ma P.,Mu J.,Chen S.L.,Xiao P.G.,Peng Y.,Huo L.,Xu L.J.,and Sun C.,2012,De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum,Zhongguo Kexue(Scientia Sinica(Vitae)),42(5):398-412,431-433(郝大程,马培,穆军,陈士林,肖培根,彭勇,霍利,徐利嘉,孙超,2012,中药植物虎杖根的高通量转录组测序及转录组特征分析,中国科学:生命科学,42(5):398-412,431-433)
Hong D.Y.,and Pan K.Y.,1999,Taxonomical history and revision of Paeonia sect.Moutan(Paeoniaceae),Zhiwu Fenlei Xuebao(Acta Phytotaxonomica Sinica),37(4):351-368(洪德元,潘开玉,1999,芍药属牡丹组的分类历史和分类处理,植物分类学报,37(4):351-368)
Huang Q.L.,He R.,and Zhan R.T.,2017,Analysis on differential expressed genes from Nervilia fordii based on transcriptome Sequencing,Zhongyao Xinyao Yu Linchuang Yaoli(Traditional Chinese Drug Research and Clinical Pharmacology),28(5):687-691(黄琼林,何瑞,詹若挺,2017,基于转录组测序的青天葵差异表达基因分析,中药新药与临床药理,28(5):687-691)
Kanehisa M.,Araki M.,Goto S.,Hattori M.,Hirakawa M.,Itoh M.,Katayama T.,Kawashima S.,Okuda S.,Tokimatsu T.,and Yamanishi Y.,2008,KEGG for linking genomes to life and the environment,Nucleic Acids Res.,36(1):D480-484
Kanehisa M.,Sato Y.,Kawashima M.,Furumichi M.,and Tanabe M.,2016,KEGG as a reference resource for gene and protein annotation,Nucleic Acids Res.,44(1):457-462
Li C.F.,Zhu Y.J.,Guo X.,Sun C.,Luo H.M.,Song J.Y.,Li Y.,Wang L.Z.,Qian J.,and Chen S.L.,2013,Tanscriptome analysis reveals ginsenosides biosynthetic genes,microRNSs and simple repeats in Panax gensen CA Meyer,BMC Genomics,14:245
Li Y.,Sun C.,Luo H.M.,Li X.W.,Niu Y.Y.,and Chen S.L.,2010,Transcriptome characterization for Salvia miltiorrhiza using 454 GS FLX,Yaoxue Xuebao(Acta Pharmaceutica),45(4):524-529(李滢,孙超,罗红梅,李西文,牛云云,陈士林,2010,基于高通量测序454GS FLX的丹参转录组学研究,药学学报,45(4):524-529)
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)
Mao S.Q.,and Li X.J.,2017,Progress in peony seed oil and comprehensive utilization value of oil peony,Zhongguo Youzhi(China Oils and Fats),42(5):123-126(毛善巧,李西俊,2017,牡丹籽油的研究进展及油用牡丹综合利用价值分析,中国油脂,42(5):123-126)
Mao X.Z.,Cai T.,Olyarchuk J.G.,and Wei L.P.,2005,Automated genome annotation and pathway identification using the KEGG Orthology(KO)as a controlled vocabulary,Bioinformatics,21(19):3787-3793
Peng H.S.,Wang D.Q.,Peng D.Y.,and Huang L.Q.,2017,Research and investigation on original plants of medicinal Moutan,Zhongguo Zhongyao Zazhi(China Journal of Chinese Materia Medica),42(9):1632-1636(彭华胜,王德群,彭代银,黄璐琦,2017,药用牡丹基原的考证和调查,中国中药杂志,42(9):1632-1636)
Song J.,Guo H.Y.,Li Z.D.,You P.S.,Long Y.H.,and Xing C.B.,2016,Analysis of transicriptomes and differentially expressed genes in Eleutherococcus senticosus,Zhongcaoyao(Chinese Traditional and Herbal Drugs),47(22):4049-4053(宋菊,国红玉,李志栋,尤鹏升,龙月红,邢朝斌,2016,刺五加转录组和差异性表达分析,中草药,47(22):4049-4053)
Trapnell C.,Williams B.A.,Pertea G.,Mortazavi A.,Kwan G.,van Baren M.J.,Salzberg S.L.,Wold B.J.,and Pachter L.,2010,Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms,Nat.Biotechnol.,28(5):511-515
Wu J.,Chen F.Y.,and Zhong Y.,2016,The numerical classification of flower color phenotype in flare tree peony,Yuanyi Xuebao(Acta Horticulturae Sinica),43(5):947-956(吴静,成仿云,钟原,2016,紫斑牡丹花色表型数量分类研究,园艺学报,43(5):947-956)
Xie D.M.,Yu N.J.,Huang L.Q.,Peng D.Y.,Liu C.B.,Zhu Y.J.,and Huang H.,2017,Next generation sequencing and transcriptome analysis of root bark from Paeonia suffruticosa cv.Feng Dan,Zhongguo Zhongyao Zazhi(China Journal of Chinese Materia Medica),42(15):2954-2961(谢冬梅,俞年军,黄璐琦,彭代银,刘丛彬,朱月健,黄浩,2017,基于高通量测序的药用植物“凤丹”根皮的转录组分析,中国中药杂志,42(15):2954-2961)
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Yin L.,Huang C.H.,and Ni J.,2006,Custering of gene expressions data:performance and similarity analysis,BMC Bioinformatics,S4:S19
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