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Volumn 46, Issue 1, 2019, Pages 933-945

Transcriptome-based gene expression profiling of diploid radish (Raphanus sativus L.) and the corresponding autotetraploid

Author keywords

Autotetraploid; DEGs; Radish (Raphanus sativus L.); Reverse transcription quantitative PCR (RT qPCR); Transcriptome sequencing

Indexed keywords

AUXIN; COLCHICINE; HYDROLASE; PECTINESTERASE; PROTEIN XYLOGLUCAN ENDOTRANSGLUCOSYLASE; UNCLASSIFIED DRUG; TRANSCRIPTOME;

EID: 85058823109     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-018-4549-1     Document Type: Article
Times cited : (7)

References (53)
  • 2
    • 0035344021 scopus 로고    scopus 로고
    • Yesterday’s polyploids and the mystery of diploidization
    • Wolfe KH (2001) Yesterday’s polyploids and the mystery of diploidization. Nat Rev Genet 2:333–341
    • (2001) Nat Rev Genet , vol.2 , pp. 333-341
    • Wolfe, K.H.1
  • 4
    • 0034500239 scopus 로고    scopus 로고
    • Polyploid incidence and evolution
    • Otto SP, Whitton J (2000) Polyploid incidence and evolution. Annu Rev Genet 34:401–437
    • (2000) Annu Rev Genet , vol.34 , pp. 401-437
    • Otto, S.P.1    Whitton, J.2
  • 5
    • 84858865242 scopus 로고    scopus 로고
    • Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors
    • Ng DWK, Zhang C, Miller M, Shen Z, Briggs SP, Chen ZJ (2012) Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity 108:419–430
    • (2012) Heredity , vol.108 , pp. 419-430
    • Ng, D.W.K.1    Zhang, C.2    Miller, M.3    Shen, Z.4    Briggs, S.P.5    Chen, Z.J.6
  • 6
    • 0033974956 scopus 로고    scopus 로고
    • Genome evolution in polyploids
    • Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42:225–249
    • (2000) Plant Mol Biol , vol.42 , pp. 225-249
    • Wendel, J.F.1
  • 8
    • 84950310903 scopus 로고    scopus 로고
    • Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression
    • Zhang J, Liu Y, Xia EH, Yao QY, Liu XD, Gao LZ (2015) Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression. Proc Natl Acad Sci USA 112:7022–7029
    • (2015) Proc Natl Acad Sci USA , vol.112 , pp. 7022-7029
    • Zhang, J.1    Liu, Y.2    Xia, E.H.3    Yao, Q.Y.4    Liu, X.D.5    Gao, L.Z.6
  • 9
    • 0034691216 scopus 로고    scopus 로고
    • The role of genetic and genomic attributes in the success of polyploids
    • Soltis PS, Soltis DE (2000) The role of genetic and genomic attributes in the success of polyploids. Proc Natl Acad Sci USA 97:7051–7057
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 7051-7057
    • Soltis, P.S.1    Soltis, D.E.2
  • 11
  • 13
    • 84901821115 scopus 로고    scopus 로고
    • Different drought-stress responses in photosynthesis and reactive oxygen metabolism between autotetraploid and diploid rice
    • Yang PM, Huang QC, Qin GY, Zhao SP, Zhou JG (2014) Different drought-stress responses in photosynthesis and reactive oxygen metabolism between autotetraploid and diploid rice. Photosynthetica 52(2):193–202
    • (2014) Photosynthetica , vol.52 , Issue.2 , pp. 193-202
    • Yang, P.M.1    Huang, Q.C.2    Qin, G.Y.3    Zhao, S.P.4    Zhou, J.G.5
  • 14
    • 84949580155 scopus 로고    scopus 로고
    • Polyploidy enhances F1 pollen sterility loci interactions that increase meiosis abnormalities and pollen sterility in autotetraploid rice
    • Wu JW, Shahid MQ, Chen L, Chen ZX, Wang L, Liu XD, Lu YG (2015) Polyploidy enhances F1 pollen sterility loci interactions that increase meiosis abnormalities and pollen sterility in autotetraploid rice. Plant Physiol 169:2700–2717
    • (2015) Plant Physiol , vol.169 , pp. 2700-2717
    • Wu, J.W.1    Shahid, M.Q.2    Chen, L.3    Chen, Z.X.4    Wang, L.5    Liu, X.D.6    Lu, Y.G.7
  • 15
