Genome wide characterization of WUSCHEL-related homeobox (WOX) gene family in Apostasia shenzhenica, a primeval orchid
DOI:
https://doi.org/10.14719/pst.2020.7.2.703Keywords:
WOX, WUSCHEL, Apostasia shenzhenicaAbstract
In the present study, we report identification and characterization of the plant-specific WUSCHEL-related homeobox (WOX) gene family in Apostasia shenzhenica, a primeval orchid. WOX proteins are DNA-binding WUSCHEL-related homeobox (WOX) encoding transcription factors that play critical role in zygote patterning, embryo development, organogenesis, florigenesis, stress responses etc. Ten putative AsWOX genes were predicted in the A. shenzhenica genome and were characterized by the presence of DNA-binding helix-loop-helix-turn-helix motif. AsWOX proteins were grouped into three clades, ancient, intermediate and WUS on the basis of sequence homology with Arabidopsis thaliana (AtWOX), Oryza sativa (OsWOX), Phalaenopsis equestris (PeWOX) and Dendrobium catenatum (DcWOX) and their phylogenetic relationship was established. Gene structure analysis revealed that three AsWOX genes had two introns, six genes had a single intron, and one gene was intron-less. Expression profiling in a variety of tissue (tubers, seeds and pollens) was analysed in light of the presence of specific cis-regulatory elements in the promoter region and their role in various developmental processes was discussed. Three dimensional structures were predicted for three selected AsWOX proteins representing the three clades. The present study provides insights to the role of AsWOX gene family in various vital developmental processes, establishes phylogenetic relationships with related plant species and provides a platform for functional validation of specific AsWOX genes.
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References
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3. Costanzo E, Trehin C, Vandenbussche M. The role of WOX genes in flower development. Annals of Botany. 2014; 114(7):1545-53. https://doi.org/10.1093/aob/mcu123
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7. Deveaux Y, Toffano-Nioche C, Claisse G, Thareau V, Morin H, Laufs P, Moreau H, Kreis M, Lecharny A. Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis. BMC Evolutionary Biology. 2008;8(1):291. https://doi.org/10.1186/1471-2148-8-291
8. Ge Y, Liu J, Zeng M, He J, Qin P, Huang H, Xu L. Identification of WOX family genes in Selaginella kraussiana for studies on stem cells and regeneration in lycophytes. Frontiers in Plant Science. 2016;7:93. https://doi.org/10.3389/fpls.2016.00093
9. Hedman H, Zhu T, von Arnold S, Sohlberg JJ. Analysis of the WUSCHEL-RELATED HOMEOBOX gene family in the conifer Picea abies reveals extensive conservation as well as dynamic patterns. BMC Plant Biology. 2013;13(1):89. https://doi.org/10.1186/1471-2229-13-89
10. Zhang X, Zong J, Liu J, Yin J, Zhang D. Genome?wide analysis of WOX gene family in rice, sorghum, maize, Arabidopsis and poplar. Journal of Integrative plant biology. 2010; 52(11):1016-26. https://doi.org/10.1111/j.1744-7909.2010.00982.x
11. Li XX, Liu C, Li W, Zhang ZL, Gao XM, Zhou H, Guo YF. Genome-wide identification, phylogenetic analysis and expression profiling of the WOX family genes in Solanum lycopersicum. Yi chuan= Hereditas. 2016;38(5):444-60. http://www.cnki.net/kcms/detail/11.1913.R.20160331.1108.006.html
12. Shchennikova AV, Shulga OA, Kochieva EZ, Beletsky AV, Filyushin MA, Ravin NV, Skryabin KG. Homeobox genes encoding WOX transcription factors in the flowering parasitic plant Monotropa hypopitys. Russian Journal of Genetics: Applied Research. 2017;7(7):781-88. https://doi.org/10.1134/S2079059717070085
13. Tang F, Chen N, Zhao M, Wang Y, He R, Peng X, Shen S. Identification and functional divergence analysis of WOX gene family in paper mulberry. International Journal of Molecular Sciences. 2017;18(8):1782. https://doi.org/10.3390/ijms18081782
14. Cao Y, Han Y, Meng D, Li G, Li D, Abdullah M, Jin Q, Lin Y, Cai Y. Genome-wide analysis suggests the relaxed purifying selection affect the evolution of WOX genes in Pyrus bretschneideri, Prunus persica, Prunus mume and Fragaria vesca. Frontiers in Genetics. 2017;8:78. https://doi.org/10.3389/fgene.2017.00078
15. Li Y, Zhu Y, Yao J, Zhang S, Wang L, Guo C, Van Nocker S, Wang X. Genome-wide identification and expression analyses of the homeobox transcription factor family during ovule development in seedless and seeded grapes. Scientific Reports. 2017;7(1):1-6. https://doi.org/10.1038/s41598-017-12988-y
