Genome-Wide Identification and Analysis of Auxin Response Factor Transcription Factor Gene Family in <i>Populus euphratica</i>
Auxin response factor (ARF) is a plant-specific transcription factor that responds to changes in auxin levels, regulating various biological processes in plants such as flower development, senescence, lateral root formation, stress response, and secondary metabolite accumulation. In this study, we i...
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2025-04-01
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| author | Yunzhu Shi Zixuan Mu Xiangyu Meng Xiang Li Lingxuan Zou Xuli Zhu Wenhao Bo |
| author_facet | Yunzhu Shi Zixuan Mu Xiangyu Meng Xiang Li Lingxuan Zou Xuli Zhu Wenhao Bo |
| author_sort | Yunzhu Shi |
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| description | Auxin response factor (ARF) is a plant-specific transcription factor that responds to changes in auxin levels, regulating various biological processes in plants such as flower development, senescence, lateral root formation, stress response, and secondary metabolite accumulation. In this study, we identified the ARF gene family in <i>Populus euphratica</i> Oliv. using bioinformatics analysis, examining their conserved structural domains, gene structure, expression products, and evolutionary relationships. We found that the 34 <i>PeARF</i> genes were unevenly distributed on 19 chromosomes of <i>P. euphratica</i>. All 56 PeARF proteins were hydrophilic and unstable proteins localized in the nucleus, with secondary structures containing α-helices, extended strands, random coils, and β-turns but lacking transmembrane helices (TM-helices) and signal peptides. Evolutionary analysis divided the PeARF proteins into five subfamilies (A–E), with high conservation observed in the order and number of motifs, domains, gene structure, and other characteristics within each subfamily. Expression pattern analysis revealed that 17 <i>PeARF</i> genes were upregulated during cell growth and heterophylly development. This comprehensive analysis provides insights into the molecular mechanisms of ARF genes in <i>P. euphratica</i> growth, development, and stress response, serving as a basis for further studies on the auxin signaling pathway in <i>P. euphratica</i>. |
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| spelling | doaj-art-3c76e33d352649faa6a6342af1e103cb2025-08-20T02:28:19ZengMDPI AGPlants2223-77472025-04-01148124810.3390/plants14081248Genome-Wide Identification and Analysis of Auxin Response Factor Transcription Factor Gene Family in <i>Populus euphratica</i>Yunzhu Shi0Zixuan Mu1Xiangyu Meng2Xiang Li3Lingxuan Zou4Xuli Zhu5Wenhao Bo6State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, ChinaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, ChinaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, ChinaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, ChinaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, ChinaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, ChinaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, ChinaAuxin response factor (ARF) is a plant-specific transcription factor that responds to changes in auxin levels, regulating various biological processes in plants such as flower development, senescence, lateral root formation, stress response, and secondary metabolite accumulation. In this study, we identified the ARF gene family in <i>Populus euphratica</i> Oliv. using bioinformatics analysis, examining their conserved structural domains, gene structure, expression products, and evolutionary relationships. We found that the 34 <i>PeARF</i> genes were unevenly distributed on 19 chromosomes of <i>P. euphratica</i>. All 56 PeARF proteins were hydrophilic and unstable proteins localized in the nucleus, with secondary structures containing α-helices, extended strands, random coils, and β-turns but lacking transmembrane helices (TM-helices) and signal peptides. Evolutionary analysis divided the PeARF proteins into five subfamilies (A–E), with high conservation observed in the order and number of motifs, domains, gene structure, and other characteristics within each subfamily. Expression pattern analysis revealed that 17 <i>PeARF</i> genes were upregulated during cell growth and heterophylly development. This comprehensive analysis provides insights into the molecular mechanisms of ARF genes in <i>P. euphratica</i> growth, development, and stress response, serving as a basis for further studies on the auxin signaling pathway in <i>P. euphratica</i>.https://www.mdpi.com/2223-7747/14/8/1248ARF gene familyauxin response factor<i>Populus euphratica</i>genomics |
| spellingShingle | Yunzhu Shi Zixuan Mu Xiangyu Meng Xiang Li Lingxuan Zou Xuli Zhu Wenhao Bo Genome-Wide Identification and Analysis of Auxin Response Factor Transcription Factor Gene Family in <i>Populus euphratica</i> Plants ARF gene family auxin response factor <i>Populus euphratica</i> genomics |
| title | Genome-Wide Identification and Analysis of Auxin Response Factor Transcription Factor Gene Family in <i>Populus euphratica</i> |
| title_full | Genome-Wide Identification and Analysis of Auxin Response Factor Transcription Factor Gene Family in <i>Populus euphratica</i> |
| title_fullStr | Genome-Wide Identification and Analysis of Auxin Response Factor Transcription Factor Gene Family in <i>Populus euphratica</i> |
| title_full_unstemmed | Genome-Wide Identification and Analysis of Auxin Response Factor Transcription Factor Gene Family in <i>Populus euphratica</i> |
| title_short | Genome-Wide Identification and Analysis of Auxin Response Factor Transcription Factor Gene Family in <i>Populus euphratica</i> |
| title_sort | genome wide identification and analysis of auxin response factor transcription factor gene family in i populus euphratica i |
| topic | ARF gene family auxin response factor <i>Populus euphratica</i> genomics |
| url | https://www.mdpi.com/2223-7747/14/8/1248 |
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