    • 33644681986 scopus 로고    scopus 로고
    • The advantages and disadvantages of being polyploid
    • Comai L (2005) The advantages and disadvantages of being polyploid. Nat Rev Genet 6:836–846
    • (2005) Nat Rev Genet , vol.6 , pp. 836-846
    • Comai, L.1
  • 16
    • 0035810998 scopus 로고    scopus 로고
    • Protein-coding genes are epigenetically regulated in Arabidopsis polyploids
    • Lee HS, Chen ZJ (2001) Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc Natl Acad Sci USA 98:6753–6758
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 6753-6758
    • Lee, H.S.1    Chen, Z.J.2
  • 17
    • 4344642732 scopus 로고    scopus 로고
    • Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids
    • Wang J, Tian L, Madlung A et al (2004) Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167:1961–1973
    • (2004) Genetics , vol.167 , pp. 1961-1973
    • Wang, J.1    Tian, L.2    Madlung, A.3
  • 18
    • 0030003670 scopus 로고    scopus 로고
    • Dosage effects on gene expression in a maize ploidy series
    • Guo M, Davis D, Birchler JA (1996) Dosage effects on gene expression in a maize ploidy series. Genetics 142: 1349–1355
    • (1996) Genetics , vol.142 , pp. 1349-1355
    • Guo, M.1    Davis, D.2    Birchler, J.A.3
  • 19
    • 81255175641 scopus 로고    scopus 로고
    • Genomically biased accumulation of seed storage proteins in allopolyploid cotton
    • Hu G, Houston NL, Pathak D, Schmidt L, Thelen JJ, Wendel JF (2011) Genomically biased accumulation of seed storage proteins in allopolyploid cotton. Genetics 189:1103–1115
    • (2011) Genetics , vol.189 , pp. 1103-1115
    • Hu, G.1    Houston, N.L.2    Pathak, D.3    Schmidt, L.4    Thelen, J.J.5    Wendel, J.F.6
  • 20
    • 33745335890 scopus 로고    scopus 로고
    • Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids
    • Albertin W, Balliau T, Brabant P, Chèvre AM, Eber F, Malosse C, Thlellement H (2006) Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids. Genetics 173:1101–1113
    • (2006) Genetics , vol.173 , pp. 1101-1113
    • Albertin, W.1    Balliau, T.2    Brabant, P.3    Chèvre, A.M.4    Eber, F.5    Malosse, C.6    Thlellement, H.7
  • 22
    • 84968903135 scopus 로고    scopus 로고
    • Coming of age: ten years of next-generation sequencing technologies
    • Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351
    • (2016) Nat Rev Genet , vol.17 , pp. 333-351
    • Goodwin, S.1    McPherson, J.D.2    McCombie, W.R.3
  • 23
    • 85054125237 scopus 로고    scopus 로고
    • Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish (Raphanus sativus L.)
    • Xie Y, Xu L, Wang Y, Fan L, Chen Y, Tang M, Luo X, Liu L (2018) Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish (Raphanus sativus L.). Horticult Res 5(1):51
    • (2018) Horticult Res , vol.5 , Issue.1 , pp. 51
    • Xie, Y.1    Xu, L.2    Wang, Y.3    Fan, L.4    Chen, Y.5    Tang, M.6    Luo, X.7    Liu, L.8
  • 24
    • 84911988385 scopus 로고    scopus 로고
    • Comparative cytological and transcriptomic analysis of pollen development in autotetraploid and diploid rice
    • Wu JW, Shahid MQ, Guo HB, Yin W, Chen ZX, Wang L, Liu XD, Lu YG (2014) Comparative cytological and transcriptomic analysis of pollen development in autotetraploid and diploid rice. Plant Reprod 27:181–196
    • (2014) Plant Reprod , vol.27 , pp. 181-196
    • Wu, J.W.1    Shahid, M.Q.2    Guo, H.B.3    Yin, W.4    Chen, Z.X.5    Wang, L.6    Liu, X.D.7    Lu, Y.G.8
  • 25
    • 84897398835 scopus 로고    scopus 로고
    • Differential transcriptome analysis between Paulownia fortunei and its synthesized autopolyploid
    • Zhang X, Deng M, Fan G (2014) Differential transcriptome analysis between Paulownia fortunei and its synthesized autopolyploid. Int J Mol Sci 15:5079–5093
