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Genes & Genomics

, Volume 40, Issue 3, pp 265–279 | Cite as

Molecular characterization and expression analysis of WRKY family genes in Dendrobium officinale

  • Tao Wang
  • Zheng Song
  • Li Wei
  • Lubin Li
Research Article

Abstract

The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators, and the members regulate multiple biological processes. However, there is limited information on WRKYs in Dendrobium officinale. In this study, 52 WRKY family genes of D. officinale were surveyed for the first time. Conserved domain, phylogenetic, exon–intron construction, and expression analyses were performed for the DoWRKY genes. Two major types of intron splicing (PR and VQR introns) were found, and the intron insertion position was observed to be relatively conserved in the conserved DoWRKY domains. The expression profiles of nine DoWRKYs were analyzed in cold- and methyl jasmonate (MeJA)-treated D. officinale seedlings; the DoWRKYs showed significant expression changes at different levels, which suggested their vital roles in stress tolerance. Moreover, the expression trends of most of the DoWRKYs after the simultaneous cold stress and MeJA treatment were the opposite of those of DoWRKYs after the individual cold stress and MeJA treatments, suggesting that the two stresses might have antagonistic effects and affect the adaptive capacity of the plants to stresses. Twelve DoWRKY genes were differentially expressed between symbiotic and asymbiotic germinated seeds; all were upregulated in the symbiotic germinated seeds except DoWRKY16. These differences in expression of DoWRKYs might be involved in promoting in vitro symbiotic germination of seeds with Tulasnella-like fungi. Our findings will be useful for further studies on the WRKY family genes in orchids.

Keywords

WRKY Dendrobium officinale Gene family Abiotic stress Symbiotic germination seeds 

Notes

Acknowledgements

This work was supported by grants from the National High Technology Research and Development Program of China (863 Program) (No. 2013AA102607).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest. Tao Wang declares that she has no conflict of interest. Zheng Song declares that he has no conflict of interest. Li Wei declares that she has no conflict of interest. Lubin Li declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human subjects or animals performed by any of the authors.

Supplementary material

13258_2017_602_MOESM1_ESM.xlsx (27 kb)
Supplementary material 1 (XLSX 27 KB)

