title: 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.
abstract: 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.
authors.affiliation: Laboratory of Plant Breeding and Utilization, Yunnan University, Kunming 650091, China; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100039, China.
authors.forename: Qiu-Yang
authors.initials: QY
authors.lastname: Yao
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100039, China.
authors.forename: En-Hua
authors.initials: EH
authors.lastname: Xia
authors.affiliation: Laboratory of Plant Breeding and Utilization, Yunnan University, Kunming 650091, China. Electronic address: dmzpynu@126.com.
authors.forename: Fei-Hu
authors.initials: FH
authors.lastname: Liu
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China. Electronic address: Lgao@mail.kib.ac.cn.
authors.forename: Li-Zhi
authors.initials: LZ
authors.lastname: Gao
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D001937:Brassica / Q000235:genetics*; D018744:DNA, Plant / Q000032:analysis / Q000235:genetics; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D020131:Genes, Duplicate; D018745:Genome, Plant / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000145:classification / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; D014157:Transcription Factors
keywords: Cabbage; Duplicated gene; Expression divergence; Tissue-specific expression; WRKY transcription factor