RNA-Seq mediated root transcriptome analysis of Chlorophytum borivilianum for identification of genes involved in saponin biosynthesis
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Abe I, Rohmer M, Prestwich GD (1993) Enzymatic cyclization of squalene and oxidosqualene to sterols and triterpenes. Chem Rev 93:2189–2206
Acharya D, Mitaine-Offer AC, Kaushik N (2009) Cytotoxic spirostane-type saponins from the roots of Chlorophytum borivilianum. J Natl Products 72:177–181
Allardyce JA, Rookes JE, Hussain HI, Cahill DM (2013) Transcriptional profiling of Zea mays roots reveals roles for jasmonic acid and terpenoids in resistance against Phytophthora cinnamomi. Funct Integr Genomics 13:217–228
Anderson MS, Yarger JG, Burck CL, Poulter CD (1989) Farnesyl diphosphate synthetase molecular cloning, sequence, and expression of an essential gene from Saccharomyces cerevisiae. J Biol Chem 264:19176–19184
Bak S, Kahn RA, Olsen CE, Halkier BA (1997) Cloning and expression in Escherichia coli of the obtusifoliol 1, 4 alpha-demethylase of Sorghum bicolor (L.) Moench, a cytochrome P450 orthologous to the sterol 1,4 alpha-demethylases (CYP51) from fungi and mammals. Plant J 11:191–201
Bowles D, Lim EK, Poppenberger B, Vaistij FE (2006) Glycosyltransferases of lipophilic small molecules. Annu Rev Plant Biol 57:567–597
Brown MS, Goldstein JL (1997) The SREBP pathway: regulation of cholesterol metabolism by proteolysis of a membrane-bound transcription factor. Cell 2:89(3):331–340
Cabello HF, Zimmerlin A, Rahier A, Taton M, DeRose R, Nedelkina S, Batard Y, Durst F, Pallett KE, Werck RD (1997) Cloning and functional expression in yeast of a cDNA coding for an obtusifoliol 1,4–demethylase (CYP51) in wheat. Biophys Biochem Res Commun 230:38–385
Caelles C, Ferrer A, Balcells L, Hegardt FG, Boronat A (1989) Isolation and structural characterization of a cDNA encoding Arabidopsis thaliana 3-hydroxy-3-methylglutarylcoenzyme A reductase. Plant Mol Biol 13:627–638
Closa M, Vranova′ E, Bortolotti C, Bigler L, Arro′ M, Ferrer A, Gruissem W (2010) The Arabidopsis thaliana FPP synthase isozymes have overlapping and specific functions in isoprenoid biosynthesis, and complete loss of FPP synthase activity causes early developmental arrest. Plant J 63:512–525
Dabur R, Gupta A, Mandal TK, Singh DD, Bajpai V, Gurav AM, Lavekar GS (2007) Antimicrobial activity of some Indian medicinal plants. Afr J Tradit Complement Altern Med 4:313–318
Dalton-Morgan J, Hayward A, Alamery S et al (2014) A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes. Funct Integr Genomics 14(4):643–655
Furuno M, Kasukawa T, Saito R, Adachi J, Suzuki H, Baldarelli R, Hayashizaki Y, Okazaki Y (2003) CDS annotation in full-length cDNA sequence. Genome Res 13:1478–1487
Geetha KA, Maiti S (2001) Reproductive biology of Safed musli (Chlorophytum borivilianum Sant. & Fern.). J Trop Med Plants 2(2):287–290
Ghawana S, Paul A, Kumar H, Kumar A, Singh H (2011) An RNA isolation system for plant tissues rich in secondary metabolites. BMC Res Notes 4:85–94
Gibbons GF, Goad LJ, Goodwin TW, Nes WR (1971) Concerning the role of lanosterol and cycloartenol in steroid biosynthesis. J Biol Chem 246:3967–3976
Gurielidze KG, Pasehnichenko VA, Vasil’eva IS (1987) Glucohydrolase from the leaves and roots of Dioscorea deltoidea wall. Biokhimia 52:362–370
Gurielidze K, Gogoberidze M, Dadeshidze I, Vardosanidze M, Djaoshvili M, Lomkatsi N (2004) Tissue and subcellular localization of oligofurostanosides and their specific degrading glucosidase in Dioscorea caucasica. Phytochemistry 65:555–559
