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Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera)
The plant-specific IQ67-domain (IQD) protein family members are downstream targets of calcium sensors, known to regulate plant growth and lateral organ polarity, and basal defense response against environmental cues. No systematic study of IQD gene family has been performed on grapevine. The public...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073947/ https://www.ncbi.nlm.nih.gov/pubmed/32102395 http://dx.doi.org/10.3390/genes11020235 |
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author | Liu, Zhongjie Haider, Muhammad Salman Khan, Nadeem Fang, Jinggui |
author_facet | Liu, Zhongjie Haider, Muhammad Salman Khan, Nadeem Fang, Jinggui |
author_sort | Liu, Zhongjie |
collection | PubMed |
description | The plant-specific IQ67-domain (IQD) protein family members are downstream targets of calcium sensors, known to regulate plant growth and lateral organ polarity, and basal defense response against environmental cues. No systematic study of IQD gene family has been performed on grapevine. The public availability of grapevine genome enables us to perform identification, phylogeny, chromosomal orientation, and gene structure analysis of the IQD genes in grapevine. We identified 49 VvIQD genes (VvIQD1–VvIQD49) and further classified them into eight subgroups based on phylogenetic relationships. The 49 VvIQD genes were assigned to 19 different chromosomal positions. The collinear relationship between grapevine and Arabidopsis IQDs (VvIQD and AtIQD), and within grapevine VvIQDs, was highly conserved. In addition, most of duplicated gene pairs showed Ka/Ks ratio less than 1.00, indicating purifying selection within these gene pairs, implying functional discrepancy after duplication. Transcription profiling of VvIQD genes shed light on their specific role in grapevine tissue and organ development. The qRT-PCR validation of the 49 VvIQD genes in grape berry tissue from cultivars with distinct berry shape during developmental phases suggested candidate genes involved in the shape of grape berries. The subcellular prediction of VvIQD22, VvIQD23, VvIQD38, and VvIQD49 genes validated their localization in the nucleus and plasma membrane. The VvIQD49 protein interaction with VvCaM2 was also verified by bimolecular fluorescence complementation (BiFC) analysis in the plasma membrane. Our findings will be valuable for the functional genomic studies for desirable shape development of grape berries. |
format | Online Article Text |
id | pubmed-7073947 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-70739472020-03-19 Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera) Liu, Zhongjie Haider, Muhammad Salman Khan, Nadeem Fang, Jinggui Genes (Basel) Article The plant-specific IQ67-domain (IQD) protein family members are downstream targets of calcium sensors, known to regulate plant growth and lateral organ polarity, and basal defense response against environmental cues. No systematic study of IQD gene family has been performed on grapevine. The public availability of grapevine genome enables us to perform identification, phylogeny, chromosomal orientation, and gene structure analysis of the IQD genes in grapevine. We identified 49 VvIQD genes (VvIQD1–VvIQD49) and further classified them into eight subgroups based on phylogenetic relationships. The 49 VvIQD genes were assigned to 19 different chromosomal positions. The collinear relationship between grapevine and Arabidopsis IQDs (VvIQD and AtIQD), and within grapevine VvIQDs, was highly conserved. In addition, most of duplicated gene pairs showed Ka/Ks ratio less than 1.00, indicating purifying selection within these gene pairs, implying functional discrepancy after duplication. Transcription profiling of VvIQD genes shed light on their specific role in grapevine tissue and organ development. The qRT-PCR validation of the 49 VvIQD genes in grape berry tissue from cultivars with distinct berry shape during developmental phases suggested candidate genes involved in the shape of grape berries. The subcellular prediction of VvIQD22, VvIQD23, VvIQD38, and VvIQD49 genes validated their localization in the nucleus and plasma membrane. The VvIQD49 protein interaction with VvCaM2 was also verified by bimolecular fluorescence complementation (BiFC) analysis in the plasma membrane. Our findings will be valuable for the functional genomic studies for desirable shape development of grape berries. MDPI 2020-02-24 /pmc/articles/PMC7073947/ /pubmed/32102395 http://dx.doi.org/10.3390/genes11020235 Text en © 2020 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Liu, Zhongjie Haider, Muhammad Salman Khan, Nadeem Fang, Jinggui Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera) |
title | Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera) |
title_full | Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera) |
title_fullStr | Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera) |
title_full_unstemmed | Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera) |
title_short | Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera) |
title_sort | comprehensive sequence analysis of iqd gene family and their expression profiling in grapevine (vitis vinifera) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073947/ https://www.ncbi.nlm.nih.gov/pubmed/32102395 http://dx.doi.org/10.3390/genes11020235 |
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