메뉴 건너뛰기




Volumn 57, Issue 6, 2014, Pages 337-348

Comparative transcriptome analysis of RNA-seq data for cold-tolerant and cold-sensitive rice genotypes under cold stress

Author keywords

Cold stress; Rice; RNA seq; Transcriptome analysis

Indexed keywords


EID: 84911460983     PISSN: 12269239     EISSN: 18670725     Source Type: Journal    
DOI: 10.1007/s12374-014-0183-1     Document Type: Article
Times cited : (80)

References (41)
  • 1
    • 84865265257 scopus 로고    scopus 로고
    • Cold stress-induced acclimation in rice is mediated by root-specific aquaporins
    • PID: 22711693
    • Hayashi H, Kawamura Y, Uemura M (2012) Cold stress-induced acclimation in rice is mediated by root-specific aquaporins. Plant Cell Physiol 53:1445–145.
    • (2012) Plant Cell Physiol , vol.53 , pp. 1445-1145
    • Hayashi, H.1    Kawamura, Y.2    Uemura, M.3
  • 2
    • 84911473626 scopus 로고    scopus 로고
    • Preliminary study on cold-resistance of seedling of near-isogenic lines from Dongxiang wild rice
    • Chen DZ, Xiao YQ, Pi YH, Hu LX, Yu MJ (2003) Preliminary study on cold-resistance of seedling of near-isogenic lines from Dongxiang wild rice. Acta Agric Jiangxi 15:54–5.
    • (2003) Acta Agric Jiangxi , vol.15 , pp. 54-55
    • Chen, D.Z.1    Xiao, Y.Q.2    Pi, Y.H.3    Hu, L.X.4    Yu, M.J.5
  • 6
    • 0033133863 scopus 로고    scopus 로고
    • Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families
    • PID: 10322435
    • De la Cruz J, Kressler D, Linder P (1999) Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. Trends Biochem Sci 24:192–198
    • (1999) Trends Biochem Sci , vol.24 , pp. 192-198
    • De la Cruz, J.1    Kressler, D.2    Linder, P.3
  • 7
    • 79959472680 scopus 로고    scopus 로고
    • The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing
    • Ge G, Xiao P, Zhang Y, Yang L (2011) The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing. PLoS One 6:e21220
    • (2011) PLoS One , vol.6 , pp. 21220
    • Ge, G.1    Xiao, P.2    Zhang, Y.3    Yang, L.4
  • 8
    • 21444454906 scopus 로고    scopus 로고
    • A DEAD box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis
    • COI: 1:CAS:528:DC%2BD2MXotlanug%3D%3D, PID: 15598798
    • Gong ZZ, Dong CH, Lee H, Zhu JH, Xiong LM, Gong DM, Stevenson B, Zhu JK (2005) A DEAD box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis. Plant Cell 17:256–26.
    • (2005) Plant Cell , vol.17 , pp. 256-226
    • Gong, Z.Z.1    Dong, C.H.2    Lee, H.3    Zhu, J.H.4    Xiong, L.M.5    Gong, D.M.6    Stevenson, B.7    Zhu, J.K.8
  • 9
    • 0026261995 scopus 로고
    • Expression of antifreeze proteins in transgenic plants
    • COI: 1:CAS:528:DyaK3MXmslamtro%3D, PID: 1932678
    • Hightower R, Baden C, Penzes E, Lund P, Dunsmuir P (1991) Expression of antifreeze proteins in transgenic plants. Plant Mol Biol 17:1013–102.
    • (1991) Plant Mol Biol , vol.17 , pp. 1013-1102
    • Hightower, R.1    Baden, C.2    Penzes, E.3    Lund, P.4    Dunsmuir, P.5
  • 10
    • 84861169493 scopus 로고    scopus 로고
    • Deep sequencing-based transcriptome profiling analysis of Oryzias melastigma exposed to PFOS
    • PID: 22613580
    • Huang Q, Dong S, Fang C, Wu X, Ye T, Lin Y (2012) Deep sequencing-based transcriptome profiling analysis of Oryzias melastigma exposed to PFOS. Aquat Toxicol 120–121:54–5.
    • (2012) Aquat Toxicol , vol.120-121 , pp. 54-55