    • (2014) Int J Mol Sci , vol.15 , pp. 5079-5093
    • Zhang, X.1    Deng, M.2    Fan, G.3
  • 26
    • 84908248102 scopus 로고    scopus 로고
    • Identification of genes related to the phenotypic variations of a synthesized Paulownia (Paulownia tomentosa × Paulownia fortunei) autotetraploid
    • Li Y, Fan G, Dong Y, Zhao Z, Deng M, Cao X, Xu E, Niu S (2014) Identification of genes related to the phenotypic variations of a synthesized Paulownia (Paulownia tomentosa × Paulownia fortunei) autotetraploid. Gene 553:75
    • (2014) Gene , vol.553 , pp. 75
    • Li, Y.1    Fan, G.2    Dong, Y.3    Zhao, Z.4    Deng, M.5    Cao, X.6    Xu, E.7    Niu, S.8
  • 27
    • 84924368511 scopus 로고    scopus 로고
    • Differential gene expression and alternative splicing between diploid and tetraploid watermelon
    • Saminathan T, Nimmakayala P, Manohar S et al (2014) Differential gene expression and alternative splicing between diploid and tetraploid watermelon. J Exp Bot 66:1369–1385
    • (2014) J Exp Bot , vol.66 , pp. 1369-1385
    • Saminathan, T.1    Nimmakayala, P.2    Manohar, S.3
  • 28
    • 84958092827 scopus 로고    scopus 로고
    • Induction of autotetraploidy using colchicine and its identification in radish (Raphanus sativus L.)
    • Limera C, Wang K, Xu L, Wang Y, Zhu X, Feng H, Sha Y, Gong Y, Liu L (2016) Induction of autotetraploidy using colchicine and its identification in radish (Raphanus sativus L.). J Hortic Sci Biotech 91:63–70
    • (2016) J Hortic Sci Biotech , vol.91 , pp. 63-70
    • Limera, C.1    Wang, K.2    Xu, L.3    Wang, Y.4    Zhu, X.5    Feng, H.6    Sha, Y.7    Gong, Y.8    Liu, L.9
  • 29
    • 84929339186 scopus 로고    scopus 로고
    • De novo sequencing of root transcriptome reveals complex cadmium-responsive regulatory networks in radish (Raphanus sativus L.)
    • Xu L, Wang Y, Liu W et al (2015) De novo sequencing of root transcriptome reveals complex cadmium-responsive regulatory networks in radish (Raphanus sativus L.). Plant Sci 236:313–323
    • (2015) Plant Sci , vol.236 , pp. 313-323
    • Xu, L.1    Wang, Y.2    Liu, W.3
  • 30
    • 0345532642 scopus 로고
    • Changes in the pattern of phospholipid synthesis during the induction by cytokinin of cell division in soybean suspension cultures
    • Connett RJA, Hanke DE (1987) Changes in the pattern of phospholipid synthesis during the induction by cytokinin of cell division in soybean suspension cultures. Planta, 170(2):161–167
    • (1987) Planta , vol.170 , Issue.2 , pp. 161-167
    • Connett, R.J.A.1    Hanke, D.E.2
  • 31
    • 84991387650 scopus 로고    scopus 로고
    • Morphological, genome and gene expression changes in newly induced autopolyploid Chrysanthemum lavandulifolium (Fisch. ex Trautv.) Makino
    • Gao R, Wang H, Dong B et al (2016) Morphological, genome and gene expression changes in newly induced autopolyploid Chrysanthemum lavandulifolium (Fisch. ex Trautv.) Makino. Int J Mol Sci 17:1690
    • (2016) Int J Mol Sci , vol.17 , pp. 1690
    • Gao, R.1    Wang, H.2    Dong, B.3
  • 32
    • 84864768408 scopus 로고    scopus 로고
    • Evaluation of reference genes for gene expression studies in radish (Raphanus sativus L.) using quantitative real-time PCR
    • Xu Y, Zhu X, Gong Y et al (2012) Evaluation of reference genes for gene expression studies in radish (Raphanus sativus L.) using quantitative real-time PCR. Biochem Biophl Res Co 424:398–403
    • (2012) Biochem Biophl Res Co , vol.424 , pp. 398-403
    • Xu, Y.1    Zhu, X.2    Gong, Y.3
  • 34
    • 75249095274 scopus 로고    scopus 로고
    • DEGseq: an R package for identifying differentially expressed genes from RNA-Seq data
    • Wang L, Feng Z, Wang X et al (2009) DEGseq: an R package for identifying differentially expressed genes from RNA-Seq data. Bioinformatics 26:136–138
