Generation and analysis of expressed sequence tags from leaf and root of Withania somnifera (Ashwgandha)

Molecular Biology Reports

Volumn 37, Issue 2, 2010, Pages 893-902

  Senthil, Kalaiselvi ^b   Wasnik, Neha G ^a,b   Kim, Yu Jin ^a   Yang, Deok Chun ^a  

^a Kyung Hee University   (South Korea)

^b AVINASHILINGAM INSTITUTE FOR HOME SCIENCE AND HIGHER EDUCATION FOR WOMEN   (India)

Author keywords

ESTs; Root; Withania somnifera; Withanolides

Indexed keywords

ALKALOID; ARGININE DECARBOXYLASE; CDP ME KINASE; CHITINASE; COMPLEMENTARY DNA; CYTOCHROME P450; GLUCOSYLTRANSFERASE; HYDROXYMETHYLGLUTARYL COENZYME A SYNTHASE; PHOSPHOTRANSFERASE; SQUALENE MONOOXYGENASE; TRANSCRIPTOME; UNCLASSIFIED DRUG; WITHANOLIDE;

ARTICLE; BIOSYNTHESIS; CELL FUNCTION; DNA LIBRARY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC IDENTIFICATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; IN VITRO STUDY; MOLECULAR BIOLOGY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOSYNTHESIS; PLANT LEAF; PLANT ROOT; WITHANIA SOMNIFERA; BIOLOGICAL MODEL; CLUSTER ANALYSIS; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; METABOLISM; WITHANIA;

WITHANIA SOMNIFERA;

CLONING, MOLECULAR; CLUSTER ANALYSIS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; PLANT LEAVES; PLANT ROOTS; SEQUENCE ANALYSIS, DNA; WITHANIA; WITHANOLIDES;

EID: 77950876064     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-009-9696-y     Document Type: Article

References (50)

