Comparative transcriptome analysis of genes involved in GA-GID1-DELLA regulatory module in symbiotic and asymbiotic seed germination of anoectochilus roxburghii (Wall.) Lindl. (Orchidaceae)

International Journal of Molecular Sciences

Volumn 16, Issue 12, 2015, Pages 30190-30203

  Liu, Si Si ^a   Chen, Juan ^a   Li, Shu Chao ^a   Zeng, Xu ^a   Meng, Zhi Xia ^a   Guo, Shun Xing ^a  

^a INSTITUTE OF MEDICINAL PLANT DEVELOPMENT   (China)

Author keywords

Anoectochilus roxburghii; Asymbiotic; GA GID1 DELLA; Orchidaceae; Seed germination; Symbiotic; Transcriptome

Indexed keywords

GIBBERELLIN; TRANSCRIPTOME; PLANT PROTEIN;

ANOECTOCHILUS ROXBURGHII; ARTICLE; DELLA GENE; GENE; GENE EXPRESSION; GENE ONTOLOGY; GENETIC ANALYSIS; GERMINATION; GID1 GENE; GID2 GENE; METABOLISM; MYCORRHIZA; MYCORRHIZAL INOCULATION; NONHUMAN; ORCHIDACEAE; PROTEIN EXPRESSION; REGULATORY MECHANISM; RNA EXTRACTION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SYMBIOSIS; COMPARATIVE STUDY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; PLANT GENE; PLANT SEED;

DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE ONTOLOGY; GENE REGULATORY NETWORKS; GENES, PLANT; GERMINATION; MOLECULAR SEQUENCE ANNOTATION; MYCORRHIZAE; ORCHIDACEAE; PLANT PROTEINS; SEEDS; SYMBIOSIS; TRANSCRIPTOME;

EID: 84950147117     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms161226224     Document Type: Article

References (54)

