滇杨正/倒扦插苗叶片和树皮组织的转录组比较分析
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摘要
该研究以滇杨正、倒扦插苗为对象,于速生期(8月)收集插穗主枝萌发处下侧树皮组织和主枝的叶片组织进行转录组比较分析。结果显示:(1)正、倒扦插滇杨苗于2种组织中的转录调控变化存在差异;测序得到358 587条Unigenes,并于叶片组织和树皮组织中分别筛选得到6 512和12 020条DEGs。(2)KEGG在叶片组织中成功注释了552个DEGs,被分配至122个通路中;显著富集通路主要为植物病原菌互作、氨基糖和核苷酸糖代谢、戊糖和葡糖醛酸互换、半乳糖代谢、氨基酸生物合成、抗坏血酸和新陈代谢,其中39个DEGs编码了USPase,影响叶片正常的细胞壁代谢。(3)树皮组织中,分布于128个通路中的1 623个DEGs被KEGG成功注释,主要的富集通路为碳代谢、核糖体、氨基酸生物合成、苯丙素生物合成。(4)大量DEGs富集到与ROS代谢相关的作用酶中,包括ROS产生机制相关的卡尔文循环相关酶、ROS清除机制相关的氧化还原酶(POD)和半胱氨酸合成酶(如cysK和MET17)等。研究认为,上述关键酶类的基因变化,表明倒插扰乱了树皮组织的ROS浓度平衡,激发了倒插苗的生理保护机制。
Two tissues,the bark located at downside of shoot site of cuttings and leaf located at top of shoot,were sampled to compare the transcriptome profiles between upright and inverted cuttings of P.yunnanensisin vegetative growth stage(August).The results showed:(1)a different transcriptome profiling changing induced by cutting inversion from the two tissues.A total of 358 587 unigenes was obtained by transcriptome sequencing.Then,6 512 DEGs were selected in leaf samples and 12 020 DEGs were selected in bark samples.(2)In total,552 DEGs were identified by KEGG databases in leaf tissue and assigned to 122 metabolic pathways.The main significant enriched pathways were plant-pathogen interaction,amino sugar and nucleotide sugar metabolism,pentose and glucuronate interconversions,galactose metabolism,biosynthesis of amino acids,and ascorbate and aldarate metabolism.The changing USPase encoded by 39 DEGs impacted on cell wall metabolism of leaf tissue.(3)In bark tissue,1 623 DEGs identified by KEGG databases were mapped to 128 pathways,among which carbon metabolism,ribosome,biosynthesis of amino acids,and phenylpropanoid biosynthesis were main enriched pathways.(4)Furthermore,a large number of DEGs were found in ROS metabolic reactions,including enzymes in Calvin cycle related to ROS production system and POD and cysteine synthase(i.e.cysK and MET17)related to ROS removal system have large number of DEGs,indicated a change of ROS concentration balance induced by inversion and a activated defend system in bark tissue of cuttings.
Two tissues,the bark located at downside of shoot site of cuttings and leaf located at top of shoot,were sampled to compare the transcriptome profiles between upright and inverted cuttings of P.yunnanensisin vegetative growth stage(August).The results showed:(1)a different transcriptome profiling changing induced by cutting inversion from the two tissues.A total of 358 587 unigenes was obtained by transcriptome sequencing.Then,6 512 DEGs were selected in leaf samples and 12 020 DEGs were selected in bark samples.(2)In total,552 DEGs were identified by KEGG databases in leaf tissue and assigned to 122 metabolic pathways.The main significant enriched pathways were plant-pathogen interaction,amino sugar and nucleotide sugar metabolism,pentose and glucuronate interconversions,galactose metabolism,biosynthesis of amino acids,and ascorbate and aldarate metabolism.The changing USPase encoded by 39 DEGs impacted on cell wall metabolism of leaf tissue.(3)In bark tissue,1 623 DEGs identified by KEGG databases were mapped to 128 pathways,among which carbon metabolism,ribosome,biosynthesis of amino acids,and phenylpropanoid biosynthesis were main enriched pathways.(4)Furthermore,a large number of DEGs were found in ROS metabolic reactions,including enzymes in Calvin cycle related to ROS production system and POD and cysteine synthase(i.e.cysK and MET17)related to ROS removal system have large number of DEGs,indicated a change of ROS concentration balance induced by inversion and a activated defend system in bark tissue of cuttings.
