Genome-wide identification and expression pattern analysis of BRI1-EMS-suppressor transcription factors in tomato under abiotic stresses

Journal of the American Society for Horticultural Science

Volumn 143, Issue 1, 2018, Pages 84-90

  Gao, Yingmei ^a   Hu, Jingkang ^a   Zhao, Tingting ^a   Xu, Xiangyang ^a   Jiang, Jingbin ^a   Li, Jingfu ^a  

^a NORTHEAST AGRICULTURAL UNIVERSITY   (China)

Author keywords

BES1; Expression characteristics; Gene structure; Phylogeny; Solanum lycopersicum; Stress resistance

Indexed keywords

EID: 85042110016     PISSN: 00031062     EISSN: 23279788     Source Type: Journal    
DOI: 10.21273/JASHS04312-17     Document Type: Article

References (43)

1. Artimo, P., M. Jonnalagedda, K. Arnold, D. Baratin, G. Csardi, E. Castro, S. Duvaud, V. Flegel, A. Fortier, E. Gasteiger, A. Grosdidier, C. Hernandez, V. Ioannidis, D. Kuznetsov, R. Liechti, S. Moretti, K. Mostaguir, N. Redaschi, G. Rossier, I. Xenarios, and H. Stockinger. 2012. ExPASy:SIB bioinformatics resource portal. Nucleic Acids Res. 40:597-603.
2. Bai, Y., W.B. Zhu, X.C. Hu, C.C. Sun, Y.L. Li, D.D. Wang, Q.H. Wang, G.L. Pei, Y.F. Zhang, A.G. Guo, H.X. Zhao, H.B. Lu, X.Q. Mu, J.J. Hu, X.N. Zhou, and C.G. Xie. 2016. Genome-wide analysis of the bZIP gene family identifies two ABI5-Like bZIP transcription factors, BrABI5a and BrABI5b, as positive modulators of ABA signalling in chinese cabbage. PLoS One 11(7):1-19.
3. Baloglu,M.C., V. Eldem,M. Hajyzadeh, and T. Unver. 2014. Genomewide analysis of the bZIP transcription factors in cucumber. PLoS One 9(4):e96014.
4. Bo, H., J. Jin, A. Guo, H. Zhang, J. Luo, and G. Gao. 2015. GSDS 2.0:An upgraded gene feature visualization server. Bioinformatics 31:1296-1297.
5. Broun, P. 2004. Transcription factors as tools for metabolic engineering in plants. Curr. Opin. Plant Biol. 7:202-209.
6. Center for Bioinformatics. 2015. Gene structure display server. 17 May 2017. .
7. Century, K., T.L. Reuber, and O.J. Ratcliffe. 2008. Regulating the regulators: The future prospects for transcription-factor-based agricultural biotechnology products. Plant Physiol. 147:20-29.
8. Chen, L., W. Hu, S. Tan, M. Wang, Z. Ma, S. Zhou, X. Deng, Y. Zhang, C. Huang, G. Yang, and G. He. 2012. Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon. PLoS One 7(10):e46744.
9. Chen,Y.,M. Li, X.Wu, Y. Huang, J. Ma, and A. Xiong. 2015.Genomewide analysis of basic helix-loop-helix family transcription factors and their role in responses to abiotic stress in carrot. Mol. Breed. 35:125.
10. Cheng, F., S. Liu, J. Wu, L. Fang, S. Sun, B. Liu, P. Li, W. Hua, and X. Wang. 2011. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol. 11(1):136.
11. Crooks, G.E., G. Hon, J.M. Chandonia, and S.E. Brenner. 2004. WebLogo: A sequence logo generator. Genome Res. 14:1188-1190.
12. Cui, L., K. Feng, M. Wang, M. Wang, P. Deng, W. Song, and X. Nie. 2016. Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon. BMC Genomics 17(1):636.
13. Energy’s Joint Genome Institute. 1997. Phytozome. 21 June 2017. .
14. Espinosa-Ruiz, A., C. Martinez, M. Lucas, N. Fabregas, N. Bosch, A. Cano-Delgado, and S. Prat. 2017. Topless mediates brassinosteroid control of shoot boundaries and root meristem development in Arabidopsis thaliana. Development 144:1619-1628.
15. Fujioka, S. and T. Yokota. 2003. Biosynthesis and metabolism of brassinosteroids. Annu. Rev. Plant Biol. 54:137-164.
16. Gene Denovo. 2015. Omicshare. 8 May 2017. .
17. Guo, R., H. Qian, W. Shen, L. Liu, M. Zhang, C. Cai, Y. Zhao, J. Qiao, and Q. Wang. 2013. BZR1 and BES1 participate in regulation of glucosinolate biosynthesis by brassinosteroids in Arabidopsis. J. Expt. Bot. 64:2401-2412.
18. Hoagland, D.R. and D.I. Arnon. 1937. The water-culture method for growing plants without soil. California Agr. Expt. Sta. Circ. 347.
19. Huala, E., A. Dickerman, M. Garcia-Hernandez, D. Weems, L. Reiser, F. LaFond, D. Hanley, D. Kiphart, J. Zhuang, W. Huang, L. Mueller, D. Bhattacharyya, D. Bhaya, B. Sobral, B. Beavis, C. Somerville, and S.Y. Rhee. 2001. The Arabidopsis information resource (TAIR): A comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res. 29:102-105.
