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Volumn 6, Issue , 2016, Pages

De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis

Author keywords

[No Author keywords available]

Indexed keywords

APOCAROTENAL; CAROTENOID; PLANT PROTEIN; TRANSCRIPTOME;

EID: 84960092984     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep22456     Document Type: Article
Times cited : (82)

References (53)
  • 2
    • 33746143206 scopus 로고    scopus 로고
    • HPLC quantification of major active components from 11 different saffron (Crocus sativus L.) sources
    • Caballero-Ortega, H., Pereda-Miranda, R. & Abdullaev, F. I. HPLC quantification of major active components from 11 different saffron (Crocus sativus L.) sources. Food Chem. 100, 1126-1131 (2007).
    • (2007) Food Chem. , vol.100 , pp. 1126-1131
    • Caballero-Ortega, H.1    Pereda-Miranda, R.2    Abdullaev, F.I.3
  • 3
    • 33644653603 scopus 로고    scopus 로고
    • Implications of carotenoid biosynthetic genes in apocarotenoid formation during the stigma development of Crocus sativus and its closer relatives
    • Castillo, R., Fernandez, J.-A. & Gomez-Gomez, L. Implications of carotenoid biosynthetic genes in apocarotenoid formation during the stigma development of Crocus sativus and its closer relatives. Plant Physiol. 139, 674-89 (2005).
    • (2005) Plant Physiol. , vol.139 , pp. 674-689
    • Castillo, R.1    Fernandez, J.-A.2    Gomez-Gomez, L.3
  • 4
    • 84867745625 scopus 로고    scopus 로고
    • Relative expression of CsZCD gene and apocarotenoid biosynthesis during stigma development in
    • Mir, J. I., Ahmed, N., Wafai, A. H. & Qadri, R. A. Relative expression of CsZCD gene and apocarotenoid biosynthesis during stigma development in. Crocus sativus L. 18, 371-375 (2012).
    • (2012) Crocus Sativus L. , vol.18 , pp. 371-375
    • Mir, J.I.1    Ahmed, N.2    Wafai, A.H.3    Qadri, R.A.4
  • 5
    • 0346664458 scopus 로고    scopus 로고
    • Oxidative remodeling of chromoplast carotenoids: Identification of the carotenoid dioxygenase CsCCD and CsZCD genes involved in Crocus secondary metabolite biogenesis
    • Bouvier, F., Suire, C., Mutterer, J. & Camara, B. Oxidative remodeling of chromoplast carotenoids: identification of the carotenoid dioxygenase CsCCD and CsZCD genes involved in Crocus secondary metabolite biogenesis. Plant Cell 15, 47-62 (2003).
    • (2003) Plant Cell , vol.15 , pp. 47-62
    • Bouvier, F.1    Suire, C.2    Mutterer, J.3    Camara, B.4
  • 6
    • 85004693575 scopus 로고
    • Synthesis of crocin, picrocrocin and safranal by saffron stigma-like structures proliferated in vitro
    • Himeno, H. & Sano, K. Synthesis of crocin, picrocrocin and safranal by saffron stigma-like structures proliferated in vitro. Agric. Biol. Chem. 51, 2395-2400 (1987).
    • (1987) Agric. Biol. Chem. , vol.51 , pp. 2395-2400
    • Himeno, H.1    Sano, K.2
  • 7
    • 84872832475 scopus 로고    scopus 로고
    • Safranal: From an aromatic natural product to a rewarding pharmacological agent
    • Rezaee, R. & Hosseinzadeh, H. Safranal: from an aromatic natural product to a rewarding pharmacological agent. Iran. J. Basic Med. Sci. 16, 12-26 (2013).
    • (2013) Iran. J. Basic Med. Sci. , vol.16 , pp. 12-26
    • Rezaee, R.1    Hosseinzadeh, H.2
  • 8
    • 0036377909 scopus 로고    scopus 로고
    • Cancer chemopreventive and tumoricidal properties of saffron (Crocus sativus L.)
    • Abdullaev, F. I. Cancer chemopreventive and tumoricidal properties of saffron (Crocus sativus L.). Exp. Biol. Med. 227, 20-25 (2002).
