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.

A genome-wide survey of homeodomain-leucine zipper genes and analysis of cold-responsive HD-Zip I members’ expression in tomato

“…Tandem duplication was two or more genes located on the same chromosome within the range of 100 kb distance, while the segmental duplication means the homologous genes duplicated on different chromosomomes. 65,66) In this study, the results showed the SlHZ genes were distributed at all the 12 chromosomes. SlHZ genes were distributed with high density at chromosome II and III, each contained nine genes.…”

Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses

“…The results showed that 69 SiWRKY proteins contained one or two identical WRKYGQK domains. Although the WRKYGQK domain is highly conserved in WRKY proteins, SiWRKY59 and SiWRKY60 differed at one residue, with a glutamine being replaced by a lysine residue; this change is also found in WRKYs from tomato, Arabidopsis, and other plant species [13,15,19,22]. Additionally, most of the SiWRKY proteins contained the C-X 4-7 -C-X 23 -H motif that forms the C 2 H 2 /C 2 HC-type zinc-finger structure.…”

“…The first identified WRKY gene, SPF1, was cloned from sweet potato (Ipomoea batatas) 20 years ago [16]. Since then, a large number of WRKY genes have been identified, including 74 from Arabidopsis thaliana [17], 103 from Oryza sativa [18], 45 from Hordeum vulgare [19], 119 from Zea mays [20], and many more from other plant species [21][22][23].…”

In silico analysis of gene content in tomato genomic regions mapped to the Ty-2 resistance gene

“…Among the 22 candidate genes, 5 belonged to the NBS-LRR family, 3 were receptor-like protein kinase family members, 3 were transcription factors, 2 were protein isomerases, 2 were involved in oxidation reduction in organisms, 1 encoded structural proteins, 1 encoded allergic pathogenic proteins, 2 were ubiquitin ligases, and 1 was related to cytochromes. According to the gene clusters and tandem repeats criteria used in previous studies (Meyers et al, 2003;Yang et al, 2008;Huang et al, 2012), further analysis revealed that the 5 NBS-LRR family genes in the Ty-2 disease-resistant genes region belonged to 2 gene clusters. Solyc11g069620.1.1 and Solyc11g069660.1.1 belonged to the same gene cluster, and exhibited tandem repeat modes; the other 3 NBS-LRR family genes (Solyc11g069920.1.1, Solyc11g069990.1.1, and Solyc11g070000.1.1) belonged to another cluster.…”