Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus <i>Oryza</i>
Dirigent (DIR) members have been shown to play essential roles in plant growth, development and adaptation to environmental changes. However, to date, there has been no systematic analysis of the DIR members in the genus <i>Oryza</i>. Here, 420 genes were identified from nine rice specie...
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MDPI AG
2023-04-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/8/7189 |
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| author | Wen Duan Baoping Xue Yaqian He Shenghao Liao Xuemei Li Xueying Li Yun-Kuan Liang |
| author_facet | Wen Duan Baoping Xue Yaqian He Shenghao Liao Xuemei Li Xueying Li Yun-Kuan Liang |
| author_sort | Wen Duan |
| collection | DOAJ |
| description | Dirigent (DIR) members have been shown to play essential roles in plant growth, development and adaptation to environmental changes. However, to date, there has been no systematic analysis of the DIR members in the genus <i>Oryza</i>. Here, 420 genes were identified from nine rice species to have the conserved DIR domain. Importantly, the cultivated rice species <i>Oryza sativa</i> has more DIR family members than the wild rice species. DIR proteins in rice could be classified into six subfamilies based on phylogeny analysis. Gene duplication event analysis suggests that whole genome/segmental duplication and tandem duplication are the primary drivers for <i>DIR</i> genes’ evolution in <i>Oryza</i>, while tandem duplication is the main mechanism of gene family expansion in the DIR-b/d and DIR-c subfamilies. Analysis of the RNA sequencing data indicates that <i>OsjDIR</i> genes respond to a wide range of environmental factors, and most <i>OsjDIR</i> genes have a high expression level in roots. Qualitative reverse transcription PCR assays confirmed the responsiveness of <i>OsjDIR</i> genes to the undersupply of mineral elements, the excess of heavy metals and the infection of <i>Rhizoctonia solani</i>. Furthermore, there exist extensive interactions between DIR family members. Taken together, our results shed light on and provide a research foundation for the further exploration of <i>DIR</i> genes in rice. |
| first_indexed | 2024-03-11T04:56:42Z |
| format | Article |
| id | doaj.art-01c81485b589470fa7a403d15220c446 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T04:56:42Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-01c81485b589470fa7a403d15220c4462023-11-17T19:36:35ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-04-01248718910.3390/ijms24087189Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus <i>Oryza</i>Wen Duan0Baoping Xue1Yaqian He2Shenghao Liao3Xuemei Li4Xueying Li5Yun-Kuan Liang6State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaState Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaState Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaState Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaState Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaState Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaState Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, ChinaDirigent (DIR) members have been shown to play essential roles in plant growth, development and adaptation to environmental changes. However, to date, there has been no systematic analysis of the DIR members in the genus <i>Oryza</i>. Here, 420 genes were identified from nine rice species to have the conserved DIR domain. Importantly, the cultivated rice species <i>Oryza sativa</i> has more DIR family members than the wild rice species. DIR proteins in rice could be classified into six subfamilies based on phylogeny analysis. Gene duplication event analysis suggests that whole genome/segmental duplication and tandem duplication are the primary drivers for <i>DIR</i> genes’ evolution in <i>Oryza</i>, while tandem duplication is the main mechanism of gene family expansion in the DIR-b/d and DIR-c subfamilies. Analysis of the RNA sequencing data indicates that <i>OsjDIR</i> genes respond to a wide range of environmental factors, and most <i>OsjDIR</i> genes have a high expression level in roots. Qualitative reverse transcription PCR assays confirmed the responsiveness of <i>OsjDIR</i> genes to the undersupply of mineral elements, the excess of heavy metals and the infection of <i>Rhizoctonia solani</i>. Furthermore, there exist extensive interactions between DIR family members. Taken together, our results shed light on and provide a research foundation for the further exploration of <i>DIR</i> genes in rice.https://www.mdpi.com/1422-0067/24/8/7189<i>Oryza</i>dirigent gene familyphylogenetic analysisexpression profilesenvironmental stress |
| spellingShingle | Wen Duan Baoping Xue Yaqian He Shenghao Liao Xuemei Li Xueying Li Yun-Kuan Liang Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus <i>Oryza</i> International Journal of Molecular Sciences <i>Oryza</i> dirigent gene family phylogenetic analysis expression profiles environmental stress |
| title | Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus <i>Oryza</i> |
| title_full | Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus <i>Oryza</i> |
| title_fullStr | Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus <i>Oryza</i> |
| title_full_unstemmed | Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus <i>Oryza</i> |
| title_short | Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus <i>Oryza</i> |
| title_sort | genome wide identification and expression pattern analysis of dirigent members in the genus i oryza i |
| topic | <i>Oryza</i> dirigent gene family phylogenetic analysis expression profiles environmental stress |
| url | https://www.mdpi.com/1422-0067/24/8/7189 |
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