Identifying strawberry Whirly family transcription factors and their expressions in response to crown rot
Keywords:crown rot, gene structure, phylogenetic analysis, strawberry, transcriptional expression
Crown rot is one of the most destructive diseases of cultivated strawberry. The correlation between Whirly family transcription factors, the one class of known resistance genes, and strawberry crown rot resistance has not been studied. In this study, the Whirlys of Fragaria × ananassa, F. iinumae, F. vesca, F. viridis and F. nilgerrensis were characterized by searching the strawberry genome database and analyzing the presence of Whirly domains. Five FaWHYs, two FiWHYs, three FnWHYs, two FviWHYs and four FvWHYs were identified from their respective genome. Two gene clusters with segmental duplications were obtained from the gene cluster analysis with two and three FaWHYs, and three FaWHYs showed syntenic relationships with AtWHYs of Arabidopsis thaliana. FiWHY1, FvWHY2 and FviWHY1 showed syntenic relationships with FaWHY1 and FaWHY2. At the same time, FiWHY2, FvWHY3, FviWHY2 and FnWHY3 exhibited similar syntenic relationships with FaWHY4 and FaWHY5. In addition, FnWHY1 and FnWHY2 corresponded to both FaWHY1 and FaWHY2. Gene expression analysis revealed that five FaWHYs were expressed in crowns, and the regulation of FaWHYs was always consistent with the cis-elements in their promoters. All of them were downregulated by crown rot infected. Together, these results provided a basis for further functional studies of the FaWHYs proteins and their responses to crown rot.
Akbudak MA, Filiz E (2019). Whirly (Why) transcription factors in tomato (Solanum lycopersicum): genome-wide identification and transcriptional profiling under drought and salt stresses. Molecular Biology Report 46(4):4139-4150. https://doi.org/10.1007/s11033-019-04863-y DOI: https://doi.org/10.1007/s11033-019-04863-y
Anciro A, Mangandi J, Verma S, Peres N, Whitaker VM, Lee S (2018). FaRCg1: a quantitative trait locus conferring resistance to Colletotrichum crown rot caused by Colletotrichum gloeosporioides in octoploid strawberry. Theoretical and Applied Genetics 131(10):2167-2177. https://doi.org/10.1007/s00122-018-3145-z DOI: https://doi.org/10.1007/s00122-018-3145-z
Cappadocia L, Parent JS, Sygusch J, Brisson N (2013). A family portrait: structural comparison of the Whirly proteins from Arabidopsis thaliana and Solanum tuberosum. Acta Crystallographica. Section F Structural Biology Crystallization Communications 69(11):1207-1211. https://doi.org/10.1107/S1744309113028698 DOI: https://doi.org/10.1107/S1744309113028698
Cappadocia L, Parent JS, Zampini, E, Lepage E, Sygusch J, Brisson N (2012). A conserved lysine residue of plant Whirly proteins is necessary for higher order protein assembly and protection against DNA damage. Nucleic Acids Research 40(1):258-269. https://doi.org/10.1093/nar/gkr740 DOI: https://doi.org/10.1093/nar/gkr740
