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The IQD Gene Family in Soybean: Structure, Phylogeny, Evolution and Expression

Members of the plant-specific IQ67-domain (IQD) protein family are involved in plant development and the basal defense response. Although systematic characterization of this family has been carried out in Arabidopsis, tomato (Solanum lycopersicum), Brachypodium distachyon and rice (Oryza sativa), sy...

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Autores principales: Feng, Lin, Chen, Zhu, Ma, Hui, Chen, Xue, Li, Yuan, Wang, Yiyi, Xiang, Yan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4208818/
https://www.ncbi.nlm.nih.gov/pubmed/25343341
http://dx.doi.org/10.1371/journal.pone.0110896
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author Feng, Lin
Chen, Zhu
Ma, Hui
Chen, Xue
Li, Yuan
Wang, Yiyi
Xiang, Yan
author_facet Feng, Lin
Chen, Zhu
Ma, Hui
Chen, Xue
Li, Yuan
Wang, Yiyi
Xiang, Yan
author_sort Feng, Lin
collection PubMed
description Members of the plant-specific IQ67-domain (IQD) protein family are involved in plant development and the basal defense response. Although systematic characterization of this family has been carried out in Arabidopsis, tomato (Solanum lycopersicum), Brachypodium distachyon and rice (Oryza sativa), systematic analysis and expression profiling of this gene family in soybean (Glycine max) have not previously been reported. In this study, we identified and structurally characterized IQD genes in the soybean genome. A complete set of 67 soybean IQD genes (GmIQD1–67) was identified using Blast search tools, and the genes were clustered into four subfamilies (IQD I–IV) based on phylogeny. These soybean IQD genes are distributed unevenly across all 20 chromosomes, with 30 segmental duplication events, suggesting that segmental duplication has played a major role in the expansion of the soybean IQD gene family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the GmIQD family primarily underwent purifying selection. Microsynteny was detected in most pairs: genes in clade 1–3 might be present in genome regions that were inverted, expanded or contracted after the divergence; most gene pairs in clade 4 showed high conservation with little rearrangement among these gene-residing regions. Of the soybean IQD genes examined, six were most highly expressed in young leaves, six in flowers, one in roots and two in nodules. Our qRT-PCR analysis of 24 soybean IQD III genes confirmed that these genes are regulated by MeJA stress. Our findings present a comprehensive overview of the soybean IQD gene family and provide insights into the evolution of this family. In addition, this work lays a solid foundation for further experiments aimed at determining the biological functions of soybean IQD genes in growth and development.
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spelling pubmed-42088182014-10-27 The IQD Gene Family in Soybean: Structure, Phylogeny, Evolution and Expression Feng, Lin Chen, Zhu Ma, Hui Chen, Xue Li, Yuan Wang, Yiyi Xiang, Yan PLoS One Research Article Members of the plant-specific IQ67-domain (IQD) protein family are involved in plant development and the basal defense response. Although systematic characterization of this family has been carried out in Arabidopsis, tomato (Solanum lycopersicum), Brachypodium distachyon and rice (Oryza sativa), systematic analysis and expression profiling of this gene family in soybean (Glycine max) have not previously been reported. In this study, we identified and structurally characterized IQD genes in the soybean genome. A complete set of 67 soybean IQD genes (GmIQD1–67) was identified using Blast search tools, and the genes were clustered into four subfamilies (IQD I–IV) based on phylogeny. These soybean IQD genes are distributed unevenly across all 20 chromosomes, with 30 segmental duplication events, suggesting that segmental duplication has played a major role in the expansion of the soybean IQD gene family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the GmIQD family primarily underwent purifying selection. Microsynteny was detected in most pairs: genes in clade 1–3 might be present in genome regions that were inverted, expanded or contracted after the divergence; most gene pairs in clade 4 showed high conservation with little rearrangement among these gene-residing regions. Of the soybean IQD genes examined, six were most highly expressed in young leaves, six in flowers, one in roots and two in nodules. Our qRT-PCR analysis of 24 soybean IQD III genes confirmed that these genes are regulated by MeJA stress. Our findings present a comprehensive overview of the soybean IQD gene family and provide insights into the evolution of this family. In addition, this work lays a solid foundation for further experiments aimed at determining the biological functions of soybean IQD genes in growth and development. Public Library of Science 2014-10-24 /pmc/articles/PMC4208818/ /pubmed/25343341 http://dx.doi.org/10.1371/journal.pone.0110896 Text en © 2014 Feng et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Feng, Lin
Chen, Zhu
Ma, Hui
Chen, Xue
Li, Yuan
Wang, Yiyi
Xiang, Yan
The IQD Gene Family in Soybean: Structure, Phylogeny, Evolution and Expression
title The IQD Gene Family in Soybean: Structure, Phylogeny, Evolution and Expression
title_full The IQD Gene Family in Soybean: Structure, Phylogeny, Evolution and Expression
title_fullStr The IQD Gene Family in Soybean: Structure, Phylogeny, Evolution and Expression
title_full_unstemmed The IQD Gene Family in Soybean: Structure, Phylogeny, Evolution and Expression
title_short The IQD Gene Family in Soybean: Structure, Phylogeny, Evolution and Expression
title_sort iqd gene family in soybean: structure, phylogeny, evolution and expression
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4208818/
https://www.ncbi.nlm.nih.gov/pubmed/25343341
http://dx.doi.org/10.1371/journal.pone.0110896
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