title: Genome-wide identification and expression analysis of the WRKY gene family in common tobacco (Nicotiana tabacum L.).
abstract: The coding products of WRKY gene family plays important roles in plant growth and development as well as in various stress responses. They have been identified in various plants, but only few in common tobacco (Nicotiana tabacum L.). In this study, 164 putative WRKY proteins in the common tobacco genome were identified by using the conserved WRKY sequence (PF03106) from the Pfam database. Phylogenetic trees, functional domain analysis, chromosomal localization, subcellular localization and tissue expression patterns were analyzed with the bioinformatics softwares, including DNAMAN 5.0, Weblogo 3, MEGA 5.1, MG2C and MEME. First of all, phylogenetic trees divided all the candidate genes into three subfamilies: Ⅰ, Ⅱ and Ⅲ, respectively, and subfamily Ⅱ could be further divided into five subgroups: group Ⅱ-a, -b, -c, -d and -e. Secondly, the WRKY regions contained a highly conserved heptapeptide stretch WRKYGQK followed by a zinc-finger motif. Most of the NtWRKY genes contained 2-5 exons and a highly conserved gene structure. Thirdly, 154 out of 164 NtWRKY genes were distributed with different densities on 24 chromosomes, and each subfamily with different patterns and frequency. The largest number of NtWRKY genes was found on chromosome VI, and only one on chromosome X. Fourthly, the majority of NtWRKY members located in the nucleus, with 74 percent of subfamily Ⅲ in the extracellular matrix. Lastly, the members in the same subfamily had different spatial and temporal expression profiles, with 11 NtWRKY genes in roots, stems and leaves expressed at various levels. The expression of genes NtWRKY26, NtWRKY30 and NtWRKY32 can be induced by Phytophthora nicotianae. Our research thus provides valuable information for NtWRKY gene cloning and functional characterization in common tobacco.
authors.affiliation: 1. Tobacco Research Institute of CAAS, Key Laboratory of Tobacco Genetic Improvement and Biotechnology, CAAS, Qingdao 266100, China; 2. Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Xiao-hua
authors.initials: XH
authors.lastname: Xiang
authors.affiliation: Tobacco Research Institute of CAAS, Key Laboratory of Tobacco Genetic Improvement and Biotechnology, CAAS, Qingdao 266100, China.
authors.forename: Xin-ru
authors.initials: XR
authors.lastname: Wu
authors.affiliation: Tobacco Research Institute of CAAS, Key Laboratory of Tobacco Genetic Improvement and Biotechnology, CAAS, Qingdao 266100, China.
authors.forename: Jiang-tao
authors.initials: JT
authors.lastname: Chao
authors.affiliation: 1. Tobacco Research Institute of CAAS, Key Laboratory of Tobacco Genetic Improvement and Biotechnology, CAAS, Qingdao 266100, China; 2. Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Ming-lei
authors.initials: ML
authors.lastname: Yang
authors.affiliation: Yunnan Tobacco Company Dalizhou Branch, Dali 671000, China.
authors.forename: Fan
authors.initials: F
authors.lastname: Yang
authors.affiliation: 1. Tobacco Research Institute of CAAS, Key Laboratory of Tobacco Genetic Improvement and Biotechnology, CAAS, Qingdao 266100, China; 2. Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Guo
authors.initials: G
authors.lastname: Chen
authors.affiliation: Tobacco Research Institute of CAAS, Key Laboratory of Tobacco Genetic Improvement and Biotechnology, CAAS, Qingdao 266100, China.
authors.forename: Guan-shan
authors.initials: GS
authors.lastname: Liu
authors.affiliation: Tobacco Research Institute of CAAS, Key Laboratory of Tobacco Genetic Improvement and Biotechnology, CAAS, Qingdao 266100, China.
authors.forename: Yuan-ying
authors.initials: YY
authors.lastname: Wang
mesh_terms: D000595:Amino Acid Sequence; D032461:Chromosomes, Plant / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D016415:Sequence Alignment; D013312:Stress, Physiological / Q000235:genetics; D014026:Nicotiana / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors