Transcriptomic analysis of floral organs from Phalaenopsis orchid by using oligonucleotide microarray

Gene

Volumn 518, Issue 1, 2013, Pages 91-100

  Hsiao, Yu Yun ^a   Huang, Tian Hsiang ^a   Fu, Chih Hsiung ^a   Huang, Shi Ching ^a   Chen, Yi Jun ^a   Huang, Yueh Min ^a   Chen, Wen Huei ^a   Tsai, Wen Chieh ^a   Chen, Hong Hwa ^a  

^a NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

Author keywords

Labellum; Oligomicroarray; Orchids; Phalaenopsis; Transcriptome

Indexed keywords

OLIGONUCLEOTIDE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR WRKY; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; ENERGY METABOLISM; EXPRESSED SEQUENCE TAG; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE IDENTIFICATION; LIPID METABOLISM; MICROARRAY ANALYSIS; MOLECULAR GENETICS; NONHUMAN; ORCHIDACEAE; PETAL; PHALAENOPSIS; PRIORITY JOURNAL; SEPAL; TRANSCRIPTOMICS;

ENERGY METABOLISM; EXPRESSED SEQUENCE TAGS; FLOWERS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; LIPID METABOLISM; MADS DOMAIN PROTEINS; METABOLIC NETWORKS AND PATHWAYS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORCHIDACEAE; PLANT PROTEINS; TRANSCRIPTION FACTORS;

MAGNOLIOPHYTA; ORCHIDACEAE; PHALAENOPSIS;

EID: 84875374770     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.11.069     Document Type: Article

References (54)