Chen CJ, Chen H, Zhang Y, Thomas HR, Frank MH, He YH, Xia R (2020). TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant 13(8):1194-1202. https://doi.org/10.1101/289660 DOI: https://doi.org/10.1016/j.molp.2020.06.009
Chitnis VR, Gao F, Yao Z, Jordan MC, Park S, Ayele BT (2014). After-ripening induced transcriptional changes of hormonal genes in wheat seeds: the cases of brassinosteroids, ethylene, cytokinin and salicylic acid. PloS One 9(1):e87543. https://doi.org/10.1371/journal.pone.0087543 DOI: https://doi.org/10.1371/journal.pone.0087543
Desveaux D, Allard J, Brisson N, Sygusch J (2002). A new family of plant transcription factors displays a novel ssDNA-binding surface. Nature Structural Biology 9(7):512-517. https://doi.org/10.1038/nsb814 DOI: https://doi.org/10.1038/nsb814
Desveaux D, Després C, Joyeux A, Subramaniam R, Brisson N (2000). PBF-2 is a novel single-stranded DNA binding factor implicated in PR-10a gene activation in potato. The Plant Cell 12(8):1477-1489. https://doi.org/10.2307/3871144 DOI: https://doi.org/10.1105/tpc.12.8.1477
Desveaux D, Maréchal A, Brisson N (2005). Whirly transcription factors: defense gene regulation and beyond. Trends in Plant Science 10(2):95-102. https://doi.org/10.1016/j.tplants.2004.12.008 DOI: https://doi.org/10.1016/j.tplants.2004.12.008
Desveaux D, Subramanian R, Després C, Mess J, Lévesque C, Fobert P, Dangl J (2004). A WHIRLY transcription factor is required for salicylic acid dependent disease resistance in Arabidopsis. Developmental Cell 6(2):229-240. https://doi.org/10.1016/s1534-5807(04)00028-0 DOI: https://doi.org/10.1016/S1534-5807(04)00028-0
Edgar RC (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5):1792-1797. https://doi.org/10.1093/nar/gkh340 DOI: https://doi.org/10.1093/nar/gkh340
Edger PP, McKain MR, Yocca AE, Knapp SJ, Qiao Q, Zhang TC (2020). Reply to: Revisiting the origin of octoploid strawberry. Nature Genetics 52(1):5-7. https://doi.org/10.1038/s41588-019-0544-2 DOI: https://doi.org/10.1038/s41588-019-0544-2
Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, … Knapp PS (2019) Origin and evolution of the octoploid strawberry genome. Nature Genetics 51:541-547. https://doi.org/10.1038/s41588-019-0356-4 DOI: https://doi.org/10.1038/s41588-019-0356-4
Feng C, Wang J, Harris AJ, Folta KM, Zhao M, Kang M (2021). Tracing the diploid ancestry of the cultivated octoploid strawberry. Molecular Biology and Evolution 38(2):478-485. https://doi.org/10.1093/molbev/msaa238 DOI: https://doi.org/10.1093/molbev/msaa238
Foyer CH, Karpinska B, Krupinska K (2013). The functions of WHIRLY1 and REDOX-RESPONSIVE TRANSCRIPTION FACTOR1 in cross tolerance responses in plants: a hypothesis. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 369(1640):20130226. https://doi.org/10.1098/rstb.2013.0226 DOI: https://doi.org/10.1098/rstb.2013.0226
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 Research 31(13):3784-3788. https://doi.org/10.1093/nar/gkg563 DOI: https://doi.org/10.1093/nar/gkg563
He YT, Ju CM, Chen JG (2020). Cloning of OsWHY1 gene in rice and construction of overexpression and RNAi vectors. School of Life Sciences, Hubei University 42:390-397.
