Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Shi, Cheng Ying ^a   Yang, Hua ^a   Wei, Chao Ling ^a   Yu, Oliver ^a,b   Zhang, Zheng Zhu ^a   Jiang, Chang Jun ^a   Sun, Jun ^a   Li, Ye Yun ^a   Chen, Qi ^a   Xia, Tao ^a   Wan, Xiao Chun ^a  

^a ANHUI AGRICULTURAL UNIVERSITY   (China)

^b DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAFFEINE; COMPLEMENTARY DNA; FLAVONOID; NATURAL PRODUCT; POLYADENYLATED RNA; THEANINE; PLANT RNA;

ARTICLE; BASE PAIRING; CONTIG MAPPING; CONTROLLED STUDY; DNA LIBRARY; EXPRESSED SEQUENCE TAG; FUNCTIONAL GENOMICS; GENE CLUSTER; GENE EXPRESSION; GENETIC CONSERVATION; GENOME SIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLANT METABOLISM; PROTEIN DOMAIN; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TEA; TRANSCRIPTOMICS; CHEMISTRY; CLUSTER ANALYSIS; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PLANT GENOME;

CAMELLIA SINENSIS;

CAMELLIA SINENSIS; CLUSTER ANALYSIS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE ANNOTATION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, PLANT; SEQUENCE ANALYSIS, DNA; TEA;

EID: 79952045110     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-131     Document Type: Article

References (59)

