The banana (Musa acuminata) MYB gene family and MaMYB14, MaMYB63 and MaMYB110 expression in response to salinity-stress in cv. Berangan

References

• Agarwal M, Hao Y, Kapoor A, Dong CH, Fujii H, Zheng X, Zhu JK. 2006. A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. J Biol Chem. 281(49):37636–37645.
   PubMed Web of Science ®Google Scholar
• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403–410. DOI: 10.1016/S0022-2836(05)80360-2.
   PubMed Web of Science ®Google Scholar
• Anand L. 2019. chromoMap: An R package for interactive visualization and annotation of chromosomes. BioRxiv. DOI: 10.1101/605600.
   Google Scholar
• Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths‐Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32(1):138–141.
   Web of Science ®Google Scholar
• Baumann K, Perez-Rodriguez M, Bradley D, Venail J, Bailey P, Jin H, Koes R, Roberts K, Martin C. 2007. Control of cell and petal morphogenesis by R2R3 MYB transcription factors. Development. 134(9):1691–1701. DOI: 10.1242/dev.02836.
   PubMed Web of Science ®Google Scholar
• Cao ZH, Zhang SZ, Wang RK, Zhang RF, Hao YJ. 2013. Genome wide analysis of the apple MYB transcription factor family allows the identification of MdoMYB121 gene conferring abiotic stress tolerance in plants. PLoS One 8(7):e69955.
   PubMed Web of Science ®Google Scholar
• Chen S, Niu X, Guan Y, Li H. 2017. Genome-wide analysis and expression profiles of the MYB genes in Brachypodium distachyon. Plant Cell Physiol. 58(10):1777–1788.
   PubMed Web of Science ®Google Scholar
• Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676.
   PubMed Web of Science ®Google Scholar
• Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: A sequence logo generator. Genome Res. 14(6):1188–1190.
   PubMed Web of Science ®Google Scholar
• Du H, Feng BR, Yang SS, Huang YB, Tang YX. 2012. The R2R3-MYB transcription factor gene family in maize. PLoS One 7(6):e37463.
   PubMed Web of Science ®Google Scholar
• Du H, Liang Z, Zhao S, Nan MG, Tran LS, Lu K, Huang YB, Li JN. 2015. The evolutionary history of R2R3-MYB proteins across 50 eukaryotes: new insights into subfamily classification and expansion. Sci Rep. 5:11037.
   PubMed Web of Science ®Google Scholar
• Du HA, Wang YB, Xie YI, Liang ZH, Jiang SJ, Zhang SS, Huang YB, Tang YX. 2013. Genome-wide identification and evolutionary and expression analyses of MYB-related genes in land plants. DNA Res. 20(5):437–448.
   PubMed Web of Science ®Google Scholar
• D’Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, et al. 2012. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213–217.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792–1797.
   PubMed Web of Science ®Google Scholar
• Espley RV, Hellens RP, Putterill J, Stevenson DE, Kutty‐Amma S, Allan AC. 2007. Red colouration in Apple fruit is due to the activity of the MYB transcription factor, MdMYB10. Plant J. 49(3):414–427.
   PubMed Web of Science ®Google Scholar
• Fan ZQ, Ba LJ, Shan W, Xiao YY, Lu WJ, Kuang JF, Chen JY. 2018. A banana R2R3-MYB transcription factor MaMYB3 is involved in fruit ripening through modulation of starch degradation by repressing starch degradation-related genes and MabHLH6. Plant J. 96(6):1191–1205.
   PubMed Web of Science ®Google Scholar
• FAO. 2017. Banana facts and figures; [accessed 2020 January 8]. http://www.fao.org/economic/est/est-commodities/bananas/bananafacts/en/#.XhU81OgzY2w.
   Google Scholar
• Feng G, Burleigh JG, Braun EL, Mei W, Barbazuk WB. 2017. Evolution of the 3R-MYB gene family in plants. Genome Biol Evol. 9(4):1013–1029.
   PubMed Web of Science ®Google Scholar
• Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. 2003. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31(13):3784–3788. 2003
   PubMed Web of Science ®Google Scholar
• Gonçalves S. 2016. MYB transcription factors for enhanced drought tolerance in plants. Water stress and crop plants: A sustainable approach. In: Ahmad, P, editor. Water stress and crop plants: A sustainable approach. Hoboken (NJ): Wiley; p. 194–205.
