Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants
The NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, 207 NGA gen...
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MDPI AG
2022-06-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/13/7063 |
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| author | Hymavathi Salava Sravankumar Thula Adrià Sans Sánchez Tomasz Nodzyński Fatemeh Maghuly |
| author_facet | Hymavathi Salava Sravankumar Thula Adrià Sans Sánchez Tomasz Nodzyński Fatemeh Maghuly |
| author_sort | Hymavathi Salava |
| collection | DOAJ |
| description | The NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, 207 NGA gene family members were identified from a genome-wide search against <i>Arabidopsis thaliana</i> in the genome data of 18 dicots and seven monocots. The phylogenetic and sequence alignment analyses divided NGA genes into different clusters and revealed that the numbers of genes varied depending on the species. The phylogeny was followed by the characterization of the Solanaceae (tomato, potato, capsicum, tobacco) and Poaceae (<i>Brachypodium distachyon</i>, <i>Oryza sativa</i> L. japonica, and <i>Sorghum bicolor</i>) family members in comparison with <i>A. thaliana</i>. The gene and protein structures revealed a similar pattern for NGA and NGA-like sequences, suggesting that both are conserved during evolution. Promoter <i>cis</i>-element analysis showed that phytohormones such as abscisic acid, auxin, and gibberellins play a crucial role in regulating the NGA gene family. Gene ontology analysis revealed that the NGA gene family participates in diverse biological processes such as flower development, leaf morphogenesis, and the regulation of transcription. The gene duplication analysis indicates that most of the genes are evolved due to segmental duplications and have undergone purifying selection pressure. Finally, the gene expression analysis implicated that the NGA genes are abundantly expressed in lateral organs and flowers. This analysis has presented a detailed and comprehensive study of the NGA gene family, providing basic knowledge of the gene, protein structure, function, and evolution. These results will lay the foundation for further understanding of the role of the NGA gene family in various plant developmental processes. |
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| language | English |
| last_indexed | 2024-03-09T21:50:38Z |
| publishDate | 2022-06-01 |
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| spelling | doaj.art-2d4691883000409e85d710d73fa93a4a2023-11-23T20:07:17ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-06-012313706310.3390/ijms23137063Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop PlantsHymavathi Salava0Sravankumar Thula1Adrià Sans Sánchez2Tomasz Nodzyński3Fatemeh Maghuly4Plant Functional Genomics, Institute of Molecular Biotechnology, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, 1190 Vienna, AustriaMendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech RepublicMendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech RepublicMendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech RepublicPlant Functional Genomics, Institute of Molecular Biotechnology, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, 1190 Vienna, AustriaThe NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, 207 NGA gene family members were identified from a genome-wide search against <i>Arabidopsis thaliana</i> in the genome data of 18 dicots and seven monocots. The phylogenetic and sequence alignment analyses divided NGA genes into different clusters and revealed that the numbers of genes varied depending on the species. The phylogeny was followed by the characterization of the Solanaceae (tomato, potato, capsicum, tobacco) and Poaceae (<i>Brachypodium distachyon</i>, <i>Oryza sativa</i> L. japonica, and <i>Sorghum bicolor</i>) family members in comparison with <i>A. thaliana</i>. The gene and protein structures revealed a similar pattern for NGA and NGA-like sequences, suggesting that both are conserved during evolution. Promoter <i>cis</i>-element analysis showed that phytohormones such as abscisic acid, auxin, and gibberellins play a crucial role in regulating the NGA gene family. Gene ontology analysis revealed that the NGA gene family participates in diverse biological processes such as flower development, leaf morphogenesis, and the regulation of transcription. The gene duplication analysis indicates that most of the genes are evolved due to segmental duplications and have undergone purifying selection pressure. Finally, the gene expression analysis implicated that the NGA genes are abundantly expressed in lateral organs and flowers. This analysis has presented a detailed and comprehensive study of the NGA gene family, providing basic knowledge of the gene, protein structure, function, and evolution. These results will lay the foundation for further understanding of the role of the NGA gene family in various plant developmental processes.https://www.mdpi.com/1422-0067/23/13/7063transcription factorNGATHA (NGA)phylogenetic analysisevolutionplant development |
| spellingShingle | Hymavathi Salava Sravankumar Thula Adrià Sans Sánchez Tomasz Nodzyński Fatemeh Maghuly Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants International Journal of Molecular Sciences transcription factor NGATHA (NGA) phylogenetic analysis evolution plant development |
| title | Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants |
| title_full | Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants |
| title_fullStr | Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants |
| title_full_unstemmed | Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants |
| title_short | Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants |
| title_sort | genome wide identification and annotation of ngatha transcription factor family in crop plants |
| topic | transcription factor NGATHA (NGA) phylogenetic analysis evolution plant development |
| url | https://www.mdpi.com/1422-0067/23/13/7063 |
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