Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata

• Published in: Gene 2015-02, Vol.557 (1), p.35-42
• Main Authors: Yao, Qiu-Yang, Xia, En-Hua, Liu, Fei-Hu, Gao, Li-Zhi
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Arabidopsis - genetics; Arabidopsis thaliana; Base Sequence; Brassica; Brassica - genetics; Brassica oleracea; Cabbage; DNA, Plant - analysis; DNA, Plant - genetics; Duplicated gene; Expression divergence; Gene Duplication; Gene Expression Profiling; Gene Expression Regulation, Plant - genetics; Genes, Duplicate; Genome, Plant - genetics; Phylogeny; Plant Proteins - classification; Plant Proteins - genetics; Sequence Analysis, DNA; Tissue-specific expression; Transcription Factors - classification; Transcription Factors - genetics; Transcriptome - genetics; WRKY transcription factor
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2014.12.005

WRKY transcription factors (TFs), one of the ten largest TF families in higher plants, play important roles in regulating plant development and resistance. To date, little is known about the WRKY TF family in Brassica oleracea. Recently, the completed genome sequence of cabbage (B. oleracea var. capitata) allows us to systematically analyze WRKY genes in this species. A total of 148 WRKY genes were characterized and classified into seven subgroups that belong to three major groups. Phylogenetic and synteny analyses revealed that the repertoire of cabbage WRKY genes was derived from a common ancestor shared with Arabidopsis thaliana. The B. oleracea WRKY genes were found to be preferentially retained after the whole-genome triplication (WGT) event in its recent ancestor, suggesting that the WGT event had largely contributed to a rapid expansion of the WRKY gene family in B. oleracea. The analysis of RNA-Seq data from various tissues (i.e., roots, stems, leaves, buds, flowers and siliques) revealed that most of the identified WRKY genes were positively expressed in cabbage, and a large portion of them exhibited patterns of differential and tissue-specific expression, demonstrating that these gene members might play essential roles in plant developmental processes. Comparative analysis of the expression level among duplicated genes showed that gene expression divergence was evidently presented among cabbage WRKY paralogs, indicating functional divergence of these duplicated WRKY genes. •We characterized a total of 148 WRKY genes including 37 novel ones in cabbage.•Preferential retention after WGT may contribute to rapid expansion of WRKY family.•A large portion of WRKY genes exhibited patterns of tissue-specific expression.•Expression divergence of BolWRKY paralogs indicates their functional diversification.