西瓜含有JmjC结构域的组蛋白去甲基化酶家族的生物信息学分析

周皇经; 王翔伍; 吉逢逢; 张鹏辉; 郭清华; 郝云飞; 何世斌

doi:10.11913/PSJ.2095-0837.2020.60802

西瓜含有JmjC结构域的组蛋白去甲基化酶家族的生物信息学分析

河南大学生命科学学院, 棉花生物学国家重点实验室, 河南开封 475004

基金项目:

国家自然科学基金项目（31401044）。

详细信息

作者简介:
周皇经(1998~),男,本科生,研究方向为植物表观遗传学(E-mail:2373006425@qq.com)。

通讯作者:
何世斌,E-mail:sbhe@henu.edu.cn

中图分类号: Q943.2
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出版历程
- 收稿日期: 2020-04-09
- 修回日期: 2020-05-17
- 网络出版日期: 2022-10-31
- 发布日期: 2020-12-27

Bioinformatics analysis of JmjC domain-containing histone demethylase family in watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai)

School of Life Sciences, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, Henan 475004, China

Funds:

This work was supported by a grant from the National Natural Science Foundation of China (31401044).

摘要

摘要: 利用生物信息学方法，对西瓜（Citrullus lanatus（Thunb.）Matsum.&Nakai）JmjC基因家族的成员进行鉴定，对该基因家族的染色体定位、基因结构、蛋白结构域、选择压力和酶活位点进行分析，并对该基因家族与其它物种的系统进化及共线性关系进行研究。结果显示：西瓜全基因组含有17个JmjC候选基因，核苷酸序列长度为1209~5541 bp；这些基因均含有JmjC结构域，分别位于9条染色体上，归属8个亚族。系统进化、选择压力以及共线性分析结果表明，西瓜与黄瓜（Cucumis sativus L.）亲缘关系较近，JmjC家族基因数量相同，其中14个成员呈现一对一的共线性关系；而西瓜与拟南芥（Arabidopsis thaliana（L.）Heynh）亲缘关系较远，但西瓜和拟南芥同一亚族中JmjC基因间K_a/K_s的比值均小于1，推测西瓜各个亚族成员的编码蛋白功能与同一亚族的拟南芥成员功能极为相似。酶活位点分析结果表明西瓜JmjC基因家族中有10个成员具有潜在的组蛋白去甲基化酶活性。
- 西瓜 /
- 组蛋白去甲基化酶 /
- JmjC结构域 /
- 生物信息学分析
Abstract: Jumonji C (JmjC) domain-containing proteins are a class of histone demethylases responsible for removing histone methylation marks. They also play important roles in plant growth and development. Using bioinformatics, we identified the JmjC genes in Citrullus lanatus (Thunb.) Matsum. & Nakai, and analyzed their location, gene structure, protein domain, enzyme activity site, and selection pressure. In addition, the phylogenetic relationships and collinearity among C. lanatus, Cucumis sativus L., and Arabidopsis thaliana (L.) Heynh were also analyzed. A total of 17 JmjC genes were identified in C. lanatus, which ranged in size from 1209 to 5541 bp. These genes all contained the JmjC domain and were located on nine chromosomes and classified into eight subfamilies. Both C. lanatus and closely related species C. sativus shared the same number of JmjC genes, with 14 members showing a one-to-one collinear relationship, while C. lanatus and distant species A. thaliana showed lower collinearity. The K_a/K_s ratios of JmjC genes in the same subfamily were less than One between C. lanatus and A. thaliana, indicating that orthologous genes between the two species should have similar functions. In addition, according to enzyme activity site prediction, we speculated that 10 of them may confer histone demethylase activity.
- Citrullus lanatus /
- Histone demethylase /
- JmjC domain /
- Bioinformatics analysis

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