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Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots

SHORT VEGETATIVE PHASE (SVP) genes are members of the well-known MADS-box gene family that regulates vital developmental processes in plants. In Arabidopsis, there are two SVP paralogs, SVP/AGAMOUS-LIKE22 (SVP/AGL22) and AGL24. SVP protein suppresses the flowering process, whereas AGL24 acts as a fl...

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Autores principales: Liu, Xing, Sun, Zhichao, Dong, Wei, Wang, Zhengjia, Zhang, Liangsheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251477/
https://www.ncbi.nlm.nih.gov/pubmed/30364940
http://dx.doi.org/10.1093/gbe/evy235
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author Liu, Xing
Sun, Zhichao
Dong, Wei
Wang, Zhengjia
Zhang, Liangsheng
author_facet Liu, Xing
Sun, Zhichao
Dong, Wei
Wang, Zhengjia
Zhang, Liangsheng
author_sort Liu, Xing
collection PubMed
description SHORT VEGETATIVE PHASE (SVP) genes are members of the well-known MADS-box gene family that regulates vital developmental processes in plants. In Arabidopsis, there are two SVP paralogs, SVP/AGAMOUS-LIKE22 (SVP/AGL22) and AGL24. SVP protein suppresses the flowering process, whereas AGL24 acts as a flowering activator. Phylogenetic analysis of SVP genes representing most of the sequenced eudicot species showed that the SVP gene family could be divided into three major clades in eudicots (SVP1, SVP2, and SVP3), most likely resulting from an ancient whole-genome triplication in core eudicots. Among them, the SVP1 (SVP) and SVP2 (AGL24) clades are retained in nearly all species, whereas the SVP3 clade has been lost in Brassicaceae, Myrtaceae, and some species in other families. Reflecting lineage-specific tandem duplication and whole-genome duplication, SVP gene copy numbers ranged from 3 to 11 in the analyzed species. Sequence analysis showed that SVP3 proteins have obvious differences with SVP1 and SVP2 in the C-terminal (C) domain and intervening (I) domain. Positive selection analysis also showed that the ω (dN/dS) value was highest in the SVP3 clade, with 17 positive selection sites detected in the SVP3 clade. Promoter analysis for cis-regulatory elements showed that some genes in the SVP2 and SVP3 clades may be regulated by abscisic acid, ethylene, and gibberellin. RNA-seq data from grape, poplar, and apple revealed that genes in SVP3 group are highly expressed in vegetative organs such as buds, leaves, cotyledons, and dormant buds in particular, indicating the involvement of genes belong to SVP3 group in the dormancy process. Overall, the findings underscore the functional diversity of the SVP genes in eudicots.
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spelling pubmed-62514772018-11-28 Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots Liu, Xing Sun, Zhichao Dong, Wei Wang, Zhengjia Zhang, Liangsheng Genome Biol Evol Research Article SHORT VEGETATIVE PHASE (SVP) genes are members of the well-known MADS-box gene family that regulates vital developmental processes in plants. In Arabidopsis, there are two SVP paralogs, SVP/AGAMOUS-LIKE22 (SVP/AGL22) and AGL24. SVP protein suppresses the flowering process, whereas AGL24 acts as a flowering activator. Phylogenetic analysis of SVP genes representing most of the sequenced eudicot species showed that the SVP gene family could be divided into three major clades in eudicots (SVP1, SVP2, and SVP3), most likely resulting from an ancient whole-genome triplication in core eudicots. Among them, the SVP1 (SVP) and SVP2 (AGL24) clades are retained in nearly all species, whereas the SVP3 clade has been lost in Brassicaceae, Myrtaceae, and some species in other families. Reflecting lineage-specific tandem duplication and whole-genome duplication, SVP gene copy numbers ranged from 3 to 11 in the analyzed species. Sequence analysis showed that SVP3 proteins have obvious differences with SVP1 and SVP2 in the C-terminal (C) domain and intervening (I) domain. Positive selection analysis also showed that the ω (dN/dS) value was highest in the SVP3 clade, with 17 positive selection sites detected in the SVP3 clade. Promoter analysis for cis-regulatory elements showed that some genes in the SVP2 and SVP3 clades may be regulated by abscisic acid, ethylene, and gibberellin. RNA-seq data from grape, poplar, and apple revealed that genes in SVP3 group are highly expressed in vegetative organs such as buds, leaves, cotyledons, and dormant buds in particular, indicating the involvement of genes belong to SVP3 group in the dormancy process. Overall, the findings underscore the functional diversity of the SVP genes in eudicots. Oxford University Press 2018-10-26 /pmc/articles/PMC6251477/ /pubmed/30364940 http://dx.doi.org/10.1093/gbe/evy235 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Research Article
Liu, Xing
Sun, Zhichao
Dong, Wei
Wang, Zhengjia
Zhang, Liangsheng
Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots
title Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots
title_full Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots
title_fullStr Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots
title_full_unstemmed Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots
title_short Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots
title_sort expansion and functional divergence of the short vegetative phase (svp) genes in eudicots
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251477/
https://www.ncbi.nlm.nih.gov/pubmed/30364940
http://dx.doi.org/10.1093/gbe/evy235
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