    • (2009) Bioinformatics , vol.26 , pp. 136-138
    • Wang, L.1    Feng, Z.2    Wang, X.3
  • 35
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc B 57:289–300
    • (1995) J R Stat Soc B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 36
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323
    • (2011) BMC Bioinform , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 37
    • 77953212372 scopus 로고    scopus 로고
    • Gene ontology analysis for RNA-Seq: accounting for selection bias
    • Young MD, Wakefield MJ, Smyth GK et al (2010) Gene ontology analysis for RNA-Seq: accounting for selection bias. Genome Biol 11:R14
    • (2010) Genome Biol , vol.11 , pp. R14
    • Young, M.D.1    Wakefield, M.J.2    Smyth, G.K.3
  • 38
    • 84895878929 scopus 로고    scopus 로고
    • Genome-wide analysis of the bHlH transcription factor family in Chinese cabbage (Brassica rapa ssp. pekinensis)
    • Song XM, Huang ZN, Duan WK, Ren J, Liu TK, Li Y, Hou XL (2014) Genome-wide analysis of the bHlH transcription factor family in Chinese cabbage (Brassica rapa ssp. pekinensis). Mol Genet Genomics 289:77–91
    • (2014) Mol Genet Genom , vol.289 , pp. 77-91
    • Song, X.M.1    Huang, Z.N.2    Duan, W.K.3    Ren, J.4    Liu, T.K.5    Li, Y.6    Hou, X.L.7
  • 40
    • 84893083276 scopus 로고    scopus 로고
    • APETALA2/Ethylene responsive factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs
    • Licausi F, Ohmetakagi M, Perata P (2013) APETALA2/Ethylene responsive factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs. New Phytol 199:639–649
    • (2013) New Phytol , vol.199 , pp. 639-649
    • Licausi, F.1    Ohmetakagi, M.2    Perata, P.3
  • 41
    • 84955406431 scopus 로고    scopus 로고
    • The polyploidy and its key role in plant breeding
    • Sattler MC, Carvalho CR, Clarindo WR (2016) The polyploidy and its key role in plant breeding. Planta 243: 281–296
    • (2016) Planta , vol.243 , pp. 281-296
    • Sattler, M.C.1    Carvalho, C.R.2    Clarindo, W.R.3
  • 42
    • 85021266879 scopus 로고    scopus 로고
    • Cytogenetic and molecular evidences revealing genomic changes after autopolyploidization: a case study of synthetic autotetraploid Phlox drummondii Hook
    • Dar TH, Raina SN, Goel S (2017) Cytogenetic and molecular evidences revealing genomic changes after autopolyploidization: a case study of synthetic autotetraploid Phlox drummondii Hook. Physiol Mol Biol Pla 23:641–650
    • (2017) Physiol Mol Biol Plants , vol.23 , pp. 641-650
    • Dar, T.H.1    Raina, S.N.2    Goel, S.3
  • 43
    • 27644525170 scopus 로고    scopus 로고
    • Growth of the plant cell wall
    • Cosgrove DJ (2005) Growth of the plant cell wall. Nat Rev Mol Cell Biol 6:850–861
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 850-861
    • Cosgrove, D.J.1
  • 44
    • 0034760628 scopus 로고    scopus 로고
    • A comprehensive expression analysis of all members of a gene family encoding cell-wall enzymes allowed us to predict cis-regulatory regions involved in cell-wall construction in specific organs of Arabidopsis
    • Yokoyama R, Nishitani K (2001) A comprehensive expression analysis of all members of a gene family encoding cell-wall enzymes allowed us to predict cis-regulatory regions involved in cell-wall construction in specific organs of Arabidopsis. Plant Cell Physiol 42:1025–1033
    • (2001) Plant Cell Physiol , vol.42 , pp. 1025-1033
    • Yokoyama, R.1    Nishitani, K.2
  • 45
    • 0036953722 scopus 로고    scopus 로고
    • The XTH family of enzymes involved in xyloglucan endotransglucosylation and endohydrolysis: current perspectives and a new unifying nomenclature
