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Volumn 17, Issue 3, 2013, Pages 391-403

Next-generation sequencing-based transcriptome profiling analysis of Pohlia nutans reveals insight into the stress-relevant genes in Antarctic moss

Author keywords

Cold treatment; Gene expression profiling; High throughput RNA sequencing; Mosses; Transcriptome

Indexed keywords

BRYOPHYTA; POHLIA NUTANS;

EID: 84876688441     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-013-0528-6     Document Type: Article
Times cited : (31)

References (46)
  • 2
    • 84355162181 scopus 로고    scopus 로고
    • Cold acclimation in the moss Physcomitrella patens involves abscisic acid-dependent signaling
    • Bhyan SB, Minami A, Kaneko Y, Suzuki S, Arakawa K, Sakata Y, Takezawa D (2012) Cold acclimation in the moss Physcomitrella patens involves abscisic acid-dependent signaling. J Plant Physiol 169(2): 137-145.
    • (2012) J Plant Physiol , vol.169 , Issue.2 , pp. 137-145
    • Bhyan, S.B.1    Minami, A.2    Kaneko, Y.3    Suzuki, S.4    Arakawa, K.5    Sakata, Y.6    Takezawa, D.7
  • 3
    • 62249203564 scopus 로고    scopus 로고
    • Transcriptomics: the digital generation
    • Blow N (2009) Transcriptomics: the digital generation. Nature 458: 239-242.
    • (2009) Nature , vol.458 , pp. 239-242
    • Blow, N.1
  • 4
    • 39049111525 scopus 로고    scopus 로고
    • The effect of environmental change on vascular plant and cryptogam communities from the Falkland Islands and the Maritime Antarctic
    • Bokhorst S, Huiskes A, Convey P, Aerts R (2007) The effect of environmental change on vascular plant and cryptogam communities from the Falkland Islands and the Maritime Antarctic. BMC Ecol 7: 15.
    • (2007) BMC Ecol , vol.7 , pp. 15
    • Bokhorst, S.1    Huiskes, A.2    Convey, P.3    Aerts, R.4
  • 6
    • 34848912307 scopus 로고    scopus 로고
    • Antarctic Biodiversity
    • Convey P, Stevens MI (2007) Antarctic Biodiversity. Science 317: 1877-1878.
    • (2007) Science , vol.317 , pp. 1877-1878
    • Convey, P.1    Stevens, M.I.2
  • 7
    • 79953254419 scopus 로고    scopus 로고
    • The RLK/Pelle family of kinases
    • Gish LA, Clark SE (2011) The RLK/Pelle family of kinases. Plant J 66: 117-127.
    • (2011) Plant J , vol.66 , pp. 117-127
    • Gish, L.A.1    Clark, S.E.2
  • 9
    • 50649122770 scopus 로고    scopus 로고
    • EagleView: a genome assembly viewer for nextgeneration sequencing technologies
    • Huang W, Marth G (2008) EagleView: a genome assembly viewer for nextgeneration sequencing technologies. Genome Res 18: 1538-1543.
    • (2008) Genome Res , vol.18 , pp. 1538-1543
    • Huang, W.1    Marth, G.2
  • 10
    • 42149115630 scopus 로고    scopus 로고
    • LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana
    • Hundertmark M, Hincha DK (2008) LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC Genomics 9: 118.
    • (2008) BMC Genomics , vol.9 , pp. 118
    • Hundertmark, M.1    Hincha, D.K.2
  • 11
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: 355-360.
    • (2010) Nucleic Acids Res , vol.38 , pp. 355-360
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 12
    • 66149113974 scopus 로고    scopus 로고
    • Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes
    • Lehti-Shiu MD, Zou C, Hanada K, Shiu SH (2009) Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. Plant Physiol 150: 12-26.
    • (2009) Plant Physiol , vol.150 , pp. 12-26
    • Lehti-Shiu, M.D.1    Zou, C.2    Hanada, K.3    Shiu, S.H.4
  • 13
    • 80053350637 scopus 로고    scopus 로고
    • Transcriptome profiling of Pinus radiata juvenile wood with contrasting stiffness identifies putative candidate genes involved in microfibril orientation and cell wall mechanics
    • Li XG, Wu HX, Southerton SG (2011) Transcriptome profiling of Pinus radiata juvenile wood with contrasting stiffness identifies putative candidate genes involved in microfibril orientation and cell wall mechanics. BMC Genomics 12: 480.
    • (2011) BMC Genomics , vol.12 , pp. 480
    • Li, X.G.1    Wu, H.X.2    Southerton, S.G.3
  • 15
    • 77952427556 scopus 로고    scopus 로고
