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Open Access Highly Accessed Research article

Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles

Riccardo Aiese Cigliano1, Walter Sanseverino2, Gaetana Cremona1, Maria R Ercolano2, Clara Conicella1 and Federica M Consiglio1*

  • * Corresponding author: Federica M Consiglio marconsi@unina.it

  • † Equal contributors

Author Affiliations

1 CNR, National Research Council of Italy, Institute of Plant Genetics, Research Division Portici, Via Università 133, 80055, Portici, Italy

2 DISSPAPA, Department of Soil, Plant and Environmental Sciences, University of Naples “Federico II”, Via Università 100, 80055, Portici, Italy

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BMC Genomics 2013, 14:57  doi:10.1186/1471-2164-14-57

Published: 28 January 2013

Abstract

Background

Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although Solanum lycopersicum is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (HMs) in tomato are sketchy.

Results

Based on recently released tomato whole-genome sequences, we identified in silico 32 histone acetyltransferases (HATs), 15 histone deacetylases (HDACs), 52 histone methytransferases (HMTs) and 26 histone demethylases (HDMs), and compared them with those detected in Arabidopsis (Arabidopsis thaliana), maize (Zea mays) and rice (Oryza sativa) orthologs. Comprehensive analysis of the protein domain architecture and phylogeny revealed the presence of non-canonical motifs and new domain combinations, thereby suggesting for HATs the existence of a new family in plants. Due to species-specific diversification during evolutionary history tomato has fewer HMs than Arabidopsis. The transcription profiles of HMs within tomato organs revealed a broad functional role for some HMs and a more specific activity for others, suggesting key HM regulators in tomato development. Finally, we explored S. pennellii introgression lines (ILs) and integrated the map position of HMs, their expression profiles and the phenotype of ILs. We thereby proved that the strategy was useful to identify HM candidates involved in carotenoid biosynthesis in tomato fruits.

Conclusions

In this study, we reveal the structure, phylogeny and spatial expression of members belonging to the classical families of HMs in tomato. We provide a framework for gene discovery and functional investigation of HMs in other Solanaceae species.

Keywords:
Solanum lycopersicum; Epigenetics; Development