1. Kulkarni AA, Thengane SR, Krishnamurthy KV (1996) Direct in vitro regeneration of leaf explants of Withania somnifera (L.) Dunal. Plant Sci (Limerick) 119:163-168
2. RajaSankar S, Manivasagam T, Surendran S (2009) Ashwagandha leaf extract: A potential agent in treating oxidative damage and physiological abnormalities seen in a mouse model of Parkinson's disease. Neurosci Lett 454:11-15
3. Ali M, Shuaib M, Ansari SH (1997) Withanolides from the stem bark of Withania somnifera. Phytochemistry 44:1163-1168
4. Ohlrogge J, Benning C (2000) Unraveling plant metabolism by EST analysis. Curr Opin Plant Biol 3:224-228
5. Nagaraj SH, Gasser RB, Nisbet AJ, Ranganathan S (2008) In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): Comparison of the automated ESTExplorer workflow platform with conventional database searches. BMC Bioinform 9:S10
6. Shelton D, Leach D, Baverstock P, Henry RJ (2002) Isolation of genes involved in secondary metabolism from Melaleuca alternifolia (Cheel) using expressed sequence tags (ESTs). Plant Sci 162:9-15
7. Suzuki H, Achnine L, Xu R, Matsuda S, Dixon RA (2002) A genomics approach to the early stages of triterpene saponin biosynthesis in Medicago truncatula. Plant J 32:1033-1048
8. Lange BM, Wildung MR, Stauber EJ, Sanchez C, Pouchnik D, Croteau R (2000) Probing essential oil biosynthesis and secretion by functional evaluation of expressed sequence tags from mint glandular trichomes. Proc Natl Acad Sci 97:2934-2939
9. Goossens A, Hakkinen ST, Laakso I, Seppanen-Laakso T, Biondi S, De Sutter V, Lammertyn F, Nuutila AM, Soderlund H, Zabeau M (2003) A functional genomics approach toward the understanding of secondary metabolism in plant cells. Proc Natl Acad Sci 100:8595-8600
10. Jako C, Coutu C, Roewer I, Reed DW, Pelcher LE, Covello PS (2002) Probing carotenoid biosynthesis in developing seed coats of Bixa orellana (Bixaceae) through expressed sequence tag analysis. Plant Sci (Limerick) 163:141-145
11. Gang DR, Wang J, Dudareva N, Nam KH, Simon JE, Lewinsohn E, Pichersky E (2001) An investigation of the storage and biosynthesis of phenylpropenes in sweet basil. Plant Physiol 125: 539-555
12. Asamizu E, Nakamura Y, Sato S, Tabata S (2000) A large scale analysis of cDNA in Arabidopsis thaliana: Generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries. DNA Res 7:175-180
13. Yamamoto K, Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35:135-144
14. Sterky F, Regan S, Karlsson J, Hertzberg M, Rohde A, Holmberg A, Amini B, Bhalerao R, Larsson M, Villarroel R (1998) Gene discovery in the wood-forming tissues of poplar: Analysis of 5,692 expressed sequence tags. Proc Natl Acad Sci 95:13330-13335
15. 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
16. Lichtenthaler HK (1999) The 1-deoxy-D-xylulose-5-phosphate pathway of isoprenoid biosynthesis in plants. Annu Rev Plant Biol 50:47-65
17. Sangwan RS, Chaurasiya ND, Lal P, Misra L, Uniyal GC, Tuli R, Sangwan NS (2007) Withanolide A biogeneration in in vitro shoot cultures of Ashwagandha (Withania somnifera Dunal), a main medicinal plant in Ayurveda. Chem Pharm Bull 55:1371-1375
18. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco cultures. Physiol Plant 15:473-497
19. Birnboim HC, Doly J (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7:1513-1523
20. Kelley JM, Field CE, Craven MB, Bocskai D, Kim UJ, Rounsley SD, Adams MD (1999) High throughput direct end sequencing of BAC clones. Nucleic Acids Res 27:1539
21. Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 186-194
22. Ewing B, Hillier LD, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 175-185
23. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B (2003) TIGR Gene Indices clustering tools (TGICL): A software system for fast clustering of large EST datasets. Oxford University Press, New York, pp 651-652
24. Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 868-877
25. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
26. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
27. Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196:261
28. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer ELL (2007) The Pfam protein families database. Nucleic Acids Res 36:D281-D288
29. Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960
30. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: A universal tool for annotation visualization and analysis in functional genomics research. Oxford University Press, New York, pp 3674-3676
31. Jung JD, Park HW, Hahn Y, Hur CG, In DS, Chung HJ, Liu JR, Choi DW (2003) Discovery of genes for ginsenoside biosynthesis by analysis of ginseng expressed sequence tags. Plant Cell Rep 22:224-230
32. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36:3420-3435
33. Lindqvist C, Scheen AC, Yoo MJ, Grey P, Oppenheimer DG, Leebens-Mack JH, Soltis DE, Soltis PS, Albert VA (2006) An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): Characterization and microsatellite markers. BMC Plant Biol 6:16
34. Scheideler M, Schlaich NL, Fellenberg K, Beissbarth T, Hauser NC, Vingron M, Slusarenko AJ, Hoheisel JD (2002) Monitoring the switch from housekeeping to pathogen defense metabolism in Arabidopsis thaliana using cDNA arrays. J Biol Chem 277: 10555-10561
35. Guilleroux M, Osbourn A (2004) Gene expression during infection of wheat roots by the 'take-all' fungus Gaeumannomyces graminis. Mol Plant Pathol 5:203-216
36. Sangwan RS, Chaurasiya ND, Lal P, Misra L, Tuli R, Sangwan NS (2008) Withanolide-A is inherently de novo biosynthesized in roots of the medicinal plant Ashwagandha (Withania somnifera). Physiol Plant 133:278-287
37. Park JS, Kim JB, Hahn BS, Kim KH, Ha SH, Kim YH (2004) EST analysis of genes involved in secondary metabolism in Camellia sinensis (tea), using suppression subtractive hybridization. Plant Sci 166:953-961
38. Browne GJ, Finn SG, Proud CG (2004) Stimulation of the AMPactivated protein kinase leads to activation of eukaryotic elongation factor 2 kinase and to its phosphorylation at a novel site, serine 398. J Biol Chem 279:12220-12231
39. Shaneka S, Hari C, Rajendram R, Dwayne S, Isokpehi R (2008) Abundance of universal stress protein family in finished prokaryotic genomes. In: An official conference of the international society for computational biology, CO, pp 29-30
40. Leclerc D, Wilson A, Dumas R, Gafuik C, Song D, Watkins D, Heng HHQ, Rommens JM, Scherer SW, Rosenblatt DS (1998) Cloning and mapping of a cDNA for methionine synthase reductase, a flavoprotein defective in patients with homocystinuria. Proc Natl Acad Sci 95:3059-3064
41. Tiburcio AF, Kaur-Sawhney R, Galston AW (1990) Polyamine metabolism. Biochem Plants 16:283-325
42. Lee GJ, Roseman AM, Saibil HR, Vierling E (1997) A small heat shock protein stably binds heat-denatured model substrates and can maintain a substrate in a folding-competent state. EMBO J 16:659-671
43. Hendry G (1986) Why do plants have cytochrome P-450? Detoxification versus defence. New Phytol 102:239-247
44. Ashikawa I (2001) Gene-associated CpG islands in plants as revealed by analyses of genomic sequences. Plant J 26:617-625
45. Glotter E (1991) Withanolides and related ergostane-type steroids. Nat Prod Rep 8:415-440
46. Kajikawa M, Yamato KT, Kohzu Y, Sakata R, Fukuzawa H, Uchida H, Ohyama K (2004) Expressed sequence tags from callus of Euphorbia tirucalli: A resource for genes involved in triterpenoid and sterol biosynthesis. Plant Biotechnol 21:349-353
47. Vogt T, Jones P (2000) Glycosyltransferases in plant natural product synthesis: Characterization of a supergene family. Trends Plant Sci 5:380-386
48. Hyung Ko J, Gyu Kim B, Joong-Hoon A (2006) Glycosylation of flavonoids with a glycosyltransferase from Bacillus cereus. FEMS Microbiol Lett 258:263-268
49. Sharma LK, Madina BR, Chaturvedi P, Sangwan RS, Tuli R (2007) Molecular cloning and characterization of one member of 3β-hydroxy sterol glucosyltransferase gene family in Withania somnifera. Arch Biochem Biophys 460:48-55
50. Hunter WN (2007) The non-mevalonate pathway of isoprenoid precursor biosynthesis. J Biol Chem 282:21573-21577