    • Complementary DNA library construction and expressed sequence tag analysis of an Arctic moss, Aulacomnium turgidum
    • Liu SH, Lee HS, Kang PS, Huang XH, Yim JH, Lee HK, Kim Il-C (2010) Complementary DNA library construction and expressed sequence tag analysis of an Arctic moss, Aulacomnium turgidum. Polar Biol 33: 617-626.
    • (2010) Polar Biol , vol.33 , pp. 617-626
    • Liu, S.H.1    Lee, H.S.2    Kang, P.S.3    Huang, X.H.4    Yim, J.H.5    Lee, H.K.6    Kim, I.-C.7
  • 16
    • 0029186849 scopus 로고
    • Reversible photoinhibition in Antarctic moss during freezing and thawing
    • Lovelock CE, Jackson AE, Melick DR, Seppelt RD (1995) Reversible photoinhibition in Antarctic moss during freezing and thawing. Plant Physiol 109: 955-961.
    • (1995) Plant Physiol , vol.109 , pp. 955-961
    • Lovelock, C.E.1    Jackson, A.E.2    Melick, D.R.3    Seppelt, R.D.4
  • 17
    • 14944367017 scopus 로고    scopus 로고
    • Cold acclimation in bryophytes: low-temperature-induced freezing tolerance in Physcomitrella patens is associated with increases in expression levels of stress-related genes but not with increase in level of endogenous abscisic acid
    • Minami A, Nagao M, Ikegami K, Koshiba T, Arakawa K, Fujikawa S, Takezawa D (2005) Cold acclimation in bryophytes: low-temperature-induced freezing tolerance in Physcomitrella patens is associated with increases in expression levels of stress-related genes but not with increase in level of endogenous abscisic acid. Planta 220(3): 414-423.
    • (2005) Planta , vol.220 , Issue.3 , pp. 414-423
    • Minami, A.1    Nagao, M.2    Ikegami, K.3    Koshiba, T.4    Arakawa, K.5    Fujikawa, S.6    Takezawa, D.7
  • 18
    • 79951571893 scopus 로고    scopus 로고
    • Unusual P450 reactions in plant secondary metabolism
    • Mizutani M, Sato F (2011) Unusual P450 reactions in plant secondary metabolism. Arch Biochem Biophys 507(1): 194-203.
    • (2011) Arch Biochem Biophys , vol.507 , Issue.1 , pp. 194-203
    • Mizutani, M.1    Sato, F.2
  • 21
    • 49249107677 scopus 로고    scopus 로고
    • Climate change and the microbiology of the Antarctic Peninsula region
    • Pearce DA (2008) Climate change and the microbiology of the Antarctic Peninsula region. Sci Prog 91: 203-217.
    • (2008) Sci Prog , vol.91 , pp. 203-217
    • Pearce, D.A.1
  • 22
    • 20244386700 scopus 로고    scopus 로고
    • Genomics: applications to Antarctic ecosystems
    • Peck LS, Clark MS, Clarke A et al (2005) Genomics: applications to Antarctic ecosystems. Polar Biol 28: 351-365.
    • (2005) Polar Biol , vol.28 , pp. 351-365
    • Peck, L.S.1    Clark, M.S.2    Clarke, A.3
  • 23
    • 84862778928 scopus 로고    scopus 로고
    • Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile
    • Qi XH, Xu XW, Lin XJ, Zhang WJ, Chen XH (2012) Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile. Genomics 99: 160-168.
    • (2012) Genomics , vol.99 , pp. 160-168
    • Qi, X.H.1    Xu, X.W.2    Lin, X.J.3    Zhang, W.J.4    Chen, X.H.5
  • 24
    • 73149112186 scopus 로고    scopus 로고
    • Natural variation reveals relationships between pre-stress carbohydrate nutritional status and subsequent responses to xenobiotic and oxidative stress in Arabidopsis thaliana
    • Ramel F, Sulmon C, Gouesbet G, Couée I (2009) Natural variation reveals relationships between pre-stress carbohydrate nutritional status and subsequent responses to xenobiotic and oxidative stress in Arabidopsis thaliana. Ann Bot 104(7): 1323-1337.
    • (2009) Ann Bot , vol.104 , Issue.7 , pp. 1323-1337
    • Ramel, F.1    Sulmon, C.2    Gouesbet, G.3    Couée, I.4
  • 25
    • 84858668893 scopus 로고    scopus 로고
    • Role of trehalose in salinity and temperature tolerance in the model halophilic bacterium Chromohalobacter salexigens
    • Reina-Bueno M, Argandoña M, Salvador M, Rodríguez-Moya J, Iglesias-Guerra F et al (2012) Role of trehalose in salinity and temperature tolerance in the model halophilic bacterium Chromohalobacter salexigens. PLoS ONE 7(3): e33587.
    • (2012) PLoS ONE , vol.7 , Issue.3
    • Reina-Bueno, M.1    Argandoña, M.2    Salvador, M.3    Rodríguez-Moya, J.4    Iglesias-Guerra, F.5