16. Yang Z, Gong Q, Qin W, Yang Z, Cheng Y, Lu L, Ge X, Zhang C, Wu Z, Li F. Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses. BMC Plant Biology. 2017;17(1):113. https://doi.org/10.1186/s12870-017-1065-8
17. Zhang N, Huang X, Bao Y, Wang B, Liu L, Dai L, Chen J, An X, Sun Y, Peng D. Genome-wide identification and expression profiling of WUSCHEL-related homeobox (WOX) genes during adventitious shoot regeneration of watermelon (Citrullus lanatus). Acta physiologiae Plantarum. 2015;37(11):224. https://doi.org/10.1007/s11738-015-1964-y
18. Rahman ZU, Azam SM, Liu Y, Yan C, Ali H, Zhao L, Chen P, Yi L, Priyadarshani SV, Yuan Q. Expression profiles of Wuschel-related homeobox gene family in pineapple (Ananas comosus L.). Tropical Plant Biology. 2017;4(10):204-15. https://doi.org/10.1007/s12042-017-9192-9
19. Ramkumar TR, Kanchan M, Upadhyay SK, Sembi JK. Identification and characterization of WUSCHEL-related homeobox (WOX) gene family in economically important orchid species Phalaenopsis equestris and Dendrobium catenatum. Plant Gene. 2018;14:37-45. https://doi.org/10.1016/j.plgene.2018.04.004
20. Wang X, Bi C, Wang C, Ye Q, Yin T, Ye N. Genome-wide identification and characterization of WUSCHEL-related homeobox (WOX) genes in Salix suchowensis. Journal of Forestry Research. 2019;30(5):1811-22.https://doi.org/10.1007/s11676-018-0734-2
21. Wang P, Guo Y, Chen X, Zheng Y, Sun Y, Yang J, Ye N. Genome-wide identification of WOX genes and their expression patterns under different hormone and abiotic stress treatments in tea plant (Camellia sinensis). Trees. 2019; 33(4):1129-42. https://doi.org/10.1007/s00468-019-01847-0
22. Li M, Wang R, Liu Z, Wu X, Wang J. Genome-wide identification and analysis of the WUSCHEL-related homeobox (WOX) gene family in allotetraploid Brassica napus reveals changes in WOX genes during polyploidization. BMC Genomics. 2019; 20(1): 317. https://doi.org/10.1186/s12864-019-5684-3
23. Chang Y, Song X, Zhang Q, Liu H, Bai Y, Lei X, Pei D. Genome-Wide Identification of WOX Gene Family and Expression Analysis during Rejuvenational Rhizogenesis in Walnut (Juglans regia L.). Forests. 2020;11(1):16. https://doi.org/10.3390/f11010016
24. Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z. The genome sequence of the orchid Phalaenopsis equestris. Nature Genetics. 2015; 47(1): 65-72. https://doi.org/10.1038/ng.3149
25. Zhang GQ, Xu Q, Bian C, Tsai WC, Yeh CM, Liu KW, Yoshida K, Zhang LS, Chang SB, Chen F, Shi Y. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. Scientific Reports. 2016;6(1):1-10. https://doi.org/10.1038/srep19029
26. Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q, Chen LJ, Yoshida K. The Apostasia genome and the evolution of orchids. Nature. 2017;549(7672):379-83. https://doi.org/10.1038/nature23897
27. Givnish TJ, Spalink D, Ames M, Lyon SP, Hunter SJ, Zuluaga A, Iles WJ, Clements MA, Arroyo MT, Leebens-Mack J, Endara L. Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proceedings of the Royal Society B: Biological Sciences. 2015;282(1814):20151553. https://doi.org/10.1098/rspb.2015.1553
28. Schultz J, Copley RR, Doerks T, Ponting CP, Bork P. SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Research. 2000;28(1):231-34. https://doi.org/10.1093/nar/28.1.231
29. Sigrist CJ, De Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I. New and continuing developments at PROSITE. Nucleic Acids Research. 2012;41(D1):D344-7. https://doi.org/10.1093/nar/gks1067
30. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research. 1988;16(22):10881-90. https://doi.org/10.1093/nar/16.22.10881
31. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research. 2009; 37(suppl_2):W202-8. https://doi.org/10.1093/nar/gkp335
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33. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. Protein identification and analysis tools on the ExPASy server. Springer. 2005:571-607. https://doi.org/10.1385/1-59259-890-0:571
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Published
01-04-2020
How to Cite
1.
Ramkumar TR, Kanchan M, Sembi JK. Genome wide characterization of WUSCHEL-related homeobox (WOX) gene family in Apostasia shenzhenica, a primeval orchid. Plant Sci. Today [Internet]. 2020 Apr. 1 [cited 2024 Nov. 21];7(2):164-71. Available from: https://horizonepublishing.com/journals/index.php/PST/article/view/703
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