20. International Solanaceae Initiative. 2015. The Sol Genomics Network. 2 Jan. 2017. .
21. Jie, W., J. Cui, and H. Zhu. 2013. Suppression of type I collagen in human scleral fibroblaststreated with extremely low-frequency electromagnetic fields. Mol. Vis. 19:885-893.
22. Jin, J.P., F. Tian, D.C. Yang, Y.Q. Meng, L. Kong, J.C. Luo, and G. Gao. 2017. PlantTFDB 4.0: Toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 45:1040-1045.
23. Larkin,M.A., G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J.D. Thompson, T.J. Gibson, and D.G. Higgins. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
24. Li, D., F. Fu, H. Zhang, and F. Song. 2015. Genome-wide systematic characterization of the bZIP transcriptional factor family in tomato (Solanum lycopersicum L.). BMC Genomics 16(1):771.
25. Li, J. and J. Chory. 1999. Brassinosteroid actions in plants. J. Expt. Bot. 50:275-282.
26. Li, L., X. Yu, A. Thompson, M. Guo, S. Yoshida, T. Asami, J. Chory, and Y. Yin. 2009. Arabidopsis MYB30 is a direct target of BES1 and cooperates with BES1 to regulate brassinosteroid-induced gene expression. Plant J. 58:275-286.
27. Magadum, S., U. Banerjee, P. Murugan, D. Gangapur, and R. Ravikesavan. 2013. Gene duplication as a major force in evolution. J. Genet. 92:155-161.
28. National Institutes of Health. 2015. Mutiple Em for motif elicitation. 15 May 2017. .
29. Pfaffl, M.W. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29:e45-e51.
30. Phoenix Bioinformatics Corporation. 2013. The arabidopsis information resource. 20 Apr. 2017. .
31. Rio, D.C., M. Ares, Jr., G.J. Hannon, and T.W. Nilsen. 2010. Purification of RNA using TRIzol (TRI reagent)Cold Spring Harb.Protoc.20106pdb.prot5439.
32. Ryu, H., K. Kim, H. Cho, and I. Hwang. 2010. Predominant actions of cytosolic BSU1 and nuclear BIN2 regulate subcellular localization of BES1 in brassinosteroid signaling. Mol. Cells 29:291-296.
33. Salazarhenao, J.E., R. Lehner, I. Betegónputze, J. Vilarrasablasi, and A.I. Cañodelgado. 2016. BES1 regulates the localization of the brassinosteroid receptor BRL3 within the provascular tissue of the Arabidopsis primary root. J. Expt. Bot. 67:4951.
34. Song,H., P.Wang, Z.Nan, andX.Wang. 2014. TheWRKYtranscription factor genes in Lotus japonicus. Intl. J. Genomics 2014:420128.
35. Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
36. Wang, C., W. Duan, A.R. Riquicho, Z. Jing, T. Liu, X. Hou, and Y. Li. 2015. Genome-wide survey and expression analysis of the PUB family in chinese cabbage (Brassica rapa ssp. pekinesis). Mol. Genet. Genomics 290:2241-2260.
37. Wei, G., L. Long, X. Tian, J. Jin, H. Liu, H. Zhang, F. Xu, and C. Song. 2016. Genome-wide identification and expression analysis of stressassociated proteins (SAPs) containing A20/AN1 zinc finger in cotton. Mol. Genet. Genomics 291:1-15.
38. Wei, X., L. Wang, J. Yu, Y. Zhang, D. Li, and X. Zhang. 2015. Genome-wide identification and analysis of the MADS-box gene family in sesame. Gene 569:66-76.
39. Wenkai, A.N., D. Chang, and F. Zhang. 2015. Expression characteristics of transcription factor BES1/BZR1 of cotton seedling in response to brassinosteroid under drought stress. Acta Botanica Boreali-Occidentalia Sinica 35:1311.
40. Wu, P., X. Song, Z. Wang, W. Duan, R. Hu, W. Wang, Y. Li, and X. Hou. 2016. Genome-wide analysis of the BES1 transcription factor family in chinese cabbage (Brassica rapa ssp. pekinensis). Plant Growth Regulat. 80:291-301.
41. Yin, Y., D. Vafeados, Y. Tao, S. Yoshida, T. Asami, and J. Chory. 2005. A new class of transcription factors mediates brassinosteroidregulated gene expression in Arabidopsis. Cell 120:249-259.
42. Yin, Y., Z.Y. Wang, S. Mora-Garcia, J. Li, S. Yoshida, T. Asami, and J. Chory. 2002. BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell 109(2):181.
43. Zhao, T., D. Liang, P. Wang, J. Liu, and F. Ma. 2012. Genome-wide analysis and expression profiling of the DREB transcription factor gene family in Malus under abiotic stress. Mol. Genet. Genomics 287:423-436.