  • 26
    • 37849032457 scopus 로고    scopus 로고
    • The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
    • Rensing SA, Lang D, Zimmer AD et al (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319: 64-69.
    • (2008) Science , vol.319 , pp. 64-69
    • Rensing, S.A.1    Lang, D.2    Zimmer, A.D.3
  • 27
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: the European molecular biology open software suite
    • Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16: 276-277.
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 28
    • 77952478526 scopus 로고    scopus 로고
    • Mitogen-activated protein kinase signaling in plants
    • Rodriguez MC, Petersen M, Mundy J (2010) Mitogen-activated protein kinase signaling in plants. Annu Rev Plant Biol 61: 621-649.
    • (2010) Annu Rev Plant Biol , vol.61 , pp. 621-649
    • Rodriguez, M.C.1    Petersen, M.2    Mundy, J.3
  • 29
    • 51749102658 scopus 로고    scopus 로고
    • Characterizing the mouse ES cell transcriptome with Illumina sequencing
    • Rosenkranz R, Borodina T, Lehrach H, Himmelbauer H (2008) Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics 92: 187-194.
    • (2008) Genomics , vol.92 , pp. 187-194
    • Rosenkranz, R.1    Borodina, T.2    Lehrach, H.3    Himmelbauer, H.4
  • 30
    • 84859768479 scopus 로고    scopus 로고
    • Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
    • Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28: 1086-1092.
    • (2012) Bioinformatics , vol.28 , pp. 1086-1092
    • Schulz, M.H.1    Zerbino, D.R.2    Vingron, M.3    Birney, E.4
  • 31
    • 37749031255 scopus 로고    scopus 로고
    • Next-generation sequencing transforms today's biology
    • Schuster SC (2008) Next-generation sequencing transforms today's biology. Nat Methods 5: 16-18.
    • (2008) Nat Methods , vol.5 , pp. 16-18
    • Schuster, S.C.1
  • 32
    • 0033805958 scopus 로고    scopus 로고
    • Genetic diversity, mutagenesis and dispersal of Antarctic mosses-a review of progress with molecular studies
    • Skotnicki ML, Ninham JA, Selkirk PM (2000) Genetic diversity, mutagenesis and dispersal of Antarctic mosses-a review of progress with molecular studies. Antarct Sci 12: 363-373.
    • (2000) Antarct Sci , vol.12 , pp. 363-373
    • Skotnicki, M.L.1    Ninham, J.A.2    Selkirk, P.M.3
  • 33
    • 24644477084 scopus 로고    scopus 로고
    • DNA sequencing and genetic diversity of the 18S-26S nuclear ribosomal internal transcribed spacers (ITS) in nine Antarctic moss species
    • Skotnicki ML, Mackenzie AM, Clements MA, Selkirk PM (2005) DNA sequencing and genetic diversity of the 18S-26S nuclear ribosomal internal transcribed spacers (ITS) in nine Antarctic moss species. Antarctic Sci 17: 377-384.
    • (2005) Antarctic Sci , vol.17 , pp. 377-384
    • Skotnicki, M.L.1    Mackenzie, A.M.2    Clements, M.A.3    Selkirk, P.M.4
  • 34
    • 36949023148 scopus 로고    scopus 로고
    • Differentially expressed genes under cold acclimation in Physcomitrella patens
    • Sun MM, Li LH, Xie H, Ma RC, He YK (2007) Differentially expressed genes under cold acclimation in Physcomitrella patens. J Biochem Mol Biol 40(6): 986-1001.
    • (2007) J Biochem Mol Biol , vol.40 , Issue.6 , pp. 986-1001
    • Sun, M.M.1    Li, L.H.2    Xie, H.3    Ma, R.C.4    He, Y.K.5
  • 35
    • 0036928033 scopus 로고    scopus 로고
    • Low-temperature-induced changes in trehalose, mannitol and arabitol associated with enhanced tolerance to freezing in ectomycorrhizal basidiomycetes (Hebeloma spp.)
    • Tibbett M, Sanders F, Cairney J (2002) Low-temperature-induced changes in trehalose, mannitol and arabitol associated with enhanced tolerance to freezing in ectomycorrhizal basidiomycetes (Hebeloma spp.). Mycorrhiza 12(5): 249-255.
    • (2002) Mycorrhiza , vol.12 , Issue.5 , pp. 249-255
    • Tibbett, M.1    Sanders, F.2    Cairney, J.3
  • 36
    • 70350223958 scopus 로고    scopus 로고
    • Proteomic analysis of the cold stress response in the moss, Physcomitrella patens
    • Wang X, Yang P, Zhang X, Xu Y, Kuang T, Shen S, He Y (2009) Proteomic analysis of the cold stress response in the moss, Physcomitrella patens. Proteomics 9(19): 4529-4538.
