메뉴 건너뛰기




Volumn 4, Issue 2, 2011, Pages 129-136

Transcriptome sequencing of a highly salt tolerant mangrove species Sonneratia alba using Illumina platform

Author keywords

Adaptation; Codon usage bias; De novo assemble; High throughput sequencing; Mangroves

Indexed keywords

ADAPTATION; ARTICLE; CODON; COMPARATIVE STUDY; DNA SEQUENCE; EVALUATION; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENETIC MARKER; GENETIC SELECTION; GENETICS; LYTHRACEAE; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SALINITY; SPECIES DIFFERENCE; VARIABLE NUMBER OF TANDEM REPEAT;

EID: 79956356376     PISSN: 18747787     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.margen.2011.03.005     Document Type: Article
Times cited : (49)

References (66)
  • 2
    • 0028973932 scopus 로고
    • Growth responses to salinity in relation to distribution of two mangrove species, Sonneratia alba and S. lanceolata, in Northern Australia
    • Ball M.C., Pidsley S.M. Growth responses to salinity in relation to distribution of two mangrove species, Sonneratia alba and S. lanceolata, in Northern Australia. Funct. Ecol. 1995, 9:77-85.
    • (1995) Funct. Ecol. , vol.9 , pp. 77-85
    • Ball, M.C.1    Pidsley, S.M.2
  • 3
    • 70349487694 scopus 로고    scopus 로고
    • Expression of terpenoid synthase mRNA terpenoid content in salt stressed mangrove
    • Basyuni M., Baba S., Inafuku M., Iwasaki H., Kinjo K., Oku H. Expression of terpenoid synthase mRNA terpenoid content in salt stressed mangrove. J. Plant Physiol. 2009, 166:1786-1800.
    • (2009) J. Plant Physiol. , vol.166 , pp. 1786-1800
    • Basyuni, M.1    Baba, S.2    Inafuku, M.3    Iwasaki, H.4    Kinjo, K.5    Oku, H.6
  • 5
    • 25444472044 scopus 로고    scopus 로고
    • TransAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences
    • Bininda-Emonds O.R.P. transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics 2005, 6:156.
    • (2005) BMC Bioinformatics , vol.6 , pp. 156
    • Bininda-Emonds, O.R.P.1
  • 7
    • 0037237973 scopus 로고    scopus 로고
    • Antioxidants, oxidative damage and oxygen deprivation stress: a review
    • Blokhina O., Virolainen E., Fagerstedt K.V. Antioxidants, oxidative damage and oxygen deprivation stress: a review. Ann. Bot. 2003, 91:179-194.
    • (2003) Ann. Bot. , vol.91 , pp. 179-194
    • Blokhina, O.1    Virolainen, E.2    Fagerstedt, K.V.3
  • 10
    • 43949138227 scopus 로고    scopus 로고
    • Blast2GO: a comprehensive suite for functional analysis in plant genomics
    • Conesa A., Gotz S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics 2008, 2008:619832.
    • (2008) Int. J. Plant Genomics , vol.2008 , pp. 619832
    • Conesa, A.1    Gotz, S.2
  • 11
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: a universal tool for annotation, visualization analysis in functional genomics research
    • Conesa A., Gotz S., Garcia-Gomez J.M., Terol J., Talon M., Robles M. Blast2GO: a universal tool for annotation, visualization analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676.
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1    Gotz, S.2    Garcia-Gomez, J.M.3    Terol, J.4    Talon, M.5    Robles, M.6
  • 12
    • 51749119885 scopus 로고    scopus 로고
    • Synonymous codon usage bias dependent on local nucleotide context in the class Deinococci
    • Cutler R.W., Chantawannakul P. Synonymous codon usage bias dependent on local nucleotide context in the class Deinococci. J. Mol. Evol. 2008, 67:301-314.
    • (2008) J. Mol. Evol. , vol.67 , pp. 301-314
    • Cutler, R.W.1    Chantawannakul, P.2
  • 13
    • 67650915750 scopus 로고    scopus 로고
    • Shedding light on an extremophile lifestyle through transcriptomics
    • Dassanayake M., Haas J.S., Bohnert H.J., Cheeseman J.M. Shedding light on an extremophile lifestyle through transcriptomics. New Phytol. 2009, 183:764-775.
