Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development
详细信息 查看全文
- 作者：Jianxia Zhang (1) (2)
Kunlin Wu (1)
Songjun Zeng (1)
Jaime A Teixeira da Silva (3)
Xiaolan Zhao (4)
Chang-En Tian (5)
Haoqiang Xia (6)
Jun Duan (1) - 关键词：Floral development ; Flowering time ; Digital gene expression ; Transcriptome ; Cymbidium sinense
- 刊名：BMC Genomics
- 出版年：2013
- 出版时间：December 2013
- 年：2013
- 卷：14
- 期：1
- 全文大小：714KB
- 参考文献：1. Leitch IJ, Kahandawala I, Suda J, Hanson L, Ingrouille MJ, Chase MW, Fay MF: Genome size diversity in orchids: consequences and evolution. / Ann Bot 2009,104(3):469鈥?81. CrossRef
2. Wu ZY, Raven PH, Hong DY: / Flora of China. Volume 25 (Orchidaceae). Beijing, St. Louis: Science Press and Missouri Botanical Garden Press; 2009:260.
3. Bernier G, Havelange A, Houssa C, Petitjean A, Lejeune P: Physiological signals that induce flowering. / Plant Cell 1993, 5:1147鈥?155.
4. Komeda Y: Genetic regulation of time to flower in Arabidopsis thaliana . / Annu Rev Plant Biol 2004, 55:521鈥?35. CrossRef
5. Yu H, Yang SH, Goh CJ: DOH1 , a class 1 knox gene, is required for maintenance of the basic plant architecture and floral transition in orchid. / Plant Cell 2000,12(11):2143鈥?159.
6. Yu H, Yang SH, Goh CJ: Spatial and temporal expression of the orchid floral homeotic gene DOMADS1 is mediated by its upstream regulatory regions. / Plant Mol Biol 2002,49(2):225鈥?37. CrossRef
7. Xu Y, Teo LL, Zhou J, Kumar PP, Yu H: Floral organ identity genes in the orchid Dendrobium crumenatum . / Plant J 2006, 46:54鈥?8. CrossRef
8. Hsu HF, Yang CH: An orchid ( Oncidium Gower Ramsey) AP3 -like MADS gene regulates floral formation and initiation. / Plant Cell Physiol 2002,43(10):1198鈥?209. CrossRef
9. Hsu HF, Huang CH, Chou LT, Yang CH: Ectopic expression of an orchid ( Oncidium Gower Ramsey) AGL6 -like gene promotes flowering by activating flowering time genes in Arabidopsis thaliana . / Plant Cell Physiol 2003,44(8):783鈥?94. CrossRef
10. Niwa Y, Yamashino T, Mizuno T: The circadian clock regulates the photoperiodic response of hypocotyl elongation through a coincidence mechanism in Arabidopsis thaliana . / Plant Cell Physiol 2009,50(4):838鈥?54. CrossRef
11. Putterill J, Robson F, Lee K, Simon R, Coupland G: The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. / Cell 1995, 80:847鈥?57. CrossRef
12. Suarez-Lopez P, Wheatley K, Robson F, Onouchi H, Valverde F, Coupland G: CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis . / Nature 2001, 410:1116鈥?120. CrossRef
13. Tamura K, Dudley J, Nei M, Kumar S: MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. / Mol Biol Evol 2007, 24:1596鈥?599. CrossRef
14. Audic S, Claverie JM: The significance of digital gene expression profiles. / Genome Res 1997,7(10):986鈥?5.
15. Simpson GG: Evolution of flowering in response to day length flipping the CONSTANS switch. / Bioessays 2003, 25:829鈥?32. CrossRef
16. Ahmad M, Cashmore AR: HY4 gene of A. thaliana encodes a protein with characteristics of a blue-light photoreceptor. / Nature 1993, 366:162鈥?66. CrossRef
17. Briggs WR, Beck CF, Cashmore AR, Christie JM, Hughes J, Jarillo JA, Kagawa T, Kanegae H, Liscum E, Nagatani A, Okada K, Salomon M, R眉diger , Sakai T, Takano M, Wada M, Watson JC: The phototropin family of photoreceptors. / Plant Cell 2001, 13:993鈥?97.
