title: Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum.
abstract: The WRKY transcription factors have been implicated in multiple biological processes in plants, especially in regulating defense against biotic and abiotic stresses. However, little information is available about the WRKYs in tomato (Solanum lycopersicum). The recent release of the whole-genome sequence of tomato allowed us to perform a genome-wide investigation for tomato WRKY proteins, and to compare these positively identified proteins with their orthologs in model plants, such as Arabidopsis and rice. In the present study, based on the recently released tomato whole-genome sequences, we identified 81 SlWRKY genes that were classified into three main groups, with the second group further divided into five subgroups. Depending on WRKY domains' sequences derived from tomato, Arabidopsis and rice, construction of a phylogenetic tree demonstrated distinct clustering and unique gene expansion of WRKY genes among the three species. Genome mapping analysis revealed that tomato WRKY genes were enriched on several chromosomes, especially on chromosome 5, and 16 % of the family members were tandemly duplicated genes. The tomato WRKYs from each group were shown to share similar motif compositions. Furthermore, tomato WRKY genes showed distinct temporal and spatial expression patterns in different developmental processes and in response to various biotic and abiotic stresses. The expression of 18 selected tomato WRKY genes in response to drought and salt stresses and Pseudomonas syringae invasion, respectively, was validated by quantitative RT-PCR. Our results will provide a platform for functional identification and molecular breeding study of WRKY genes in tomato and probably other Solanaceae plants.
authors.affiliation: Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, People's Republic of China. huangshengxiong@163.com
authors.forename: Shengxiong
authors.initials: S
authors.lastname: Huang
authors.forename: Yongfeng
authors.initials: Y
authors.lastname: Gao
authors.forename: Jikai
authors.initials: J
authors.lastname: Liu
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Peng
authors.forename: Xiangli
authors.initials: X
authors.lastname: Niu
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.forename: Shuqing
authors.initials: S
authors.lastname: Cao
authors.forename: Yongsheng
authors.initials: Y
authors.lastname: Liu
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D015870:Gene Expression; D017343:Genes, Plant; D018745:Genome, Plant; D018551:Solanum lycopersicum / Q000235:genetics*; D005810:Multigene Family; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D013045:Species Specificity; D014157:Transcription Factors / Q000145:classification / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors