黄肉猕猴桃中果皮和内果皮不同时期比较转录组分析
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摘要
类胡萝卜素是果实中的重要色素之一。本研究中,我们对黄肉猕猴桃(‘金实1号’)中果皮与内果皮4个不同发育时期(开花后0 d, 44 d, 81 d, 189 d,分别标注为T1时期, T2时期, T3时期, T4时期)类胡萝卜素含量测定结果表明,类胡萝卜素含量在T1时期最高,而后随着果实的发育逐步降低,在果实成熟期(T4时期)又有一定程度升高。转录组分析显示在|log2 Ratio|≥1和FDR<0.05阈值下,中果皮和内果皮在T2、T3、T4时期检测到的差异基因数目分别为5 665个、6 288个、9 293个和5 010个、5 524个、9 190个。Gene Ontology (GO)分析表明,这些差异表达基因被富集到50个GO类别,其中属于"生物学过程"的有22个类别,属于"细胞组分"的有16个类别,属于"分子功能"的有12个类别。此外我们还鉴定到14个类胡萝卜素生物合成相关基因差异表达,其中3个基因随果实发育上调表达,11个基因随果实发育下调表达,这一结果与类胡萝卜素含量变化模式相吻合。本研究有助于认识果实中类胡萝卜素调控机制,并且对今后彩色猕猴桃选育种工作有一定的指导意义。
Carotenoid is one of important pigments in fruit. In the present research, carotenoid content determination of four stages(0 day, 44 days, 81 days and 189 days after flowering, termed as T1 stage, T2 stage, T3 stage, T4 stage) of yellow-fleshed kiwifruit('Jinshi 1') sarcocarp and endocarp suggested that carotenoid content was highest in T1 stage, then gradually decreased with fruit development and partly increased at fruit maturation(T4 stage).Under the limited role(|log2 Ratio|≥1 and FDR<0.05), 5 665, 6 288, 9 293 and 5 010, 5 524, 9 190 differentially expressed genes were detected in T2, T3, T4 stages of sarcocarp and endocarp. Gene Ontology(GO) analysis showed 50 GO terms were significantly enriched. Of which, 22 terms belonged to "Biological Process", 16 terms belonged to "Cell Part", 12 terms belonged to "Molecular Function". Moreover, 14 differentially expressed genes related to carotenoid biosynthesis were further detected. With fruit development, three of them were up-regulated while the rest 11 were down-regulated, which was consistent with the change of carotenoid content. The research present here not only deepens the mechanism of fruit color formation, but also contributes to the color kiwifruit molecular breeding in future.
Carotenoid is one of important pigments in fruit. In the present research, carotenoid content determination of four stages(0 day, 44 days, 81 days and 189 days after flowering, termed as T1 stage, T2 stage, T3 stage, T4 stage) of yellow-fleshed kiwifruit('Jinshi 1') sarcocarp and endocarp suggested that carotenoid content was highest in T1 stage, then gradually decreased with fruit development and partly increased at fruit maturation(T4 stage).Under the limited role(|log2 Ratio|≥1 and FDR<0.05), 5 665, 6 288, 9 293 and 5 010, 5 524, 9 190 differentially expressed genes were detected in T2, T3, T4 stages of sarcocarp and endocarp. Gene Ontology(GO) analysis showed 50 GO terms were significantly enriched. Of which, 22 terms belonged to "Biological Process", 16 terms belonged to "Cell Part", 12 terms belonged to "Molecular Function". Moreover, 14 differentially expressed genes related to carotenoid biosynthesis were further detected. With fruit development, three of them were up-regulated while the rest 11 were down-regulated, which was consistent with the change of carotenoid content. The research present here not only deepens the mechanism of fruit color formation, but also contributes to the color kiwifruit molecular breeding in future.
引文
Ahrazem O.,Gómez-Gómez L.,Rodrigo M.J.,Avalos J.,and Limón M.C.,2016,Carotenoid cleavage oxygenases from microbes and photosynthetic organisms:features and functions,Int.J.Mol.Sci.,17(11):1781
Botella-Pavía P.,Besumbes O.,Phillips M.A.,Carretero-Paulet L.,Boronat A.,and Rodr1guez-Concepcion M.,2010,Regulation of carotenoid biosynthesis in plants:evidence for a key role of hydroxymethylbutenyl diphosphate reductase in controlling the supply of plastidial isoprenoid precursors,P-lant J.,40(2):188-199
Cao H.,Wang J.,Dong X.,Han Y.,Ma Q.,Ding Y.,Zhao F.,Zhang J.,Chen H.,Xu Q.,Xu J.,and Deng X.,2015,Caotenoid accumulation affects redox status,starch metabolism,and flavonoid/anthocyanin accumulation in citrus,BMCPlant Biol.,15(1):27
Chen D.,Song H.Y.,Gong R.G.,Li J.,Tu M.Y.,Jiang G.L.,Sun S.X.,and Tang H.R.,2017,Comparative transcriptome analysis of different stages of fruit ripening between redand white-flesh loquat,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(6):2112-2118(陈栋,宋海岩,龚荣高,李靖,涂美艳,江国良,孙淑霞,汤浩茹,2017,红肉枇杷和白肉枇杷果实成熟不同阶段的比较转录组研究,分子植物育种,15(6):2112-2118)
Gao J.,Huang C.H.,Ge C.L.,Qu X.Y.,Gu Q.Q.,and Xu X.B.,2013a,Analysis of differential gene expression during colorturning stages in yellow flesh kiwifruit(Actinidia chinensis)using DGE,Guoshu Xuebao(Journal of Fruit Science),30(3):361-368(高洁,黄春辉,葛翠莲,曲雪艳,辜青青,徐小彪,2013a,利用DGE对黄肉猕猴桃果实着色过程中相关差异基因表达的解析,果树学报,30(3):361-368)
Gao J.,Huang C.H.,Qu X.Y.,Gu Q.Q.,and Xu X.B.,2013b,Study on extracting conditions of carotenoid in kiwifruit by microwave,Beifang Yuanyi(Northern Horticulture),(1):11-14(高洁,黄春辉,曲雪艳,辜青青,徐小彪,2013b,微波法提取猕猴桃果实中类胡萝卜素的工艺研究,北方园艺,(1):11-14)
Huang C.H.,Gao J.,Zhang X.H.,Chen C.J.,Qu X.Y.,and Xu X.B.,2014,Study on the changes of contents of pigments of yellow-fleshed kiwifruit,Guoshu Xuebao(Journal of Fruit Science),31(4):617-623(黄春辉,高洁,张晓慧,陈楚佳,曲雪艳,徐小彪,2014,黄肉猕猴桃果实发育期间色素变化及呈色分析,果树学报,31(4):617-623)
Huang S.,Ding J.,Deng D.,Tang W.,Sun H.,Liu D.,Zhang L.,Niu X.,Zhang X.,Meng M.,Yu J.,Liu J.,Han Y.,Shi W.,Zhang D.,Cao S.,Wei Z.,Cui Y.,Xia Y.,Zeng H.,Bao K.,Lin L.,Min Y.,Zhang H.,Miao M.,Tang X.,Zhu Y.,Sui Y.,Li G.,Sun H.,Yue J.,Sun J.,Liu F.,Zhou L.,Lei L.,Zheng X.,Liu M.,Huang L.,Song J.,Xu C.,Li J.,Ye K.,Zhong S.,Lu R.,He G.,Xiao F.,Wang H.,Zheng H.,Fei Z.,and Liu Y.,2013,Draft genome of the kiwifruit Actinidia chinensis,Nat.Commun.,4:2640
Ibdah M.,Azulay Y.,Portnoy V.,Wasserman B.,Bar E.,Meir A.,Burger Y.,Hirschberg J.,Schaffer A.A.,Katzir N.,Tadmor Y.,and Lewinsohn E.,2006,Functional characterization of CmCCD1,a carotenoid cleavage dioxygenase from melon,Phytochemistry,67(15):1579-89
Jiang Y.,Song H.Y.,He J.R.,Wang Q.,and Liu J.,2018,Comparative transcriptome analysis provides global insight into gene expression differences between two orchid cultivars,PLoS One,13(7):e0200155
覵abaj P.P.,and Kreil D.P.,2016,Sensitivity,specificity,and reproducibility of RNA-Seq differential expression calls,Biology Direct,11(1):66
Lange B.M.,Rujan T.,Martin W.,and Croteau R.,2000,Isoprenoid biosynthesis:the evolution of two ancient and distinct pathways across genomes,Proc.Natl.Acad.Sci.USA,97(24):13172-13177
Nisar N.,Li L.,Lu S.,Khin N.C.,and Pogson B.J.,2015,Carotenoid metabolism in plants,Mol.Plant,8:68-82
Norris S.R.,Shen X.,and DellaPenna D.,1998,Complementation of the arabidopsis pds1 mutation with the gene encoding p-Hydroxyphenylpyruvate dioxygenase,Plant Physiol.,117(4):1317-1323
Qian Y.Q.,Wang D.F.,and Fu A.G.,2016,Molecular features and physiological roles of plant plastid terminal oxidase,Zhiwu Shengli Xuebao(Plant Physiology Journal),52(11):1710-1720(钱昱琪,王丹凤,付爱根,2016,植物质体末端氧化酶的分子特性与生理学功能,植物生理学报,52(11):1710-1720)
Walter M.H.,and Strack D.,2011,Carotenoids and their cleavage products:biosynthesis and functions,Nat.Prod.Rep.,28(3):663
Wang Y.S.,Wen G.Q.,and Nie F.,2016,Analysis of the young leaf transcriptome of highbush blueberry variety"Ruilan",Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(8):2145-2154(王云生,文光琴,聂飞,2016,高丛蓝莓品种“瑞蓝”的幼叶转录组分析,基因组学与应用生物学,35(8):2145-2154)
Wu D.,David A.,Wright D.A.,Wetze C.,Daniel F.,Voytas D.F.,and Rodermela S.,1999,The IMMUTANS variegation locus of Arabidopsis defines a mitochondrial alternative oxidase homolog that functions during early chloroplast biogenesis,Plant Cell,11(1):43-55
Xie Y.,Xia H.,Liang D.,Wang Y.Z.,Liu J.,Zhuang Q.G.,and Li M.Z.,2018,Genetic diversity analysis of 25 Actinidia materials and the establishment of DNA fingerprint,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(15):5001-5007(谢玥,夏惠,梁东,王永志,刘娟,庄启国,李明章,2018,25个猕猴桃材料遗传多样性分析及DNA指纹图谱的建立,分子植物育种,16(15):5001-5007)
Zhang M.,Wang H.X.,Lou X.,Zhao L.N.,and Yan D.L.,2017,The development status and breeding trend of hardy kiwifruit cultivars in the world,Shengtaixue Zazhi(Chinese Journal of Ecology),36(11):3289-3297(张敏,王贺新,娄鑫,赵丽娜,闫东玲,2017,世界软枣猕猴桃品种资源特点及育种趋势,生态学杂志,36(11):3289-3297)
Zhang X.H.,Huang C.H.,Zhong M.,Chen C.J.,Lang B.B.,Qu X.Y.,and Xu X.B.,2015,Analysis of expression of the related genes with carotenoids synthesis in yellow flesh ki wifruit(Actinidia chinensis)based on RNA-seq,Guoshu X-uebao(Journal of Fruit Science),32(3):404-412(张晓慧,黄春辉,钟敏,陈楚佳,郎彬彬,曲雪艳,徐小彪,2015,基于RNA-seq的黄肉猕猴桃类胡萝卜素合成相关基因的表达分析,果树学报,32(3):404-412)
Botella-Pavía P.,Besumbes O.,Phillips M.A.,Carretero-Paulet L.,Boronat A.,and Rodr1guez-Concepcion M.,2010,Regulation of carotenoid biosynthesis in plants:evidence for a key role of hydroxymethylbutenyl diphosphate reductase in controlling the supply of plastidial isoprenoid precursors,P-lant J.,40(2):188-199
Cao H.,Wang J.,Dong X.,Han Y.,Ma Q.,Ding Y.,Zhao F.,Zhang J.,Chen H.,Xu Q.,Xu J.,and Deng X.,2015,Caotenoid accumulation affects redox status,starch metabolism,and flavonoid/anthocyanin accumulation in citrus,BMCPlant Biol.,15(1):27
Chen D.,Song H.Y.,Gong R.G.,Li J.,Tu M.Y.,Jiang G.L.,Sun S.X.,and Tang H.R.,2017,Comparative transcriptome analysis of different stages of fruit ripening between redand white-flesh loquat,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(6):2112-2118(陈栋,宋海岩,龚荣高,李靖,涂美艳,江国良,孙淑霞,汤浩茹,2017,红肉枇杷和白肉枇杷果实成熟不同阶段的比较转录组研究,分子植物育种,15(6):2112-2118)
Gao J.,Huang C.H.,Ge C.L.,Qu X.Y.,Gu Q.Q.,and Xu X.B.,2013a,Analysis of differential gene expression during colorturning stages in yellow flesh kiwifruit(Actinidia chinensis)using DGE,Guoshu Xuebao(Journal of Fruit Science),30(3):361-368(高洁,黄春辉,葛翠莲,曲雪艳,辜青青,徐小彪,2013a,利用DGE对黄肉猕猴桃果实着色过程中相关差异基因表达的解析,果树学报,30(3):361-368)
Gao J.,Huang C.H.,Qu X.Y.,Gu Q.Q.,and Xu X.B.,2013b,Study on extracting conditions of carotenoid in kiwifruit by microwave,Beifang Yuanyi(Northern Horticulture),(1):11-14(高洁,黄春辉,曲雪艳,辜青青,徐小彪,2013b,微波法提取猕猴桃果实中类胡萝卜素的工艺研究,北方园艺,(1):11-14)
Huang C.H.,Gao J.,Zhang X.H.,Chen C.J.,Qu X.Y.,and Xu X.B.,2014,Study on the changes of contents of pigments of yellow-fleshed kiwifruit,Guoshu Xuebao(Journal of Fruit Science),31(4):617-623(黄春辉,高洁,张晓慧,陈楚佳,曲雪艳,徐小彪,2014,黄肉猕猴桃果实发育期间色素变化及呈色分析,果树学报,31(4):617-623)
Huang S.,Ding J.,Deng D.,Tang W.,Sun H.,Liu D.,Zhang L.,Niu X.,Zhang X.,Meng M.,Yu J.,Liu J.,Han Y.,Shi W.,Zhang D.,Cao S.,Wei Z.,Cui Y.,Xia Y.,Zeng H.,Bao K.,Lin L.,Min Y.,Zhang H.,Miao M.,Tang X.,Zhu Y.,Sui Y.,Li G.,Sun H.,Yue J.,Sun J.,Liu F.,Zhou L.,Lei L.,Zheng X.,Liu M.,Huang L.,Song J.,Xu C.,Li J.,Ye K.,Zhong S.,Lu R.,He G.,Xiao F.,Wang H.,Zheng H.,Fei Z.,and Liu Y.,2013,Draft genome of the kiwifruit Actinidia chinensis,Nat.Commun.,4:2640
Ibdah M.,Azulay Y.,Portnoy V.,Wasserman B.,Bar E.,Meir A.,Burger Y.,Hirschberg J.,Schaffer A.A.,Katzir N.,Tadmor Y.,and Lewinsohn E.,2006,Functional characterization of CmCCD1,a carotenoid cleavage dioxygenase from melon,Phytochemistry,67(15):1579-89