18. Lin C, Yang H, Guo H, Mockler T, Chen J, Cashmore AR: Enhancement of the blue-light sensitivity of Arabidopsis young seedlings by a blue-light receptor cry2 . / Proc Natl Acad Sci USA 1998, 95:2686鈥?690. CrossRef
19. Parks BM: Quail PH: hy8, a new class of Arabidopsis long hypocotyl mutants deficient in functional phytochrome A. / Plant Cell 1993, 5:39鈥?8.
20. Reed JW, Nagpal P, Poole DS, Furuya M, Chory J: Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development. / Plant Cell 1993, 5:147鈥?57.
21. Fowler S, Lee K, Onouchi H, Samach A, Richardson K, Morris B, Coupland G, Putterill J: GIGANTEA: a circadian clock controlled gene that regulates photoperiodic flowering in Arabidopsis and encodes a protein with several possible membrane spanning domains. / EMBO J 1999, 18:4679鈥?688. CrossRef
22. Hicks KA, Albertson TM, Wagner DR: EARLY FLOWERING3 encodes a novel protein that regulates circadian clock function and flowering in Arabidopsis . / Plant Cell 2001, 13:1281鈥?292.
23. Simpson GG, Dean C: Arabidopsis , the Rosetta stone of flowering time? / Science 2002, 296:285鈥?89. CrossRef
24. Somers DE: The physiology and molecular bases of the plant circadian clock. / Plant Physiol 1999, 121:9鈥?0. CrossRef
25. Alabadid D, Oyama T, Yanovsky MJ, Harmon FG, Mas P, Kay SA: Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. / Science 2001, 293:880鈥?83. CrossRef
26. Millar AJ: Input signals to the plant circadian clock. / J Exp Bot 2004, 55:277鈥?83. CrossRef
27. McWatters HG, Bastow RM, Hall A, Millar AJ: The ELF3 zeitnehmer regulates light signalling to the circadian clock. / Nature 2000, 408:716鈥?20. CrossRef
28. Dixon LE, Knox K, Kozma-Bognar L, Southern MM, Pokhilko A, Millar AJ: Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis . / Curr Biol 2011, 21:120鈥?25. CrossRef
29. Mizoguchi T, Wright L, Fujiwara S, Cremer F, Lee K, Onouchi H, Mouradov A, Fowler S, Kamada H, Putterill J, Coupland G: Distinct roles of GIGANTEA in promoting flowering and regulating circadian rhythms in Arabidopsis . / Plant Cell 2005, 17:2255鈥?270. CrossRef
30. Locke JCW, Kozma-Bognar L, Gould PD, Feh茅r B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ: Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana . / Mol Syst Biol 2006, 2:59. CrossRef
31. Doyle MR, Davis SJ, Bastow RM, McWatters HG, Kozma-Bognar L, Nagy E, Millar AJ, Amasino RM: The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana . / Nature 2002, 419:74鈥?7. CrossRef
32. Kardailsky I, Shukla VK, Ahn JH, Dagenais N, Christensen SK, Nguyen JT, Chory J, Harrison MJ, Weigel D: Activation tagging of the floral inducer FT . / Science 1999, 286:1962鈥?965. CrossRef
33. Samach A, Onouchi H, Gold SE, Ditta GS, Schwarz-Sommer Z, Yanofsky MF, Coupland G: Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis . / Science 2000, 288:1613鈥?616. CrossRef
34. Griffths S, Dunford RP, Coupland G, Laurie DA: The evolution of CONSTANS- like gene families in barley, rice, and Arabidopsis . / Plant Physiol 2003, 131:1855鈥?867. CrossRef
35. Robson F, Costa MMR, Hepworth SR, Vizir I, Pineiro M, Reeves PH, Putterill J, Coupland G: Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. / Plant J 2001, 28:619鈥?31. CrossRef
36. Ledger S, Strayer C, Ashton F, Kay SA, Putterill J: Analysis of the function of two circadian-regulated CONSTANS- LIKE genes. / Plant J 2001, 26:15鈥?2. CrossRef
37. Chandler J, Wilson A, Dean C: Arabidopsis mutants showing an altered response to vernalization. / Plant J 1996, 10:637鈥?44. CrossRef
38. Sheldon CC, Rouse DT, Finnegan EJ, Peacock WJ, Dennis ES: The molecular basis of vernalization: The central role of FLOWERING LOCUS C ( FLC ). / Proc Natl Acad Sci USA 2000, 97:3753鈥?758. CrossRef