    • (2009) New Phytol. , vol.183 , pp. 764-775
    • Dassanayake, M.1    Haas, J.S.2    Bohnert, H.J.3    Cheeseman, J.M.4
  • 14
    • 0001376497 scopus 로고
    • A systematic revision of the mangrove genus Sonneratia (Sonneratiaceae) in Australasia
    • Duke N.C. A systematic revision of the mangrove genus Sonneratia (Sonneratiaceae) in Australasia. Blumea 1987, 32:277-302.
    • (1987) Blumea , vol.32 , pp. 277-302
    • Duke, N.C.1
  • 15
    • 0031669284 scopus 로고    scopus 로고
    • Factors influencing biodiversity distributional gradients in mangroves
    • Duke N.C., Ball M.C., Ellison J.C. Factors influencing biodiversity distributional gradients in mangroves. Global Ecol. Biogeogr. 1998, 7:27-47.
    • (1998) Global Ecol. Biogeogr. , vol.7 , pp. 27-47
    • Duke, N.C.1    Ball, M.C.2    Ellison, J.C.3
  • 16
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: a multiple sequence alignment method with reduced time space complexity
    • Edgar R.C. MUSCLE: a multiple sequence alignment method with reduced time space complexity. BMC Bioinformatics 2004, 5:1-19.
    • (2004) BMC Bioinformatics , vol.5 , pp. 1-19
    • Edgar, R.C.1
  • 18
    • 79956344090 scopus 로고    scopus 로고
    • Vitamins minimize the salt-induced oxidative stress hazards
    • Emam M.M., Helal N.M. Vitamins minimize the salt-induced oxidative stress hazards. Aust. J. Basic Appl. Sci. 2008, 2:1110-1119.
    • (2008) Aust. J. Basic Appl. Sci. , vol.2 , pp. 1110-1119
    • Emam, M.M.1    Helal, N.M.2
  • 19
    • 57649177915 scopus 로고    scopus 로고
    • Identification of salt tolerance genes from the mangrove plant Bruguiera gymnorhiza using Agrobacterium functional screening
    • Ezawa S., Tada Y. Identification of salt tolerance genes from the mangrove plant Bruguiera gymnorhiza using Agrobacterium functional screening. Plant Sci. 2009, 176:272-278.
    • (2009) Plant Sci. , vol.176 , pp. 272-278
    • Ezawa, S.1    Tada, Y.2
  • 20
    • 70449701942 scopus 로고    scopus 로고
    • Sense from sequence reads: methods for alignment assembly
    • Flicek P., Birney E. Sense from sequence reads: methods for alignment assembly. Nat. Methods 2009, 6:S6-S12.
    • (2009) Nat. Methods , vol.6
    • Flicek, P.1    Birney, E.2
  • 21
    • 0000622084 scopus 로고
    • Effects of salt stress on amino acid, organic acid, carbohydrate composition of roots, bacteroids, and cytosol of Alfalfa (Medicago sativa L.)
    • Fougere F., Le Rudulier D., Streeter J.G. Effects of salt stress on amino acid, organic acid, carbohydrate composition of roots, bacteroids, and cytosol of Alfalfa (Medicago sativa L.). Plant Physiol. 1991, 96:1228-1236.
    • (1991) Plant Physiol. , vol.96 , pp. 1228-1236
    • Fougere, F.1    Le Rudulier, D.2    Streeter, J.G.3
  • 25
    • 43149085041 scopus 로고    scopus 로고
    • De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer
    • Hernandez D., Francois P., Farinelli L., Osteras M., Schrenzel J. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 2008, 18:802-809.
    • (2008) Genome Res. , vol.18 , pp. 802-809
    • Hernandez, D.1    Francois, P.2    Farinelli, L.3    Osteras, M.4    Schrenzel, J.5
  • 27
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: a DNA sequence assembly program
    • Huang X.Q., Madan A. CAP3: a DNA sequence assembly program. Genome Res. 1999, 9:868-877.
    • (1999) Genome Res. , vol.9 , pp. 868-877
    • Huang, X.Q.1    Madan, A.2
  • 28
    • 77954546853 scopus 로고    scopus 로고
    • Pathway analysis of the transcriptome metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms
    • Janz D., Behnke K., Schnitzler J.P., Kanawati B., Schmitt-Kopplin P., Polle A. Pathway analysis of the transcriptome metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms. BMC Plant Biol. 2010, 10:150.