    • (2002) Exp. Biol. Med. , vol.227 , pp. 20-25
    • Abdullaev, F.I.1
  • 9
    • 0242266951 scopus 로고    scopus 로고
    • Use of in vitro assays to assess the potential antigenotoxic and cytotoxic effects of saffron (Crocus sativus L.)
    • Abdullaev, F. I. et al. Use of in vitro assays to assess the potential antigenotoxic and cytotoxic effects of saffron (Crocus sativus L.). Toxicol. in Vitro 17, 731-736 (2003).
    • (2003) Toxicol. in Vitro , vol.17 , pp. 731-736
    • Abdullaev, F.I.1
  • 10
    • 9644268896 scopus 로고    scopus 로고
    • Biomedical properties of saffron and its potential use in cancer therapy and chemoprevention trials
    • Abdullaev, F. I. & Espinosa-Aguirre, J. J. Biomedical properties of saffron and its potential use in cancer therapy and chemoprevention trials. Cancer Detect. Prev. 28, 426-32 (2004).
    • (2004) Cancer Detect. Prev. , vol.28 , pp. 426-432
    • Abdullaev, F.I.1    Espinosa-Aguirre, J.J.2
  • 12
    • 0034367581 scopus 로고    scopus 로고
    • Saffron-renewed interest in an ancient spice
    • Winterhalter, P. & Straubinger, M. Saffron-Renewed interest in an ancient spice. Food Rev. Int. 16, 39-59 (2000).
    • (2000) Food Rev. Int. , vol.16 , pp. 39-59
    • Winterhalter, P.1    Straubinger, M.2
  • 13
    • 84868530644 scopus 로고    scopus 로고
    • Adulteration and marketing of saffron (Crocus sativus Linn.)
    • Rekha, K., Koul, S. & Ram, G. Adulteration and marketing of saffron (Crocus sativus Linn.). J. Trop. Med. Plants 12, 135-140 (2011).
    • (2011) J. Trop. Med. Plants , vol.12 , pp. 135-140
    • Rekha, K.1    Koul, S.2    Ram, G.3
  • 14
    • 76149100956 scopus 로고    scopus 로고
    • Molecular marker based adulteration detection in traded food and agricultural commodities of plant origin with special reference to spices
    • Dhanya, K. & Sasikumar, B. Molecular marker based adulteration detection in traded food and agricultural commodities of plant origin with special reference to spices. Curr. Trends Biotechnol. Pharm. 4, 454-489 (2010).
    • (2010) Curr. Trends Biotechnol. Pharm. , vol.4 , pp. 454-489
    • Dhanya, K.1    Sasikumar, B.2
  • 15
    • 36549010906 scopus 로고    scopus 로고
    • Use of random amplified polymorphic DNA analysis for economically important food crops
    • Salem, H. H. et al. Use of random amplified polymorphic DNA analysis for economically important food crops. J. Integr. Plant Biol. 49, 1670-1680 (2007).
    • (2007) J. Integr. Plant Biol. , vol.49 , pp. 1670-1680
    • Salem, H.H.1
  • 16
    • 84857219324 scopus 로고    scopus 로고
    • Next-generation sequencing technologies for gene expression profiling in plants
    • Jain, M. Next-generation sequencing technologies for gene expression profiling in plants. Brief. Funct. Genomics 11, 63-70 (2011).
    • (2011) Brief. Funct. Genomics , vol.11 , pp. 63-70
    • Jain, M.1
  • 18
    • 84941561702 scopus 로고    scopus 로고
    • Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis
    • Baba, S. A. et al. Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis. BMC Genomics 16, 698 (2015).
    • (2015) BMC Genomics , vol.16 , pp. 698
    • Baba, S.A.1
  • 19
    • 84906319224 scopus 로고    scopus 로고
    • Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis
    • Frusciante, S. et al. Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis. Proc. Natl. Acad. Sci. USA 111, 12246-12251 (2014).
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 12246-12251
    • Frusciante, S.1
  • 20
    • 7044231921 scopus 로고    scopus 로고
    • Glucosylation of the saffron apocarotenoid crocetin by a glucosyltransferase isolated from
    • Ferna, A. Glucosylation of the saffron apocarotenoid crocetin by a glucosyltransferase isolated from. Crocus sativus stigmas. 219, 955-966 (2004).
