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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...

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Autores principales: Yuan, Jiale, Liu, Ying, Wang, Zhenyi, Lei, Tianyu, Hu, Yanfang, Zhang, Lan, Yuan, Min, Wang, Jinpeng, Li, Yuxian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
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.
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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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