Genome-wide identification of WRKY transcription factors and their target genes associated with drought and salt stress tolerance in Robinia pseudoacacia L.
Subject Areas : Genetics
Sergey Vishnyakov
1
*
,
Pavel Krylov
2
1 - Federal State Budget Scientific Institution “Federal Scientific Centre of Agroecology, Complex Melioration and Protective Afforestation of the Russian Academy of Sciences”, Volgograd, Russia
2 - Federal State Budget Scientific Institution “Federal Scientific Centre of Agroecology, Complex Melioration and Protective Afforestation of the Russian Academy of Sciences”
Keywords: afforestation, drought tolerance, Robinia pseudoacacia L., salt tolerance, W-box, WRKY,
Abstract :
Robinia pseudoacacia L. (black locust) is a valuable tree species widely used in afforestation and land reclamation. This species plays a crucial role in establishing resilient forest ecosystems in arid regions, contributing to soil erosion prevention and environmental improvement. The high adaptability of R. pseudoacacia makes it one of the key species for restoring degraded lands. In this study, a comprehensive bioinformatics analysis was conducted, including multiple sequence alignment, phylogenetic analysis, gene structure examination, and conserved motif identification of WRKY transcription factors. Special attention was given to the promoter regions of R. pseudoacacia genes associated with drought and salt stress responses to identify WRKY-recognized motifs (W-box) within their sequences. The results highlight the diversity of biological processes regulated by the WRKY transcription factor family. The findings provide valuable insights for selecting candidate genes that can be utilized in breeding new R. pseudoacacia cultivars with enhanced drought and salt stress tolerance.
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Chen, X., C. Li, H. Wang and Z. Guo. 2019. WRKY transcription factors: evolution, binding, and action. Phytopathology Research, 1, (1) 1-15.
Dai, W.-S., T. Peng, M. Wang and J.-H. Liu. 2023. Genome-wide identification and comparative expression profiling of the WRKY transcription factor family in two Citrus species with different Candidatus Liberibacter asiaticus susceptibility. BMC Plant Biology, 23, (1) 159.
Ding, Z. J., J. Y. Yan, C. X. Li, G. X. Li, Y. R. Wu and S. J. Zheng. 2015. Transcription factor WRKY 46 modulates the development of Arabidopsis lateral roots in osmotic/salt stress conditions via regulation of ABA signaling and auxin homeostasis. The Plant Journal, 84, (1) 56-69.
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Grant, C. E., T. L. Bailey and W. S. Noble. 2011. FIMO: scanning for occurrences of a given motif. Bioinformatics, 27, (7) 1017-1018.
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Rinerson, C. I., R. C. Rabara, P. Tripathi, Q. J. Shen and P. J. Rushton. 2015. The evolution of WRKY transcription factors. BMC plant biology, 15, 1-18.
Schwärzel, K., L. Zhang, L. Montanarella, Y. Wang and G. Sun. 2020. How afforestation affects the water cycle in drylands: A process‐based comparative analysis. Global change biology, 26, (2) 944-959.
Song, H., W. Sun, G. Yang and J. Sun. 2018. WRKY transcription factors in legumes. BMC plant biology, 18, 1-13.
Supek, F., M. Bošnjak, N. Škunca and T. Šmuc. 2011. REVIGO summarizes and visualizes long lists of gene ontology terms. PloS one, 6, (7) e21800.
Törönen, P. and L. Holm. 2022. PANNZER—a practical tool for protein function prediction. Protein Science, 31, (1) 118-128.
Wang, H., X. Cheng, D. Yin, D. Chen, C. Luo, H. Liu and C. Huang. 2023a. Advances in the research on plant WRKY transcription factors responsive to external stresses. Current issues in molecular biology, 45, (4).
Bailey, T. L., J. Johnson, C. E. Grant and W. S. Noble. 2015. The MEME suite. Nucleic acids research, 43, (W1) W39-W49.
Banerjee, A. and A. Roychoudhury. 2015. WRKY proteins: signaling and regulation of expression during abiotic stress responses. The Scientific World Journal, 2015, (1) 807560.
Chen, F., Y. Hu, A. Vannozzi, K. Wu, H. Cai, Y. Qin, A. Mullis, Z. Lin and L. Zhang. 2017a. The WRKY transcription factor family in model plants and crops. Critical Reviews in Plant Sciences, 36, (5-6) 311-335.
Chen, J., T. M. Nolan, H. Ye, M. Zhang, H. Tong, P. Xin, J. Chu, C. Chu, Z. Li and Y. Yin. 2017b. Arabidopsis WRKY46, WRKY54, and WRKY70 transcription factors are involved in brassinosteroid-regulated plant growth and drought responses. The Plant Cell, 29, (6) 1425-1439.
Chen, X., C. Li, H. Wang and Z. Guo. 2019. WRKY transcription factors: evolution, binding, and action. Phytopathology Research, 1, (1) 1-15.
Dai, W.-S., T. Peng, M. Wang and J.-H. Liu. 2023. Genome-wide identification and comparative expression profiling of the WRKY transcription factor family in two Citrus species with different Candidatus Liberibacter asiaticus susceptibility. BMC Plant Biology, 23, (1) 159.