1. Aarts M.G., Keijzer C.J., Stiekema W.J., Pereira A. Molecular characterization of the CER1 gene of Arabidopsis involved in epicuticular wax biosynthesis and pollen fertility. Plant Cell 1995, 7:2115-2127.
2. Abbruscato P., et al. OsWRKY22, a monocot WRKY gene, plays a role in the resistance response to blast. Mol. Plant Pathol. 2012, 13:828-841.
3. Bai Y., Meng Y., Huang D., Qi Y., Chen M. Origin and evolutionary analysis of the plant-specific TIFY transcription factor family. Genomics 2011, 98:128-136.
4. Chang Y.Y., et al. Characterization of the possible roles for B class MADS box genes in regulation of perianth formation in orchid. Plant Physiol. 2010, 152:837-853.
5. Chase M.W., Williams N.H., Donisete de Faria A., Neubig K.M., Amaral M.C.E., Whitten W.M. Floral convergence in Oncidiinae (Cymbidieae; Orchidaceae): an expanded concept of Gomesa and a new genus Nohawilliamsia. Ann. Bot. 2009, 104:387-402.
6. Chen Y.Y., et al. C- and D-class MADS-box genes from Phalaenopsis equestris (Orchidaceae) display functions in gynostemium and ovule development. Plant Cell Physiol. 2012, 53:1053-1067.
7. Cozzolino S., Widmer A. Orchid diversity: an evolutionary consequence of deception?. Trends Ecol. Evol. 2005, 20:487-494.
8. Deluc L.G., et al. Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development. BMC Genomics 2007, 8:429.
9. Dressler R.L. How many orchid species?. Selbyana 2005, 26:155-158.
10. Duan H., Schuler M.A. Differential expression and evolution of the Arabidopsis CYP86A subfamily. Plant Physiol. 2005, 137:1067-1081.
11. Fu C.H., et al. OrchidBase: a collection of sequences of transcriptome derived from orchids. Plant Cell Physiol. 2011, 52:238-243.
12. Godard K.-A., White R., Bohlmann J. Monoterpene-induced molecular responses in Arabidopsis thaliana. Phytochemistry 2008, 69:1838-1849.
13. Golz J.F., Hudson A. Plant development: YABBYs claw to the fore. Curr. Biol. 1999, 9:R861-R863.
14. Guilfoyle T.J., Hagen G. Auxin response factors. Curr. Opin. Plant Biol. 2007, 10:453-460.
15. Hsiao Y.Y., et al. Comparison of transcripts in Phalaenopsis bellina and Phalaenopsis equestris (Orchidaceae) flowers to deduce the monoterpene biosynthesis pathway. BMC Plant Biol. 2006, 6:14.
16. Hsiao Y.Y., et al. Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids. BMC Genomics 2011, 12:360.
17. Hsiao Y.Y., et al. Research on orchid biology and biotechnology. Plant Cell Physiol. 2011, 52:1467-1486.
18. Hsu C.C., et al. An overview of the Phalaenopsis orchid genome through BAC end sequence analysis. BMC Plant Biol. 2011, 11:3.
19. Hu W., Ma H. Characterization of a novel putative zinc finger gene MIF1: involvement in multiple hormonal regulation of Arabidopsis development. Plant J. 2006, 45:399-422.
20. Huang P., et al. Molecular and physiological characterization of the Arabidopsis thaliana Oxidation-related Zinc Finger 2, a plasma membrane protein involved in ABA and salt stress response through the ABI2-mediated signaling pathway. Plant Cell Physiol. 2012, 53:193-203.
21. Jakoby M., et al. bZIP transcription factors in Arabidopsis. Trends Plant Sci. 2002, 7:106-111.
22. Joubès J., et al. The VLCFA elongase gene family in Arabidopsis thaliana: phylogenetic analysis, 3D modelling and expression profiling. Plant Mol. Biol. 2008, 67:547-566.
23. Kim S.Y., et al. Expression of a DEFICIENS-like gene correlates with the differentiation between sepal and petal in the orchid, Habenaria radiata (Orchidaceae). Plant Sci. 2007, 172:319-326.
24. Li H., et al. The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice. Cell Res. 2010, 20:299-313.
25. Li Y., Pi L., Huang H., Xu L. ATH1 and KNAT2 proteins act together in regulation of plant inflorescence architecture. J. Exp. Bot. 2012, 63:1423-1433.
26. Liu Z.J., et al. Paraholcoglossum and Tsiorchis, two new orchid genera established by molecular and morphological analyses of the Holcoglossum alliance. PLoS One 2011, 6:e24864.
27. Lynch D.V., Dunn T.M. An introduction to plant sphingolipids and a review of recent advances in understanding their metabolism and function. New Phytol. 2004, 161:677-702.
28. Meyers B.C., Galbraith D.W., Nelson T., Agrawal V. Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiol. 2004, 135:637-652.
29. Mondragon-Palomino M., Theissen G. MADS about the evolution of orchid flowers. Trends Plant Sci. 2008, 13:51-59.
30. Nakashima K., et al. Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J. 2007, 51:617-630.
31. Otero J.T., Flanagan N.S. Orchid diversity-beyond deception. Trends Ecol. Evol. 2006, 21:64-65.
32. Pan Z.J., et al. The duplicated B-class MADS-box genes display dualistic characters in orchid floral organ identity and growth. Plant Cell Physiol. 2011, 52:1515-1531.
33. Rowland O., Zheng H., Hepworth S.R., Lam P., Jetter R., Kunst L. CER4 encodes an alcohol-forming fatty acyl-coenzyme A reductase involved in cuticular wax production in Arabidopsis. Plant Physiol. 2006, 142:866-877.
34. Rushton D.L., et al. WRKY transcription factors: key components in abscisic acid signalling. Plant Biotechnol. J. 2012, 10:2-11.
35. Silvera K., Santiago L.S., Cushman J.C., Winter K. Crassulacean acid metabolism and epiphytism linked to adaptive radiations in the Orchidaceae. Plant Physiol. 2009, 149:1838-1847.
36. Skipper M., Johansen L.B., Pedersen K.B., Frederiksen S., Johansen B.B. Cloning and transcription analysis of an AGAMOUS- and SEEDSTICK ortholog in the orchid Dendrobium thyrsiflorum (Reichb. f.). Gene 2006, 366:266-274.
37. Song I.-J., et al. Spatiotemporal expression of duplicate AGAMOUS orthologues during floral development in Phalaenopsis. Dev. Genes Evol. 2006, 216:301-313.
38. Swarbreck D., et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 2007, 36:D1009-D1014.
39. Tholl D., Chen F., Petri J., Gershenzon J., Pichersky E. Two sesquiterpene synthases are responsible for the complex mixture of sesquiterpenes emitted from Arabidopsis flowers. Plant J. 2005, 42:757-771.
40. Tremblay R.L., Ackerman J.D., Zimmerman J.K., Calvo R.N. Variation in sexual reproduction in orchids and its evolutionary consequences: a spasmodic journey to diversification. Biol. J. Linn. Soc. 2005, 84:1-54.
41. Tsai W.C., Chuang M.H., Kuoh C.S., Chen W.H., Chen H.H. Four DEF-like MADS box genes displayed distinct floral morphogenetic roles in Phalaenopsis orchid. Plant Cell Physiol. 2004, 45:831-844.
42. Tsai W.C., et al. PeMADS6, a GLOBOSA/PISTILLATA-like gene in Phalaenopsis equestris involved in petaloid formation, and correlated with flower longevity and ovary development. Plant Cell Physiol. 2005, 46:1125-1139.
43. Tsai W.C., et al. Expression analysis of the ESTs derived from the flower buds of Phalaenopsis equestris. Plant Sci. 2006, 170:426-432.
44. Tsai W.C., et al. Molecular biology of orchid flowers: with emphasis on Phalaenopsis. Adv. Bot. Res. 2008, 47:99-145.
45. Tsai W.C., et al. Interaction of B-class complex proteins involved in tepal development in Phalaenopsis orchid. Plant Cell Physiol. 2008, 49:814-824.
46. Voelckel C., Borevitz J.O., Kramer E.M., Hodges S.A. Within and between whorls: comparative transcriptional profiling of Aquilegia and Arabidopsis. PLoS One 2010, 5:e9735.
47. Wang C.Y., et al. Carbohydrate mobilization and gene regulatory profile in the pseudobulb of Oncidium orchid during the flowering process. Planta 2008, 227:1063-1077.
48. Wang S.Y., et al. Duplicated C-class MADS-box genes reveal distinct roles in gynostemium development in Cymbidium ensifolium (Orchidaceae). Plant Cell Physiol. 2011, 52:563-577.
49. Wechter W.P., et al. Gene expression in developing watermelon fruit. BMC Genomics 2008, 9:275.
50. Weigel D., Meyerowitz E.M. The ABCs of floral homeotic genes. Cell 1994, 78:203-209.
51. Wellmer F., Riechmann J.L., Alves-Ferreira M., Meyerowitz Genome-wide analysis of spatial gene expression in Arabidopsis flowers. Plant Cell 2004, 16:1314-1326.
52. Xu Y.H., Wang J.W., Wang S., Wang J.Y., Chen X.Y. Characterization of GaWRKY1, a cotton transcription factor that regulates the sesquiterpene synthase gene (1)-δ-cadinene synthase-A. Plant Physiol. 2004, 135:507-515.
53. Xu Y., Teo L.L., Zhou J., Kumar P.P., Yu H. Floral organ identity genes in the orchid Dendrobium crumenatum. Plant J. 2006, 46:54-68.
54. Zheng H., Rowland O., Kunst L. Disruptions of the Arabidopsis Enoyl-CoA reductase gene reveal an essential role for very-long-chain fatty acid synthesis in cell expansion during plant morphogenesis. Plant Cell 2005, 17:1467-1481.