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Title: Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare)WRKY transcription factor family reveals putatively retained functions betweenmonocots and dicots

Abstract

WRKY proteins belong to the WRKY-GCM1 superfamily of zinc finger transcription factors that have been subject to a large plant-specific diversification. For the cereal crop barley (Hordeum vulgare), three different WRKY proteins have been characterized so far, as regulators in sucrose signaling, in pathogen defense, and in response to cold and drought, respectively. However, their phylogenetic relationship remained unresolved. In this study, we used the available sequence information to identify a minimum number of 45 barley WRKY transcription factor (HvWRKY) genes. According to their structural features the HvWRKY factors were classified into the previously defined polyphyletic WRKY subgroups 1 to 3. Furthermore, we could assign putative orthologs of the HvWRKY proteins in Arabidopsis and rice. While in most cases clades of orthologous proteins were formed within each group or subgroup, other clades were composed of paralogous proteins for the grasses and Arabidopsis only, which is indicative of specific gene radiation events. To gain insight into their putative functions, we examined expression profiles of WRKY genes from publicly available microarray data resources and found group specific expression patterns. While putative orthologs of the HvWRKY transcription factors have been inferred from phylogenetic sequence analysis, we performed a comparative expression analysis of WRKYmore » genes in Arabidopsis and barley. Indeed, highly correlative expression profiles were found between some of the putative orthologs. HvWRKY genes have not only undergone radiation in monocot or dicot species, but exhibit evolutionary traits specific to grasses. HvWRKY proteins exhibited not only sequence similarities between orthologs with Arabidopsis, but also relatedness in their expression patterns. This correlative expression is indicative for a putative conserved function of related WRKY proteins in mono- and dicot species.« less

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Earth Sciences Division
OSTI Identifier:
937445
Report Number(s):
LBNL-222E
TRN: US200819%%131
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 9
Country of Publication:
United States
Language:
English
Subject:
54; 58; ARABIDOPSIS; BARLEY; CEREALS; CROPS; DIVERSIFICATION; GENES; PATHOGENS; PROTEINS; RADIATIONS; RICE; SACCHAROSE; STRUCTURAL CHEMICAL ANALYSIS; TRANSCRIPTION FACTORS; ZINC; gene expression analysis, WRKY transcription factor, monocots, dicots

Citation Formats

Mangelsen, Elke, Kilian, Joachim, Berendzen, Kenneth W, Kolukisaoglu, Uner, Harter, Klaus, Jansson, Christer, and Wanke, Dierk. Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare)WRKY transcription factor family reveals putatively retained functions betweenmonocots and dicots. United States: N. p., 2008. Web. doi:10.1186/1471-2164-9-194.
Mangelsen, Elke, Kilian, Joachim, Berendzen, Kenneth W, Kolukisaoglu, Uner, Harter, Klaus, Jansson, Christer, & Wanke, Dierk. Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare)WRKY transcription factor family reveals putatively retained functions betweenmonocots and dicots. United States. https://doi.org/10.1186/1471-2164-9-194
Mangelsen, Elke, Kilian, Joachim, Berendzen, Kenneth W, Kolukisaoglu, Uner, Harter, Klaus, Jansson, Christer, and Wanke, Dierk. 2008. "Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare)WRKY transcription factor family reveals putatively retained functions betweenmonocots and dicots". United States. https://doi.org/10.1186/1471-2164-9-194. https://www.osti.gov/servlets/purl/937445.
@article{osti_937445,
title = {Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare)WRKY transcription factor family reveals putatively retained functions betweenmonocots and dicots},
author = {Mangelsen, Elke and Kilian, Joachim and Berendzen, Kenneth W and Kolukisaoglu, Uner and Harter, Klaus and Jansson, Christer and Wanke, Dierk},
abstractNote = {WRKY proteins belong to the WRKY-GCM1 superfamily of zinc finger transcription factors that have been subject to a large plant-specific diversification. For the cereal crop barley (Hordeum vulgare), three different WRKY proteins have been characterized so far, as regulators in sucrose signaling, in pathogen defense, and in response to cold and drought, respectively. However, their phylogenetic relationship remained unresolved. In this study, we used the available sequence information to identify a minimum number of 45 barley WRKY transcription factor (HvWRKY) genes. According to their structural features the HvWRKY factors were classified into the previously defined polyphyletic WRKY subgroups 1 to 3. Furthermore, we could assign putative orthologs of the HvWRKY proteins in Arabidopsis and rice. While in most cases clades of orthologous proteins were formed within each group or subgroup, other clades were composed of paralogous proteins for the grasses and Arabidopsis only, which is indicative of specific gene radiation events. To gain insight into their putative functions, we examined expression profiles of WRKY genes from publicly available microarray data resources and found group specific expression patterns. While putative orthologs of the HvWRKY transcription factors have been inferred from phylogenetic sequence analysis, we performed a comparative expression analysis of WRKY genes in Arabidopsis and barley. Indeed, highly correlative expression profiles were found between some of the putative orthologs. HvWRKY genes have not only undergone radiation in monocot or dicot species, but exhibit evolutionary traits specific to grasses. HvWRKY proteins exhibited not only sequence similarities between orthologs with Arabidopsis, but also relatedness in their expression patterns. This correlative expression is indicative for a putative conserved function of related WRKY proteins in mono- and dicot species.},
doi = {10.1186/1471-2164-9-194},
url = {https://www.osti.gov/biblio/937445}, journal = {BMC Genomics},
number = ,
volume = 9,
place = {United States},
year = {Fri Feb 01 00:00:00 EST 2008},
month = {Fri Feb 01 00:00:00 EST 2008}
}