References

  1. An Y, Hen Y, Wu L, Zhang Z (2006) A change of phenolic acids content in poplar leaves induced by methyl salicylate and methyl jasmonate. J Forest Res 17:107–110CrossRefGoogle Scholar
  2. Bencke-Malato M, Cabreira C, Wiebke-Strohm B, Bücker-Neto L, Mancini E, Osorio MB, Homrich MS, Turchetto-Zolet AC, De Carvalho MC, Stolf R et al (2014) Genome-wide annotation of the soybean WRKY family and functional characterization of genes involved in response to Phakopsora pachyrhizi infection. BMC Plant Biol 14:236CrossRefPubMedPubMedCentralGoogle Scholar
  3. Brand LH, Fischer NM, Harter K, Kohlbacher O, Wanke D (2013) Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Res 41:1–15CrossRefGoogle Scholar
  4. Consortium TIBG (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–717Google Scholar
  5. Deng W, Wang Y, Liu Z, Cheng H, Xue Y (2014) HemI: a toolkit for illustrating heatmaps. PLoS ONE 11:e111988CrossRefGoogle Scholar
  6. Diao W, Snyder J, Wang SB, Liu JB, Pan BG, Guo G, Wei G (2016) Genome-wide identification and expression analysis of WRKY gene family in Capsicum annuum L. Front Plant Sci 7:1–15CrossRefGoogle Scholar
  7. Dou F, Xuan W, Huang Z, Deng F, Tan X (2009) Effects of MeJA on cold tolerance of banana seedlings. J Fruit Sci 26:390–393Google Scholar
  8. Dou L, Zhang X, Pang C, Song M, Wei H, Fan S, Yu S (2014) Genome-wide analysis of the WRKY gene family in cotton. Mol Genet Genomics 289:1103–1121CrossRefPubMedGoogle Scholar
  9. Duan X, Deng Z, Bin J (2009) Efects of Methyl Jasmonate on cold resistance of rice (Oryza sativa L.) seedlings. Plant Physiol Commun 45:881–884Google Scholar
  10. Eulgem T, Rushton PJ, Robatzek S, Somssich IE (2000) The WRKY superfamily of plant transcription factors. Trends Plant Sci 5:199–206CrossRefPubMedGoogle Scholar
  11. Gaude N, Bortfeld S, Duensing N, Lohse M, Krajinski F (2012) Arbuscule-containing and non-colonized cortical cells of mycorrhizal roots undergo a massive and specific reprogramming during arbuscular mycorrhizal development. Plant J 69:510–528CrossRefPubMedGoogle Scholar
  12. Guan L, Chi W, Xiao W, Chen L, He S (2014) Analysis of hypoxia-inducible factor alpha polyploidization reveals adaptation to Tibetan plateau in the evolution of schizothoracine fish. BMC Evol Biol 14:192CrossRefPubMedPubMedCentralGoogle Scholar
  13. Guo X, Li Y, Li C, Luo H, Wang L, Qian J, Luo X, Xiang L, Song J, Sun C, Xu H, Yao H, Chen S (2013) Analysis of the Dendrobium officinale transcriptome reveals putative alkaloid biosynthetic. Gene 527:131–138CrossRefPubMedGoogle Scholar
  14. Huang S, Liu Y (2013) Genome-wide analysis of WRKY transcription factors in Solanum tuberosum. Chin J Appl Environ Biol 19:205–214CrossRefGoogle Scholar
  15. Huang S, Gao Y, Liu J, Peng X, Niu X, Fei Z, Cao S, Liu Y (2012) Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Mol Genet Genomics 287:495–513CrossRefPubMedGoogle Scholar
  16. Hung KT, Hsu YT, Kao CH (2006) Hydrogen peroxide is involved in methyl jasmonate-induced senescence of rice leaves. Physiol Plantarum 127:293–303CrossRefGoogle Scholar
  17. Jiang Y, Duan Y, Yin J, Ye S, Zhu J, Zhang F, Lu W, Di Fan, Luo K (2014) Genome-wide identification and characterization of the Populus WRKY transcription factor family and analysis of their expression in response to biotic and abiotic stresses. J Exp Bot 65:1–16CrossRefGoogle Scholar
  18. Jiang Y, Zhu Y, Gao Y, Si J (2016) Cloning and expression analysis of WRKY5 gene in Dendrobium officinale. Chin Tradit Herbal Drugs 47:301–308Google Scholar
  19. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948CrossRefPubMedGoogle Scholar
  20. Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S (2002) PlantCARE: a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucl Acids Res 30:325–327CrossRefPubMedPubMedCentralGoogle Scholar
  21. Li H, Zhang L, Guo D, Li C, Peng S (2012) Identification and expression profiles of the WRKY transcription factor family in Ricinus communis. Gene 503:248–253CrossRefPubMedGoogle Scholar
  22. Li X, Luo J, Yan T, Xiang L, Jin F, Qin D, Sun C, Xie M (2013) Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome. PLoS ONE 12:e85480CrossRefGoogle Scholar
  23. Li H, Guo D, Yang Z, Tang X, Peng S (2014) Genome-wide identification and characterization of WRKY gene family in Hevea brasiliensis. Genomics 104:14–23CrossRefPubMedGoogle Scholar