Haralampadis K, Trojanowska M, Osbourn AE (2002) Biosynthesis of triterpenoid saponins in plants. Adv Biochem Eng Biotechnol 75:31–49
Heim MA, Jakoby M, Werber M, Martin C, Weisshaar B, Bailey PC (2003) The basic helix loop helix transcription factor family in plants: a genome—wide study of protein structure and functional diversity. Mol Biol Evol 20:735–747
Herz S, Wungsintaweekul J, Schuhr CA, Hecht S, Luttgen H, Sagner S, Fellermeier M, Eisenreich W, Zenk MH, Bacher A, Rohdich F (2000) Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate to 2C-methyl-D-erythritol-2,4-cyclodiphosphate. Proc Natl Acad Sci U S A 97:2486–2490
Inoue K, Ebizuka Y (1996) Purification and characterization of furostanol glycoside 26-O-b-glucosidase from Costus speciosus rhizomes. FEBS Lett 378:157–160
Jat RD, Bordia PC (1990) Propagation studies in safed musli (Chlorophytum species). In: BL Chaudhary, NC Aery & SS Katewa (Eds.) Proceedings of the national symposium on advances in plant sciences: current status and emerging challenges. Udaipur: Department of Botany, M. L. Sukhadia University, pp 46
Jiang H, Wong WH (2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25:1026–1032
Joly RA, Bonner J, Benett RD, Heftmann E (1969) The biosynthesis of steroidal sapogenins in Dioscorea floribunda from doubly labelled cholesterol. Phytochemistry 8:1709–1711
Kalra S, Kumar S, Lakhanpal N, Kaur J, Singh K (2013a) Characterization of Squalene synthase gene from Chlorophytum borivilianum (Sant and Fernand). Mol Biotechnol 54:944–953
Kalra S, Puniya BL, Kulshreshtha D et al (2013b) De novo transcriptome sequencing reveals important molecular networks and metabolic pathways of the plant, Chlorophytum borivilianum. PLoS ONE 8:e83336
Kalra S, Kumar S, Singh K (2014) Molecular analysis of squalene epoxidase gene from Chlorophytum borivilianum (Sant. and Fernand.). J Plant Biochem Biotechnol. doi: 10.1007/s13562-014-0292-4
Kirtikar KR, Basu BD (1975) Liliaceae: Chlorophytum. In: Kirtikar, K. R.; Basu, B. D., eds. Indian medicinal plants. Allahabad: L. M. Basu: 2508–2509
Kumar S, Kalra S, Kumar S, Kaur J, Singh K (2012) Differentially expressed transcripts from leaf and root tissue of Chlorophytum borivilianum: a plant with high medicinal value. Gene 511:79–87. doi: 10.1016/j.gene.2012.09.046
Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659
Li Z, Thomas TL (1998) PEI1, an embryo–specific zinc finger protein gene required for heart-stage embryo formation in Arabidopsis. Plant Cell 10:383–398
Maiti S, Geetha KA (2005) Characterization genetic improvement and cultivation of Chlorophytum borivilianum-an important medicinal plant of India. Plant Genet Res 3:264–272
Marisa M, Magaria SL, Kimberly AD, Timothy FO (1997) Sterol regulation of acetyl coenzyme A carboxylase promoter requires two interdependent binding sites for sterol regulatory element binding proteins. J Lipid Res 38:1630–1638
Matsushita Y, Kang WY, Charlwood BV (1996) Cloning and analysis of a cDNA encoding farnesyl diphosphate synthase from Artemisia annua. Gene 172:207–209
Morikawa T, Mizutani M, Aoki N, Watanabe B, Saga H et al (2006) Cytochrome P450 CYP710A encodes the sterol C–22 desaturase in Arabidopsis and tomato. Plant Cell 18:1008–1022
Morozova O, Hirst M, Marra MA (2009) Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 10:135–151
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628