    • Huang, Q.1    Dong, S.2    Fang, C.3    Wu, X.4    Ye, T.5    Lin, Y.6
  • 11
    • 0037004330 scopus 로고    scopus 로고
    • Acclimative response to temperature stress in higher plants: approaches of gene engineering for temperature tolerance
    • COI: 1:CAS:528:DC%2BD38XlsVWhtbY%3D, PID: 12221974
    • Iba K (2002) Acclimative response to temperature stress in higher plants: approaches of gene engineering for temperature tolerance. Annu Rev Plant Biol 53:225–24.
    • (2002) Annu Rev Plant Biol , vol.53 , pp. 225-224
    • Iba, K.1
  • 12
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: an improved ultrafast tool for short read alignment
    • COI: 1:CAS:528:DC%2BD1MXovVeku7w%3D, PID: 19497933
    • Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–196.
    • (2009) Bioinformatics , vol.25 , pp. 1966-1196
    • Li, R.1    Yu, C.2    Li, Y.3    Lam, T.W.4    Yiu, S.M.5    Kristiansen, K.6    Wang, J.7
  • 14
    • 84911464199 scopus 로고    scopus 로고
    • Cloning of the DREB-like transcription the construction of plant factor from Chaling wild vector rice and expression
    • COI: 1:CAS:528:DC%2BC3MXjsl2ku7Y%3D
    • Liu JY, Cheng JQ, Gong JH, Kang M, Hong YH (2010) Cloning of the DREB-like transcription the construction of plant factor from Chaling wild vector rice and expression. J Hunan Agric univ (Nat Sci) 36:630–63.
    • (2010) J Hunan Agric univ (Nat Sci) , vol.36 , pp. 630-663
    • Liu, J.Y.1    Cheng, J.Q.2    Gong, J.H.3    Kang, M.4    Hong, Y.H.5
  • 15
    • 77956675063 scopus 로고    scopus 로고
    • Identification for cold tolerance at different growth stages in rice (Oryza sativa L.) and physiological mechanism of differential cold tolerance
    • Li X, Dai C, Cheng Y, Chen T, Jiao D (2006) Identification for cold tolerance at different growth stages in rice (Oryza sativa L.) and physiological mechanism of differential cold tolerance. Acta Agron Sin 32:76
    • (2006) Acta Agron Sin , vol.32 , pp. 76
    • Li, X.1    Dai, C.2    Cheng, Y.3    Chen, T.4    Jiao, D.5
  • 16
    • 0037188887 scopus 로고    scopus 로고
    • RNA chaperones exist and DEAD box proteins get a life
    • COI: 1:CAS:528:DC%2BD38Xlt1eiur0%3D, PID: 12110176
    • Lorsch JR (2002) RNA chaperones exist and DEAD box proteins get a life. Cell 109:797–80.
    • (2002) Cell , vol.109 , pp. 797-780
    • Lorsch, J.R.1
  • 17
    • 77952884377 scopus 로고    scopus 로고
    • Profiling of cold-stress-responsive miRNAs in rice by microarrays
    • COI: 1:CAS:528:DC%2BC3cXmtVGku7o%3D, PID: 20350593
    • Lv DK, Bai X, Li Y, Ding XD, Ge Y, Cai H, Ji W, Wu N, Zhu YM (2010) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene 459:39–4.
    • (2010) Gene , vol.459 , pp. 39-34
    • Lv, D.K.1    Bai, X.2    Li, Y.3    Ding, X.D.4    Ge, Y.5    Cai, H.6    Ji, W.7    Wu, N.8    Zhu, Y.M.9
  • 18
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    • COI: 1:CAS:528:DC%2BD1cXhtV2qsr3E, PID: 18550803
    • Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509–151.
    • (2008) Genome Res , vol.18 , pp. 1509-1151
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 21
    • 0001641104 scopus 로고    scopus 로고
    • Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor
    • COI: 1:CAS:528:DyaK1MXit1alt7g%3D, PID: 10090722
    • Morita MT, Tanaka Y, Kodama TS, Kyogoku Y, Yanagi H, Yura T (1999) Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor. Gene Dev 13:655–66.