   Google Scholar
• Guo AY, Zhu QH, Chen X, Luo JC. 2007. GSDS: A gene structure display server. Yi Chuan. 29(8):1023–1026.
   PubMedGoogle Scholar
• Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K. 2007. WoLF PSORT: Protein localization predictor. Nucleic Acids Res. 35(2):585–587.
   Web of Science ®Google Scholar
• Jian W, Cao H, Yuan S, Liu Y, Lu J, Lu W, Li N, Wang J, Zou J, Tang N, et al. 2019. SlMYB75, an MYB-type transcription factor, promotes anthocyanin accumulation and enhances volatile aroma production in tomato fruits. Horticulture Res. 6:22.
   PubMed Web of Science ®Google Scholar
• Jiang C, Gu J, Chopra S, Gu X, Peterson T. 2004. Ordered origin of the typical two- and three-repeat Myb genes. Gene 326:13–22.
   PubMed Web of Science ®Google Scholar
• Katiyar A, Smita S, Lenka SK, Rajwanshi R, Chinnusamy V, Bansal KC. 2012. Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC Genomics 13(1):544.
   PubMed Web of Science ®Google Scholar
• Kelemen Z, Sebastian A, Xu W, Grain D, Salsac F, Avon A, Berger N, Tran J, Dubreucq B, Lurin C, et al. 2015. Analysis of the DNA-binding activities of the Arabidopsis R2R3-MYB transcription factor family by one-hybrid experiments in yeast. PLoS One 10(10):e0141044.
   PubMed Web of Science ®Google Scholar
• Kiefer E, Heller W, Ernst D. 2000. A simple and efficient protocol for isolation of functional RNA from plant tissues rich in secondary metabolites. Plant Mol Biol Rep. 18(1):33–39.
   Web of Science ®Google Scholar
• Klempnauer KH, Gonda TJ, Bishop JM. 1982. Nucleotide sequence of the retroviral leukemia gene v-myb and its cellular progenitor c-myb: The architecture of a transduced oncogene. Cell 31(2 Pt 1):453–463.
   PubMed Web of Science ®Google Scholar
• Kosová K, Vítámvás P, Urban MO, Prášil IT, Renaut J. 2018. Plant abiotic stress proteomics: The major factors determining alterations in cellular proteome. Front Plant Sci. 8(9):122.
   Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 33(7):1870–1874.
   PubMed Web of Science ®Google Scholar
• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948.
   PubMed Web of Science ®Google Scholar
• Lee TH, Tang H, Wang X, Paterson AH. 2012. PGDD: A database of gene and genome duplication in plants. Nucleic Acids Res. 41:1152–1158.
   Web of Science ®Google Scholar
• Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P. 2004. SMART 4.0: Towards genomic data integration. Nucleic Acids Res. 32(1):142–144.
   Web of Science ®Google Scholar
• Li Z, Peng R, Tian Y, Han H, Xu J, Yao Q. 2016. Genome-wide identification and analysis of the MYB transcription factor superfamily in Solanum lycopersicum. Plant Cell Physiol. 57(8):1657–1677.
   PubMed Web of Science ®Google Scholar
• Li X, Xue C, Li J, Qiao X, Li L, Yu LA, Huang Y, Wu J. 2016. Genome-wide identification, evolution and functional divergence of MYB transcription factors in Chinese white pear (Pyrus bretschneideri). Plant Cell Physiol. 57(4):824–847.
   PubMed Web of Science ®Google Scholar
• Li Q, Zhang C, Li J, Wang L, Ren Z. 2012. Genome-wide identification and characterization of R2R3MYB family in Cucumis sativus. PLoS One 7(10):e47576.
   PubMed Web of Science ®Google Scholar
• Li J, Liu H, Yang C, Wang J, Yan G, Si P, Bai Q, Lu Z, Zhou W, Xu L. 2020. Genome-wide identification of MYB genes and expression analysis under different biotic and abiotic stresses in Helianthus annuus L. Ind Crops Prod. 143(143):111924.
   Web of Science ®Google Scholar
• Liang YK, Dubos C, Dodd IC, Holroyd GH, Hetherington AM, Campbell MM. 2005. AtMYB61, an R2R3-MYB transcription factor controlling stomatal aperture in Arabidopsis thaliana. Curr Biol. 15(13):1201–1206.