    • (2004) Crocus Sativus Stigmas , vol.219 , pp. 955-966
    • Ferna, A.1
  • 21
    • 79961197602 scopus 로고    scopus 로고
    • Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development
    • Garg, R. et al. Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol. 156, 1661-1678 (2011).
    • (2011) Plant Physiol. , vol.156 , pp. 1661-1678
    • Garg, R.1
  • 22
    • 78649294100 scopus 로고    scopus 로고
    • Optimization of de novo transcriptome assembly from next-generation sequencing data
    • Surget-Groba, Y. & Montoya-Burgos, J. I. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res. 20, 1432-1440 (2010).
    • (2010) Genome Res. , vol.20 , pp. 1432-1440
    • Surget-Groba, Y.1    Montoya-Burgos, J.I.2
  • 23
    • 84867388620 scopus 로고    scopus 로고
    • Transcriptional regulation of plant secondary metabolism
    • Yang, C.-Q. et al. Transcriptional regulation of plant secondary metabolism. J. Integr. Plant Biol. 54, 703-712 (2012).
    • (2012) J. Integr. Plant Biol. , vol.54 , pp. 703-712
    • Yang, C.-Q.1
  • 24
    • 33846597097 scopus 로고    scopus 로고
    • Identification of a WRKY protein as a transcriptional regulator of benzylisoquinoline alkaloid biosynthesis in Coptis japonica
    • Kato, N. et al. Identification of a WRKY protein as a transcriptional regulator of benzylisoquinoline alkaloid biosynthesis in Coptis japonica. Plant Cell Physiol. 48, 8-18 (2006).
    • (2006) Plant Cell Physiol. , vol.48 , pp. 8-18
    • Kato, N.1
  • 25
    • 82755176592 scopus 로고    scopus 로고
    • The transcription factor CrWRKY1 positively regulates the terpenoid indole alkaloid biosynthesis in Catharanthus roseus
    • Suttipanta, N. et al. The transcription factor CrWRKY1 positively regulates the terpenoid indole alkaloid biosynthesis in Catharanthus roseus. Plant Physiol. 157, 2081-2093 (2011).
    • (2011) Plant Physiol. , vol.157 , pp. 2081-2093
    • Suttipanta, N.1
  • 26
    • 79958829032 scopus 로고    scopus 로고
    • The basic helix-loop-helix transcription factor CrMYC2 controls the jasmonate-responsive expression of the ORCA genes that regulate alkaloid biosynthesis in Catharanthus roseus
    • Zhang, H. et al. The basic helix-loop-helix transcription factor CrMYC2 controls the jasmonate-responsive expression of the ORCA genes that regulate alkaloid biosynthesis in Catharanthus roseus. Plant J. 67, 61-71 (2011).
    • (2011) Plant J. , vol.67 , pp. 61-71
    • Zhang, H.1
  • 27
    • 84885987125 scopus 로고    scopus 로고
    • Transcriptional regulation of secondary metabolite biosynthesis in plants
    • Patra, B., Schluttenhofer, C., Wu, Y., Pattanaik, S. & Yuan, L. Transcriptional regulation of secondary metabolite biosynthesis in plants. Biochim. Biophys. Acta 1829, 1236-1247 (2013).
    • (2013) Biochim. Biophys. Acta , vol.1829 , pp. 1236-1247
    • Patra, B.1    Schluttenhofer, C.2    Wu, Y.3    Pattanaik, S.4    Yuan, L.5
  • 28
    • 7944238456 scopus 로고    scopus 로고
    • Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice
    • Varshney, R. K. et al. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci. 168, 195-202 (2005).
    • (2005) Plant Sci. , vol.168 , pp. 195-202
    • Varshney, R.K.1
  • 29
    • 64549147083 scopus 로고    scopus 로고
    • RAPD-based method for the quality control of Mediterranean oregano and its contribution to pharmacognostic techniques
    • Marieschi, M., Torelli, A., Poli, F., Sacchetti, G. & Bruni, R. RAPD-based method for the quality control of Mediterranean oregano and its contribution to pharmacognostic techniques. J. Agric. Food Chem. 57, 1835-1840 (2009).
