Genome-Wide Analysis of the Almond <i>AP2/ERF</i> Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress
The AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays an important role in regulating plant growth and development and the response to biotic and abiotic stresses. However, there is no report on the AP2/ERF gene family in almond (<i>Pru...
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MDPI AG
2022-10-01
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| author | Zhenfan Yu Dongdong Zhang Shaobo Hu Xingyue Liu Bin Zeng Wenwen Gao Yawen He Huanxue Qin Xintong Ma |
| author_facet | Zhenfan Yu Dongdong Zhang Shaobo Hu Xingyue Liu Bin Zeng Wenwen Gao Yawen He Huanxue Qin Xintong Ma |
| author_sort | Zhenfan Yu |
| collection | DOAJ |
| description | The AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays an important role in regulating plant growth and development and the response to biotic and abiotic stresses. However, there is no report on the AP2/ERF gene family in almond (<i>Prunus dulcis</i>). In this study, a total of 136 <i>PdAP2/ERF</i> genes were identified from the almond genome, and their protein physicochemical properties were analyzed. The <i>PdAP2/ERF</i> members were divided into five subgroups: AP2, RAV, ERF, DREB, and Soloist. The <i>PdAP2/ERF</i> members in each subgroup had conserved motif types and exon/intron numbers. <i>PdAP2/ERFS</i> members are distributed on eight chromosomes, with 22 pairs of segmental duplications and 28 pairs of tandem duplications. We further explored the colinear relationship between almond and <i>Arabidopsis thaliana</i>, <i>Oryza sativa</i>, <i>Malus domestica</i>, and <i>Prunus persica</i><i>AP2/ERF</i> genes and their evolution. The results of <i>cis</i>-acting elements showed that <i>PdAP2</i>/ERF members are widely involved in various processes, such as growth and development, hormone regulation, and stress response. The results based on transcriptome expression patterns showed that <i>PdAP2/ERF</i> genes had significant tissue-specific expression characteristics and were involved in the response of annual dormant branches of almond to low-temperature freezing stress. In addition, the fluorescence quantitative relative expression results of 13 representative <i>PdAP2/ERF</i> genes in four tissues of ‘Wanfeng’ almond and under six low-temperature freezing treatments of annual dormant branches were consistent with the transcriptome results. It is worth noting that the fluorescence quantitative expression level showed that the <i>PdERF24</i> gene was extremely significant at −30 °C, suggesting that this gene may play an important role in the response of almond dormancy to ultralow temperature freezing stress. Finally, we identified 7424 and 6971 target genes based on AP2 and ERF/DREB DNA-binding sites, respectively. The GO and KEGG enrichment results showed that these target genes play important roles in protein function and multiple pathways. In summary, we conducted bioinformatics and expression pattern studies on <i>PdAP2/ERF</i> genes, including 13 PdAP2/ERF genes, and performed fluorescence quantitative analysis of annual dormant shoots under different low-temperature freezing stress treatments to understand the tolerance of almond dormancy to freezing stress and suggest future improvements. |
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| language | English |
| last_indexed | 2024-03-09T20:39:47Z |
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| spelling | doaj.art-560da33523644576be430e0fd8ea584c2023-11-23T23:00:57ZengMDPI AGBiology2079-77372022-10-011110152010.3390/biology11101520Genome-Wide Analysis of the Almond <i>AP2/ERF</i> Superfamily and Its Functional Prediction during Dormancy in Response to Freezing StressZhenfan Yu0Dongdong Zhang1Shaobo Hu2Xingyue Liu3Bin Zeng4Wenwen Gao5Yawen He6Huanxue Qin7Xintong Ma8College of Horticulture, Xinjiang Agricultural University, Urumqi 830000, ChinaCollege of Horticulture, Xinjiang Agricultural University, Urumqi 830000, ChinaCollege of Horticulture, Xinjiang Agricultural University, Urumqi 830000, ChinaCollege of Horticulture, Xinjiang Agricultural University, Urumqi 830000, ChinaCollege of Horticulture, Xinjiang Agricultural University, Urumqi 830000, ChinaCollege of Horticulture, Xinjiang Agricultural