引文
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[2]李佳蔓,员涛,王军民,等.滇杨倒置插穗的生长素极性运输[J].植物生理学报,2015,51(6):935-940.LI J M,YUN T,WANG J M,et al.The polarity of auxin transport in inverted cuttings of Populus yunnanensis[J].Plant Physiology Communications,2015,51(6):935-940.
[3]NICK P,FURUYA M.Induction and fixation of polarityearly steps in plant morphogenesis[J].Development,Growth and Differentiation,1992,34(2):115-125.
[4]ESHED Y,BAUM S F,PEREA J V,et al.Establishment of polarity in lateral organs of plants[J].Current Biology,2001,11(16):1 251-1 260.
[5]周银丽,胡先奇,张虹,等.影响植物枝条倒插成活的因素初探[J].现代农业科学,2008,(5):3,5.ZHOU Y L,HU X Q,ZHANG H,et al.Studies on the factor which effect plant tress turned down cottage[J].Modern Agricultural Sciences,2008,(5):3,5.
[6]SACHS T.Polarity and the induction of organized vascular tissues[J].Annals of Botany,1969,33(2):263-275.
[7]杜珲,陈晓德,范庭兴.匍匐茎克隆植物可倒插繁殖研究[J].北方园艺,2015,(4):26-30.DU H,CHEN X D,FAN T X.Study on stoloniferous clonal plants that can reverse cuttage[J].Northern Horticulture,2015,(4):26-30.
[8]陈发军,汤小凤,黄作喜.不同基质中正插和倒插对锦屏藤插条重量及幼苗生长的影响[J].北方园艺,2015,(5):67-70.CHEN F J,TANG X F,HUANG Z X.Effect of normal and reverse cuttage on the cutting weight and seedling growth of Cissus sicyoide in different substrate[J].Northern Horticulture,2015,(5):67-70.
[9]何承忠,车鹏燕,周修涛,等.滇杨基因资源及其研究概况[J].西南林学院学报,2010,30(1):83-88,94.HE C Z,CHE P Y,ZHOU X T,et al.A survey of research progress on gene resources of Populus yunnanensis[J].Journal of Southwest Forestry University,2010,30(1):83-88,94.
[10]于雷,何小帆,周安佩,等.滇杨与毛白杨插穗内源激素含量的比较研究[J].云南农业大学学报(自然科学),2018,33(4):715-720.YU L,HE X F,ZHOU A P,et al.Comparative study on the endogenous hormone contents in cuttings of Populus yunnanensis and P.tomentosa[J].Journal of Yunnan Agricultural University(Natural Science),2018,33(4):715-720.
[11]颜璐茜,李佳蔓,员涛,等.滇杨遗传多样性的SRAP分析[J].生物技术通报,2016,32(4):159-167.YAN L X,LI J M,YUN T,et al.Genetic diversity analysis of Populus yunnanensis by SRAP markers[J].Biotechnology Bulletin,2016,32(4):159-167.
[12]李佳蔓.滇杨倒插穗条生根过程中生长素含量变化规律研究[D].昆明:西南林业大学,2016.
[13]颜璐茜.滇杨倒插苗生长特征及内源激素含量与氧化酶活性研究[D].昆明:西南林业大学,2017.
[14]HANSEN K D,BRENNER S E,DUDOIT S.Biases in Illumina transcriptome sequencing caused by random hexamer priming[J].Nucleic Acids Research,2010,38(12):e131.
[15]YANG Y X,WANG M M,YIN Y L,et al.RNA-seq analysis reveals the role of red light in resistance against Pseudomonas syringae pv.tomato DC3000in tomato plants[J].BMC Genomics,2015,16(1):120.
[16]王炜,郑伟,徐晓丹,等.基于转录组测序的滇山茶花叶呈色机理分析[J].西北植物学报,2017,37(9):1 720-1 727.WANG W,ZHENG W,XU X D,et al.Coloring mechanism analysis of mosaic leaves in Camellia reticulata Lindl.based on sequencing of transcriptome[J].Acta Botanica BorealiOccidentalia Sinica,2017,37(9):1 720-1 727.
[17]CHEN L N,GUO X J,CUI Y Z,et al.Comparative transcriptome analysis reveals hormone signaling genes involved in the launch of culm-shape differentiation in Dendrocalamus sinicus[J].Genes,2018,9:E4.
