Identifying strawberry DOF family transcription factors and their expressions in response to crown rot

Authors

  • Chun LUO Yangtze University, College of Horticulture and Gardening, 1 Nanhuan road, Jingzhou (CN)
  • Yuyang HU Yangtze University, College of Horticulture and Gardening, 1 Nanhuan road, Jingzhou (CN)
  • Bo SHU Yangtze University, College of Horticulture and Gardening, 1 Nanhuan road, Jingzhou (CN)

DOI:

https://doi.org/10.15835/nbha50112640

Keywords:

crown rot, gene family, gene structure, phylogenetic analysis, strawberry, transcriptional expression

Abstract

Crown rot is one of the most destructive diseases of cultivated strawberry. The DOF family transcription factors, which involved in biotic stress, has not been studied in responding to strawberry crown rot. In this study, the DOFs of Fragaria × ananassa, F. iinumae, F. nilgerrensis, F. viridis, and F. vesca were characterized. One hundred and eighteen FaDOFs, twenty-two FiDOFs, twenty-three FnDOFs, twenty-five FviDOFs and thirty-seven FvDOFs were identified. Gene cluster analysis showed nearly seventy segmental duplication and seventeen tandem duplications for DOF family expansion in octaploid strawberry. In addition, 59 FaDOFs showed syntenic relationships with 32 AtDOFs, which were located on all F.×ananassa chromosomes except Fvb4-1 and Fvb4-2. Except for five DOFs of diploid strawberries had syntenic relationships to one FaDOF, most of them corresponded to multiple FaDOFs. Gene expression analysis revealed that 107 FaDOFs were expressed in crown, and most of them were downregulated by crown rot, while some FaDOFs such as FaDOF107, 12, 82, 91, 90 and 101 were upregulated, whose regulation was not always consistent with the cis-elements in their promoters. Together, these results provided a basis for further functional studies of the FaDOFs.