    • (2010) BMC Plant Biol. , vol.10 , pp. 150
    • Janz, D.1    Behnke, K.2    Schnitzler, J.P.3    Kanawati, B.4    Schmitt-Kopplin, P.5    Polle, A.6
  • 29
    • 0346732986 scopus 로고    scopus 로고
    • Patterns of codon usage bias in three dicot and four monocot plant species
    • Kawabe A., Miyashita N.T. Patterns of codon usage bias in three dicot and four monocot plant species. Genes Genet. Syst. 2003, 78:343-352.
    • (2003) Genes Genet. Syst. , vol.78 , pp. 343-352
    • Kawabe, A.1    Miyashita, N.T.2
  • 30
    • 0036133146 scopus 로고    scopus 로고
    • Correlations between mRNA expression levels GC contents of coding untranslated regions of genes in rodents
    • Konu O., Li M.D. Correlations between mRNA expression levels GC contents of coding untranslated regions of genes in rodents. J. Mol. Evol. 2002, 54:35-41.
    • (2002) J. Mol. Evol. , vol.54 , pp. 35-41
    • Konu, O.1    Li, M.D.2
  • 31
    • 33745198703 scopus 로고    scopus 로고
    • High guanine cytosine content increases mRNA levels in mammalian cells
    • Kudla G., Lipinski L., Caffin F., Helwak A., Zylicz M. High guanine cytosine content increases mRNA levels in mammalian cells. PLoS Biol. 2006, 4:e180.
    • (2006) PLoS Biol. , vol.4
    • Kudla, G.1    Lipinski, L.2    Caffin, F.3    Helwak, A.4    Zylicz, M.5
  • 32
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering comparing large sets of protein or nucleotide sequences
    • Li W., Godzik A. Cd-hit: a fast program for clustering comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 33
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads calling variants using mapping quality scores
    • Li H., Ruan J., Durbin R. Mapping short DNA sequencing reads calling variants using mapping quality scores. Genome Res. 2008, 18:1851-1858.
    • (2008) Genome Res. , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 34
    • 44849094868 scopus 로고    scopus 로고
    • Adaptation to salinity in mangroves: implication on the evolution of salt-tolerance
    • Liang S., Zhou R.C., Dong S.S., Shi S.H. Adaptation to salinity in mangroves: implication on the evolution of salt-tolerance. Chin. Sci. Bull. 2008, 53:8.
    • (2008) Chin. Sci. Bull. , vol.53 , pp. 8
    • Liang, S.1    Zhou, R.C.2    Dong, S.S.3    Shi, S.H.4
  • 36
    • 19444363142 scopus 로고    scopus 로고
    • Comparative studies on codon usage pattern of chloroplasts their host nuclear genes in four plant species
    • Liu Q.P., Xue Q.Z. Comparative studies on codon usage pattern of chloroplasts their host nuclear genes in four plant species. J. Genet. 2005, 84:55-62.
    • (2005) J. Genet. , vol.84 , pp. 55-62
    • Liu, Q.P.1    Xue, Q.Z.2
  • 37
    • 79956369051 scopus 로고    scopus 로고
    • Comparative analysis of amino acid between transgenic non transgenic Egyptian cotton (Gossypium barbadense) lines under different salt stress conditions
    • Momtaz O.A., Fahmy A.H., Diab A.A., Ahmad A.H. Comparative analysis of amino acid between transgenic non transgenic Egyptian cotton (Gossypium barbadense) lines under different salt stress conditions. American-Eurasian J. Agric. Environ. Sci. 2007, 2:6-15.
    • (2007) American-Eurasian J. Agric. Environ. Sci. , vol.2 , pp. 6-15
    • Momtaz, O.A.1    Fahmy, A.H.2    Diab, A.A.3    Ahmad, A.H.4
  • 38
    • 0033541967 scopus 로고    scopus 로고
    • Infectious virus in transgenic plants inoculated with a nonviable, P1-proteinase defective mutant of a potyvirus
    • Moreno M., Brandwagt B.F., Shaw J.G., Rodriguez-Cerezo E. Infectious virus in transgenic plants inoculated with a nonviable, P1-proteinase defective mutant of a potyvirus. Virology 1999, 257:322-329.