Nagai M, Sakakibara J, Nakamura Y, Gejyo F, Ono T (2002) SREBP-2 and NF-Y are involved in the transcriptional regulation of squalene epoxidase. Biochem Biophys Res Commun 295:74–80
Negi KS, Tiwari JK, Gaur RD, Pant KC (1993) Notes on ethnobotany of five districts of Garhwal Himalaya, Uttar Pradesh, India. Ethnobotany 5:73–81
Oudhia P (2001) My experiences with wonder crop Safed Musli In: Sovenier International Seminar on Medicinal Plants and Quality Standardization, VHERDS, Chennai, India. 9–10
Parkinson J (2009) In expressed sequence tags (ESTs): generation and analysis. New York: Humana Press; Methods Mol Biol 533
Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652
Pfaffl MW, Horgan GW, Dempfle L (2002) Relative Expression Software Tool (REST©) for group wise comparison and statistical analysis of relative expression results in real-time PCR. Nucl Acids Res 30:e36
Purohit SD, Dave A, Kukda G (2004) Micropropagation of safed musli (Chlorphytum borivilianum) a rare Indian medicinal herb. Plant Cell Tissue Organ 39:93–96
Rees HH, Goad LJ, Goodwin TS (1968) Cyclization of 2,3-oxidosqualene to cycloartenol in a cell-free system from higher plants. Tetrahedron Lett 9:723–725
Rees HH, Goad LJ, Goodwin TW (1969) 2,3-Oxidosqualene cycloartenol cyclase from Ochromonas malhamensis. Biochem Biophys Acta 176:892–894
Rohdich F, Kis K, Bacher A, Eisenreich W (2001) The non-mevalonate pathway of isoprenoids: genes, enzymes and intermediates. Curr Opin Chem Biol 5:535–540
Rohdich F, Wungsintaweekul J, Lüttgen H, Fischer M, Eisenreich W, Schuhr CA, Fellermeier M, Schramek N, Zenk MH, Bacher A (2000) Biosynthesis of terpenoids: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase from tomato. Proc Natl Acad Sci U S A 97:8251–8256
Rohmer M (1999) The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria algae and higher plants. Nat Prod Rep 16:565–574
Senthilvel S, Jayashree B, Mahalakshmi V, Kumar PS, Nakka S, Nepolean T, Hash C (2008) Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biol 8:119
Singh K, Foley RC, Onate-Sanchez L (2002) Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 5:430–436
Sung S, Schmitz RJ, Amasino RM (2006) A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis. Genes Dev 20:3244–3248
Takahashi S, Koyama T (2006) Structure and function of cis-prenyl chain elongating enzymes. Chem Rec 6:194–205
Takahashi S, Kuzuyama T, Watanabe H, Seto H (1998) A 1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in an alternative nonmevalonate pathway for terpenoid biosynthesis. Proc Natl Acad Sci U S A 95:9879–9884
Tansey TR, Shechter I (2001) Structure and regulation of mammalian squalene synthase. Biochim Biophys Acta 1529:49–62
Thompson PA, Harrison PJ, Whyte NC (1990) Influence of irradiance on the fatty acid composition of phytoplankton. J Phycol 26:278–288
Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7:537–546
Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12:451–476
Xiao CW (2011) Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics 12:131–163
Yamashita S, Hemmi H, Ikeda Y, Nakayama T, Nishino T (2004) Type 2 isopentenyl diphosphate isomerase from a thermoacidophilic archaeon Sulfolobus shibatae. Eur J Biochem 271(6):1087–1093
Yanhui C, Xiaoyuan Y, Kun H, Meihua L, Jigang L, Zhaofeng G, Zhiqiang L, Yunfei Z, Xiaoxiao W, Xiaoming Q et al (2006) The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol 60:107–124
Yang Y, Li X, Kong X, Lan M, Hu X, Yang Y (2015) Transcriptome analysis reveals diversified adaptation of Stipa purpurea along a drought gradient on the Tibetan Plateau. Funct Integr Genomics 15(3):295–307