39. Gendall AR, Levy YY, Wilson A, Dean C: The VERNALIZATION 2 gene mediates the epigenetic regulation of vernalization in Arabidopsis . / Cell 2001, 107:525鈥?35. CrossRef
40. Amador V, Monte E, Garcia-Martinez JL, Prat S: Gibberellins signal nuclear import of PHOR1, a photoperiod-responsive protein with homology to Drosophila armadillo . / Cell 2001,106(3):343鈥?54. CrossRef
41. Hepworth SR, Valverde F, Ravenscroft D, Mouradov A, Coupland G: Antagonistic regulation of flowering-time gene SOC1 by CONSTANS and FLC via separate promoter motifs. / EMBO J 2002, 21:4327鈥?337. CrossRef
42. Bradley D, Ratcliffe O, Vincent C, Carpenter R, Coen E: Inflorescence commitment and architecture in Arabidopsis . / Science 1997, 275:80鈥?3. CrossRef
43. Alvarez J, Guli CL, Yu XH, Smyth DR: Terminal flower: a gene affecting inflorescence development in Arabidopsis thaliana . / Plant J 1992, 2:103鈥?16. CrossRef
44. Mandel MA, Gustafson-Brown C, Savidge B, Yanofsky MF: Molecular characterization of the Arabidopsis floral homeotic gene APETALA1 . / Nature 1992, 360:273鈥?77. CrossRef
45. Jofuku KD, den Boer BGW, Van Montagu M, Okamuro JK: Control of Arabidopsis flower and seed development by homeotic gene APETALA2 . / Plant Cell 1994, 6:1211鈥?225.
46. Kempin SA, Savidge B, Yanofsky MF: Molecular basis of the cauliflower phenotype of Arabidopsis . / Science 1994, 267:522鈥?25. CrossRef
47. Yanofsky MF: Floral meristems to floral organs: genes controlling early events in Arabidopsis flower development. / Annu Rev Plant Physiol Plant Mol Biol 1995, 46:167鈥?88. CrossRef
48. Schultz EA, Haughn GW: LEAFY , a homeotic gene that regulates inflorescence development in Arabidopsis . / Plant Cell 1991, 3:771鈥?81.
49. Weigel D, Alvarez J, Smyth DR, Yanofsky MF, Meyerowitz EM: LEAFY controls floral meristem identity in Arabidopsis . / Cell 1992,69(5):843鈥?59. CrossRef
50. Pidkowich MS, Klenz JE, Haughn GW: The making of a flower: control of floral meristem identity in Arabidopsis . / Plant Sci 1999, 4:64鈥?0. CrossRef
51. Coen ES, Romero JM, Doyle S, Elliott R, Murphy G, Carpenter R: floricaula : a homeotic gene required for flower development in Antirrhinum majus . / Cell 1990, 63:1311鈥?322. CrossRef
52. Nilsson O, Lee Y, Blazquez MA, Weigel D: Flowering time genes modulate the response to LEAFY activity. / Genetics 1998, 150:403鈥?10.
53. Parcy F, Nilsson O, Busch MA, Lee I, Weigel D: A genetic framework for floral patterning. / Nature 1998, 395:561鈥?66. CrossRef
54. Irish VF, Sussex IM: Function of the APETALA1 gene during Arabidopsis floral development. / Plant Cell 1990, 2:741鈥?53.
55. Huala E, Sussex IM: LEAFY interacts with floral homeotic genes to regulate Arabidopsis floral development. / Plant Cell 1992, 4:901鈥?13.
56. Bowman JL, Alvarez J, Weigel D, Meyerowitz EM, Smyth DR: Control of flower development in Arabidopsis thaliana by APETALA1 and interacting genes. / Development 1993, 119:721鈥?43.
57. Shannon S, Meeks-Wagner DR: Genetic interactions that regulate inflorescence development in Arabidopsis . / Plant Cell 1993, 5:639鈥?55.
58. Mandel MA, Yanofsky MF: A gene triggering flower formation in Arabidopsis . / Nature 1995, 377:522鈥?24. CrossRef
59. Bai C, Sen P, Hofmann K, Ma L, Goebl M, Harper JW, Elledge SJ: SKP1 connects cell cycle regulators to the ubiquitin proteolysis machinery through a novel motif, the F-box. / Cell 1996, 86:263鈥?74. CrossRef
60. Ferrandiz C, Gu Q, Martienssen R, Yanofsky MF: Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1 and CAULIFLOWER . / Development 2000, 127:725鈥?34.
