Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Liu, Zhongjie, Haider, Muhammad Salman, Khan, Nadeem, Fang, Jinggui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
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
_version_ 1783506726480248832
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
work_keys_str_mv AT liuzhongjie comprehensivesequenceanalysisofiqdgenefamilyandtheirexpressionprofilingingrapevinevitisvinifera
AT haidermuhammadsalman comprehensivesequenceanalysisofiqdgenefamilyandtheirexpressionprofilingingrapevinevitisvinifera
AT khannadeem comprehensivesequenceanalysisofiqdgenefamilyandtheirexpressionprofilingingrapevinevitisvinifera
AT fangjinggui comprehensivesequenceanalysisofiqdgenefamilyandtheirexpressionprofilingingrapevinevitisvinifera