Isemer R, Mulisch M, Schäfer A, Kirchner S, Koop HU, Krupinska K (2012). Recombinant Whirly1 translocates from transplastomic chloroplasts to the nucleus. FEBS Letters 586(1):85-88. https://doi.org/10.1016/j.febslet.2011.11.029 DOI: https://doi.org/10.1016/j.febslet.2011.11.029
Kong FY, Deng YS, Zhou B, Meng QW (2012). Research advancement of Whirly transcription factors. Plant Physiology Journal 48(7):643-653. https://doi.org/10.13592/j.cnki.ppj.2012.07.014
Kumar S, Stecher G, Tamura K (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7):1870-1874. https://doi.org/10.1093/molbev/msw054 DOI: https://doi.org/10.1093/molbev/msw054
Lepage É, Zampini É, Brisson N (2013). Plastid genome instability leads to reactive oxygen species production and plastid-to-nucleus retrograde signalling in Arabidopsis. Plant Physiology 163(2):867-881. https://doi.org/10.1104/pp.113.223560 DOI: https://doi.org/10.1104/pp.113.223560
Li Q, Wang H, Guo LQ, Luo QL (2019). Identification and expression analysis of the Whirly gene family in soybean. Soybean Science 38:204-211. DOI: https://doi.org/10.7287/peerj.preprints.27606
Li Z, Wang YT, Gao L, Wang F, Ye JL, Li GH (2014). Biochemical changes and defence responses during the development of peach gummosis caused by Lasiodiplodia theobromae. European Journal of Plant Pathology 138(1):195-207. https://doi.org/10.1007/s10658-013-0322-4 DOI: https://doi.org/10.1007/s10658-013-0322-4
Liston A, Wei N, Tennessen JA, Li JM, Dong M, Ashman TL (2020) Revisiting the origin of octoploid strawberry. Nature Genetics 52(1):2-4. https://doi.org/10.1038/s41588-019-0543-3 DOI: https://doi.org/10.1038/s41588-019-0543-3
Liu W, Yan Y, Zeng HQ, Li XL, Wei YX, Liu GY, … Shi HT (2018). Functional characterization of WHY-WRKY75 transcriptional module in plant response to cassava bacterial blight. Tree Physiology 38(10):1502-1512. https://doi.org/10.1093/treephys/tpy053 DOI: https://doi.org/10.1093/treephys/tpy053
Lu YY, Wei XC, Zhao YY, Yuan YX, Wang ZY, Yang SJ, … Zhang XW (2019). Identification and expression analysis of Whirly gene family in Capsicum annuum L. Acta Agriculturae Boreali-Sinica 34:72-78.
Mangandi J, Peres NA, Whitaker VM (2015). Identifying resistance to crown rot caused by Colletotrichum gloeosporioides in strawberry. Plant Disease 99(7):954-961. https://doi.org/10.1094/pdis-09-14-0907-re DOI: https://doi.org/10.1094/PDIS-09-14-0907-RE
Maréchal A, Parent JS, Sabar M, Véronneau-Lafortune F, Abou-Rached C, Brisson N (2008). Overexpression of mtDNA-associated AtWhy2 compromises mitochondrial function. BMC Plant Biology 8(1):42. https://doi.org/10.1186/1471-2229-8-42 DOI: https://doi.org/10.1186/1471-2229-8-42
Rombauts S, Déhais P, Montagu MV, Rouzé P (1999). PlantCARE, a plant cis-acting regulatory element database. Nucleic Acids Research 27(1):295-296. https://doi.org/10.1093/nar/27.1.295 DOI: https://doi.org/10.1093/nar/27.1.295
Shu B, Li WC, Liu LQ, Wei YZ, Shi SY (2016). Transcriptomes of arbuscular mycorrhizal fungi and litchi host interaction after tree girdling. Frontiers in Microbiology 7:408. https://doi.org/10.3389/fmicb.2016.00408 DOI: https://doi.org/10.3389/fmicb.2016.00408
Wang YP, Tang HB, Debarry JD, Tan X, Li JP, Wang XY, … Paterson AH (2012). MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research 40(7):e49. https://doi.org/10.1093/nar/gkr1293 DOI: https://doi.org/10.1093/nar/gkr1293
Yao QT, Zhang WW, Liu L, Han R, Jian GL, Qi FJ (2008). Negative regulation of rice Whirly transcription factor for the hypersensitive response induced by non-host pathogen bacterium. Journal of Agriculture Science and Technology 10:53-58.
Zhao SY, Wang GD, Zhao WY, Zhang S, Kong FY, Dong XC, Meng QW (2018). Overexpression of tomato WHIRLY protein enhances tolerance to drought stress and resistance to Pseudomonas solanacearum in transgenic tobacco. Biologia Plantarum 62:55-68. https://doi.org/10.1007/s10535-017-0714-y DOI: https://doi.org/10.1007/s10535-017-0714-y
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