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Genome-wide identification and characterization of R2R3MYB family in Solanum lycopersicum

Abstract

The R2R3MYB proteins comprise one of the largest families of transcription factors and play regulatory roles in developmental processes and defense responses in plants. However, there has been relatively little effort to systematically carry out comprehensive genomic and functional analyses of these genes in tomato (Solanum lycopersicum L.), a reference species for Solanaceae plants, and the model plant for fruit development. In this study, a total of 121 R2R3MYB genes were identified in the tomato genome released recently and further classified into 29 subgroups based on the phylogenetic analysis of the complete protein sequences. Phylogenetic comparison of the members of this superfamily among tomato, Arabidopsis, grape, rice, poplar, soybean, cucumber and apple revealed that the putative functions of some tomato R2R3MYB proteins were clustered into the Arabidopsis functional clades. The chromosome distribution pattern revealed that tomato R2R3MYB genes were enriched on several chromosomes and 52 % of the family members were tandemly duplicated genes. Tissue specificity or different expression levels of SlR2R3MYBs in different tissues suggested differential regulation of tissue development as well as metabolic regulation. The transcript abundance level analysis during abiotic conditions identified a group of R2R3MYB genes that responded to one or more treatments suggesting that the SlR2R3MYBs played major roles in the plant response to abiotic conditions and involved in signal transduction pathways. This study not only provides a solid foundation for further functional dissection of tomato R2R3MYB family genes, but may also be profitable for, in the future, the improvement of tomato stress tolerance and fruit quality.

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Acknowledgments

This work was supported by fundings from ‘Taishan Scholar’ Foundation of the People’s Government of Shandong Province, the National Natural Science Foundation of China (NSFC; 31222048 and 31171977), and the Program for Changjiang Scholars and Innovative Research Team in University (IRT1155).

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Correspondence to Zhonghai Ren.

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Communicated by S. Hohmann.

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Zhao, P., Li, Q., Li, J. et al. Genome-wide identification and characterization of R2R3MYB family in Solanum lycopersicum . Mol Genet Genomics 289, 1183–1207 (2014). https://doi.org/10.1007/s00438-014-0879-4

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Keywords

  • Tomato
  • R2R3MYB
  • Phylogenetic analysis
  • Intron–exon structure
  • Expression profile