Comprehensive Analyses of NAC Transcription Factor Family in Almond (<i>Prunus dulcis</i>) and Their Differential Gene Expression during Fruit Development
As plant specific transcription factors, NAC (NAM, ATAF1/2, CUC2) domain is involved in the plant development and stress responses. Due to the vitality of NAC gene family, BLASTp was performed to identify NAC genes in almond (<i>Prunus dulcis</i>). Further, phylogenetic and syntenic anal...
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| Format: | Article |
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MDPI AG
2021-10-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/10/10/2200 |
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| author | Zeeshan Zafar Sidra Fatima Muhammad Faraz Bhatti |
| author_facet | Zeeshan Zafar Sidra Fatima Muhammad Faraz Bhatti |
| author_sort | Zeeshan Zafar |
| collection | DOAJ |
| description | As plant specific transcription factors, NAC (NAM, ATAF1/2, CUC2) domain is involved in the plant development and stress responses. Due to the vitality of NAC gene family, BLASTp was performed to identify NAC genes in almond (<i>Prunus dulcis</i>). Further, phylogenetic and syntenic analyses were performed to determine the homology and evolutionary relationship. Gene duplication, gene structure, motif, subcellular localization, and <i>cis</i>-regulatory analyses were performed to assess the function of <i>PdNAC</i>. Whereas RNA-seq analysis was performed to determine the differential expression of <i>PdNAC</i> in fruits at various developmental stages. We identified 106 NAC genes in <i>P. dulcis</i> genome and were renamed according to their chromosomal distribution. Phylogenetic analysis in both <i>P. dulcis</i> and <i>Arabidopsis thaliana</i> revealed the presence of 14 subfamilies. Motif and gene structure followed a pattern according to the <i>PdNAC</i> position in phylogenetic subfamilies. Majority of NAC are localized in the nucleus and have ABA-responsive elements in the upstream region of <i>PdNAC</i>. Differential gene expression analyses revealed one and six <i>PdNAC</i> that were up and down-regulated, respectively, at all development stages. This study provides insights into the structure and function of <i>PdNAC</i> along with their role in the fruit development to enhance an understanding of NAC in <i>P. dulcis</i>. |
| first_indexed | 2024-03-10T06:15:29Z |
| format | Article |
| id | doaj.art-a946d2664c5544c795e7979ec728a2c9 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T06:15:29Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-a946d2664c5544c795e7979ec728a2c92023-11-22T19:45:29ZengMDPI AGPlants2223-77472021-10-011010220010.3390/plants10102200Comprehensive Analyses of NAC Transcription Factor Family in Almond (<i>Prunus dulcis</i>) and Their Differential Gene Expression during Fruit DevelopmentZeeshan Zafar0Sidra Fatima1Muhammad Faraz Bhatti2Atta-ur-Rahman School of Applied Bioscience, National University of Sciences and Technology, H-12, Kashmir Highway, Islamabad 44000, PakistanAtta-ur-Rahman School of Applied Bioscience, National University of Sciences and Technology, H-12, Kashmir Highway, Islamabad 44000, PakistanAtta-ur-Rahman School of Applied Bioscience, National University of Sciences and Technology, H-12, Kashmir Highway, Islamabad 44000, PakistanAs plant specific transcription factors, NAC (NAM, ATAF1/2, CUC2) domain is involved in the plant development and stress responses. Due to the vitality of NAC gene family, BLASTp was performed to identify NAC genes in almond (<i>Prunus dulcis</i>). Further, phylogenetic and syntenic analyses were performed to determine the homology and evolutionary relationship. Gene duplication, gene structure, motif, subcellular localization, and <i>cis</i>-regulatory analyses were performed to assess the function of <i>PdNAC</i>. Whereas RNA-seq analysis was performed to determine the differential expression of <i>PdNAC</i> in fruits at various developmental stages. We identified 106 NAC genes in <i>P. dulcis</i> genome and were renamed according to their chromosomal distribution. Phylogenetic analysis in both <i>P. dulcis</i> and <i>Arabidopsis thaliana</i> revealed the presence of 14 subfamilies. Motif and gene structure followed a pattern according to the <i>PdNAC</i> position in phylogenetic subfamilies. Majority of NAC are localized in the nucleus and have ABA-responsive elements in the upstream region of <i>PdNAC</i>. Differential gene expression analyses revealed one and six <i>PdNAC</i> that were up and down-regulated, respectively, at all development stages. This study provides insights into the structure and function of <i>PdNAC</i> along with their role in the fruit development to enhance an understanding of NAC in <i>P. dulcis</i>.https://www.mdpi.com/2223-7747/10/10/2200genome wide identificationNACtranscription factorphylogenetic analysissyntenic analysisgene duplication |
| spellingShingle | Zeeshan Zafar Sidra Fatima Muhammad Faraz Bhatti Comprehensive Analyses of NAC Transcription Factor Family in Almond (<i>Prunus dulcis</i>) and Their Differential Gene Expression during Fruit Development Plants genome wide identification NAC transcription factor phylogenetic analysis syntenic analysis gene duplication |
| title | Comprehensive Analyses of NAC Transcription Factor Family in Almond (<i>Prunus dulcis</i>) and Their Differential Gene Expression during Fruit Development |
| title_full | Comprehensive Analyses of NAC Transcription Factor Family in Almond (<i>Prunus dulcis</i>) and Their Differential Gene Expression during Fruit Development |
| title_fullStr | Comprehensive Analyses of NAC Transcription Factor Family in Almond (<i>Prunus dulcis</i>) and Their Differential Gene Expression during Fruit Development |
| title_full_unstemmed | Comprehensive Analyses of NAC Transcription Factor Family in Almond (<i>Prunus dulcis</i>) and Their Differential Gene Expression during Fruit Development |
| title_short | Comprehensive Analyses of NAC Transcription Factor Family in Almond (<i>Prunus dulcis</i>) and Their Differential Gene Expression during Fruit Development |
| title_sort | comprehensive analyses of nac transcription factor family in almond i prunus dulcis i and their differential gene expression during fruit development |
| topic | genome wide identification NAC transcription factor phylogenetic analysis syntenic analysis gene duplication |
| url | https://www.mdpi.com/2223-7747/10/10/2200 |
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