    • (2009) J. Agric. Food Chem. , vol.57 , pp. 1835-1840
    • Marieschi, M.1    Torelli, A.2    Poli, F.3    Sacchetti, G.4    Bruni, R.5
  • 30
    • 77249151476 scopus 로고    scopus 로고
    • Saffron is a monomorphic species as revealed by RAPD, ISSR and microsatellite analyses
    • Rubio-Moraga, A., Castillo-López, R., Gómez-Gómez, L. & Ahrazem, O. Saffron is a monomorphic species as revealed by RAPD, ISSR and microsatellite analyses. BMC Res. Notes 2, 189 (2009).
    • (2009) BMC Res. Notes , vol.2 , pp. 189
    • Rubio-Moraga, A.1    Castillo-López, R.2    Gómez-Gómez, L.3    Ahrazem, O.4
  • 31
    • 84863730087 scopus 로고    scopus 로고
    • Computational identification of miRNAs and their targets from Crocus sativus L
    • Guleria, P., Goswami, D. & Yadav, K. Computational identification of miRNAs and their targets from Crocus sativus L. Arch. Biol. Sci. 64, 65-70 (2012).
    • (2012) Arch. Biol. Sci. , vol.64 , pp. 65-70
    • Guleria, P.1    Goswami, D.2    Yadav, K.3
  • 32
    • 84868584519 scopus 로고    scopus 로고
    • Quality control of saffron (Crocus sativus L.): Development of SCAR markers for the detection of plant adulterants used as bulking agents
    • Marieschi, M., Torelli, A. & Bruni, R. Quality control of saffron (Crocus sativus L.): development of SCAR markers for the detection of plant adulterants used as bulking agents. J. Agric. Food Chem. 60, 10998-11004 (2012).
    • (2012) J. Agric. Food Chem. , vol.60 , pp. 10998-11004
    • Marieschi, M.1    Torelli, A.2    Bruni, R.3
  • 33
    • 78751570979 scopus 로고    scopus 로고
    • RNA sequencing: Advances, challenges and opportunities
    • Ozsolak, F. & Milos, P. M. RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet. 12, 87-98 (2011).
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 87-98
    • Ozsolak, F.1    Milos, P.M.2
  • 34
    • 33746363847 scopus 로고    scopus 로고
    • Importance of transcription factors in the regulation of plant secondary metabolism and their relevance to the control of terpenoid accumulation
    • Broun, P. et al. Importance of transcription factors in the regulation of plant secondary metabolism and their relevance to the control of terpenoid accumulation. Phytochem. Rev. 5, 27-38 (2006).
    • (2006) Phytochem. Rev. , vol.5 , pp. 27-38
    • Broun, P.1
  • 35
    • 0141907262 scopus 로고    scopus 로고
    • Maize phytoene desaturase and ξ -carotene desaturase catalyse a poly-Z desaturation pathway: Implications for genetic engineering of carotenoid content among cereal crops
    • Matthews, P. D., Luo, R. & Wurtzel, E. T. Maize phytoene desaturase and ξ -carotene desaturase catalyse a poly-Z desaturation pathway: Implications for genetic engineering of carotenoid content among cereal crops. J. Exp. Bot. 54, 2215-2230 (2003).
    • (2003) J. Exp. Bot. , vol.54 , pp. 2215-2230
    • Matthews, P.D.1    Luo, R.2    Wurtzel, E.T.3
  • 37
    • 0035049993 scopus 로고    scopus 로고
    • Carotenoid biosynthesis in flowering plants
    • Hirschberg, J. Carotenoid biosynthesis in flowering plants. Curr. Opin. Plant Biol. 4, 210-218 (2001).
    • (2001) Curr. Opin. Plant Biol. , vol.4 , pp. 210-218
    • Hirschberg, J.1
  • 38
    • 0033587751 scopus 로고    scopus 로고
    • The violaxanthin cycle protects plants from photooxidative damage by more than one mechanism
    • Havaux, M. & Niyogi, K. K. The violaxanthin cycle protects plants from photooxidative damage by more than one mechanism. Proc. Natl. Acad. Sci. USA 96, 8762-8767 (1999).
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 8762-8767
    • Havaux, M.1    Niyogi, K.K.2
  • 39
    • 2942700872 scopus 로고    scopus 로고
    • Violaxanthin de-epoxidase, the xanthophyll cycle enzyme, requires lipid inverted hexagonal structures for its activity
    • Latowski, D., Akerlund, H. & Strzałka, K. Violaxanthin de-epoxidase, the xanthophyll cycle enzyme, requires lipid inverted hexagonal structures for its activity. Biochemistry 43, 15-18 (2004).