Jiang Y.,Song H.Y.,He J.R.,Wang Q.,and Liu J.,2018,Comparative transcriptome analysis provides global insight into gene expression differences between two orchid cultivars,PLoS One,13(7):e0200155
覵abaj P.P.,and Kreil D.P.,2016,Sensitivity,specificity,and reproducibility of RNA-Seq differential expression calls,Biology Direct,11(1):66
Lange B.M.,Rujan T.,Martin W.,and Croteau R.,2000,Isoprenoid biosynthesis:the evolution of two ancient and distinct pathways across genomes,Proc.Natl.Acad.Sci.USA,97(24):13172-13177
Nisar N.,Li L.,Lu S.,Khin N.C.,and Pogson B.J.,2015,Carotenoid metabolism in plants,Mol.Plant,8:68-82
Norris S.R.,Shen X.,and DellaPenna D.,1998,Complementation of the arabidopsis pds1 mutation with the gene encoding p-Hydroxyphenylpyruvate dioxygenase,Plant Physiol.,117(4):1317-1323
Qian Y.Q.,Wang D.F.,and Fu A.G.,2016,Molecular features and physiological roles of plant plastid terminal oxidase,Zhiwu Shengli Xuebao(Plant Physiology Journal),52(11):1710-1720(钱昱琪,王丹凤,付爱根,2016,植物质体末端氧化酶的分子特性与生理学功能,植物生理学报,52(11):1710-1720)
Walter M.H.,and Strack D.,2011,Carotenoids and their cleavage products:biosynthesis and functions,Nat.Prod.Rep.,28(3):663
Wang Y.S.,Wen G.Q.,and Nie F.,2016,Analysis of the young leaf transcriptome of highbush blueberry variety"Ruilan",Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(8):2145-2154(王云生,文光琴,聂飞,2016,高丛蓝莓品种“瑞蓝”的幼叶转录组分析,基因组学与应用生物学,35(8):2145-2154)
Wu D.,David A.,Wright D.A.,Wetze C.,Daniel F.,Voytas D.F.,and Rodermela S.,1999,The IMMUTANS variegation locus of Arabidopsis defines a mitochondrial alternative oxidase homolog that functions during early chloroplast biogenesis,Plant Cell,11(1):43-55
Xie Y.,Xia H.,Liang D.,Wang Y.Z.,Liu J.,Zhuang Q.G.,and Li M.Z.,2018,Genetic diversity analysis of 25 Actinidia materials and the establishment of DNA fingerprint,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(15):5001-5007(谢玥,夏惠,梁东,王永志,刘娟,庄启国,李明章,2018,25个猕猴桃材料遗传多样性分析及DNA指纹图谱的建立,分子植物育种,16(15):5001-5007)
Zhang M.,Wang H.X.,Lou X.,Zhao L.N.,and Yan D.L.,2017,The development status and breeding trend of hardy kiwifruit cultivars in the world,Shengtaixue Zazhi(Chinese Journal of Ecology),36(11):3289-3297(张敏,王贺新,娄鑫,赵丽娜,闫东玲,2017,世界软枣猕猴桃品种资源特点及育种趋势,生态学杂志,36(11):3289-3297)
Zhang X.H.,Huang C.H.,Zhong M.,Chen C.J.,Lang B.B.,Qu X.Y.,and Xu X.B.,2015,Analysis of expression of the related genes with carotenoids synthesis in yellow flesh ki wifruit(Actinidia chinensis)based on RNA-seq,Guoshu X-uebao(Journal of Fruit Science),32(3):404-412(张晓慧,黄春辉,钟敏,陈楚佳,郎彬彬,曲雪艳,徐小彪,2015,基于RNA-seq的黄肉猕猴桃类胡萝卜素合成相关基因的表达分析,果树学报,32(3):404-412)
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