    • Rose JKC, Braam J, Fry SC, Nishitani K (2002) The XTH family of enzymes involved in xyloglucan endotransglucosylation and endohydrolysis: current perspectives and a new unifying nomenclature. Plant Cell Physiol 43:1421–1435
    • (2002) Plant Cell Physiol , vol.43 , pp. 1421-1435
    • Rose, J.K.C.1    Braam, J.2    Fry, S.C.3    Nishitani, K.4
  • 46
    • 0035202023 scopus 로고    scopus 로고
    • Characterization of a tomato xyloglucan endotransglycosylase gene that is down-regulated by auxin in etiolated hypocotyls
    • Catalá C, Rose JKC, York WS, Albersheim P, Darvill AG, Bennett AB (2001) Characterization of a tomato xyloglucan endotransglycosylase gene that is down-regulated by auxin in etiolated hypocotyls. Plant Physiol 127:1180–1192
    • (2001) Plant Physiol , vol.127 , pp. 1180-1192
    • Catalá, C.1    Rose, J.K.C.2    York, W.S.3    Albersheim, P.4    Darvill, A.G.5    Bennett, A.B.6
  • 47
    • 0032706658 scopus 로고    scopus 로고
    • Roles of cellulose and xyloglucan in determining the mechanical properties of primary plant cell walls
    • Whitney SEC, Gothard MGE, Mitchell JT, Gidley MJ (1999) Roles of cellulose and xyloglucan in determining the mechanical properties of primary plant cell walls. Plant Physiol 121:657–664
    • (1999) Plant Physiol , vol.121 , pp. 657-664
    • Whitney, S.E.C.1    Gothard, M.G.E.2    Mitchell, J.T.3    Gidley, M.J.4
  • 48
    • 84864331272 scopus 로고    scopus 로고
    • Developmental, cytological and transcriptional analysis of autotetraploid Arabidopsis
    • Li X, Yu E, Fan C, Zhang C, Fu T, Zhou Y (2012) Developmental, cytological and transcriptional analysis of autotetraploid Arabidopsis. Planta 236:579–596
    • (2012) Planta , vol.236 , pp. 579-596
    • Li, X.1    Yu, E.2    Fan, C.3    Zhang, C.4    Fu, T.5    Zhou, Y.6
  • 49
    • 84904396503 scopus 로고    scopus 로고
    • The causes and molecular consequences of polyploidy in flowering plants
    • Moghe GD, Shiu SH (2014) The causes and molecular consequences of polyploidy in flowering plants. Ann NY Acad Sci 1320:16
    • (2014) Ann NY Acad Sci , vol.1320 , pp. 16
    • Moghe, G.D.1    Shiu, S.H.2
  • 50
    • 85040513475 scopus 로고    scopus 로고
    • Patterns and consequences of subgenome differentiation provide insights into the nature of paleopolyploidy in plants
    • Zhao M, Zhang B, Lisch D, Ma J (2017) Patterns and consequences of subgenome differentiation provide insights into the nature of paleopolyploidy in plants. Plant Cell 29:2974–2994
    • (2017) Plant Cell , vol.29 , pp. 2974-2994
    • Zhao, M.1    Zhang, B.2    Lisch, D.3    Ma, J.4
  • 51
    • 74549221016 scopus 로고    scopus 로고
    • Genome sequence of the palaeopolyploid soybean
    • Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178
    • (2010) Nature , vol.463 , pp. 178
    • Schmutz, J.1    Cannon, S.B.2    Schlueter, J.3
  • 52
    • 84960421688 scopus 로고    scopus 로고
    • Gene duplicability of core genes is highly consistent across all angiosperms
    • Li Z, Defoort J, Tasdighian S, Maere S, De Peer YV, Smet RD (2016) Gene duplicability of core genes is highly consistent across all angiosperms. Plant Cell 28:326–344
    • (2016) Plant Cell , vol.28 , pp. 326-344
    • Li, Z.1    Defoort, J.2    Tasdighian, S.3    Maere, S.4    De Peer, Y.V.5    Smet, R.D.6
  • 53
    • 85037719494 scopus 로고    scopus 로고
    • Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana
    • Smet RD, Sabaghian E, Li Z, Saeys Y, De Peer YV (2017) Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana. Plant Cell 29:2786–2800
    • (2017) Plant Cell , vol.29 , pp. 2786-2800
    • Smet, R.D.1    Sabaghian, E.2    Li, Z.3    Saeys, Y.4    De Peer, Y.V.5


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