    • (1999) Virology , vol.257 , pp. 322-329
    • Moreno, M.1    Brandwagt, B.F.2    Shaw, J.G.3    Rodriguez-Cerezo, E.4
  • 40
    • 25444461374 scopus 로고    scopus 로고
    • Genes and salt tolerance: bringing them together
    • Munns R. Genes and salt tolerance: bringing them together. New Phytol. 2005, 167:645-663.
    • (2005) New Phytol. , vol.167 , pp. 645-663
    • Munns, R.1
  • 42
    • 77951894310 scopus 로고    scopus 로고
    • Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery
    • Parchman T.L., Geist K.S., Grahnen J.A., Benkman C.W., Buerkle C.A. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 2010, 11:180.
    • (2010) BMC Genomics , vol.11 , pp. 180
    • Parchman, T.L.1    Geist, K.S.2    Grahnen, J.A.3    Benkman, C.W.4    Buerkle, C.A.5
  • 43
    • 0022202002 scopus 로고
    • Osmotic adaption in Australian mangroves
    • Popp M., Larher F., Weigel P. Osmotic adaption in Australian mangroves. Vegetation 1985, 61:247-253.
    • (1985) Vegetation , vol.61 , pp. 247-253
    • Popp, M.1    Larher, F.2    Weigel, P.3
  • 45
    • 56849102145 scopus 로고    scopus 로고
    • Molecular evidence for natural hybridization between Sonneratia alba and S. griffithii
    • Qiu L., Zhou R.C., Li Y.Q., Havanond S., Jaengjai C., Shi S.H. Molecular evidence for natural hybridization between Sonneratia alba and S. griffithii. J. Syst. Evol. 2008, 46:391-395.
    • (2008) J. Syst. Evol. , vol.46 , pp. 391-395
    • Qiu, L.1    Zhou, R.C.2    Li, Y.Q.3    Havanond, S.4    Jaengjai, C.5    Shi, S.H.6
  • 46
    • 0142129176 scopus 로고    scopus 로고
    • Salinity, osmolytes and compatible solutes
    • Kluwer Academic publishers, Netherlands, A. Laüchli, U. Lüttge (Eds.)
    • Rhodes D., Nadolska-Orczyk A., Rich P.J. Salinity, osmolytes and compatible solutes. Salinity: Environment - Plants - Molecules 2002, 181-204. Kluwer Academic publishers, Netherlands. A. Laüchli, U. Lüttge (Eds.).
    • (2002) Salinity: Environment - Plants - Molecules , pp. 181-204
    • Rhodes, D.1    Nadolska-Orczyk, A.2    Rich, P.J.3
  • 47
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European molecular biology open software suite
    • Rice P., Longden I., Bleasby A. EMBOSS: The European molecular biology open software suite. Trends Genet. 2000, 16:276-277.
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 48
    • 0036239958 scopus 로고    scopus 로고
    • Recent studies on metallothionein: Protection against toxicity of heavy metals and oxygen free radicals
    • Sato M., Kondoh M. Recent studies on metallothionein: Protection against toxicity of heavy metals and oxygen free radicals. Tohoku J. Exp. Med. 2002, 196:9-22.
    • (2002) Tohoku J. Exp. Med. , vol.196 , pp. 9-22
    • Sato, M.1    Kondoh, M.2
  • 49
    • 0034765914 scopus 로고    scopus 로고
    • Exogenous ascorbic acid (vitamin C) increases resistance to salt stress and reduces lipid peroxidation
    • Shalata A., Neumann P.M. Exogenous ascorbic acid (vitamin C) increases resistance to salt stress and reduces lipid peroxidation. J. Exp. Bot. 2001, 52:2207-2211.
    • (2001) J. Exp. Bot. , vol.52 , pp. 2207-2211
    • Shalata, A.1    Neumann, P.M.2
  • 50
    • 0023650543 scopus 로고
    • The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp P.M., Li W.H. The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987, 15:1281-1295.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 51
    • 0023046874 scopus 로고
    • Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes
    • Sharp P.M., Tuohy T.M. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986, 14:5125-5143.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 5125-5143
    • Sharp, P.M.1    Tuohy, T.M.2
  • 53
    • 85040853075 scopus 로고
    • Cambridge University Press, Cambridge Cambridgeshire; New York
    • Tomlinson P.B. The Botany of Mangroves 1986, Cambridge University Press, Cambridge Cambridgeshire; New York.
