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Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum.
Mol Genet Genomics. 2012 Jun; 287(6):495-513.MG

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+Show Affiliations

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.comNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

22570076

Citation

Huang, Shengxiong, et al. "Genome-wide Analysis of WRKY Transcription Factors in Solanum Lycopersicum." Molecular Genetics and Genomics : MGG, vol. 287, no. 6, 2012, pp. 495-513.
Huang S, Gao Y, Liu J, et al. Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Mol Genet Genomics. 2012;287(6):495-513.
Huang, S., Gao, Y., Liu, J., Peng, X., Niu, X., Fei, Z., Cao, S., & Liu, Y. (2012). Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Molecular Genetics and Genomics : MGG, 287(6), 495-513. https://doi.org/10.1007/s00438-012-0696-6
Huang S, et al. Genome-wide Analysis of WRKY Transcription Factors in Solanum Lycopersicum. Mol Genet Genomics. 2012;287(6):495-513. PubMed PMID: 22570076.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. AU - Huang,Shengxiong, AU - Gao,Yongfeng, AU - Liu,Jikai, AU - Peng,Xiaoli, AU - Niu,Xiangli, AU - Fei,Zhangjun, AU - Cao,Shuqing, AU - Liu,Yongsheng, Y1 - 2012/05/09/ PY - 2011/12/11/received PY - 2012/04/23/accepted PY - 2012/5/10/entrez PY - 2012/5/10/pubmed PY - 2012/7/28/medline SP - 495 EP - 513 JF - Molecular genetics and genomics : MGG JO - Mol Genet Genomics VL - 287 IS - 6 N2 - 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. SN - 1617-4623 UR - https://www.unboundmedicine.com/medline/citation/22570076/Genome_wide_analysis_of_WRKY_transcription_factors_in_Solanum_lycopersicum_ L2 - https://doi.org/10.1007/s00438-012-0696-6 DB - PRIME DP - Unbound Medicine ER -