Identification and Expression Analysis of Histone Modification Gene Family in Tomato

Abstract

【Objective】Functional modifications of plant histones, including acetylation modification and methylation modification, play important roles in plant growth and development and in response to adversity. The biological functions and molecular mechanisms of the histone modification (HM) gene family in tomato are still unclear. The present study aims to further clarify the biological functions of the HM genes in tomato, and to lay a foundation for the study of their molecular mechanisms and genetic improvement of tomato.【Method】We identified tomato HM members based on the tomato genome database, systematically analyzed the phylogeny, gene structure, and chromosomal localization of its HM gene family members with bioinformatics methods, and analyzed the spatio-temporal expression patterns of the tomato HM gene family through an online transcriptome database.【Result】A total of 148 tomato HM genes were identified in this study, including 32 encoded histone acetyltransferase (HAT), 11 encoded histone deacetylase (HDAC), 50 encoded histone methyltransferase (HMT), and 55 encoded histone demethylase (HDM). The 148 genes were unevenly distributed on different chromosomes, with the highest number of genes on chromosome 3 (21 genes) and the lowest number of genes on chromosome 12 (4 genes). Gene structure characterization showed that the exons varied greatly among tomato HM genes, with the most exons amounting to 34 and the least to only 1. Protein structure domain analysis showed that Solyc07g064130, Solyc11g005670 and Solyc10g006480 contained only the Ubl structure domains, Solyc07g062100, Solyc10g077110 and Solyc03g083310 contained only the Zn-finger structure domain, another 10 proteins contain the Bromo structure domain, 48 proteins contained only the SET structure domain, and other proteins contained other structure domains such as PLN02529 and PRMT5. In addition, the homologous proteins of tomato HM were distantly related to those of both Arabidopsis and Oryza sativa, and the protein sequences of the tomato HM were more closely related to those of the Arabidopsis thaliana than to those of Oryza sativa. Based on the clustering analysis, the tomato HM members were divided into four families, HAT, HDAC, HMT, and HDM. Tissue expression analysis showed that the HAT family was highly expressed in flowers at 30 d after germination (F30), fruits at 10 d post-anthesis (10DPA), flowers (fr), roots (rr), and immature fruits (Plgfr); the HDAC family was highly expressed in flowers (F30) and immature fruits (Plgfr); the HMT family was highly expressed in flowers (F30), when 50% of the whole plant flowers open (F45), flower buds (br), 3 cm fruits (3fr), and immature 5 cm fruits (PB+5fr); the HDM family was highly expressed in flowers (F30), when 50% of the whole plant flowers open (F45), flower buds (br), flowers (fr), roots (rr), 3 cm fruits (3fr), and immature 5 cm fruits (PB+5fr).【Conclusion】The gene structures of different tomato HM vary greatly and contain multiple functional structural domains. The homologous members of tomato HM are distant from those of Arabidopsis thaliana and Oryza sativa, and tomato HM are expressed in different growth and developmental stages of plants and in different organ tissues, suggesting that this class of genes may be involved in a variety of growth and developmental processes in tomato.

Keywords

• lycopersicum esculentum
• histone modification gene family
• gene structure
• protein structure
• phylogeny
• expression pattern