    • (2009) Proteomics , vol.9 , Issue.19 , pp. 4529-4538
    • Wang, X.1    Yang, P.2    Zhang, X.3    Xu, Y.4    Kuang, T.5    Shen, S.6    He, Y.7
  • 37
    • 75249095274 scopus 로고    scopus 로고
    • DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
    • Wang L, Feng Z, Wang X, Wang X, Zhang X (2010a) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26: 136-138.
    • (2010) Bioinformatics , vol.26 , pp. 136-138
    • Wang, L.1    Feng, Z.2    Wang, X.3    Wang, X.4    Zhang, X.5
  • 38
    • 77951998724 scopus 로고    scopus 로고
    • Exploring plant transcriptomes using ultra high-throughput sequencing
    • Wang L, Li PH, Brutnell TP (2010b) Exploring plant transcriptomes using ultra high-throughput sequencing. Brief Funct Genomics 9: 118-128.
    • (2010) Brief Funct Genomics , vol.9 , pp. 118-128
    • Wang, L.1    Li, P.H.2    Brutnell, T.P.3
  • 39
    • 80052825742 scopus 로고    scopus 로고
    • Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers
    • Wei WL, Qi XQ, Wang LH, Zhang YX, Hua W, Li DH, Lv HX, Zhang XR (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12: 451.
    • (2011) BMC Genomics , vol.12 , pp. 451
    • Wei, W.L.1    Qi, X.Q.2    Wang, L.H.3    Zhang, Y.X.4    Hua, W.5    Li, D.H.6    Lv, H.X.7    Zhang, X.R.8
  • 40
    • 33749063413 scopus 로고    scopus 로고
    • Overexpression of carnation S-adenosylmethionine decarboxylase gene generates a broad-spectrum tolerance to abiotic stresses in transgenic tobacco plants
    • Wi SJ, Kim WT, Park KY (2006) Overexpression of carnation S-adenosylmethionine decarboxylase gene generates a broad-spectrum tolerance to abiotic stresses in transgenic tobacco plants. Plant Cell Rep 25: 1111-1121.
    • (2006) Plant Cell Rep , vol.25 , pp. 1111-1121
    • Wi, S.J.1    Kim, W.T.2    Park, K.Y.3
  • 41
    • 77955487334 scopus 로고    scopus 로고
    • Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune relevant genes in marine fish
    • Xiang LX, He D, Dong WR, Zhang YW, Shao JZ (2010) Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune relevant genes in marine fish. BMC Genomics 11: 472.
    • (2010) BMC Genomics , vol.11 , pp. 472
    • Xiang, L.X.1    He, D.2    Dong, W.R.3    Zhang, Y.W.4    Shao, J.Z.5
  • 42
    • 83455195465 scopus 로고    scopus 로고
    • Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens
    • Xiao L, Wang H, Wan P, Kuang T, He Y (2011) Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens. BMC Plant Biol 11: 177.
    • (2011) BMC Plant Biol , vol.11 , pp. 177
    • Xiao, L.1    Wang, H.2    Wan, P.3    Kuang, T.4    He, Y.5
  • 43
    • 77951247055 scopus 로고    scopus 로고
    • A calcium/calmodulin-regulated member of the receptor-like kinase family confers cold tolerance in plants
    • Yang T, Chaudhuri S, Yang L, Du L, Poovaiah BW (2010) A calcium/calmodulin-regulated member of the receptor-like kinase family confers cold tolerance in plants. J Biol Chem 285(10): 7119-7126.
    • (2010) J Biol Chem , vol.285 , Issue.10 , pp. 7119-7126
    • Yang, T.1    Chaudhuri, S.2    Yang, L.3    Du, L.4    Poovaiah, B.W.5
  • 44
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 45
    • 78651337578 scopus 로고    scopus 로고
    • PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database
    • Zhang H, Jin JP, Tang L, Zhao Y, Gu XC, Gao G, Luo JC (2011) PlantTFDB 2. 0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res 39: D1114-D1117.
    • (2011) Nucleic Acids Res , vol.39
    • Zhang, H.1    Jin, J.P.2    Tang, L.3    Zhao, Y.4    Gu, X.C.5    Gao, G.6    Luo, J.C.7
  • 46
    • 79952653330 scopus 로고    scopus 로고
    • CBF-dependent signaling pathway: a key responder to low temperature stress in plants
    • Zhou MQ, Shen C, Wu LH, Tang KX, Lin J (2011) CBF-dependent signaling pathway: a key responder to low temperature stress in plants. Crit Rev Biotechnol 31(2): 186-192.
    • (2011) Crit Rev Biotechnol , vol.31 , Issue.2 , pp. 186-192
    • Zhou, M.Q.1    Shen, C.2    Wu, L.H.3    Tang, K.X.4    Lin, J.5


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