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Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato
NAC transcription factors play an important regulatory role in tomato fruit ripening. We chose a novel perspective to explore the traces left by two paleopolyploidizations in the NAC family using a bioinformatics approach. We found that 85 (S. lycopersicum) and 88 (S. pennellii) members of the NAC f...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9410287/ https://www.ncbi.nlm.nih.gov/pubmed/36013415 http://dx.doi.org/10.3390/life12081236 |
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author | Yuan, Jiale Liu, Ying Wang, Zhenyi Lei, Tianyu Hu, Yanfang Zhang, Lan Yuan, Min Wang, Jinpeng Li, Yuxian |
author_facet | Yuan, Jiale Liu, Ying Wang, Zhenyi Lei, Tianyu Hu, Yanfang Zhang, Lan Yuan, Min Wang, Jinpeng Li, Yuxian |
author_sort | Yuan, Jiale |
collection | PubMed |
description | NAC transcription factors play an important regulatory role in tomato fruit ripening. We chose a novel perspective to explore the traces left by two paleopolyploidizations in the NAC family using a bioinformatics approach. We found that 85 (S. lycopersicum) and 88 (S. pennellii) members of the NAC family were present in two tomatoes, and most of them were amplified from two paleohexaploidizations. We differentiated NAC family members from the different paleohexaploidizations and found that the SWGT-derived NAC genes had more rearrangement events, so it was different from the DWGT-derived NAC genes in terms of physicochemical properties, phylogeny, and gene location. The results of selection pressure show that DWGT-derived NAC genes tended to be positively selected in S. lycopersicum and negatively selected in S. pennellii. A comprehensive analysis of paleopolyploidization and expression reveals that DWGT-derived NAC genes tend to promote fruit ripening, and are expressed at the early and middle stages, whereas SWGT-derived NAC genes tend to terminate fruit growth and are expressed at the late stages of fruit ripening. This study obtained NAC genes from different sources that can be used as materials for tomato fruit development, and the method in the study can be extended to the study of other plants. |
format | Online Article Text |
id | pubmed-9410287 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-94102872022-08-26 Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato Yuan, Jiale Liu, Ying Wang, Zhenyi Lei, Tianyu Hu, Yanfang Zhang, Lan Yuan, Min Wang, Jinpeng Li, Yuxian Life (Basel) Article NAC transcription factors play an important regulatory role in tomato fruit ripening. We chose a novel perspective to explore the traces left by two paleopolyploidizations in the NAC family using a bioinformatics approach. We found that 85 (S. lycopersicum) and 88 (S. pennellii) members of the NAC family were present in two tomatoes, and most of them were amplified from two paleohexaploidizations. We differentiated NAC family members from the different paleohexaploidizations and found that the SWGT-derived NAC genes had more rearrangement events, so it was different from the DWGT-derived NAC genes in terms of physicochemical properties, phylogeny, and gene location. The results of selection pressure show that DWGT-derived NAC genes tended to be positively selected in S. lycopersicum and negatively selected in S. pennellii. A comprehensive analysis of paleopolyploidization and expression reveals that DWGT-derived NAC genes tend to promote fruit ripening, and are expressed at the early and middle stages, whereas SWGT-derived NAC genes tend to terminate fruit growth and are expressed at the late stages of fruit ripening. This study obtained NAC genes from different sources that can be used as materials for tomato fruit development, and the method in the study can be extended to the study of other plants. MDPI 2022-08-15 /pmc/articles/PMC9410287/ /pubmed/36013415 http://dx.doi.org/10.3390/life12081236 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Yuan, Jiale Liu, Ying Wang, Zhenyi Lei, Tianyu Hu, Yanfang Zhang, Lan Yuan, Min Wang, Jinpeng Li, Yuxian Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato |
title | Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato |
title_full | Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato |
title_fullStr | Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato |
title_full_unstemmed | Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato |
title_short | Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato |
title_sort | genome-wide analysis of the nac family associated with two paleohexaploidization events in the tomato |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9410287/ https://www.ncbi.nlm.nih.gov/pubmed/36013415 http://dx.doi.org/10.3390/life12081236 |
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