1. Jiang, C.; Fu, X. GA action: Turning on de-DELLA repressing signaling. Curr. Opin. Plant Biol. 2007, 10, 461-465. [CrossRef] [PubMed].
2. Sun, T.-P.; Gubler, F. Molecular mechanism of gibberellin signaling in plant. Annu. Rev. Plant Biol. 2004, 55, 197-223. [CrossRef] [PubMed].
3. Voegele, A.; Linkies, A.; Müller, K.; Leubner-Metzger, G. Members of the gibberellin receptor gene family GID1 (GIBBERELLIN INSENSITIVE DWARF1) play distinct roles during Lepidium. sativum and Arabidopsis thaliana seed germination. J. Exp. Bot. 2011, 62, 5131-5147. [CrossRef] [PubMed].
4. Achard, P.; Genschik, P. Releasing the brakes of plant growth: How GAs shutdown DELLA proteins. J. Exp. Bot. 2009, 60, 1085-1092. [CrossRef] [PubMed].
5. Sun, T.-P. The molecular mechanism and evolution of the GA-GID1-DELLA signaling module in plants. Curr. Biol. 2011, 21, R338-R345. [CrossRef] [PubMed].
6. Bari, R.; Jones, J.D.G. Role of plant hormones in plant defence responses. Plant Mol. Biol. 2009, 69, 473-488. [CrossRef] [PubMed].
7. Yamaguchi, S. Gibberellin metabolism and its regulation. Annu. Rev. Plant Biol. 2008, 59, 225-251. [CrossRef] [PubMed].
8. Wang, Y.-J.; Deng, D.-X. Molecular basis and evolutionary pattern of GA-GID1-DELLA regulatory module. Mol. Genet. Genom. 2014, 289, 1-9. [CrossRef] [PubMed].
9. Delectis Florae Reipublicae Popularis Sinicae, Agendae Academiae Sinicae Edita. In Flora Reipublicae Popularis Sinicae; Tomus 27; Science Press: Beijing, China, 1999; p. 220.
10. He, C.-N.; Wang, C.-L.; Guo, S.-X.; Yang, J.-S.; Xiao, P.-G. A novel flavonoid glucoside from Anoectochilus roxburghii (Wall.) Lindl. J. Integr. Plant Biol. 2006, 48, 359-363. [CrossRef].
11. Gutiérrez, R.M.P. Orchids: A review of uses in traditional medicine, its phytochemistry and pharmacology. J. Med. Plant Res. 2010, 4, 592-638.
12. Fujian Institute of Traditional Chinese Medicine. Record of Fujian Materia Medica, 2nd ed.; Fujian Science and Technology Press: Fuzhou, China, 1982.
13. Stewart, S.L.; Kane, M.E. Asymbiotic seed germination and in vitro seedling development of Habenaria. macroceratitis (Orchidaceae), a rare Florida terrestrial orchid. Plant Cell Tissue Organ 2006, 86, 147-158. [CrossRef].
14. Arditti, J. Factors affecting the germination of orchid seeds. Bot. Rev. 1967, 33, 1-97. [CrossRef].
15. Johnson, T.R.; Stewart, S.L.; Dutra, D.; Kane, M.E.; Richardson, L. Asymbiotic and symbiotic seed germination of Eulophia. alta (Orchidaceae)-Preliminary evidence for the symbiotic culture advantage. Plant Cell Tissue Organ 2007, 90, 313-323. [CrossRef].
16. Zhao, M.-M.; Zhang, G.; Zhang, D.-W.; Hsiao, Y.-Y.; Guo, S.-X. ESTs analysis reveals putative genes involved in symbiotic seed germination in Dendrobium officinale PLoS ONE 2013, 8, e72705. [CrossRef] [PubMed].
17. Perotto, S.; Rodda, M.; Benetti, A.; Sillo, F.; Ercole, E.; Rodda, M.; Girlanda, M.; Murat, C.; Balestrini, R. Gene expression in mycorrhizal orchid protocorms suggests a friendly plant-fungus relationship. Planta 2014, 239, 1337-1349. [CrossRef] [PubMed].
18. Tyler, L.; Thomas, S.G.; Hu, J.; Dill, A.; Alonso, J.M.; Ecker, J.R.; Sun, T.-P. DELLA proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiol. 2004, 135, 1008-1019. [CrossRef] [PubMed].
19. Seo, M.; Nambara, E.; Choi, G.; Yamaguchi, S. Interaction of light and hormone signals in germinating seeds. Plant Mol. Biol. 2009, 69, 463-472. [CrossRef] [PubMed].
20. Hedden, P.; Phillips, A.L. Gibberellin metabolism: New insights revealed by the genes. Trends Plant Sci. 2000, 5, 523-530. [CrossRef].
21. Hu, J.; Mitchum, M.G.; Barnaby, N.; Ayele, B.T.; Ogawa, M.; Nam, E.; Lai,W.-C.; Hanada, A.; Alonso, J.M.; Ecker, J.R.; et al. Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis. Plant Cell 2008, 20, 320-336. [CrossRef] [PubMed].
22. Murase, K.; Hirano, Y.; Sun, T.P.; Hakoshima, T. Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. Nature 2008, 456, 459-463. [CrossRef] [PubMed].
23. Floss, D.S.; Levy, J.G.; Lévesque-Tremblay, V.; Pumplin, N.; Harrison, M.J. DELLA proteins regulate arbuscule formation in arbuscular mycorrhizal symbiosis. Proc. Natl. Acad. Sci. USA 2013, 110, E5025-E5034. [CrossRef] [PubMed].
24. Rajjou, L.; Duval, M.; Gallardo, K.; Catusse, J.; Bally, J.; Job, C.; Job, D. Seed germination and vigor. Annu. Rev. Plant Biol. 2012, 63, 507-533. [CrossRef] [PubMed].
25. Rasmussen, H.N. Terrestrial Orchids: From Seed to Mycotrophic Plant; Cambridge University Press: Cambridge, UK, 1995.
26. Zettler, L.W.; Hofer, C.J. Propagation of the little club-spur orchid (Platanthera. clavellata) by symbiotic seed germination and its ecological implications. Environ. Exp. Bot. 1998, 39, 189-195. [CrossRef].
27. Weiss, D.; Ori, N. Mechanisms of cross talk between gibberellin and other hormones. Plant Physiol. 2007, 144, 1240-1246. [CrossRef] [PubMed].