  24. Ling J, Jiang W, Zhang Y, Yu H, Mao Z, Gu X, Huang S, Xie B (2011) Genome-wide analysis of WRKY gene family in Cucumis sativus. BMC Genomics 12:471CrossRefPubMedPubMedCentralGoogle Scholar
  25. Liu XQ, Zhu JJ, Wei CJ, Guo Q, Bian CK, Xing ZH, Zhao AC (2015) Genome-wide identification and characterization of the DREB transcription factor gene family in mulberry. Biol Plantarum 59:253–265CrossRefGoogle Scholar
  26. Ma J, Lu J, Xu J, Duan B, He X, Liu J (2015) Genome-wide identification of WRKY genes in the desert poplar Populus euphratica and adaptive evolution of the genes in response to salt stress. Evol Bioinform 11:47–55CrossRefGoogle Scholar
  27. Mangelsen E, Kilian J, Berendzen KW, Kolukisaoglu ÜH, Harter K, Jansson C, Wanke D (2008) Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots. BMC Genomics 9:194CrossRefPubMedPubMedCentralGoogle Scholar
  28. Muthamilarasan M, Bonthala VS, Khandelwal R, Jaishankar J, Shweta S, Nawaz K, Prasad M (2015) Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling. Front Plant Sci 6:910PubMedPubMedCentralGoogle Scholar
  29. Park CY, Lee JH, Yoo JH, Moon BC, Choi MS, Kang YH, Lee SM, Kim HS, Kang KY, Chung WS, Lima CO, Cho MJ (2005) WRKY group IId transcription factors interact with calmodulin. FEBS 579:1545–1550CrossRefGoogle Scholar
  30. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time PCR. Nucl Acids Res 29(9):e45CrossRefPubMedPubMedCentralGoogle Scholar
  31. Qi F, Li J, Duan L, Li Z (2006) Inductions of coronatine and MeJA to low-temperature resistance of wheat seedlings. Acta Bot Boreal-Occident Sin 26:1776–1780Google Scholar
  32. Rao G, Sui J, Zhang J (2015) In silico genome-wide analysis of the WRKY gene family in Salix Arbutifolia. Plant Omics 4:353–360Google Scholar
  33. Ross CA, Liu Y, Shen QJ (2007) The WRKY gene family in rice (Oryza sativa). J Integr Plant Biol 6:827–842CrossRefGoogle Scholar
  34. Rossberg M, Theres K, Acarkan A, Herrero R, Schmitt T, Schumacher K, Schmitz G, Schmidt R (2001) Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes. Plant cell 13:979–988CrossRefPubMedPubMedCentralGoogle Scholar
  35. Savkur RS, Burris TP (2004) The coactivator LXXLL nuclear receptor recognition motif. J Pept Res 63:207–212CrossRefPubMedGoogle Scholar
  36. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183CrossRefPubMedGoogle Scholar
  37. Stewart S, Zetter L (2002) Symbiotic germination of three semiaquatic rein orchids (Habenaria repens, H. quinquiseta, H. macroceratitis) from florida. Aquat Bot 72:25–35CrossRefGoogle Scholar
  38. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony. Mol Biol Evol 11:2731–2739CrossRefGoogle Scholar
  39. Tang J, Wang F, Hou X, Wang Z, Huang Z (2013) Genome-wide fractionation and identification of WRKY transcription factors in Chinese cabbage (Brassica rapa ssp. pekinensis) reveals collinearity and their expression patterns under abiotic and biotic stresses. Plant Mol Biol Rep 32:781–795CrossRefGoogle Scholar
  40. Tripathi P, Rabara RC, Langum TJ, Boken AK, Rushton DL, Boomsma DD, Rinerson CI, Rabara J, Reese RN, Chen X, Rohila JS, Rushton PJ (2012) The WRKY transcription factor family in Brachypodium distachyon. BMC Genomics 13:270CrossRefPubMedPubMedCentralGoogle Scholar
  41. Verger A, Perdomo J, Crossley M (2003) Modification with SUMO, a role in transcriptional regulation. EMBO Rep 4:137–142CrossRefPubMedPubMedCentralGoogle Scholar
  42. Wang C (2013) Cloning and preliminary function analysis of DnWRKY29 gene. Dissertation, Hangzhou Normal UniversityGoogle Scholar
  43. Wang L, Zhu W, Fang LC, Sun XM, Su LY, Liang ZC, Wang N, Londo JP, Li SH, Xin HP (2014) Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera. BMC Plant Biol 14:103CrossRefPubMedPubMedCentralGoogle Scholar
  44. Wang H, Jina M, Paek K, Piao X, Lian M (2016) An efficient strategy for enhancement of bioactive compounds by protocorm-like body culture of Dendrobium candidum. Ind Crop Prod 84:121–130CrossRefGoogle Scholar
  45. Wasternack C (2007) Jasmonates: An update on biosynthesis, signal transduction and action in plant stress response, growth and development. Ann Bot-London 100:681–697CrossRefGoogle Scholar
  46. Wasternack C (2014) Action of jasmonates in plant stress responses and development applied aspects. Biotechnol Adv 32:31CrossRefPubMedGoogle Scholar