Ding, Z. J., J. Y. Yan, C. X. Li, G. X. Li, Y. R. Wu and S. J. Zheng. 2015. Transcription factor WRKY 46 modulates the development of Arabidopsis lateral roots in osmotic/salt stress conditions via regulation of ABA signaling and auxin homeostasis. The Plant Journal, 84, (1) 56-69.
Duan, D., R. Yi, Y. Ma, Q. Dong, K. Mao and F. Ma. 2023. Apple WRKY transcription factor MdWRKY56 positively modulates drought stress tolerance. Environmental and Experimental Botany, 212, 105400.
Goyal, P., R. Devi, B. Verma, S. Hussain, P. Arora, R. Tabassum and S. Gupta. 2023. WRKY transcription factors: Evolution, regulation, and functional diversity in plants. Protoplasma, 260, (2) 331-348.
Grant, C. E., T. L. Bailey and W. S. Noble. 2011. FIMO: scanning for occurrences of a given motif. Bioinformatics, 27, (7) 1017-1018.
Grzechowiak, M., A. Ruszkowska, J. Sliwiak, A. Urbanowicz, M. Jaskolski and M. Ruszkowski. 2022. New aspects of DNA recognition by group II WRKY transcription factor revealed by structural and functional study of AtWRKY18 DNA binding domain. International journal of biological macromolecules, 213, 589-601.
Gu, L., L. Dou, Y. Guo, H. Wang, L. Li, C. Wang, L. Ma, H. Wei and S. Yu. 2019. The WRKY transcription factor GhWRKY27 coordinates the senescence regulatory pathway in upland cotton (Gossypium hirsutum L.). BMC plant biology, 19, 1-14.
Hu, B., J. Jin, A.-Y. Guo, H. Zhang, J. Luo and G. Gao. 2015. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31, (8) 1296-1297.
Huang, Z., J. Wang, Y. Li, L. Song, D. E. Chen, L. Liu and C.-Z. Jiang. 2022. A WRKY protein, MfWRKY40, of resurrection plant Myrothamnus flabellifolia plays a positive role in regulating tolerance to drought and salinity stresses of Arabidopsis. International Journal of Molecular Sciences, 23, (15) 8145.
Jones, P., D. Binns, H.-Y. Chang, M. Fraser, W. Li, C. Mcanulla, H. Mcwilliam, J. Maslen, A. Mitchell and G. Nuka. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics, 30, (9) 1236-1240.
Kuzmin, P. and P. Krylov.2024. GENETIC DIVERSITY ROBINIA PSEUDOACACIA L. GROWING IN DROUGHT CONDITIONS USING ISSR. AGRICULTURAL SCIENCE DIGEST, 1-6.
Li, Q., M. Zhao, N. Wang, S. Liu, J. Wang, W. Zhang, N. Yang, P. Fan, R. Wang and H. Wang. 2020. Water use strategies and drought intensity define the relative contributions of hydraulic failure and carbohydrate depletion during seedling mortality. Plant Physiology and Biochemistry, 153, 106-118.
Minh, B. Q., H. A. Schmidt, O. Chernomor, D. Schrempf, M. D. Woodhams, A. Von Haeseler and R. Lanfear. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular biology and evolution, 37, (5) 1530-1534.
Phukan, U. J., G. S. Jeena and R. K. Shukla. 2016. WRKY transcription factors: molecular regulation and stress responses in plants. Frontiers in plant science, 7, 760.
Rauluseviciute, I., R. Riudavets-Puig, R. Blanc-Mathieu, J. A. Castro-Mondragon, K. Ferenc, V. Kumar, R. B. Lemma, J. Lucas, J. Chèneby and D. Baranasic. 2024. JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Nucleic acids research, 52, (D1) D174-D182.
Rinerson, C. I., R. C. Rabara, P. Tripathi, Q. J. Shen and P. J. Rushton. 2015. The evolution of WRKY transcription factors. BMC plant biology, 15, 1-18.
Schwärzel, K., L. Zhang, L. Montanarella, Y. Wang and G. Sun. 2020. How afforestation affects the water cycle in drylands: A process‐based comparative analysis. Global change biology, 26, (2) 944-959.
Song, H., W. Sun, G. Yang and J. Sun. 2018. WRKY transcription factors in legumes. BMC plant biology, 18, 1-13.
Supek, F., M. Bošnjak, N. Škunca and T. Šmuc. 2011. REVIGO summarizes and visualizes long lists of gene ontology terms. PloS one, 6, (7) e21800.
Törönen, P. and L. Holm. 2022. PANNZER—a practical tool for protein function prediction. Protein Science, 31, (1) 118-128.
Wang, H., X. Cheng, D. Yin, D. Chen, C. Luo, H. Liu and C. Huang. 2023a. Advances in the research on plant WRKY transcription factors responsive to external stresses. Current issues in molecular biology, 45, (4).
Wang, Z., X. Zhang, W. Lei, H. Zhu, S. Wu, B. Liu and D. Ru. 2023b. Chromosome-level genome assembly and population genomics of Robinia pseudoacacia reveal the genetic basis for its wide cultivation. Communications Biology, 6, (1) 797.
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