Complete Genome Expression Analysis of the Auxin Response Factor Gene Family in Sandalwood and Their Potential Roles in Drought Stress
Auxin response factors (ARFs) are essential transcription factors in plants that play an irreplaceable role in controlling the expression of auxin response genes and participating in plant growth and stress. The <i>ARF</i> gene family has been found in <i>Arabidopsis thaliana</i...
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MDPI AG
2022-11-01
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| Series: | Forests |
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| Online Access: | https://www.mdpi.com/1999-4907/13/11/1934 |
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| author | Xiaojing Liu Yunshan Liu Shengkun Wang Fangcuo Qin Dongli Wang Yu Chen Lipan Hu Sen Meng Junkun Lu |
| author_facet | Xiaojing Liu Yunshan Liu Shengkun Wang Fangcuo Qin Dongli Wang Yu Chen Lipan Hu Sen Meng Junkun Lu |
| author_sort | Xiaojing Liu |
| collection | DOAJ |
| description | Auxin response factors (ARFs) are essential transcription factors in plants that play an irreplaceable role in controlling the expression of auxin response genes and participating in plant growth and stress. The <i>ARF</i> gene family has been found in <i>Arabidopsis thaliana</i>, apple (<i>Malus domestica</i>), poplar (<i>Populus trichocarpa</i>) and other plants with known whole genomes. However, <i>S. album</i> (<i>Santalum album</i> L.), has not been studied. In this study, we analyzed and screened the whole genome of <i>S. album</i> and obtained 18 <i>S. album ARF</i>s (<i>SaARF</i>s), which were distributed on eight chromosomes. Through the prediction of conserved domains, we found that 13 of the 18 SaARFs had three intact conserved domains, named DBD, MR, Phox and Bem1 (PB1), while the extra five SaARFs (SaARF3, SaARF10, SaARF12, SaARF15, SaARF17) had only two conserved domains, and the C-terminal PB1 domain was missing. By establishing a phylogenetic tree, 62 <i>ARF</i> genes in <i>S. album</i>, poplar and <i>Arabidopsis</i> were divided into four subgroups, named Ⅰ, Ⅱ, Ⅲ and Ⅳ. According to the results of collinearity analysis, we found that ten of the eighteen <i>ARF</i> genes were involved in five segmental duplication events and these genes had short distance intervals and high homology in the <i>SaARF</i> gene family. Finally, tissue-specific and drought-treatment expression of <i>SaARF</i> genes was observed by quantitative real-time polymerase chain reaction (qRT-PCR), and six genes were significantly overexpressed in haustorium. Meanwhile we found <i>SaARF5</i>, <i>SaARF10</i>, and <i>SaARF16</i> were significantly overexpressed under drought stress. These results provide a basis for further analysis of the related functions of the <i>S. album ARF</i> gene and its relationship with haustorium formation. |
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| institution | Directory Open Access Journal |
| issn | 1999-4907 |
| language | English |
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| spelling | doaj.art-62d263df26aa4154bcb72b130303cca92023-11-24T08:24:18ZengMDPI AGForests1999-49072022-11-011311193410.3390/f13111934Complete Genome Expression Analysis of the Auxin Response Factor Gene Family in Sandalwood and Their Potential Roles in Drought StressXiaojing Liu0Yunshan Liu1Shengkun Wang2Fangcuo Qin3Dongli Wang4Yu Chen5Lipan Hu6Sen Meng7Junkun Lu8State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, ChinaCollege of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, ChinaCollege of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, ChinaAuxin response factors (ARFs) are essential transcription factors in plants that play an irreplaceable role in controlling the expression of auxin response genes and participating in plant growth and stress. The <i>ARF</i> gene family has been found in <i>Arabidopsis thaliana</i>, apple (<i>Malus domestica</i>), poplar (<i>Populus trichocarpa</i>) and other plants with known whole genomes. However, <i>S. album</i> (<i>Santalum album</i> L.), has not been studied. In this study, we analyzed and screened the whole genome of <i>S. album</i> and obtained 18 <i>S. album ARF</i>s (<i>SaARF</i>s), which were distributed on eight chromosomes. Through the prediction of conserved domains, we found that 13 of the 18 SaARFs had three intact conserved domains, named DBD, MR, Phox and Bem1 (PB1), while the extra five SaARFs (SaARF3, SaARF10, SaARF12, SaARF15, SaARF17) had only two conserved domains, and the C-terminal PB1 domain was missing. By establishing a phylogenetic tree, 62 <i>ARF</i> genes in <i>S. album</i>, poplar and <i>Arabidopsis</i> were divided into four subgroups, named Ⅰ, Ⅱ, Ⅲ and Ⅳ. According to the results of collinearity analysis, we found that ten of the eighteen <i>ARF</i> genes were involved in five segmental duplication events and these genes had short distance intervals and high homology in the <i>SaARF</i> gene family. Finally, tissue-specific and drought-treatment expression of <i>SaARF</i> genes was observed by quantitative real-time polymerase chain reaction (qRT-PCR), and six genes were significantly overexpressed in haustorium. Meanwhile we found <i>SaARF5</i>, <i>SaARF10</i>, and <i>SaARF16</i> were significantly overexpressed under drought stress. These results provide a basis for further analysis of the related functions of the <i>S. album ARF</i> gene and its relationship with haustorium formation.https://www.mdpi.com/1999-4907/13/11/1934<i>Santalum album</i> L.auxin response factorsauxinqRT-PCRdrought |
| spellingShingle | Xiaojing Liu Yunshan Liu Shengkun Wang Fangcuo Qin Dongli Wang Yu Chen Lipan Hu Sen Meng Junkun Lu Complete Genome Expression Analysis of the Auxin Response Factor Gene Family in Sandalwood and Their Potential Roles in Drought Stress Forests <i>Santalum album</i> L. auxin response factors auxin qRT-PCR drought |
| title | Complete Genome Expression Analysis of the Auxin Response Factor Gene Family in Sandalwood and Their Potential Roles in Drought Stress |
| title_full | Complete Genome Expression Analysis of the Auxin Response Factor Gene Family in Sandalwood and Their Potential Roles in Drought Stress |
| title_fullStr | Complete Genome Expression Analysis of the Auxin Response Factor Gene Family in Sandalwood and Their Potential Roles in Drought Stress |
| title_full_unstemmed | Complete Genome Expression Analysis of the Auxin Response Factor Gene Family in Sandalwood and Their Potential Roles in Drought Stress |
| title_short | Complete Genome Expression Analysis of the Auxin Response Factor Gene Family in Sandalwood and Their Potential Roles in Drought Stress |
| title_sort | complete genome expression analysis of the auxin response factor gene family in sandalwood and their potential roles in drought stress |
| topic | <i>Santalum album</i> L. auxin response factors auxin qRT-PCR drought |
| url | https://www.mdpi.com/1999-4907/13/11/1934 |
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