Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus Infection
The RAV family is part of the B3 superfamily and is one of the most abundant transcription factor families in plants. Members have highly conserved B3 or AP2 DNA binding domains. Although the <i>RAV</i> family genes of several species have been systematically identified from genome-wide...
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MDPI AG
2021-04-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/5/752 |
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| author | Changhai Chen Yanjun Li Hehong Zhang Qiang Ma Zhongyan Wei Jianping Chen Zongtao Sun |
| author_facet | Changhai Chen Yanjun Li Hehong Zhang Qiang Ma Zhongyan Wei Jianping Chen Zongtao Sun |
| author_sort | Changhai Chen |
| collection | DOAJ |
| description | The RAV family is part of the B3 superfamily and is one of the most abundant transcription factor families in plants. Members have highly conserved B3 or AP2 DNA binding domains. Although the <i>RAV</i> family genes of several species have been systematically identified from genome-wide studies, there has been no comprehensive study to identify rice <i>RAV</i> family genes. Here, we identified 15 genes of the RAV family in the rice genome and analyzed their phylogenetic relationships, gene structure, conserved domains, and chromosomal distribution. Based on domain similarity and phylogenetic topology, rice RAV transcription factors were phylogenetically clustered into four groups. qRT-PCR analyses showed that expression of these <i>RAV</i> genes was significantly up-regulated or down-regulated by plant hormone treatments, including BL, NAA, IAA, MeJA, and SA. Most of the rice <i>RAV</i> genes were dramatically down-regulated in response to rice stripe virus (RSV) and mostly up-regulated in response to Southern rice black-streaked dwarf virus (SRBSDV). These results suggest that the rice <i>RAV</i> genes are involved in diverse signaling pathways and in varied responses to virus infection. |
| first_indexed | 2024-03-10T11:59:07Z |
| format | Article |
| id | doaj.art-97f8ccb843d34ff3a79dac8e5d330bb2 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T11:59:07Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-97f8ccb843d34ff3a79dac8e5d330bb22023-11-21T17:04:05ZengMDPI AGViruses1999-49152021-04-0113575210.3390/v13050752Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus InfectionChanghai Chen0Yanjun Li1Hehong Zhang2Qiang Ma3Zhongyan Wei4Jianping Chen5Zongtao Sun6State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, ChinaThe RAV family is part of the B3 superfamily and is one of the most abundant transcription factor families in plants. Members have highly conserved B3 or AP2 DNA binding domains. Although the <i>RAV</i> family genes of several species have been systematically identified from genome-wide studies, there has been no comprehensive study to identify rice <i>RAV</i> family genes. Here, we identified 15 genes of the RAV family in the rice genome and analyzed their phylogenetic relationships, gene structure, conserved domains, and chromosomal distribution. Based on domain similarity and phylogenetic topology, rice RAV transcription factors were phylogenetically clustered into four groups. qRT-PCR analyses showed that expression of these <i>RAV</i> genes was significantly up-regulated or down-regulated by plant hormone treatments, including BL, NAA, IAA, MeJA, and SA. Most of the rice <i>RAV</i> genes were dramatically down-regulated in response to rice stripe virus (RSV) and mostly up-regulated in response to Southern rice black-streaked dwarf virus (SRBSDV). These results suggest that the rice <i>RAV</i> genes are involved in diverse signaling pathways and in varied responses to virus infection.https://www.mdpi.com/1999-4915/13/5/752genome-wide analysisRAV transcription factorhormone treatmentvirus infectionrice |
| spellingShingle | Changhai Chen Yanjun Li Hehong Zhang Qiang Ma Zhongyan Wei Jianping Chen Zongtao Sun Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus Infection Viruses genome-wide analysis RAV transcription factor hormone treatment virus infection rice |
| title | Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus Infection |
| title_full | Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus Infection |
| title_fullStr | Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus Infection |
| title_full_unstemmed | Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus Infection |
| title_short | Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus Infection |
| title_sort | genome wide analysis of the rav transcription factor genes in rice reveals their response patterns to hormones and virus infection |
| topic | genome-wide analysis RAV transcription factor hormone treatment virus infection rice |
| url | https://www.mdpi.com/1999-4915/13/5/752 |
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