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Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum


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.

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WRKY transcription factor in Arabidopsis


Nucleotide sequence database of National Center for Biotechnology Information


Hidden Markov Model


International Tomato Annotation Group


Interactive Tree of Life


Kazusa Full-Length Tomato cDNA Database


J. Craig Venter Institute


Multiple Em for Motif Elicitation


National Center for Biotechnology Information


WRKY transcription factor in rice


Plant Transcription Factor Database


Sol Genomics Network


WRKY transcription factor in tomato


Simple Modular Architecture Research Tool


The Arabidopsis Information Resource


Tomato Functional Genomics Database


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This work was supported by the National Science Fund for Distinguished Young Scholars (Grant No. 30825030), the National Natural Science Foundation of China (Grant Nos. 31171179, and 90717110), the 973 Program of China (Grant No. 2011CB100401), and Advanced Program of Doctoral Fund of Ministry of Education of China (20110181130009). We acknowledge the International Tomato Genome Sequencing Consortium for using the tomato genome sequences, which were generated and released by the international organization ( We also acknowledge other institutions and organizations for providing the public release of genome sequences used in our investigation.

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Correspondence to Shuqing Cao or Yongsheng Liu.

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Communicated by Stefan Hohmann.

S. Huang and Y. Gao are equal contributors.

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Huang, S., Gao, Y., Liu, J. et al. Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum . Mol Genet Genomics 287, 495–513 (2012).

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