[18]VASHISTH D,KUMAR R,RASTOGI S,et al.Transcriptome changes induced by abiotic stresses in Artemisia annua[J].Scientific Reports,2018,8(1):3423.
[19]谭金花,候丽秀,刘永红,等.仁用杏果肉3个发育阶段的转录组分析[J].西北植物学报,2017,37(10):2 017-2 024.TAN J H,HOU L X,LIU Y H,et al.Transcriptome analysis of kernel-apricot sarcocarps during three development stages[J].Acta Botanica Boreali-Occidentalia Sinica,2017,37(10):2 017-2 024
[20]MAHER C A,KUMAR-SINHA C,CAO X H,et al.Transcriptome sequencing to detect gene fusions in cancer[J].Nature,2009,458(7 234):97-101.
[21]GRABHERR M G,HAAS B J,YASSOUR M,et al.Fulllength transcriptome assembly from RNA-Seq data without a reference genome[J].Nature Biotechnology,2011,29(7):644-652.
[22]LI B,DEWEY C N.RSEM:accurate transcript quantification from RNA-Seq data with or without a reference genome[J].BMC Bioinformatics,2011,12(1):323.
[23]TRAPNELL C,WILLIAMS B A,PERTEA G,et al.Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J].Nature Biotechnology,2010,28(5):511-515.
[24]TARAZONA S,GARCA-ALCALDE F,DOPAZO J,et al.Differential expression in RNA-seq:A matter of depth[J].Genome Research,2011,21(12):2 213-2 223.
[25]LALITHA S.Primer premier 5[J].Biotech Software&Internet Report,2000,1(6):270-272.
[26]CARRARO N,TISDALE-ORR T E,CLOUSE R M,et al.Diversification and expression of the PIN,AUX/LAX,and ABCBfamilies of putative auxin transporters in Populus[J].Frontiers in Plant Science,2012,3:17.
[27]熊国胜,李家洋,王永红.植物激素调控研究进展[J].科学通报,2009,54(18):2 718-2 733.XIONG G S,LI J Y,WANG Y H.Advances in the regulation and crosstalks of phytohormones[J].Chinese Science Bulletin,2009,54(18):2 718-2 733.
[28]BAND L R,U'BEDA-TOMS S,DYSON R J,et al.Growth-induced hormone dilution can explain the dynamics of plant root cell elongation[J].Proceedings of the National A-cademy of Sciences of the United States of America,2012,109(19):7 577-7 582.
[29]PACIFICI E,POLVERARI L,SABATINI S.Plant hormone cross-talk:the pivot of root growth[J].Journal of Experimental Botany,2015,66(4):1 113-1 121.
[30]TIAN H Y,LB S,DING T T,et al.Auxin-BR interaction regulates plant growth and development[J].Frontiers in Plant Science,2017,8:2 256.
[31]SANTNER A,CALDERON-VILLALOBOS L I,ESTELLEM.Plant hormones are versatile chemical regulators of plant growth[J].Nature Chemical Biology,2009,5(5):301-307.
[32]WOLTERS H,JRGENS G.Survival of the flexible:Hormonal growth control and adaptation in plant development[J].Nature Reviews.Genetics,2009,10(5):305-317.
[33]DEPUYDT S,HARDTKE C S.Hormone signalling crosstalk in plant growth regulation[J].Current Biology,2011,21(9):R365-R373.
[34]DOMAGALSKA M A,LEYSER O.Signal integration in the control of shoot branching[J].Nature Reviews Molecular Cell Biology,2011,12(4):211-221.
[35]NEMHAUSER J L,MOCKLER T C,CHORY J.Interdependency of Brassinosteroid and Auxin Signaling in Arabidopsis[J].PLoS Biology,2004,2(9):e258.
[36]KLECZKOWSKI L A,GEISLER M,FITZEK E,et al.Acommon structural blueprint for plant UDP-sugar-producing pyrophosphorylases[J].The Biochemical Journal,2011,439(3):375-379.
[37]REITER W D.Biochemical genetics of nucleotide sugar interconversion reactions[J].Current Opinion in Plant Biology,2008,11(3):236-243.
[38]OKAZAKI Y,SHIMOJIMA M,SAWADA Y,et al.Achloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis[J].The Plant Cell,2009,21(3):892-909.
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