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Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum

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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.

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Abbreviations

AtWRKY:

WRKY transcription factor in Arabidopsis

Genbank:

Nucleotide sequence database of National Center for Biotechnology Information

HMM:

Hidden Markov Model

ITAG:

International Tomato Annotation Group

ITOL:

Interactive Tree of Life

KaFTom:

Kazusa Full-Length Tomato cDNA Database

JCVI:

J. Craig Venter Institute

MEME:

Multiple Em for Motif Elicitation

NCBI:

National Center for Biotechnology Information

OsWRKY:

WRKY transcription factor in rice

PlantTFDB:

Plant Transcription Factor Database

SGN:

Sol Genomics Network

SlWRKY:

WRKY transcription factor in tomato

SMART:

Simple Modular Architecture Research Tool

TAIR:

The Arabidopsis Information Resource

TFGD:

Tomato Functional Genomics Database

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Acknowledgments

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 (http://solgenomics.net/organism/solanum_lycopersicum/genome). We also acknowledge other institutions and organizations for providing the public release of genome sequences used in our investigation.

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Authors and Affiliations

  1. 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

    Shengxiong Huang, Yongfeng Gao, Jikai Liu & Yongsheng Liu

  2. School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, People’s Republic of China

    Shengxiong Huang, Yongfeng Gao, Jikai Liu, Xiaoli Peng, Xiangli Niu, Shuqing Cao & Yongsheng Liu

  3. Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA

    Zhangjun Fei

  4. USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA

    Zhangjun Fei

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  1. Shengxiong Huang
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  2. Yongfeng Gao
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  4. Xiaoli Peng
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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). https://doi.org/10.1007/s00438-012-0696-6

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