叶子花花瓣状苞片和叶片的比较转录组学研究
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摘要
叶子花(Bougainvillea spectabilis Willd.)的苞片色彩鲜艳,呈花瓣状,在景观园艺和环境美化有着广泛应用。为了进一步了解花瓣状苞片的演化机制,该研究采用RNA-seq技术分别对苞片和叶片进行测序,比较苞片和叶片在基因表达水平的差异。最终获得54.48 M对长度为150bp的双向clean reads,从头拼接出55 782条Unigenes,平均长度为1 003.79bp,N50为1 402bp。共有30 874条Unigenes能被注释到公共数据库,其中有12 631条Unigenes能被注释到基因本体。差异化表达分析确定苞片和叶片差异表达的基因共有456个。该研究分别对不同组织差异表达的基因进行GO富集分析和KEGG富集分析,结果表明,在苞片中高表达的差异化基因有黄酮类合成相关的基因,花色合成关键酶多巴双加氧酶(DODA)以及发现与花瓣发育相关的基因,在叶片中高表达的差异化基因主要是参与光合作用。
Bougainvillea spectabilis Willd.,whose bracts are colorful and petal-like,has been widely used in landscape gardening.In order to further understand the evolutionary mechanism of petal-like bracts,we used RNA-seq technology to sequence transcritomes in bracts and leaves,respectively,and compared the bracts and leaves at the level of gene expression.In total,55 782 Unigenes with an average length of 1 003.79 bp and an N50 of 1 402 bp were de novo assembled from 54.48 Mbidirectional clean reads of 150 bp in length.There were 30 874 Unigenes successfully annotated to the public database,of which 12 631 Unigenes can be annotated to Gene Ontology.Differential expression analysis identified a total of 456 differentially expressed genes(DEGs)between bract and leaf.The GO enrichment analysis and KEGG enrichment analysis of differentially expressed genes in different tissues showed that:(1)the DEGS highly expressed in bracts contained flavonoid-related genes,a key enzyme in flower color synthesis(DODA),and genes related to the development of petals;(2)The DEGs highly expressed in leaves were mainly involved in photosynthesis.
Bougainvillea spectabilis Willd.,whose bracts are colorful and petal-like,has been widely used in landscape gardening.In order to further understand the evolutionary mechanism of petal-like bracts,we used RNA-seq technology to sequence transcritomes in bracts and leaves,respectively,and compared the bracts and leaves at the level of gene expression.In total,55 782 Unigenes with an average length of 1 003.79 bp and an N50 of 1 402 bp were de novo assembled from 54.48 Mbidirectional clean reads of 150 bp in length.There were 30 874 Unigenes successfully annotated to the public database,of which 12 631 Unigenes can be annotated to Gene Ontology.Differential expression analysis identified a total of 456 differentially expressed genes(DEGs)between bract and leaf.The GO enrichment analysis and KEGG enrichment analysis of differentially expressed genes in different tissues showed that:(1)the DEGS highly expressed in bracts contained flavonoid-related genes,a key enzyme in flower color synthesis(DODA),and genes related to the development of petals;(2)The DEGs highly expressed in leaves were mainly involved in photosynthesis.
引文
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[34]SASAKI N,ABE Y,GODA Y,et al.Detection of DOPA 4,5-dioxygenase(DOD)activity using recombinant protein prepared from Escherichia coli cells harboring cDNA encoding DOD from Mirabilis jalapa[J].Plant and Cell Physiology,2009,50(5):1012-1016.
[35]柏忠良,佘文琴,潘东明,等.叶子花花色DOD基因全长cDNA克隆与序列分析[J].福建林学院学报,2014,(2):152-157.BAI Z L,SHE W Q,PAN D M.Cloning and sequence analysis of full-length cDNA of the Bougainvillea spectabilis Willd.flower color DOD gene[J].Journal of Fujian College of Forestry,2014,(2):152-157.
[36]THOMPSON E P,CHRISTOPHER W,VADIM D,et al.An Arabidopsis flavonoid transporter is required for anther dehiscence and pollen development[J].Journal of Experimental Botany,2010,61(2):439-451.
[37]MOL J,GROTEWOLD E,KOES R.How gens paint flowers and seeds[J].Trends in Plant Science,1998,3(6):212-217.
[38]SCHENK P M,KAZAN K,WILSON I,et al.Coordinated plant defense responses in Arabidopsis revealed by microarray analysis.[J].Proceedings of the National Academy of Sciences of the United States of America,2000,97(21):11 655.
[39]ESTELLE GOULAS,MARIA SCHUBERT,KIESELBACH T,et al.The chloroplast lumen and stromal proteomes of Arabidopsis thaliana,show differential sensitivity to short-and long-term exposure to low temperature[J].Plant Journal,2006,47(5):720.
[40]FOWLER S,THOMASHOW M F.Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway.[J].Plant Cell,2002,14(8):1 675-1 690.
[41]SZCSI J,JOLY C,BORDJI K,et al.BIGPETALp,a bHLH transcription factor is involved in the control of Arabidopsis petal size[J].Embo Journal,2006,25(16):3 912-3 920.
