| 刘思嘉,杨荣超.番茄组蛋白修饰基因家族鉴定及表达分析[J].广东农业科学,2024,(4):- |
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番茄组蛋白修饰基因家族鉴定及表达分析 |
| Identification and expression analysis of histone modification gene families in tomato |
| 投稿时间：2024-02-05 修订日期：2024-04-06 |
| DOI： |
| 中文关键词: 番茄 组蛋白修饰基因家族 基因结构 蛋白结构 系统进化 表达模式 |
| 英文关键词: tomato histone modifier gene family gene structure protein structure phylogeny expression pattern |
| 基金项目:本研究由国家自然科学基金面上项目(No. 32370359) |
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| 摘要点击次数: 41 |
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| 中文摘要: |
| 摘 要：【目的】植物组蛋白的功能修饰包括乙酰化修饰和甲基化修饰，在植物生长发育及逆境响应的过程中发挥着重要作用。番茄组蛋白修饰（Histone modification，HM）基因家族的生物学功能及分子机制尚不清楚，本研究旨在进一步明确番茄HM基因的生物学功能，为其分子机制研究及番茄遗传改良奠定基础。【方法】基于番茄基因组数据库鉴定番茄HM成员，利用生物信息学的方法系统分析其HM基因家族成员的系统进化、基因结构、染色体的定位，通过在线数据库分析番茄HM基因家族时空表达模式。【结果】本研究共鉴定得到148个番茄HM基因，其中32个编码组蛋白乙酰转移酶（Histone acetyltransferases，HATs），11个编码组蛋白去乙酰化酶（Histone deacetylases，HDACs），50个编码组蛋白甲基转移酶（Histone methyltransferases，HMTs），55个编码个组蛋白去甲基化酶（Histone demethylases，HDMs）；148个基因不均匀地分布在不同的染色体上，其中，在3号染色体上分布最多、达21个基因，12号染色体上分布最少、达4个基因。基因结构特征分析表明，番茄HM基因之间外显子的差异很大，外显子最多的达34个，最少的仅有1个；蛋白质结构域分析结果显示，Solyc07g064130、Solyc11g005670、Solyc10g006480仅包含Ubl结构域，Solyc07g062100、Solyc10g077110和Solyc03g083310仅含有Zn-finger结构域，另外10个基因含有Bromo结构域，48个基因仅包含存在SET结构域，其他基因还包含?PLN02529、PRMT5等其他结构域。此外，番茄HM基因与拟南芥和水稻中该类同源关系均较远，且与水稻相比，番茄HM基因的蛋白序列与拟南芥同源的蛋白序列亲缘关系较近。根据系统进化聚类分析，将番茄HM家族基因分成HAT、HDAC、HMT、HDM 4个亚家族。组织表达分析表明，HDAC亚家族在发芽后30 d的花（F30）和未成熟果实（Plgfr）中高表达；HAT亚家族在发芽后30 d的花（F30）、开花后10 d的果实（10DPA）、花（fr）、根（rr）、未成熟的果实（Plgfr）中高表达；HDM亚家族在发芽后30 d的花（F30）、在50% 的花达到开花期时的花（F45）、花蕾（br）、花（fr）、根（rr）、3 cm果实（3fr）、未成熟5cm果实（PB+5fr）中高表达；HMT亚家族在发芽后30 d的花（F30）、在50% 的花达到开花期时的花（F45）、花蕾（br）、3 cm果实（3fr）、未成熟5cm果实（PB+5fr）中高表达。【结论】不同番茄HM的基因结构差异很大，包含多种蛋白功能结构域。番茄HM与拟南芥和水稻的同源关系距离较远，并且在植物的不同生长发育阶段及不同器官组织中均有一定的表达，表明该类基因可能参与了番茄多种生长发育过程。 |
| 英文摘要: |
| 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 the 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 chromosome localization of its HM gene family members using bioinformatics methods, and analyzed the spatiotemporal and temporal expression patterns of the tomato HM gene family through an online database.【Result】A total of 148 tomato HM genes were identified in this study, of which 32 encoded histone acetyltransferases (HATs), 11 encoded histone deacetylases (HDACs), 50 encoded histone methyltransferases, and 55 encoded histone demethylases (HDMs); the 148 genes were unevenly distributed on different chromosomes, of which 55 encoded histone demethylases (HDMs). methyltransferases (HMTs), and 55 genes encoding histone demethylases (HDMs); 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 structural domain analysis showed that Solyc07g064130, Solyc11g005670, and Solyc10g006480 contained only the Ubl structural domains, Solyc07g062100, Solyc10g077110 and Solyc03g083310 contain only the Zn-finger structural domain, another 10 genes contain the Bromo structural domain, 48 genes contain only the presence of the SET structural domain, and other genes contain other structural domains such as PLN02529 and PRMT5. In addition, the tomato HM genes were distantly related to the homologous proteins of this class in both Arabidopsis and rice, and the protein sequences of the tomato HM genes were more closely related to those of the Arabidopsis homologs than to those of rice. Based on phylogenetic clustering analysis, the tomato HM family genes were divided into four subfamilies, HAT, HDAC, HMT, and HDM. Tissue expression analysis showed that the HDAC subfamily was highly expressed in flowers (F30) and immature fruits (Plgfr) at 30 d after germination; the HAT subfamily was highly expressed in flowers (F30) at 30 d after germination, in fruits (10DPA) at 10 d after flowering, in flowers (fr), in roots (rr), and in immature fruits (Plgfr); the HDM subfamily was highly expressed in flowers (F30) at 30 d after germination, in fruits at 50 d after flowering, and in fruits at 50 d after flowering. flowers (F30), at 50% of flowers reaching anthesis (F45), flower buds (br), flowers (fr), roots (rr), 3 cm fruits (3fr), and immature 5 cm fruits (PB+5fr); the HDM subfamily was highly expressed in flowers 30 d after germination (F30), at 50% of flowers reaching anthesis (F45), flower buds (br), 3 cm fruit (3fr), and immature 5 cm fruit (PB+5fr).【Conclusion】The gene structures of different tomato HMs vary greatly and contain multiple protein functional structural domains. The homologous genes of tomato HM are distant from those of Arabidopsis thaliana and rice, and 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. |
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