Comprehensive Analysis of <i>Betula platyphylla</i> Suk. PIF Gene Family and Their Potential Functions in Growth and Development
Phytochrome-interacting factors (PIFs) are transcription factors with the basic helix–loop–helix (bHLH) domain. As integration factors between different signal pathways, members of the PIF protein family regulate many aspects of plant growth and development, such as seed germination, photomorphogene...
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MDPI AG
2022-12-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/23/15326 |
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| author | Aihua Chen Peng Huang Shanshan Guo Sige Liu Xiaoqing Hu Xuemei Liu |
| author_facet | Aihua Chen Peng Huang Shanshan Guo Sige Liu Xiaoqing Hu Xuemei Liu |
| author_sort | Aihua Chen |
| collection | DOAJ |
| description | Phytochrome-interacting factors (PIFs) are transcription factors with the basic helix–loop–helix (bHLH) domain. As integration factors between different signal pathways, members of the PIF protein family regulate many aspects of plant growth and development, such as seed germination, photomorphogenesis, thermomorphogenesis, rhythm regulation, flowering response, stomatal development, and stress responses. Our previous studies have shown that the <i>BpSPL2</i> gene may regulate plants’ adventitious root development through <i>PIF</i> genes. Within the <i>Betula platyphylla</i> genome, we identified eight <i>PIF</i> (<i>BpPIFs</i>) genes. We analysed and named them based on a phylogenetic tree, gene structures, and conserved motifs. Synteny analysis indicated that transposition or segmental duplication events played a minor role in the expansion of <i>BpPIFs</i>. The comparative syntenic analysis combined with phylogenetic analysis provided a deep insight into the phylogenetic relationships of <i>BpPIF</i> genes, suggesting that <i>BpPIF</i> proteins are closer to <i>PtPIF</i> than to <i>AtPIF</i>. The analysis of cis-acting elements in promoter regions of <i>BpPIF</i> genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. In addition, we found that these promoters have the transcription factor of <i>B. platyphylla SPL2</i> (<i>BpSPL2</i>) binding motif GTAC. Expression analysis demonstrated that <i>BpPIF</i> genes, especially <i>BpPIF4</i>, <i>BpPIF9b</i>, and <i>BpPIF10,</i> might be the potential target genes of <i>BpSPL2</i> in the process of adventitious root formation. Besides providing a comprehensive understanding of the <i>BpPIF</i> family, we propose a hypothetical gene network regulatory model for adventitious root formation. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T17:44:41Z |
| publishDate | 2022-12-01 |
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| spelling | doaj.art-976c5a082dca4d30897f7fade77b92182023-11-24T11:17:08ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-12-0123231532610.3390/ijms232315326Comprehensive Analysis of <i>Betula platyphylla</i> Suk. PIF Gene Family and Their Potential Functions in Growth and DevelopmentAihua Chen0Peng Huang1Shanshan Guo2Sige Liu3Xiaoqing Hu4Xuemei Liu5College of Life Science, Northeast Forestry University, Harbin 150040, ChinaCollege of Life Science, Northeast Forestry University, Harbin 150040, ChinaCollege of Life Science, Northeast Forestry University, Harbin 150040, ChinaCollege of Life Science, Northeast Forestry University, Harbin 150040, ChinaCollege of Life Science, Northeast Forestry University, Harbin 150040, ChinaCollege of Life Science, Northeast Forestry University, Harbin 150040, ChinaPhytochrome-interacting factors (PIFs) are transcription factors with the basic helix–loop–helix (bHLH) domain. As integration factors between different signal pathways, members of the PIF protein family regulate many aspects of plant growth and development, such as seed germination, photomorphogenesis, thermomorphogenesis, rhythm regulation, flowering response, stomatal development, and stress responses. Our previous studies have shown that the <i>BpSPL2</i> gene may regulate plants’ adventitious root development through <i>PIF</i> genes. Within the <i>Betula platyphylla</i> genome, we identified eight <i>PIF</i> (<i>BpPIFs</i>) genes. We analysed and named them based on a phylogenetic tree, gene structures, and conserved motifs. Synteny analysis indicated that transposition or segmental duplication events played a minor role in the expansion of <i>BpPIFs</i>. The comparative syntenic analysis combined with phylogenetic analysis provided a deep insight into the phylogenetic relationships of <i>BpPIF</i> genes, suggesting that <i>BpPIF</i> proteins are closer to <i>PtPIF</i> than to <i>AtPIF</i>. The analysis of cis-acting elements in promoter regions of <i>BpPIF</i> genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. In addition, we found that these promoters have the transcription factor of <i>B. platyphylla SPL2</i> (<i>BpSPL2</i>) binding motif GTAC. Expression analysis demonstrated that <i>BpPIF</i> genes, especially <i>BpPIF4</i>, <i>BpPIF9b</i>, and <i>BpPIF10,</i> might be the potential target genes of <i>BpSPL2</i> in the process of adventitious root formation. Besides providing a comprehensive understanding of the <i>BpPIF</i> family, we propose a hypothetical gene network regulatory model for adventitious root formation.https://www.mdpi.com/1422-0067/23/23/15326<i>Betula platyphylla</i>phytochrome-interacting factorsPIFbasic helix–loop–helix (bHLH)adventitious root |
| spellingShingle | Aihua Chen Peng Huang Shanshan Guo Sige Liu Xiaoqing Hu Xuemei Liu Comprehensive Analysis of <i>Betula platyphylla</i> Suk. PIF Gene Family and Their Potential Functions in Growth and Development International Journal of Molecular Sciences <i>Betula platyphylla</i> phytochrome-interacting factors PIF basic helix–loop–helix (bHLH) adventitious root |
| title | Comprehensive Analysis of <i>Betula platyphylla</i> Suk. PIF Gene Family and Their Potential Functions in Growth and Development |
| title_full | Comprehensive Analysis of <i>Betula platyphylla</i> Suk. PIF Gene Family and Their Potential Functions in Growth and Development |
| title_fullStr | Comprehensive Analysis of <i>Betula platyphylla</i> Suk. PIF Gene Family and Their Potential Functions in Growth and Development |
| title_full_unstemmed | Comprehensive Analysis of <i>Betula platyphylla</i> Suk. PIF Gene Family and Their Potential Functions in Growth and Development |
| title_short | Comprehensive Analysis of <i>Betula platyphylla</i> Suk. PIF Gene Family and Their Potential Functions in Growth and Development |
| title_sort | comprehensive analysis of i betula platyphylla i suk pif gene family and their potential functions in growth and development |
| topic | <i>Betula platyphylla</i> phytochrome-interacting factors PIF basic helix–loop–helix (bHLH) adventitious root |
| url | https://www.mdpi.com/1422-0067/23/23/15326 |
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