[42]MATSUBA Y,SASAKI N,TERA M,et al.A novel glucosylation reaction on anthocyanins catalyzed by acyl-glucosedependent gucosyltransferase in the petals of carnation and delphinium[J].Plant Cell,2010,22(10):3 374-3 389.
[43]BROWN B A,CLOIX C,JIANG G H,et al.A UV-B-specific signaling component orchestrates plant UV protection[J].Proceedings of the National Academy of Sciences of the United States of America,2005,102(50):18 225-18 230.
[44]WARGENT J J,GEGAS V C,JENKINS G I,et al.UVR8in Arabidopsis thaliana,regulates multiple aspects of cellular differentiation during leaf development in response to ultraviolet B radiation[J].New Phytologist,2009,183(2):315-326.
[45]BONFIG K B,SCHREIBER U,GABLER A,et al.Infection with virulent and avirulent Pseudomonas syringae,strains differentially affects photosynthesis and sink metabolism in Arabidopsis,leaves[J].Planta,2006,225(1):1-12.
[2]MARKESTEIJN L,POORTER L,PAZ H,et al.Ecological differentiation in xylem cavitation resistance is associated with stem and leaf structural traits[J].Plant Cell&Environment,2011,34(1):137-148.
[3]SACK L,SCOFFONI C,MCKOWN A D,et al.Developmentally based scaling of leaf venation architecture explains global ecological patterns[J].Nature Communications,2012,3(837):837.
[4]CARIGLINO B.Sensitivity of leaf size and shape to climate:global patterns and paleoclimatic applications[J].New Phytologist,2011,190(3):724-39.
[5]TAO S U,XING Y W,YU S,et al.Leaf margin analysis:a new equation from humid to mesic forests in China[J].Palaios,2010,25(3/4):234-238.
[6]ZIRBEL C R,BASSETT T,GRMAN E,et al.Plant functional traits and environmental conditions shape community assembly and ecosystem functioning during restoration[J].Journal of Applied Ecology,2017,54(4):1 070-1 079.
[7]BOHNERT H J,NELSON D E,JENSEN R G.Adaptations to environmental stresses[J].Plant Cell,1995,7(7):1099.
[8]BALDISSERA T C,FRAK E,CARVALHO P C,et al.Plant development controls leaf area expansion in alfalfa plants competing for light[J].Annals of Botany,2014,113(1):145.
[9]EDWARDS E J.Correlated evolution of stem and leaf hydraulic traits in Pereskia(Cactaceae)[J].New Phytologist,2006,172(3):479-789.
[10]STEFFEN S,BALL P,MUCINA L,et al.Phylogeny,biogeography and ecological diversification of Sarcocornia(Salicornioideae,Amaranthaceae)[J].Annals of Botany,2015,115(3):353.
[11]CHEESEMAN J M.Mechanisms of salinity tolerance in plants[J].Plant Physiology,1988,87(3):547-50.
[12]TAKHTADZHIAN A L.Evolutionary Trends in Flowering Plants[M].New York:Columbia University Press,1991.
[13]BALL T,GARDNER J S,BROTHERSON J D.Identifying phytoliths produced by the inflorescence bracts of three species of wheat(Triticum monococcum L.,T.dicocconSchrank.,and T.aestivum L.)using computer-assisted image and statistical analyses[J].Journal of Archaeological Science,1996,23(4):619-632.
[14]WEBERLING F.Morphology of Flowers and Inflorescences[M].CUP Archive,1992.
[15]IRISH V F,LITT A.Flower development and evolution:gene duplication,diversification and redeployment[J].Current Opinion in Genetics&Development,2005,15(4):454-460.
[16]IRISH V F.Evolution of petal identity[J].Journal of Experimental Botany,2009,60(9):2 517-2 527.
[17]BETHKE J A,PAINE T D,NUESSLY G S.Comparative biology,morphometrics,and development of two populations of Bemisia tabaci(Homoptera:Aleyrodidae)on cotton and poinsettia[J].Annals of the Entomological Society of America,1991,84(4):407-411.
[18]REDDY K S,MENARY R C.Nitrate reductase and nitrate accumulation in relation to nitrate toxicity in Boronia megastigma[J].Physiologia Plantarum,1990,78(3):430-434.
[19]FENG C M,LIU X,YU Y,et al.Evolution of bract development and B-class MADS box gene expression in petaloid bracts of Cornus s.l.(Cornaceae)[J].New Phytologist,2012,196(2):631-643.
[20]ZHAO Y H,LARSON-RABIN Z,WANG G Y,et al.Developmental genetics of the perianthless flowers and bracts of apaleoherb species,Saururus chinensis[J].PLoS One,2013,8(1):e53019.
[21]SONG B,ZHANG Z Q,STCKLIN J,et al.Multifunctional bracts enhance plant fitness during flowering and seed development in Rheumnobile(Polygonaceae),agiant herb endemic to the high Himalayas[J].Oecologia,2013,172(2):359-370.
[22]FENG C M,XIANG Q Y J,FRANKS R G.Phylogenybased developmental analyses illuminate evolution of inflorescence architectures in dogwoods(Cornus sl,Cornaceae)[J].New Phytologist,2011,191(3):850-869.