    • (1999) Gene Dev , vol.13 , pp. 655-666
    • Morita, M.T.1    Tanaka, Y.2    Kodama, T.S.3    Kyogoku, Y.4    Yanagi, H.5    Yura, T.6
  • 22
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNASeq
    • COI: 1:CAS:528:DC%2BD1cXnslyqs7k%3D, PID: 18516045
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNASeq. Nat Methods 5:621–62.
    • (2008) Nat Methods , vol.5 , pp. 621-662
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 23
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • COI: 1:CAS:528:DC%2BD1cXmslWgtbY%3D, PID: 18451266
    • Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–134.
    • (2008) Science , vol.320 , pp. 1344-1134
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 24
    • 33746361200 scopus 로고    scopus 로고
    • Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations
    • PID: 16749918
    • Okoniewski MJ, Miller CJ (2006) Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC bioinformatics 7:276
    • (2006) BMC bioinformatics , vol.7 , pp. 276
    • Okoniewski, M.J.1    Miller, C.J.2
  • 25
    • 9144230726 scopus 로고    scopus 로고
    • Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses
    • COI: 1:CAS:528:DC%2BD2cXhvFCr, PID: 14645724
    • Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol 133:1755–1767.
    • (2003) Plant Physiol , vol.133 , pp. 1755-1767
    • Rabbani, M.A.1    Maruyama, K.2    Abe, H.3    Khan, M.A.4    Katsura, K.5    Ito, Y.6    Yoshiwara, K.7    Seki, M.8    Shinozaki, K.9    Yamaguchi-Shinozaki, K.10
  • 26
    • 34548569002 scopus 로고    scopus 로고
    • Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification
    • Royce TE, Rozowsky JS, Gerstein MB (2007) Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. Nucleic Acids Res 35:e99
    • (2007) Nucleic Acids Res , vol.35 , pp. 99
    • Royce, T.E.1    Rozowsky, J.S.2    Gerstein, M.B.3
  • 27
    • 0034028259 scopus 로고    scopus 로고
    • Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways
    • COI: 1:CAS:528:DC%2BD3cXktVOnsrk%3D, PID: 10837265
    • Shinozaki K, Yamaguchi-Shinozaki K (2000) Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways. Curr Opin Plant Biol 3:217–22.
    • (2000) Curr Opin Plant Biol , vol.3 , pp. 217-222
    • Shinozaki, K.1    Yamaguchi-Shinozaki, K.2
  • 28
    • 77956613421 scopus 로고    scopus 로고
    • The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice
    • COI: 1:CAS:528:DC%2BC3cXhtVejsrnK, PID: 20632034
    • Takasaki H, Maruyama K, Kidokoro S, Ito Y, Fujita Y, Shinozaki K, Yamaguchi-Shinozaki K, Nakashima K (2010) The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. Mol Genet Genomics 284:173–18.
    • (2010) Mol Genet Genomics , vol.284 , pp. 173-118
    • Takasaki, H.1    Maruyama, K.2    Kidokoro, S.3    Ito, Y.4    Fujita, Y.5    Shinozaki, K.6    Yamaguchi-Shinozaki, K.7    Nakashima, K.8
  • 29
    • 0034857262 scopus 로고    scopus 로고
    • DExD/H box RNA helicases: from generic motors to specific dissociation functions
    • COI: 1:CAS:528:DC%2BD3MXmvFWgsbw%3D, PID: 11545728
    • Tanner NK, Linder P (2001) DExD/H box RNA helicases: from generic motors to specific dissociation functions. Mol Cell 8:251–26.
    • (2001) Mol Cell , vol.8 , pp. 251-226
    • Tanner, N.K.1    Linder, P.2
  • 31
    • 0033498862 scopus 로고    scopus 로고
    • Plant cold acclimation: freezing tolerance genes and regulatory mechanisms