   PubMed Web of Science ®Google Scholar
• Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta C(T)) method. Methods 25(4):402–408.
   PubMed Web of Science ®Google Scholar
• Martin G, Baurens F-C, Droc G, Rouard M, Cenci A, Kilian A, Hastie A, Doležel J, Aury J-M, Alberti A, et al. 2016. Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods. BMC Genomics 17(1):243.
   PubMed Web of Science ®Google Scholar
• Matus JT, Aquea F, Arce-Johnson P. 2008. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes. BMC Plant Biol. 8(1):83.
   PubMed Web of Science ®Google Scholar
• Mazumdar P, Lau SE, Wee WY, Singh P, Harikrishna JA. 2017. Genome-wide analysis of the CCCH zinc-finger gene family in banana (Musa acuminata): An insight into motif and gene structure arrangement, evolution and salt stress responses. Tropical Plant Biol. 10(4):177–193.
   Web of Science ®Google Scholar
• Millard PS, Weber K, Kragelund BB, Burow M. 2019. Specificity of MYB interactions relies on motifs in ordered and disordered contexts. Nucleic Acids Res. 47(18):9592–9608.
   PubMed Web of Science ®Google Scholar
• Mmadi M, Dossa K, Wang L, Zhou R, Wang Y, Cisse N, Sy M, Zhang X. 2017. Functional characterization of the versatile MYB gene family uncovered their important roles in plant development and responses to drought and waterlogging in sesame. Genes 8(12):362.
   Web of Science ®Google Scholar
• Murashige T, Skoog F. 1962. A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant. 15(3):473–497.
   Web of Science ®Google Scholar
• Ng D, Abeysinghe J, Kamali M. 2018. Regulating the regulators: The control of transcription factors in plant defense signaling. IJMS. 19(12):3737.
   Web of Science ®Google Scholar
• Ogata K, Hojo H, Aimoto S, Nakai T, Nakamura H, Sarai A, Ishii S, Nishimura Y. 1992. Solution structure of a DNA-binding unit of Myb: A helix-turn-helix-related motif with conserved tryptophans forming a hydrophobic core. Proc Natl Acad Sci USA. 89(14):6428–6432.
   PubMed Web of Science ®Google Scholar
• Paz‐Ares J, Ghosal D, Wienand U, Peterson PA, Saedler H. 1987. The regulatory c1 locus of Zea mays encodes a protein with homology to myb proto‐oncogene products and with structural similarities to transcriptional activators. EMBO J. 6(12):3553–3558.
   PubMed Web of Science ®Google Scholar
• Peptide Property Calculator; (accessed 2019 December 20). http://biotools.nubic.northwestern.edu/proteincalc.html.
   Google Scholar
• Qing J, Dawei W, Jun Z, Yulan X, Bingqi S, Fan Z. 2019. Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube. Peer J. 7:6353.
   Web of Science ®Google Scholar
• Ravi I, Vaganan MM. 2016. Abiotic stress tolerance in banana. In: Rao NKS, Shivashankara KS, Laxman RH, editors. Abiotic stress physiology of horticultural crops. India: Springer; p. 207–222.
   Google Scholar
• Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud P-F, Lindquist EA, Kamisugi Y, et al. 2008. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319(5859):64–69.
   PubMed Web of Science ®Google Scholar
• Saikumar P, Murali R, Reddy EP. 1990. Role of tryptophan repeats and flanking amino acids in Myb-DNA interactions. Proc Natl Acad Sci USA. 87(21):8452–8456.
   PubMed Web of Science ®Google Scholar
• Shapira O, Israeli Y, Shani U, Schwartz A. 2013. Salt stress aggravates boron toxicity symptoms in banana leaves by impairing guttation. Plant Cell Environ. 36(2):275–287.
   PubMed Web of Science ®Google Scholar
• Shen XJ, Guo XW, Guo X, Zhao D, Zhao W, Chen JS, Li TH. 2017. PacMYBA, a sweet cherry R2R3-MYB transcription factor, is a positive regulator of salt stress tolerance and pathogen resistance. Plant Physiol Biochem. 112:302–311.
