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The barley DIR gene family: An expanded gene family that is involved in stress responses

Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food....

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Autores principales: Luo, Ruihan, Pan, Wenqiu, Liu, Wenqiang, Tian, Yuan, Zeng, Yan, Li, Yihan, Li, Zhimin, Cui, Licao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9667096/
https://www.ncbi.nlm.nih.gov/pubmed/36406120
http://dx.doi.org/10.3389/fgene.2022.1042772
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author Luo, Ruihan
Pan, Wenqiu
Liu, Wenqiang
Tian, Yuan
Zeng, Yan
Li, Yihan
Li, Zhimin
Cui, Licao
author_facet Luo, Ruihan
Pan, Wenqiu
Liu, Wenqiang
Tian, Yuan
Zeng, Yan
Li, Yihan
Li, Zhimin
Cui, Licao
author_sort Luo, Ruihan
collection PubMed
description Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products. A total of 31,750 conserved orthologous groups (OGs) were identified using eight genomes/subgenomes, of which 1,113 and 6,739 were rapidly expanded and contracted OGs in barley, respectively. Five expanded OGs containing 20 barley dirigent genes (HvDIRs) were identified. HvDIRs from the same OG were phylogenetically clustered with similar gene structure and domain organization. In particular, 7 and 5 HvDIRs from OG0000960 and OG0001516, respectively, contributed greatly to the expansion of the DIR-c subfamily. Tandem duplication was the driving force for the expansion of the barley DIR gene family. Nucleotide diversity and haplotype network analysis revealed that the expanded HvDIRs experienced severe bottleneck events during barley domestication, and can thus be considered as potential domestication-related candidate genes. The expression profile and co-expression network analysis revealed the critical roles of the expanded HvDIRs in various biological processes, especially in stress responses. HvDIR18, HvDIR19, and HvDIR63 could serve as excellent candidates for further functional genomics studies to improve the production of barley products. Our study revealed that the HvDIR family was significantly expanded in barley and might be involved in different developmental processes and stress responses. Thus, besides providing a framework for future functional genomics and metabolomics studies, this study also identified HvDIRs as candidates for use in improving barley crop resistance to biotic and abiotic stresses.
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spelling pubmed-96670962022-11-17 The barley DIR gene family: An expanded gene family that is involved in stress responses Luo, Ruihan Pan, Wenqiu Liu, Wenqiang Tian, Yuan Zeng, Yan Li, Yihan Li, Zhimin Cui, Licao Front Genet Genetics Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products. A total of 31,750 conserved orthologous groups (OGs) were identified using eight genomes/subgenomes, of which 1,113 and 6,739 were rapidly expanded and contracted OGs in barley, respectively. Five expanded OGs containing 20 barley dirigent genes (HvDIRs) were identified. HvDIRs from the same OG were phylogenetically clustered with similar gene structure and domain organization. In particular, 7 and 5 HvDIRs from OG0000960 and OG0001516, respectively, contributed greatly to the expansion of the DIR-c subfamily. Tandem duplication was the driving force for the expansion of the barley DIR gene family. Nucleotide diversity and haplotype network analysis revealed that the expanded HvDIRs experienced severe bottleneck events during barley domestication, and can thus be considered as potential domestication-related candidate genes. The expression profile and co-expression network analysis revealed the critical roles of the expanded HvDIRs in various biological processes, especially in stress responses. HvDIR18, HvDIR19, and HvDIR63 could serve as excellent candidates for further functional genomics studies to improve the production of barley products. Our study revealed that the HvDIR family was significantly expanded in barley and might be involved in different developmental processes and stress responses. Thus, besides providing a framework for future functional genomics and metabolomics studies, this study also identified HvDIRs as candidates for use in improving barley crop resistance to biotic and abiotic stresses. Frontiers Media S.A. 2022-11-02 /pmc/articles/PMC9667096/ /pubmed/36406120 http://dx.doi.org/10.3389/fgene.2022.1042772 Text en Copyright © 2022 Luo, Pan, Liu, Tian, Zeng, Li, Li and Cui. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Luo, Ruihan
Pan, Wenqiu
Liu, Wenqiang
Tian, Yuan
Zeng, Yan
Li, Yihan
Li, Zhimin
Cui, Licao
The barley DIR gene family: An expanded gene family that is involved in stress responses
title The barley DIR gene family: An expanded gene family that is involved in stress responses
title_full The barley DIR gene family: An expanded gene family that is involved in stress responses
title_fullStr The barley DIR gene family: An expanded gene family that is involved in stress responses
title_full_unstemmed The barley DIR gene family: An expanded gene family that is involved in stress responses
title_short The barley DIR gene family: An expanded gene family that is involved in stress responses
title_sort barley dir gene family: an expanded gene family that is involved in stress responses
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9667096/
https://www.ncbi.nlm.nih.gov/pubmed/36406120
http://dx.doi.org/10.3389/fgene.2022.1042772
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