61. Lee I, Wolfe DS, Nilsson O, Weigel D: A LEAFY co-regulator encoded by UNUSUAL FLORAL ORGANS . / Curr Biol 1997, 7:95鈥?04. CrossRef
62. Hagen G, Guilfoyle TJ: Auxin-responsive gene expression: genes, promoters and regulatory factors. / Plant Mol Biol 2002, 49:373鈥?85. CrossRef
63. Ellis CM, Nagpal P, Young JC, Hagen G, Guilfoyle TJ, Reed JW: AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana . / Development 2005, 132:4563鈥?574. CrossRef
64. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis Z, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A: Full-length transcriptome assembly from RNA-Seq data without a reference genome. / Nat Biotechnol 2011, 29:644鈥?52. CrossRef
65. 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鈥?676. CrossRef
66. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J: WEGO: a web tool for plotting GO annotations. / Nucleic Acids Res 2006,34(Web Server issue):W293鈥?97. CrossRef
67. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y: KEGG for linking genomes to life and the environment. / Nucleic Acids Res 2008,36(Database issue):D480鈥?84.
68. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J: SOAP2: an improved ultrafast tool for short read alignment. / Bioinformatics 2009,25(15):1966鈥?967. CrossRef
69. Xue J, Bao YY, Li BL, Cheng YB, Peng ZY, Liu H, Xu HJ, Zhu ZR, Lou YG, Cheng JA, Zhang CX: Transcriptome analysis of the brown planthopper Nilaparvata lugens . / PLoS One 2010,5(12):e14233. CrossRef
70. de Hoon MJL, Imoto S, Nolan J, Miyano S: Open Source Clustering Software. / Bioinformatics 2004,20(9):1453鈥?454. CrossRef
71. Saldanha AJ: Java Treeview-extensible visualization of microarray data. / Bioinformatics 2004,20(17):3246鈥?248. CrossRef - 作者单位：Jianxia Zhang (1) (2)
Kunlin Wu (1)
Songjun Zeng (1)
Jaime A Teixeira da Silva (3)
Xiaolan Zhao (4)
Chang-En Tian (5)
Haoqiang Xia (6)
Jun Duan (1)
1. Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
2. Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
3. Faculty of Agriculture and Graduate School of Agriculture, Kagawa University, Miki-cho, Kagawa, 761-0795, Japan
4. Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China
5. School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
6. Guangzhou Genedenovo Biotechnology Co.,Ltd, Guangzhou, 510006, China
文摘
Background Cymbidium sinense belongs to the Orchidaceae, which is one of the most abundant angiosperm families. C. sinense, a high-grade traditional potted flower, is most prevalent in China and some Southeast Asian countries. The control of flowering time is a major bottleneck in the industrialized development of C. sinense. Little is known about the mechanisms responsible for floral development in this orchid. Moreover, genome references for entire transcriptome sequences do not currently exist for C. sinense. Thus, transcriptome and expression profiling data for this species are needed as an important resource to identify genes and to better understand the biological mechanisms of floral development in C. sinense. Results In this study, de novo transcriptome assembly and gene expression analysis using Illumina sequencing technology were performed. Transcriptome analysis assembles gene-related information related to vegetative and reproductive growth of C. sinense. Illumina sequencing generated 54,248,006 high quality reads that were assembled into 83,580 unigenes with an average sequence length of 612 base pairs, including 13,315 clusters and 70,265 singletons. A total of 41,687 (49.88%) unique sequences were annotated, 23,092 of which were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with metabolic and cellular processes, cell and cell parts, catalytic activity and binding. Furthermore, 120 flowering-associated unigenes, 73 MADS-box unigenes and 28 CONSTANS-LIKE (COL) unigenes were identified from our collection. In addition, three digital gene expression (DGE) libraries were constructed for the vegetative phase (VP), floral differentiation phase (FDP) and reproductive phase (RP). The specific expression of many genes in the three development phases was also identified. 32 genes among three sub-libraries with high differential expression were selected as candidates connected with flower development. Conclusion RNA-seq and DGE profiling data provided comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the molecular mechanisms of floral development at three development phases of C. sinense. This data could be used as an important resource for investigating the genetics of the flowering pathway and various biological mechanisms in this orchid.