[23]GNIRKE A,REGEV A,HAAS B J,et al.Full-length transcriptome assembly from RNA-Seq data without a reference genome[J].Nature Biotechnology,2011,29(7):644.
[24]MORGULIS A,COULOURIS G,RAYTSELIS Y,et al.Database indexing for production MegaBLAST searches[J].Bioinformatics,2008,24(16):1 757-1 764.
[25]TATUSOV R L,KOONIN E V,LIPMAN D J.A genomic perspective on protein families[J].Science,1997,278(5338):631-637.
[26]ROLF APWEILER,AMOS BAIROCH,CATHY H.WU,et al.UniProt:the universal protein knowledgebase[J].Nucleic Acids Research,2004,32(Database issue):D115.
[27]ASHBURNER M,BALL C A,BLAKE J A,et al.Gene ontology:tool for the unification of biology[J].Nature Genetics,2000,25(1):25-29.
[28]LANGMEAD B,SALZBERG S L.Fast gapped-read alignment with Bowtie 2[J].Nature methods,2012,9(4):357-359.
[29]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.
[30]ROBINSON M D,MCCARTHY D J,SMYTH G K.edgeR:a Bioconductor package for differential expression analysis of digital gene expression data[J].Bioinformatics,2010,26(1):139-140.
[31]YOUNG M D,WAKEFIELD M J,SMYTH G K,et al.Gene ontology analysis for RNA-seq:accounting for selection bias[J].Genome Biology,2010,11(2):R14.
[32]WU J,MAO X,CAI T,et al.KOBAS server:a web-based platform for automated annotation and pathway identification[J].Nucleic Acids Research,2006,34(suppl2):W720-724.
[33]赵玉梅,任红梅.我国叶子花属植物的应用前景及展望[J].安徽农业科学,2011,39(10):5 697-5 698.ZHAO Y M,REN H M.The application prospect of Bougainvillea spectabilis Willd in China[J].Journal of Anhui Agricultural Sciences,2011,39(10):5 697-5 698.
[34]SASAKI N,ABE Y,GODA Y,et al.Detection of DOPA 4,5-dioxygenase(DOD)activity using recombinant protein prepared from Escherichia coli cells harboring cDNA encoding DOD from Mirabilis jalapa[J].Plant and Cell Physiology,2009,50(5):1012-1016.
[35]柏忠良,佘文琴,潘东明,等.叶子花花色DOD基因全长cDNA克隆与序列分析[J].福建林学院学报,2014,(2):152-157.BAI Z L,SHE W Q,PAN D M.Cloning and sequence analysis of full-length cDNA of the Bougainvillea spectabilis Willd.flower color DOD gene[J].Journal of Fujian College of Forestry,2014,(2):152-157.
[36]THOMPSON E P,CHRISTOPHER W,VADIM D,et al.An Arabidopsis flavonoid transporter is required for anther dehiscence and pollen development[J].Journal of Experimental Botany,2010,61(2):439-451.
[37]MOL J,GROTEWOLD E,KOES R.How gens paint flowers and seeds[J].Trends in Plant Science,1998,3(6):212-217.
[38]SCHENK P M,KAZAN K,WILSON I,et al.Coordinated plant defense responses in Arabidopsis revealed by microarray analysis.[J].Proceedings of the National Academy of Sciences of the United States of America,2000,97(21):11 655.
[39]ESTELLE GOULAS,MARIA SCHUBERT,KIESELBACH T,et al.The chloroplast lumen and stromal proteomes of Arabidopsis thaliana,show differential sensitivity to short-and long-term exposure to low temperature[J].Plant Journal,2006,47(5):720.
[40]FOWLER S,THOMASHOW M F.Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway.[J].Plant Cell,2002,14(8):1 675-1 690.
[41]SZCSI J,JOLY C,BORDJI K,et al.BIGPETALp,a bHLH transcription factor is involved in the control of Arabidopsis petal size[J].Embo Journal,2006,25(16):3 912-3 920.
[42]MATSUBA Y,SASAKI N,TERA M,et al.A novel glucosylation reaction on anthocyanins catalyzed by acyl-glucosedependent gucosyltransferase in the petals of carnation and delphinium[J].Plant Cell,2010,22(10):3 374-3 389.
[43]BROWN B A,CLOIX C,JIANG G H,et al.A UV-B-specific signaling component orchestrates plant UV protection[J].Proceedings of the National Academy of Sciences of the United States of America,2005,102(50):18 225-18 230.
[44]WARGENT J J,GEGAS V C,JENKINS G I,et al.UVR8in Arabidopsis thaliana,regulates multiple aspects of cellular differentiation during leaf development in response to ultraviolet B radiation[J].New Phytologist,2009,183(2):315-326.
[45]BONFIG K B,SCHREIBER U,GABLER A,et al.Infection with virulent and avirulent Pseudomonas syringae,strains differentially affects photosynthesis and sink metabolism in Arabidopsis,leaves[J].Planta,2006,225(1):1-12.