1. Yamamoto T, Juneja LR, Chu DC, Kim M, . (Eds) Chemistry and Application of Green Tea 1998, CRC Press, New York, (Eds).
2. Rogers PJ, Smith JE, Heatherley SV, Pleydell-Pearce CW. Time for tea: mood, blood pressure and cognitive performance effects of caffeine and theanine administered alone and together. Psychopharmacology 2008, 195:569-577. 10.1007/s00213-007-0938-1, 17891480.
3. Wang Y, Jiang CJ, Zhang HY. Observation on the Self-incompatibility of Pollen Tubes in Self-pollination of Tea Plant in Style in vivo. Tea Sci 2008, 28:429-435.
4. Tanaka J, Taniguchi F. Estimation of the genome size of tea (Camellia sinensis), camellia (C. japonica), and their interspecific hybrids by flow cytometry. Journal of the Remote Sensing Society of Japan 2006, 101:1-7.
5. Park JS, Kim JB, Hahn BS, Kim KH, Ha SH, Kim YH. EST analysis of genes involved in secondary metabolism in Camellia sinensis (tea), using suppression subtractive hybridization. Plant Sci 2004, 166:953-961.
6. Chen L, Zhao LP, Gao QK. Generation and analysis of expressed sequence tags from the tender shoots cDNA library of tea plant (Camellia sinensis). Plant Sci 2005, 168:359-363.
7. Shi CY, Wan XC. Construction of cDNA library for young roots of tea plant (Camellia sinensis (L.) O. Kuntze) and analysis of its expressed sequence tags. Journal of Nanjing Agricultural University 2009, 32:126-130.
8. Boguski MS, Toltoshev CM, Bassett DE. Gene discovery in dbEST. Science 1994, 265:1993-1994. 10.1126/science.8091218, 8091218.
9. Ohlrogge J, Benning C. Unravelling plant metabolism by EST analysis. Curr Opin Plant Bio 2000, 3:224-228.
10. Goossens A, Hakkinen ST, Laakso I, Seppanen-Laakso T, Biondi S, De Sutter V, Lammertyn F, Nuutila AM, Soderlund H, Zabeau M, et al. A functional genomics approach toward the understanding of secondary metabolism in plant cells. PNAS 2003, 100:8595-8600. 10.1073/pnas.1032967100, 166274, 12826618.
11. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
12. Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D, Meyers BC. Short-read sequencing technologies for transcriptional analyses. Annu Rev Plant Bio 2009, 60:305-333.
13. Morozova O, Hirst M, Marra MA. Applications of New Sequencing Technologies for Transcriptome Analysis. Annu Rev Genomics Hum Genet 2009, 10:135-151. 10.1146/annurev-genom-082908-145957, 19715439.
14. Wold B, Myers RM. Sequence census methods for functional genomics. Nature Methods 2008, 5:19-21. 10.1038/nmeth1157, 18165803.
15. Shendure J. The beginning of the end for microarrays?. Nature Methods 2008, 5:585-587. 10.1038/nmeth0708-585, 18587314.
16. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 2009, 10:57-63. 10.1038/nrg2484, 2949280, 19015660.
17. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320:1344-1349. 10.1126/science.1158441, 2951732, 18451266.
18. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008, 453:1239-1243. 10.1038/nature07002, 18488015.
19. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JA. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133(3):523-536. 10.1016/j.cell.2008.03.029, 2723732, 18423832.
20. Cloonan N, Forrest ARR, Kolle G, Gardiner BBA, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods 2008, 5:613-619. 10.1038/nmeth.1223, 18516046.
21. Marioni J, Mason C, Mane S, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18:1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
22. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, et al. A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome. Science 2008, 321:956-960. 10.1126/science.1160342, 18599741.
23. Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 2008, 45:81-94. 10.2144/000112900, 18611170.
24. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology 2008, 17:1636-1647. 10.1111/j.1365-294X.2008.03666.x, 18266620.
25. Kristiansson E, Asker N, Forlin L, Larsson DGJ. Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. BMC Genomics 2009, 10:345. 10.1186/1471-2164-10-345, 2725146, 19646242.
26. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 2009, 10:219. 10.1186/1471-2164-10-219, 2689275, 19435504.
27. Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS. De novo characterization of a whitefly transcriptome and analysis its gene expression during development. BMC Genomics 2010, 11:400. 10.1186/1471-2164-11-400, 2898760, 20573269.
28. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010, 20:265-272. 10.1101/gr.097261.109, 2813482, 20019144.
29. Pertea G, Huang XQ, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, et al. TIGR Gene Indices clustering tools (TGICL):a software system for fast clustering of large EST Datasets. Bioinformatics 2003, 19:651-652. 10.1093/bioinformatics/btg034, 12651724.
30. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al. InterPro: the integrative protein signature database. Nucleic Acids Res 2009, 37:D211-D215. 10.1093/nar/gkn785, 2686546, 18940856.
31. Sompompailin K, Makita Y, Saito K. A WD-repeat-containing putative regulatory protein in anthocyanin biosynthesis in Perilla frutescens. Plant Mol Biol 2002, 50:485-495. 10.1023/A:1019850921627, 12369624.
32. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al. The Pfam protein families database. Nucleic Acids Res 2010, 38:D211-D222. 10.1093/nar/gkp985, 2808889, 19920124.
33. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001, 29:22-28. 10.1093/nar/29.1.22, 29819, 11125040.
34. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nature Genetics 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
35. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674-3676. 10.1093/bioinformatics/bti610, 16081474.
36. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32:D277-D280. 10.1093/nar/gkh063, 308797, 14681412.
37. Khan N, Mukhtar H. Tea polyphenols for health promotion. Life Sci 2007, 81:519-533. 10.1016/j.lfs.2007.06.011, 17655876.
38. Winkel-Shirley B. Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol 2001, 126(2):485-493. 10.1104/pp.126.2.485, 1540115, 11402179.
39. Takeuchi A, Matsumoto S, Hayatsu M. Chalcone synthase from Camellia sinensis: isolation of the cDNAs and the organ-specific and sugar-responsive expression of the genes. Plant Cell Physiol 1994, 35:1011-1018.
40. Lin GZ, Lian YJ, Ryu JH, Sung MK, Park JS, Park HJ, Park BK, Shin JS, Lee MS, Cheon C. Expression and purification of His-tagged flavonol synthase of Camellia sinensis from Escherichia coli. Protein Expr Purif 2007, 55:287-292. 10.1016/j.pep.2007.05.013, 17629496.
41. Singh K, Rani A, Kumar S, Sood P, Mahajan M, Yadav SK, Singh B, Ahuja PS. An early gene of the flavonoid pathway, flavanone 3-hydroxylase, exhibits a positive relationship with the concentration of catechins in tea (Camellia sinensis). Tree Physiol 2008, 28:1349-1356.
42. Rani A, Singh K, Sood P, Kumar S, Ahuja PS. p-Coumarate:CoA ligase as a key gene in the yield of catechins in tea [Camellia sinensis (L.) O. Kuntze]. Funct Integr Genomics 2009, 9:271-275. 10.1007/s10142-008-0098-3, 18931865.
43. Singh K, Kumar S, Rani A, Gulati A, Ahuja PS. Phenylalanine ammonia-lyase (PAL) and cinnamate 4-hydroxylase (C4H) and catechins (flavan-3-ols) accumulation in tea. Funct Integr Genomics 2009, 9:125-134. 10.1007/s10142-008-0092-9, 18679731.
44. Singh K, Rani A, Paul A, Dutt S, Joshi R, Gulati A, Ahuja PS, Kumar S. Differential display mediated cloning of anthocyanidin reductase gene from tea (Camellia sinensis) and its relationship with the concentration of epicatechins. Tree Physiol 2009, 29:837-846. 10.1093/treephys/tpp022, 19380395.
45. Yu O, McGonigle B. Metabolic Engineering of Isoflavone Biosynthesis . Advances in Agronomy 2005, 86:147-190.
46. Hellens RP, Allan AC, Friel EN, Bolitho K, Grafton K, Templeton MD, Karunairetnam S, Gleave AP, Laing WA. Transient expression vectors for functional genomics, quantification of promoter activity and RNA silencing in plants. Plant Methods 2005, 1:13-26. 10.1186/1746-4811-1-13, 1334188, 16359558.
47. Sasaoka K, Kito M, Inagaki H. Biosynthesis of theanine in tea seedlings. Synthesis of theanine by homogenate of tea seedlings. Agric Biol Chem 1963, 27:467-468.
48. Sasaoka K, Kito M, Onishi Y. Some properties of the theanine synthesizing enzyme in tea seedings. Agric Biol Chem 1965, 29:984-988.
49. Takeo T. L-Alanine decarboxylase in Camellia sinensis. Phytochemistry 1978, 17:313-314.
50. Tsushida T, Takeo T. An enzyme hydrolyzing L-theanine in tea leaves. Agric Biol Chem 1985, 49:2913-2917.
51. Kidron H, Repo S, Johnson MS, Salminen TA. Functional classification of amino acid decarboxylases from the alanine racemase structural family by phylogenetic studies. Mol Biol Evo 2007, 24:79-89.
52. Miflin BJ, Habash DZ. The role of glutamine synthetase and glutamate dehydrogenase in nitrogen assimilation and possibilities for improvement in the nitrogen utilization of crops. J Exp Bot 2002, 53:979-987. 10.1093/jexbot/53.370.979, 11912240.
53. Suzuki H, Izuka S, Minami H. Use of bacterial gamma-glutamyltranspeptidase for enzymatic synthesis of gamma-D-glutamyl compounds. Appl Environ Microbiol 2003, 69:6399-6404. 10.1128/AEM.69.11.6399-6404.2003, 262288, 14602592.
54. Yamamoto S, Wakayama M, Tachiki T. Theanine production by coupled fermentation with energy transfer employing Pseudomonas taetrolens Y-30 glutamine synthetase and Baker's yeast cells. Bios Biotechnol Biochem 2005, 69:784-789.
55. Kato M, Mizuno K. Caffeine synthase and related methyltransferases in plants. Front Biosci 2004, 9:1833-1842. 10.2741/1364, 14977590.
56. Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res 1999, 9:868-877. 10.1101/gr.9.9.868, 310812, 10508846.
57. Shi CY, Wan XC, Jiang CJ, Sun J. Method for high-quality total RNA isolation from tea plants [Camellia sinensis (L.) O. Kuntze)]. Journal of Anhui Agricultural University 2007, 34:360-363.
58. Li RQ, Wei F, Geng T, Zhu HM, He L, Cai J, Li B, Bai YQ, Zhang ZH, Zhang YP, et al. The sequence and de novo assembly of the giant panda genome. Nature 2010, 463:311-317. 10.1038/nature08696, 20010809.
59. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C (T)) method. Applied Biosystems 2001, 25:402-408.