    • (1986) The Botany of Mangroves
    • Tomlinson, P.B.1
  • 54
    • 69949181554 scopus 로고    scopus 로고
    • Auxin redistribution modulates plastic development of root system and architecture under salt stress in Arabidopsis thaliana
    • Wang Y.N., Li K.X., Li X. Auxin redistribution modulates plastic development of root system and architecture under salt stress in Arabidopsis thaliana. J. Plant Physiol. 2009, 166:1637-1645.
    • (2009) J. Plant Physiol. , vol.166 , pp. 1637-1645
    • Wang, Y.N.1    Li, K.X.2    Li, X.3
  • 55
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 56
    • 78650502725 scopus 로고    scopus 로고
    • De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)
    • Wang Z., Fang B., Chen J., Zhang X., Luo Z., Huang L., Chen X., Li Y. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 2010, 11:726.
    • (2010) BMC Genomics , vol.11 , pp. 726
    • Wang, Z.1    Fang, B.2    Chen, J.3    Zhang, X.4    Luo, Z.5    Huang, L.6    Chen, X.7    Li, Y.8
  • 57
    • 3042674367 scopus 로고    scopus 로고
    • Cell cycle modulation in the response of the primary root of Arabidopsis to salt stress
    • West G., Inze D., Beemster G.T.S. Cell cycle modulation in the response of the primary root of Arabidopsis to salt stress. Plant Physiol. 2004, 135:1050-1058.
    • (2004) Plant Physiol. , vol.135 , pp. 1050-1058
    • West, G.1    Inze, D.2    Beemster, G.T.S.3
  • 59
    • 33845477041 scopus 로고    scopus 로고
    • Isolation of salinity tolerant genes from the mangrove plant, Bruguiera cylindrica by using suppression subtractive hybridization (SSH) and bacterial functional screening
    • Wong Y.Y., Ho C.L., Nguyen P.D., Teo S.S., Harikrishna J.A., Rahim R.A., Wong M.C.V.L. Isolation of salinity tolerant genes from the mangrove plant, Bruguiera cylindrica by using suppression subtractive hybridization (SSH) and bacterial functional screening. Aquat. Bot. 2007, 86:117-122.
    • (2007) Aquat. Bot. , vol.86 , pp. 117-122
    • Wong, Y.Y.1    Ho, C.L.2    Nguyen, P.D.3    Teo, S.S.4    Harikrishna, J.A.5    Rahim, R.A.6    Wong, M.C.V.L.7
  • 60
    • 0025318864 scopus 로고
    • The 'effective number of codons' used in a gene
    • Wright F. The 'effective number of codons' used in a gene. Gene 1990, 87:23-29.
    • (1990) Gene , vol.87 , pp. 23-29
    • Wright, F.1
  • 62
    • 77951822618 scopus 로고    scopus 로고
    • The effect of salinity on anatomical structure and alkaloid production in Pomegranate (abstract)
    • Zarinkamar F., Asfa A. The effect of salinity on anatomical structure and alkaloid production in Pomegranate (abstract). Rostaniha 2005, 6:97-106.
    • (2005) Rostaniha , vol.6 , pp. 97-106
    • Zarinkamar, F.1    Asfa, A.2
  • 63
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18:821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 65
    • 18144411709 scopus 로고    scopus 로고
    • Molecular criteria for determining new hybrid species-an application to the Sonneratia hybrids
    • Zhou R., Shi S., Wu C.I. Molecular criteria for determining new hybrid species-an application to the Sonneratia hybrids. Mol. Phylogenet. Evol. 2005, 35:595-601.
    • (2005) Mol. Phylogenet. Evol. , vol.35 , pp. 595-601
    • Zhou, R.1    Shi, S.2    Wu, C.I.3
  • 66
    • 0036999615 scopus 로고    scopus 로고
    • Salt and drought stress signal transduction in plants
    • Zhu J.K. Salt and drought stress signal transduction in plants. Annu. Rev. Plant Biol. 2002, 53:247-273.
    • (2002) Annu. Rev. Plant Biol. , vol.53 , pp. 247-273
    • Zhu, J.K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.