  47. Wasternack C, Strnad M (2015) Jasmonate signaling in plant stress responses and development-active and inactive compounds. New Biotechnol 33:604–613CrossRefGoogle Scholar
  48. Wei K, Chen J, Chen Y, Wu L, Xie D (2012) Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize. DNA Res 15:153–164CrossRefGoogle Scholar
  49. Wu K, Guo Z, Wang H, Li J (2005) The WRKY family of transcription factors in rice and Arabidopsis and their origins. DNA Res 12:9–26CrossRefPubMedGoogle Scholar
  50. Xie Z, Zhang Z, Zou X, Huang J, Ruas P, Thompson D, Shen QJ (2005) Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Plant Physiol 137:176–189CrossRefPubMedPubMedCentralGoogle Scholar
  51. Xiong W, Xu X, Zhang L, Wu P, Chen Y, Li M, Jiang H, Wu G (2013) Genome wide analysis of the WRKY gene family in physic nut (Jatropha carcas). Gene 524:124–132CrossRefPubMedGoogle Scholar
  52. Xu X, Pan Y, Wang C, Ying Q, Song H, Wang H (2014) Overexpression of DnWRKY11 enhanced salt and drought stress tolerance of transgenic tobacco. Biologia 69:994–1000CrossRefGoogle Scholar
  53. Xu L, Tian JN, Wang T, Li LB (2017) Symbiosis established between orchid and Tulasnella spp. Fungi. China J Nucl Agric Sci 31:0876–0883Google Scholar
  54. Yan L, Wang X, Liu H, Tian Y, Lian J, Yang R, Hao S, Wang X, Yang S, Li Q et al (2015) The genome of Dendrobium officinale illuminates the biology of the important traditional Chinese orchid herb. Mol Plant 8:922–934CrossRefPubMedGoogle Scholar
  55. Yang S, Galanis A, Witty J, Sharrocks AD (2006) An extended consensus motif enhances the specificity of substrate modification by SUMO. EMBO J 25:5083–5093CrossRefPubMedPubMedCentralGoogle Scholar
  56. Zhang Y, Feng JC (2014) Identification and characterization of the grape WRKY Family. Biomed Res Int 2014:1–14Google Scholar
  57. Zhang G, Zhao MM, Zhang Dw, Guo SX (2013) Reference gene selection for real-time quantitative PCR analysis of Dendrobium officinale. Chin Pharm J 48:1664–1668Google Scholar
  58. Zhang G, Xu Q, Bian C, Tsai W, Yeh C, Liu K, Yoshida K, Zhang L, Chang S, Chen F (2016a) The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. Scientific Rep 6:19029CrossRefGoogle Scholar
  59. Zhang J, He C, Wu K, Silva JATD, Zeng S, Zhang X, Yu Z, Xia H, Duan J (2016b) Transcriptome analysis of Dendrobium officinale and its application to the identification of genes associated with polysaccharide synthesis. Front Plant Sci 5:1–14Google Scholar
  60. Zhao MM, Zhang G, Zhang DW, HsiaoYY, Guo SX (2013) ESTs analysis reveals putative genes involved in symbiotic seed germination in Dendrobium officinale. PLoS ONE 8:e72705CrossRefPubMedPubMedCentralGoogle Scholar
  61. Zhao X, Yang J, Liu S, Chen C, Zhu H, Cao J (2014a) The colonization patterns of different fungi on roots of Cymbidium hybridum plantlets and their respective inoculation effects on growth and nutrient uptake of orchid plantlet. World J Microb Biot 30:1993–2003CrossRefGoogle Scholar
  62. Zhao XL, Zhang JX, Chen CL, Yang JZ, Zhu HY, Liu M, Lv FB (2014b) Deep sequencing-based comparative transcriptional profiles of Cymbidium hybridum roots in response to mycorrhizal and non-mycorrhizal beneficial fungi. BMC Genomics 15:747CrossRefPubMedPubMedCentralGoogle Scholar
  63. Zhao J, Meng CC, Zhao YF, Wang CX, Fan HH, Jin Q, Li DH, Lin Y, Cai YP (2015a) Cloning and expression analysis of transcription factor gene (DoWRKY2) in Dendrobium officinal. J Agr Biotechnol 23:1049–1057Google Scholar
  64. Zhao J, Sun SW, Meng CC, Jin Q, Fan HH, Lin Y, Cai YP (2015b) Cloning and expression analysis of transcription factor gene DoWRKY1 in Dendrobium officinal. China J Chin Materia Med 40:2807–2813Google Scholar
  65. Zheng Z, Qamar SA, Chen Z, Mengiste T (2006) Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens. Plant J 48:592–605CrossRefPubMedGoogle Scholar
  66. Zou Q, Zhu K, Liu H, Zhou J, Ma G (2011) Effect of exogenous Methyl Jasmonate on chlorophyll fluorescence and antioxidant characteristics in the leaves of phalaenopsis amabilis under abiotic stress. J Plant Physiol 47:913–917Google Scholar

Copyright information

© The Genetics Society of Korea and Springer Science+Business Media B.V. 2017

Authors and Affiliations

  1. 1.State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of ForestryChinese Academy of ForestryBeijingChina
  2. 2.Environmental Monitoring Center of HandanHandanChina

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