28. Sun, T.-P.; Kamiya, Y. The Arabidopsis GA1 locus encodes the cyclase ent-kaurene synthetase A of gibberellin biosynthesis. Plant Cell 1994, 6, 1509-1518. [CrossRef] [PubMed].
29. Cao, D.; Cheng, H.; Wu, W.; Soo, H.M.; Peng, J. Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis. Plant Physiol. 2006, 142, 509-525. [CrossRef] [PubMed].
30. Fu, X.; Richards, D.E.; Fleck, B.; Xie, D.; Burton, N.; Harberd, N.P. The Arabidopsis mutant sleepy1gar2_1 protein promotes plant growth by increasing the affinity of the SCFSLY1 E3 ubiquitin ligase for DELLA protein substrates. Plant Cell 2004, 16, 1406-1418. [CrossRef] [PubMed].
31. Itoh, H.; Ueguchi-Tanaka, M.; Sato, Y.; Ashikari, M.; Matsuoka, M. The gibberellin signaling pathway is regulated by the appearance and disappearance of SLENDER RICE1 in Nuclei. Plant Cell 2002, 14, 57-70. [CrossRef] [PubMed].
32. Hussain, A.; Cao, D.-N.; Cheng, H.;Wen, Z.-L.; Peng, J.-R. Identification of the conserved serine/threonine residues important for gibberellin-sensitivity of Arabidopsis RGL2 protein. Plant J. 2005, 44, 88-99. [CrossRef] [PubMed].
33. Harberd, N.P.; Belfield, E.; Yasumura, Y. The angiosperm gibberellin-GID1-DELLA growth regulatory mechanism: how an "inhibitor of an inhibitor" enables flexible response to fluctuating environments. Plant Cell 2009, 21, 1328-1339. [CrossRef] [PubMed].
34. Schomburg, F.M.; Bizzell, C.M.; Lee, D.J.; Zeevaart, J.A.; Amasino, R.M. Overexpression of a novel class of gibberellin 2-oxidases decreases gibberellin levels and creates dwarf plants. Plant Cell 2003, 15, 151-163. [CrossRef] [PubMed].
35. Thomas, S.G.; Phillips, A.L.; Hedden, P. Molecular cloning and functional expression of gibberellin 2-oxidases, multifunctional enzymes involved in gibberellin deactivation. Proc. Natl. Acad. Sci. USA 1999, 96, 4638-4703. [CrossRef].
36. Toh, S.; Imamura, A.; Watanabe, A.; Nakabayashi, K.; Okamoto, M.; Jikumaru, J.; Hanada, A.; Aso, Y.; Ishiyama, K.; Tamura, N.; et al. High temperature-induced abscisic acid biosynthesis and its role in the inhibition of gibberellin action in Arabidopsis seeds. Plant Physiol. 2008, 146, 1368-1385. [CrossRef] [PubMed].
37. Fleet, C.M.; Sun, T.-P. A DELLAcate balance: The role of gibberellin in plant morphogenesis. Curr. Opin. Plant Biol. 2005, 8, 77-85. [CrossRef] [PubMed].
38. Gutjahr, C. Phytohormone signaling in arbuscular mycorhiza development. Curr. Opin. Plant Biol. 2014, 20, 26-34. [CrossRef] [PubMed].
39. Foo, E.; Ross, J.J.; Jones, W.T.; Reid, J.B. Plant hormones in arbuscular mycorrhizal symbioses: An emerging role for gibberellins. Ann. Bot. 2013, 111, 769-779. [CrossRef] [PubMed].
40. Gismondi, A.; Rolfo, M.F.; Leonardi, D.; Rickards, O.; Canini, A. Identification of ancient Olea europaea L. and Cornus. mas L. by DNA barcoding. Cr. Biol. 2012, 335, 472-479. [CrossRef] [PubMed].
41. Gismondi, A.; Fanali, F.; Martínez Labarga, J.M.; Grilli Caiola, M.; Canini, A. Crocus sativus L. genomics and different DNA barcode applications. Plant Syst. Evol. 2013, 299, 1859-1863. [CrossRef].
42. Gismondi, A.; di Marco, G.; Delorenzo, M.; Canini, A. Upgrade of Castanea. sativa (Mill.) genetic resources by sequencing of barcode markers. J. Genet. 2015, 94, 519-524. [CrossRef] [PubMed].
43. Grabherr, M.G.; Haas, B.J.; Yassour, M.; Levin, J.Z.; Thompson, D.A.; Amit, I.; Adiconis, X.; Fan, L.; Raychowdhury, R.; Zeng, Q.; et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29, 644-652. [CrossRef] [PubMed].
44. NCBI. Available online: http://www.ncbi.nlm.nih.gov/(accessed on 25 November 2015).
45. UniProt. Available online: http://www.ebi.ac.uk/uniprot/(accessed on 25 November 2015).
46. KOG/COG. Available online: http://www.ncbi.nlm.nih.gov/COG/(accessed on 25 November 2015).
47. Pfam. Available online: http://pfam.sanger.ac.uk/(accessed on 25 November 2015).
48. Gene Ontology Consortium. Available online: http://geneontology.org/(accessed on 25 November 2015).
49. KEGG. Available online: http://www.genome.jp/kegg/(accessed on 25 November 2015).
50. Li, B.; Dewey, C. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 2011, 12, 323. [CrossRef] [PubMed].
51. Anders, S.; Huber, W. Differential expression analysis for sequence count data. Genome Biol. 2010, 11, R106. [CrossRef] [PubMed].
52. Benjamini, Y.; Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B 1995, 57, 289-300.
53. Rasmussen, H.N.; Dixon, K.W.; Jersáková, J.; Těšitelová, T. Germination and seedling establishment in orchids: A complex of requirements. Ann. Bot. 2015. [CrossRef] [PubMed].
54. Potokina, E.; Sreenivasulu, N.; Altschmied, L.; Michalek, W.; Graner, A. Differential gene expression during seed germination in barley (Hordeum vulgare L.). Funct. Integr. Genom. 2002, 2, 28-39. [CrossRef] [PubMed].