    • COI: 1:CAS:528:DyaK1MXkt1yktrw%3D
    • Thomashow MF (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu Rev Plant Biol 50:571–59.
    • (1999) Annu Rev Plant Biol , vol.50 , pp. 571-559
    • Thomashow, M.F.1
  • 32
    • 0035144222 scopus 로고    scopus 로고
    • So what’s new in the field of plant cold acclimation
    • COI: 1:CAS:528:DC%2BD3MXjslymtLY%3D
    • Thomashow MF (2001) So what’s new in the field of plant cold acclimation? Lots! Plant Physiol 125:89–9.
    • (2001) Lots! Plant Physiol , vol.125 , pp. 89
    • Thomashow, M.F.1
  • 33
    • 0000657354 scopus 로고
    • Chlorophyll-proteins: light-harvesting and reaction center components of plants
    • COI: 1:CAS:528:DyaE2MXksVSisbg%3D
    • Thornber JP (1975) Chlorophyll-proteins: light-harvesting and reaction center components of plants. Annu Rev Plant Physiol 26:127–15.
    • (1975) Annu Rev Plant Physiol , vol.26 , pp. 127-115
    • Thornber, J.P.1
  • 35
    • 77955773702 scopus 로고    scopus 로고
    • QTLs mapping for cold tolerance at seedling stage in Dongxiang Wild Rice (Oryza rufipogon Griff.)
    • COI: 1:CAS:528:DC%2BC3cXjtVyqsbw%3D
    • Xia RX, Xiao N, Hong YH, Zhang C, Su Y, Zhang XM, Chen JM (2010) QTLs mapping for cold tolerance at seedling stage in Dongxiang Wild Rice (Oryza rufipogon Griff.). Sci Agric Sin 43:443–45.
    • (2010) Sci Agric Sin , vol.43 , pp. 443-445
    • Xia, R.X.1    Xiao, N.2    Hong, Y.H.3    Zhang, C.4    Su, Y.5    Zhang, X.M.6    Chen, J.M.7
  • 36
    • 0036273511 scopus 로고    scopus 로고
    • Cell signaling during cold, drought, and salt stress
    • Xiong L, Schumaker KS, Zhu JK (2002) Cell signaling during cold, drought, and salt stress. Plant Cell 14:S165–S183
    • (2002) Plant Cell , vol.14 , pp. 165-183
    • Xiong, L.1    Schumaker, K.S.2    Zhu, J.K.3
  • 37
    • 84863081613 scopus 로고    scopus 로고
    • Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique
    • Xu H, Gao Y, Wang J (2012) Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique. PloS one 7:e30646
    • (2012) PloS one , vol.7 , pp. 30646
    • Xu, H.1    Gao, Y.2    Wang, J.3
  • 38
    • 84864117326 scopus 로고    scopus 로고
    • Physiological analysis on mechanisms of cold-tolerance of Dongxiang wild rice (I)
    • COI: 1:CAS:528:DC%2BC3cXosl2gsLk%3D
    • Xu M, Liu X, Yu L (2010) Physiological analysis on mechanisms of cold-tolerance of Dongxiang wild rice (I). Agric Sci Tech 11:39–4.
    • (2010) Agric Sci Tech , vol.11 , pp. 39-34
    • Xu, M.1    Liu, X.2    Yu, L.3
  • 39
    • 0142245708 scopus 로고    scopus 로고
    • Calcium/calmodulin-mediated signal network in plants
    • COI: 1:CAS:528:DC%2BD3sXnvFShsrY%3D, PID: 14557048
    • Yang T, Poovaiah BW (2003) Calcium/calmodulin-mediated signal network in plants. Trends Plant Sci 8:505–51.
    • (2003) Trends Plant Sci , vol.8 , pp. 505-551
    • Yang, T.1    Poovaiah, B.W.2
  • 40
    • 0036808830 scopus 로고    scopus 로고
    • Chill-induced inhibition of photosynthesis: genotypic variation within Cucumis sativus
    • COI: 1:CAS:528:DC%2BD38Xot12htb0%3D, PID: 12407198
    • Yu JQ, Zhou YH, Huang LF, Allen DJ (2002) Chill-induced inhibition of photosynthesis: genotypic variation within Cucumis sativus. Plant Cell Physiol 43:1182–118.
    • (2002) Plant Cell Physiol , vol.43 , pp. 1182-1118
    • Yu, J.Q.1    Zhou, Y.H.2    Huang, L.F.3    Allen, D.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.