University, Urumqi 830000, ChinaCollege of Horticulture, Xinjiang Agricultural University, Urumqi 830000, ChinaCollege of Horticulture, Xinjiang Agricultural University, Urumqi 830000, ChinaCollege of Horticulture, Xinjiang Agricultural University, Urumqi 830000, ChinaThe AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays an important role in regulating plant growth and development and the response to biotic and abiotic stresses. However, there is no report on the AP2/ERF gene family in almond (<i>Prunus dulcis</i>). In this study, a total of 136 <i>PdAP2/ERF</i> genes were identified from the almond genome, and their protein physicochemical properties were analyzed. The <i>PdAP2/ERF</i> members were divided into five subgroups: AP2, RAV, ERF, DREB, and Soloist. The <i>PdAP2/ERF</i> members in each subgroup had conserved motif types and exon/intron numbers. <i>PdAP2/ERFS</i> members are distributed on eight chromosomes, with 22 pairs of segmental duplications and 28 pairs of tandem duplications. We further explored the colinear relationship between almond and <i>Arabidopsis thaliana</i>, <i>Oryza sativa</i>, <i>Malus domestica</i>, and <i>Prunus persica</i><i>AP2/ERF</i> genes and their evolution. The results of <i>cis</i>-acting elements showed that <i>PdAP2</i>/ERF members are widely involved in various processes, such as growth and development, hormone regulation, and stress response. The results based on transcriptome expression patterns showed that <i>PdAP2/ERF</i> genes had significant tissue-specific expression characteristics and were involved in the response of annual dormant branches of almond to low-temperature freezing stress. In addition, the fluorescence quantitative relative expression results of 13 representative <i>PdAP2/ERF</i> genes in four tissues of ‘Wanfeng’ almond and under six low-temperature freezing treatments of annual dormant branches were consistent with the transcriptome results. It is worth noting that the fluorescence quantitative expression level showed that the <i>PdERF24</i> gene was extremely significant at −30 °C, suggesting that this gene may play an important role in the response of almond dormancy to ultralow temperature freezing stress. Finally, we identified 7424 and 6971 target genes based on AP2 and ERF/DREB DNA-binding sites, respectively. The GO and KEGG enrichment results showed that these target genes play important roles in protein function and multiple pathways. In summary, we conducted bioinformatics and expression pattern studies on <i>PdAP2/ERF</i> genes, including 13 PdAP2/ERF genes, and performed fluorescence quantitative analysis of annual dormant shoots under different low-temperature freezing stress treatments to understand the tolerance of almond dormancy to freezing stress and suggest future improvements.https://www.mdpi.com/2079-7737/11/10/1520<i>Prunus dulcis</i><i>AP2/ERF</i> gene familyevolutionary analysesfreezing stressexpression patterns |
| spellingShingle | Zhenfan Yu Dongdong Zhang Shaobo Hu Xingyue Liu Bin Zeng Wenwen Gao Yawen He Huanxue Qin Xintong Ma Genome-Wide Analysis of the Almond <i>AP2/ERF</i> Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress Biology <i>Prunus dulcis</i> <i>AP2/ERF</i> gene family evolutionary analyses freezing stress expression patterns |
| title | Genome-Wide Analysis of the Almond <i>AP2/ERF</i> Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress |
| title_full | Genome-Wide Analysis of the Almond <i>AP2/ERF</i> Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress |
| title_fullStr | Genome-Wide Analysis of the Almond <i>AP2/ERF</i> Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress |
| title_full_unstemmed | Genome-Wide Analysis of the Almond <i>AP2/ERF</i> Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress |
| title_short | Genome-Wide Analysis of the Almond <i>AP2/ERF</i> Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress |
| title_sort | genome wide analysis of the almond i ap2 erf i superfamily and its functional prediction during dormancy in response to freezing stress |
| topic | <i>Prunus dulcis</i> <i>AP2/ERF</i> gene family evolutionary analyses freezing stress expression patterns |
| url | https://www.mdpi.com/2079-7737/11/10/1520 |
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