   PubMed Web of Science ®Google Scholar
• Shen XJ, Wang YY, Zhang YX, Guo W, Jiao YQ, Zhou XA. 2018. Overexpression of the wild soybean R2R3-MYB transcription factor GsMYB15 enhances resistance to salt stress and Helicoverpa armigera in transgenic Arabidopsis. IJMS. 19(12):3958.
   Web of Science ®Google Scholar
• Singh KB, Foley RC, Oñate-Sánchez L. 2002. Transcription factors in plant defense and stress responses. Curr Opin Plant Biol. 5(5):430–436.
   PubMed Web of Science ®Google Scholar
• Song X, Li Y, Hou X. 2013. Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis). BMC Genomics 14:573.
   PubMed Web of Science ®Google Scholar
• Tak H, Negi S, Ganapathi TR. 2017. Overexpression of MusaMYB31, a R2R3 type MYB transcription factor gene indicate its role as a negative regulator of lignin biosynthesis in banana. PLoS One 12(2):e0172695.
   PubMed Web of Science ®Google Scholar
• Tanikawa J, Yasukawa T, Enari M, Ogata K, Nishimura Y, Ishii S, Sarai A. 1993. Recognition of specific DNA sequences by the c-myb protooncogene product: Role of three repeat units in the DNA-binding domain. Proc Natl Acad Sci USA. 90(20):9320–9324.
   PubMed Web of Science ®Google Scholar
• Tombuloglu H, Kekec G, Sakcali MS, Unver T. 2013. Transcriptome-wide identification of R2R3-MYB transcription factors in barley with their boron responsive expression analysis. Mol Genet Genomics 288(3–4):141–155.
   PubMed Web of Science ®Google Scholar
• Van Asten P, Fermont A, Taulya G. 2011. Drought is a major yield loss factor for rainfed East African highland banana. Agric Water Manage. 98(4):541–552.
   Web of Science ®Google Scholar
• Wang H, Wang H, Shao H, Tang X. 2016. Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology. Front Plant Sci. 9(7):67.
   Google Scholar
• Wang Y, Tang H, DeBarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, et al. 2012. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40(7):49.
   PubMed Web of Science ®Google Scholar
• Weston K. 1998. Myb proteins in life, death and differentiation. Curr Opin Genet Dev. 8(1):76–81.
   PubMed Web of Science ®Google Scholar
• Wilkins O, Nahal H, Foong J, Provart NJ, Campbell MM. 2009. Expansion and diversification of the populus R2R3-MYB family of transcription factors. Plant Physiol. 149(2):981–993.
   PubMed Web of Science ®Google Scholar
• Yang K, Li Y, Wang S, Xu X, Sun H, Zhao H, Li X, Gao Z. 2019. Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis). Peer J. 6:6242.
   Web of Science ®Google Scholar
• Zhang C, Ma R, Xu J, Yan J, Guo L, Song J, Feng R, Yu M. 2018. Genome-wide identification and classification of MYB superfamily genes in peach. PLoS One 13(6):e0199192.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Wang L. 2005. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol. 5(1):1.
   PubMed Web of Science ®Google Scholar
• Zhang L, Zhang Z, Zhang X, Yao Y, Wang R, Duan B, Fan S. 2019. Comprehensive meta-analysis and co-expression network analysis identify candidate genes for salt stress response in Arabidopsis. Plant Biosyst. 153(3):367–377.
   Web of Science ®Google Scholar
• Zhao Y, Cheng X, Liu X, Wu H, Bi H, Xu H. 2018. The wheat MYB transcription factor TaMYB31 is involved in drought stress responses in Arabidopsis. Front Plant Sci. 9:1426
   PubMed Web of Science ®Google Scholar
• Zhao Y, Yang Z, Ding Y, Liu L, Han X, Zhan J, Wei X, Diao Y, Qin W, Wang P, et al. 2019. Over-expression of an R2R3 MYB gene, GhMYB73, increases tolerance to salt stress in transgenic Arabidopsis. Plant Sci. 286:28–36.
   PubMed Web of Science ®Google Scholar
• Zhu N, Cheng S, Liu X, Du H, Dai M, Zhou DX, Yang W, Zhao Y. 2015. The R2R3-type MYB gene OsMYB91 has a function in coordinating plant growth and salt stress tolerance in rice. Plant Sci. 236:146–156.
   PubMed Web of Science ®Google Scholar