References

Cai XF, Zhang YY, Zhang CY, Zhang TY, Hu TX, Ye J, … Ye ZB (2013). Genome-wide analysis of plant-specific Dof transcription factor family in tomato. Journal of Integrative Plant Biology 55(6):552-566. https://doi.org/10.1111/jipb.12043
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/10.1016/j.molp.2020.06.009
Chow CN, Chiang-Hsieh YF, Chien CH, Zheng HQ, Lee TY, Wu NY, … Chang WC (2018). Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo-and exogenous stimuli. BMC Genomics 19(2):85. https://doi.org/10.1186/s12864-018-4469-4
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
Edger PP, McKain MR, Yocca AE, Knapp SJ, Qiao Q, Zhang TC (2020). Reply to: Revisiting the origin of octoploid strawberry. Nature Genetics 52:5-7. 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
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(7):478-485. https://doi.org/10.1093/molbev/msaa238
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
Guo Y, Qiu LJ (2013). Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics. PLoS One 8(9):e76809. https://doi.org/10.1371/journal.pone.0076809
Hernando-Amado S, González-Calle V, Carbonero P, Barrero-Sicilia C (2012). The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling. BMC Plant Biology 12:202. https://doi.org/10.1186/1471-2229-12-202
Jiang Y, Zeng B, Zhao H, Zhang M, Xie SJ, Lai JS (2012). Genome-wide transcription factor gene prediction and their expressional tissue-specificities in maize. Journal Integrative Plant Biology 54: 616-630. https://doi.org/10.1111/j.1744-7909.2012.01149.x
Kang WH, Kim S, Lee HA, Choi D, Yeom SI (2016). Genome-wide analysis of Dof transcription factors reveals functional characteristics during development and response to biotic stresses in pepper. Scientific Reports 6:33332. https://doi.org/10.1101/gr.6214107
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
Kushwaha H, Gupta S, Singh VK, Rastogi S, Yadav D (2011). Genome wide identification of Dof transcription factor gene family in sorghum and its comparative phylogenetic analysis with rice and Arabidopsis. Molecular Biology Reports 38:5037-5053. https://doi.org/10.1007/s11033-010-0650-9
Lijavetzky D, Carbonero P, Vicente-Carbajosa J (2003). Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. BMC Evolutionary Biology 3:17. https://doi.org/10.1186/1471-2148-3-17
Liston A, Wei N, Tennessen JA, Li JM, Dong M, Ashman TL (2020). Revisiting the origin of octoploid strawberry. Nature Genetics 52:2-4. https://doi.org/10.1101/665216
Liu T, Li MZ, Liu ZC, Ai XY, Li YP (2021). Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database. Horticulture Research 8:41. https://doi:org/10.1038/s41438-021-00476-4
Luo C, Sun Q, Zhang F, Zhang D, Liu C, Wu Q, Shu B (2020). Genome-wide identification and expression analysis of the Citrus malectin domain-containing receptor-like kinases in response to arbuscular mycorrhizal fungi colonization and drought. Horticulture, Environment, and Biotechnology 61:891-901. https://doi.org/10.1007/s13580-020-00273-3
Ma J, Li MY, Wang F, Tang J, Xiong AS (2015). Genome-wide analysis of Dof family transcription factors and their responses to abiotic stresses in Chinese cabbage. BMC Genomics 16:33. https://doi.org/10.1186/s12864-015-1242-9
Martínez M, Rubio-Somoza I, Fuentes R, Lara P, Carbonero P, Díaz I (2005). The barley cystatin gene (Icy) is regulated by DOF transcription factors in aleurone cells upon germination. Journal of Experimental Botany 56(412):547-556. https://doi.org/10.1093/jxb/eri033
Moreno-Risueno MA, Díaz I, Carrillo L, Fuentes R, Carbonero P (2007). The HvDOF19 transcription factor mediates the abscisic acid-dependent repression of hydrolase genes in germinating barley aleurone. the Plant Journal 51(3):352-365. https://doi.org/10.1111/j.1365-313X.2007.03146.x
Moreno-Risueno MA, Martínez M, Vicente-Carbajosa J, Carbonero P (2007). The family of DOF transcription factors: from green unicellular algae to vascular plants. Molecular Genetics and Genomics 277:379-390. https://doi.org/10.1007/s00438-006-0186-9
Negi J, Moriwaki K, Konishi M, Yokoyama R, Nakano T, Kusumi K, … Iba K (2013). A Dof transcription factor, SCAP1, is essential for the development of functional stomata in Arabidopsis. Current Biology 23(6):479-484. https://doi.org/10.1016/j.cub.2013.02.001
Shaw LM, McIntyre CL, Gresshoff PM, Xue GP (2009). Members of the Dof transcription factor family in Triticum aestivum are associated with light-mediated gene regulation. Functional and Integrative Genomics 9:485-498. https://doi.org/10.1007/s10142-009-0130-2
Shigyo M, Tabei N, Yoneyama T, Yanagisawa S (2007). Evolutionary processes during the formation of the plant-specific Dof transcription factor family. Plant & Cell Physiology 48(1):179-185. https://doi.org/10.1093/pcp/pcl044
Skirycz A, Jozefczuk S, Stobiecki M, Muth D, Zanor MI, Witt I, Mueller‐Roeber B (2007). Transcription factor AtDOF4; 2 affects phenylpropanoid metabolism in Arabidopsis thaliana. New Phytologist 175(3):425-438. https://doi.org/10.1111/j.1469-8137.2007.02129.x
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
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
Wu Z, Cheng J, Cui J, Xu X, Liang G, Luo X, … Qin C (2016). Genome-wide identification and expression profile of Dof transcription factor gene family in pepper (Capsicum annuum L.). Frontiers in Plant Science 7:574. https://doi.org/10.3389/fpls.2016.00574
Xie Y, Zhang Y, Han J, Luo J, Li G, Huang J, … Chen L (2018). The intronic cis element SE1 recruits trans-acting repressor complexes to repress the expression of ELONGATED UPPERMOST INTERNODE1 in rice. Molecular Plant 11(5):720-735. https://doi.10.1016/j.molp.2018.03.001
Yanagisawa S, Izui K (1993). Molecular cloning of two DNA-binding proteins of maize that are structurally different but interact with the same sequence motif. Journal of Biological Chemistry 268(21):16028-16036. https://doi.org/10.1016/s0021-9258(18)82353-5
Yang X, Tuskan GA, Cheng ZM (2006). Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication. Plant Physiology 142(3):820-830. https://doi.org/10.1104/pp.106.083642
Zhang B, Chen W, Foley RC, Büttner M, Singh KB (1995). Interactions between distinct types of DNA binding proteins enhance binding to ocs element promoter sequences. the Plant Cell 7(12):2241-2252. https://doi.org/10.2307/3870165
Zheng SX, Xiao S, Chye ML (2012). The gene encoding Arabidopsis acyl-CoA-binding protein 3 is pathogen inducible and subject to circadian regulation. Journal of Experimental Botany 63(8):2985-3000. https://doi.org/10.1093/jxb/ers009

Published

2022-03-11

How to Cite

LUO, C., HU, Y., & SHU, B. (2022). Identifying strawberry DOF family transcription factors and their expressions in response to crown rot. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 50(1), 12640. https://doi.org/10.15835/nbha50112640

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Section

Research Articles
CITATION
DOI: 10.15835/nbha50112640