    • (2004) Biochemistry , vol.43 , pp. 15-18
    • Latowski, D.1    Akerlund, H.2    Strzałka, K.3
  • 41
    • 84855874413 scopus 로고    scopus 로고
    • Developmental and stress regulation of gene expression for a 9-cis-epoxycarotenoid dioxygenase, CstNCED, isolated from Crocus sativus stigmas
    • Ahrazem, O., Rubio-Moraga, A., Trapero, A. & Gómez-Gómez, L. Developmental and stress regulation of gene expression for a 9-cis-epoxycarotenoid dioxygenase, CstNCED, isolated from Crocus sativus stigmas. J. Exp. Bot. 63, 681-694 (2012).
    • (2012) J. Exp. Bot. , vol.63 , pp. 681-694
    • Ahrazem, O.1    Rubio-Moraga, A.2    Trapero, A.3    Gómez-Gómez, L.4
  • 42
    • 84856468953 scopus 로고    scopus 로고
    • NGS QC Toolkit: A toolkit for quality control of next generation sequencing data
    • Patel, R. K. & Jain, M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 7, e30619 (2012).
    • (2012) PloS One , vol.7 , pp. e30619
    • Patel, R.K.1    Jain, M.2
  • 43
    • 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. 18, 821-829 (2008).
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 44
    • 84859768479 scopus 로고    scopus 로고
    • Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
    • Schulz, M. H., Zerbino, D. R., Vingron, M. & Birney, E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28, 1086-1092 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 1086-1092
    • Schulz, M.H.1    Zerbino, D.R.2    Vingron, M.3    Birney, E.4
  • 45
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • Simpson, J. T. et al. ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117-1123 (2009).
    • (2009) Genome Res. , vol.19 , pp. 1117-1123
    • Simpson, J.T.1
  • 46
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
    • (2010) Genome Res. , vol.20 , pp. 265-272
    • Li, R.1
  • 47
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644-652 (2011).
    • (2011) Nat. Biotechnol. , vol.29 , pp. 644-652
    • Grabherr, M.G.1
  • 48
    • 84904991638 scopus 로고    scopus 로고
    • Transcriptome analysis of Catharanthus roseus for gene discovery and expression profiling
    • Verma, M., Ghangal, R., Sharma, R., Sinha, A. K. & Jain, M. Transcriptome analysis of Catharanthus roseus for gene discovery and expression profiling. PLoS One 9, e103583 (2014).
    • (2014) PloS One , vol.9 , pp. e103583
    • Verma, M.1    Ghangal, R.2    Sharma, R.3    Sinha, A.K.4    Jain, M.5
  • 49
    • 0037460985 scopus 로고    scopus 로고
    • TIGR Gene Indices clustering tools (TGICL): A software system for fast clustering of large EST datasets
    • Pertea, G. et al. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19, 651-652 (2003).
    • (2003) Bioinformatics , vol.19 , pp. 651-652
    • Pertea, G.1
  • 51
    • 0037854629 scopus 로고    scopus 로고
    • Exploiting EST databases for the development and characterization of genederived SSR-markers in barley (Hordeum vulgare L.)
    • Thiel, T., Michalek, W., Varshney, R. K. & Graner, A. Exploiting EST databases for the development and characterization of genederived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106, 411-422 (2003).
    • (2003) Theor. Appl. Genet. , vol.106 , pp. 411-422
    • Thiel, T.1    Michalek, W.2    Varshney, R.K.3    Graner, A.4
  • 52
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 53
    • 77952745995 scopus 로고    scopus 로고
    • Validation of internal control genes for quantitative gene expression studies in chickpea (Cicer arietinum L.)
    • Garg, R., Sahoo, A., Tyagi, A. K. & Jain, M. Validation of internal control genes for quantitative gene expression studies in chickpea (Cicer arietinum L.). Biochem. Biophys. Res. Commun. 396, 283-288 (2010).
    • (2010) Biochem. Biophys. Res. Commun. , vol.396 , pp. 283-288
    • Garg, R.1    Sahoo, A.2    Tyagi, A.K.3    Jain, M.4


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