Journal of Agricultural Science and Technology ›› 2025, Vol. 27 ›› Issue (1): 80-95.DOI: 10.13304/j.nykjdb.2023.0156

• BIOTECHNOLOGY & LIFE SCIENCE • Previous Articles     Next Articles

Identification and Phylogenetic Analysis of Tomato CCCH-like Zinc Finger Protein Family

Xianguo LI1,2(), Qi DAI1, Zepeng WANG1,2, Zhaolong CHEN1,2, Huizhuan YAN2, Ning LI1()   

  1. 1.Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables,Institute of Horticultural Crops,Xinjiang Academy of Agricultural Sciences,Urumqi 830091,China
    2.College of Horticulture,Xinjiang Agricultural University,Urumqi 830052,China
  • Received:2023-03-06 Accepted:2023-06-14 Online:2025-01-15 Published:2025-01-21
  • Contact: Ning LI

番茄CCCH类锌指蛋白家族的鉴定及其表达分析

李贤国1,2(), 戴麒1, 王泽鹏1,2, 陈兆龙1,2, 闫会转2, 李宁1()   

  1. 1.新疆农业科学院园艺作物研究所,新疆特色果蔬基因组研究与遗传改良重点实验室,乌鲁木齐 830091
    2.新疆农业大学园艺学院,乌鲁木齐 830052
  • 通讯作者: 李宁
  • 作者简介:李贤国 E-mail:15099198840@163.com
  • 基金资助:
    国家自然科学基金项目(32260763);新疆农业科学院科技创新专项孵化项目(xjkcpy-2021001)

Abstract:

CCCH (C3H) type zinc finger proteins are evolutionarily conserved RNA-binding proteins, which primarily bind to DNA and RNA and play a role on the regulation of gene expression. They are not only involved in plant growth and development and hormone regulation, but also in response to biotic and abiotic stresses. 47 SlC3H genes in tomato were identified by bioinformatics approach, which were unevenly distributed on 12 chromosomes and mainly localised in the nucleus. They were divided into 3 subclades (Ⅰ~Ⅲ) based on phylogenetic relationships. The covariance analysis revealed the presence of gene duplication in the SlC3H gene family, which suggested that SlC3H genes might have undergone family member expansion through duplication during evolution. The tomato SlC3H gene contained 1~14 exons with elements responsive to hormonal and abiotic stresses in its promoter region. The Ka/Ks analysis indicated that members of the SlC3H gene family and C3H genes had undergone strong evolutionary selection during evolution. The qRT-PCR analysis revealed that the expression of more than half of the SlC3H gene family was up-regulated under salt stress, with SlC3H1 reaching a maximum expression at 8 h, 30 times higher than at 0 h. And the expressions of all SlC3H genes were up-regulated under 0.1 mol·L-1 2,4-epibrassinolide (EBR) treatment, with 8~150 times higher than control. In especial, the expression of SlC3H28 in other stages was almost zero, but it’s expression in green ripening stage was 150 times higher than control. Above results provided a reference for further insights into the function of the C3H gene family in tomato in response to abiotic stresses and fruit development.

Key words: CCCH, tomato, biological informatics, expression analysis

摘要:

CCCH(C3H)型锌指蛋白是进化上保守的RNA结合蛋白质,主要与DNA和RNA结合来调控基因表达,不仅参与植物的生长发育和激素调控过程,同时也响应生物和非生物胁迫。运用生物信息学方法,在番茄(Solanum Lycopersicum)中鉴定出47个SlC3H基因,不均匀地分布在12条染色体上,主要定位于细胞核中。根据系统进化树将其分为3个亚族(Ⅰ~Ⅲ)。共线性分析发现,SlC3H基因家族存在基因复制现象,表明在进化过程中SlC3H基因可能通过复制进行家族成员扩增。番茄SlC3H基因含有1~14个外显子,其启动子区域存在与激素和非生物胁迫响应的元件。Ka/Ks分析表明,SlC3H基因家族成员和C3H基因在进化过程中经历了强烈的进化选择。qRT-PCR分析发现,在盐胁迫下,SlC3H基因家族有一半以上的基因表达上调,其中SlC3H1在8 h时表达量最高,是0 h的30倍;用0.1 mol·L-1 2,4-表油菜素内酯(2,4-epibrassinolide,EBR)处理后所有SlC3H基因在绿熟期都表达上调,表达量是对照组的8~150倍,尤其是SlC3H28在其他时期表达量几乎为0,但在绿熟期其表达量是对照组的150倍,推测EBR对果实绿熟期的发育有促进作用。上述研究结果为进一步揭示番茄C3H基因家族在响应非生物胁迫以及果实发育中的功能提供了参考依据。

关键词: CCCH, 番茄, 生物信息学, 表达分析

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