| 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：2024-05-21 |
| 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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| 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，该
文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
体定位，通过在线转录组数据分析番茄 HM 基因家族时空表达模式。【结果】共鉴定到 148 个番茄 HM 基因，其中
32 个编码组蛋白乙酰转移酶（Histone acetyltransferase，HAT），11 个编码组蛋白去乙酰化酶（Histone deacetylase，
HDAC），50 个编码组蛋白甲基转移酶（Histone methyltransferase，HMT），55 个编码组蛋白去甲基化酶（Histone
demethylase，HDM）。148 个基因不均匀地分布在 12 条染色体上，其中 3 号染色体上分布最多、有 21 个基因，12
号染色体上分布最少、有 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较大，最多可达 34 个、
最少仅有 1 个。蛋白质结构域分析结果显示，Solyc07g064130、Solyc11g005670、Solyc10g006480 仅含有 Ubl 结构域，
Solyc07g062100、Solyc10g077110 和 Solyc03g083310 仅含有 Zn-finger 结构域，另有 10 个成员含有 Bromo 结构域、
48 个成员含有 SET 结构域，其他成员还包含 PLN02529、PRMT5 等结构域。此外，番茄 HM 与拟南芥和水稻中的
同源蛋白关系均较远，且与水稻相比，番茄 HM 序列与拟南芥同源蛋白序列亲缘关系较近。根据聚类分析，将番茄
HM 分成 HAT、HDAC、HMT、HDM 4 个家族。组织表达分析表明，HAT 家族在发芽后 30 d 的花（F30）、开花后
10 d 的果实（10 DPA）、花（fr）、根（rr）、未成熟的果实（Plgfr）中高表达；HDAC 家族在发芽后 30 d 的花（F30）
和未成熟果实（Plgfr）中高表达；HMT 家族在发芽后 30 d 的花（F30）、在全株 50% 的花开放时的花（F45）、花
蕾（br）、3 cm 果实（3fr）、未成熟 5 cm 果实（PB+5fr）中高表达；HDM 家族在发芽后 30 d 的花（F30）、在全
株 50% 的花开放时的花（F45）、花蕾（br）、花（fr）、根（rr）、3 cm 果实（3fr）、未成熟 5 cm 果实（PB+5fr）
中高表达。【结论】不同番茄 HM 的基因结构差异较大，包含多种功能结构域。番茄 HM 与拟南芥、水稻 HM 的同
源关系较远，且在植物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 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. |
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