Evolutionary History and Functional Diversification of the <i>JmjC</i> Domain-Containing Histone Demethylase Gene Family in Plants
Histone demethylases containing JumonjiC (<i>JmjC</i>) domains regulate gene transcription and chromatin structure by changing the methylation status of lysine residues and play an important role in plant growth and development. In this study, a total of 332 <i>JmjC</i> famil...
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MDPI AG
2022-04-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/8/1041 |
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| author | Shifeng Ma Zhiqiang Zhang Yingqiang Long Wenqi Huo Yuzhi Zhang Xiaoqing Yang Jie Zhang Xinyang Li Qiying Du Wei Liu Daigang Yang Xiongfeng Ma |
| author_facet | Shifeng Ma Zhiqiang Zhang Yingqiang Long Wenqi Huo Yuzhi Zhang Xiaoqing Yang Jie Zhang Xinyang Li Qiying Du Wei Liu Daigang Yang Xiongfeng Ma |
| author_sort | Shifeng Ma |
| collection | DOAJ |
| description | Histone demethylases containing JumonjiC (<i>JmjC</i>) domains regulate gene transcription and chromatin structure by changing the methylation status of lysine residues and play an important role in plant growth and development. In this study, a total of 332 <i>JmjC</i> family genes were identified from 21 different plant species. The evolutionary analysis results showed that the <i>JmjC</i> gene was detected in each species, that is, the gene has already appeared in algae. The phylogenetic analysis showed that the KDM3/JHDM2 subfamily genes may have appeared when plants transitioned from water to land, but were lost in lycophytes (<i>Selaginella moellendorffii</i>). During the evolutionary process, some subfamily genes may have been lost in individual species. According to the analysis of the conserved domains, all of the plant <i>JmjC</i> genes contained a typical JmjC domain, which was highly conserved during plant evolution. The analysis of <i>cis</i>-acting elements showed that the promoter region of the <i>JmjC</i> gene was rich in phytohormones and biotic and abiotic stress-related elements. The transcriptome data analysis and protein interaction analyses showed that <i>JmjC</i> genes play an important role in plant growth and development. The results clarified the evolutionary history of <i>JmjC</i> family genes in plants and lay the foundation for the analysis of the biological functions of <i>JmjC</i> family genes. |
| first_indexed | 2024-03-09T10:30:37Z |
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| last_indexed | 2024-03-09T10:30:37Z |
| publishDate | 2022-04-01 |
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| series | Plants |
| spelling | doaj.art-e9dae034b9a34756ab6f9e3aa8ced2942023-12-01T21:19:36ZengMDPI AGPlants2223-77472022-04-01118104110.3390/plants11081041Evolutionary History and Functional Diversification of the <i>JmjC</i> Domain-Containing Histone Demethylase Gene Family in PlantsShifeng Ma0Zhiqiang Zhang1Yingqiang Long2Wenqi Huo3Yuzhi Zhang4Xiaoqing Yang5Jie Zhang6Xinyang Li7Qiying Du8Wei Liu9Daigang Yang10Xiongfeng Ma11Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaZhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, ChinaZhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, ChinaCollaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaZhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, ChinaState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, ChinaZhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, ChinaCollaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, ChinaZhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, ChinaZhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, ChinaHistone demethylases containing JumonjiC (<i>JmjC</i>) domains regulate gene transcription and chromatin structure by changing the methylation status of lysine residues and play an important role in plant growth and development. In this study, a total of 332 <i>JmjC</i> family genes were identified from 21 different plant species. The evolutionary analysis results showed that the <i>JmjC</i> gene was detected in each species, that is, the gene has already appeared in algae. The phylogenetic analysis showed that the KDM3/JHDM2 subfamily genes may have appeared when plants transitioned from water to land, but were lost in lycophytes (<i>Selaginella moellendorffii</i>). During the evolutionary process, some subfamily genes may have been lost in individual species. According to the analysis of the conserved domains, all of the plant <i>JmjC</i> genes contained a typical JmjC domain, which was highly conserved during plant evolution. The analysis of <i>cis</i>-acting elements showed that the promoter region of the <i>JmjC</i> gene was rich in phytohormones and biotic and abiotic stress-related elements. The transcriptome data analysis and protein interaction analyses showed that <i>JmjC</i> genes play an important role in plant growth and development. The results clarified the evolutionary history of <i>JmjC</i> family genes in plants and lay the foundation for the analysis of the biological functions of <i>JmjC</i> family genes.https://www.mdpi.com/2223-7747/11/8/1041histone demethylation<i>JmjC</i> genephylogenygrowth and developmentstress response |
| spellingShingle | Shifeng Ma Zhiqiang Zhang Yingqiang Long Wenqi Huo Yuzhi Zhang Xiaoqing Yang Jie Zhang Xinyang Li Qiying Du Wei Liu Daigang Yang Xiongfeng Ma Evolutionary History and Functional Diversification of the <i>JmjC</i> Domain-Containing Histone Demethylase Gene Family in Plants Plants histone demethylation <i>JmjC</i> gene phylogeny growth and development stress response |
| title | Evolutionary History and Functional Diversification of the <i>JmjC</i> Domain-Containing Histone Demethylase Gene Family in Plants |
| title_full | Evolutionary History and Functional Diversification of the <i>JmjC</i> Domain-Containing Histone Demethylase Gene Family in Plants |
| title_fullStr | Evolutionary History and Functional Diversification of the <i>JmjC</i> Domain-Containing Histone Demethylase Gene Family in Plants |
| title_full_unstemmed | Evolutionary History and Functional Diversification of the <i>JmjC</i> Domain-Containing Histone Demethylase Gene Family in Plants |
| title_short | Evolutionary History and Functional Diversification of the <i>JmjC</i> Domain-Containing Histone Demethylase Gene Family in Plants |
| title_sort | evolutionary history and functional diversification of the i jmjc i domain containing histone demethylase gene family in plants |
| topic | histone demethylation <i>JmjC</i> gene phylogeny growth and development stress response |
| url | https://www.mdpi.com/2223-7747/11/8/1041 |
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