生姜 ZoNCED 基因家族鉴定及表达分析

Identification and expression analysis of ZoNCED gene family in ginger

摘要

[目的]本文旨在揭示生姜 9-顺式-环氧类胡萝卜素双加氧酶(NCED)基因家族的分子特征及非生物胁迫表达特性。[方法]基于生姜全基因组数据，筛选鉴定出 10 个具有典型 NCED 保守结构域的 ZoNCED 家族基因，并利用生物信息学系统分析其理化性质、基因结构、保守结构域、启动子顺式作用元件、染色体定位、共线性关系和蛋白互作网络；同时，结合转录组数据和 RT-qPCR 技术验证该家族基因在盐胁迫下的表达模式。[结果]ZoNCED 基因编码蛋白的氨基酸长度为 205~646 aa，相对分子质量为 23190.73~72379.95，等电点 5.64~8.98。系统进化分析将 ZoNCED 分为 4 个亚家族(Ⅰ-Ⅳ)，分别包含 2、2、1 和 5 个成员。启动子区富集 ABRE、MYB/MYC 等与非生物胁迫响应密切相关的顺式作用元件。ZoNCED 家族成员分布于 7 条染色体上，共线性分析表明串联复制和片段复制是家族扩张的主要机制。蛋白互作网络预测显示，ZoNCED05 可能作为枢纽蛋白参与调控植物生长发育和逆境响应过程。转录因子调控网络分析鉴定出 MIKE_MADS、Dof、C2H2、HD-ZIP、MYB 和 G2-like 等可能是参与 ZoNCED 表达调控的关键转录因子。此外，表达谱分析发现，ZoNCED01、ZoNCED07 和 ZoNCED08 在盐胁迫下显著上调表达。[结论]本研究首次系统解析了生姜 ZoNCED 基因家族的分子特征，揭示了其在非生物响应中的功能多样性及调控网络，为生姜抗逆分子育种提供了重要理论依据和候选基因资源。

Abstract

[Objectives] This study aimed to uncover the molecular characteristics of the ginger 9-cis-epoxycarotenoid dioxygenase (NCED) gene family and its expression patterns in response to abiotic stress. [Methods] Ten ZoNCED gene family members harboring conserved NCED domains were screened and identified from the ginger whole-genome. Systematic analyses were conducted to investigate their physicochemical properties, gene structures, conserved domains, promoter cis-acting elements, chromosomal localization, collinearity relationships and protein-protein interaction networks. Meanwhile, transcriptome data and RT-qPCR technology were employed to verify the expression patterns of these genes under salt stress. [Results] The ZoNCED-encoded proteins exhibited amino acid lengths ranging from 205 to 646 aa, molecular weights from 23190.73 to 72379.95, and isoelectric points (pI) of 5.64-8.98. Phylogenetic analysis classified the ZoNCED genes into four subfamilies (I-IV), containing 2, 2, 1 and 5 members, respectively. The promoter regions were enriched with stress-responsive cis-acting elements, such as ABRE and MYB/MYC, implicating their roles in abiotic stress responses. Chromosomal mapping indicated that ZoNCED genes were distributed across seven chromosomes, and collinearity analysis demonstrated that tandem duplication and segmental duplication were the primary mechanisms driving family expansion. Protein-protein interaction network prediction indicated that ZoNCED05 might function as a hub protein to regulate plant growth and stress responses. Transcription factor regulatory network analysis identified potential key regulators of ZoNCED expression, including MIKE_MADS, Dof, C2H2, HD-ZIP, MYB, and G2-like families. Furthermore, expression profiling demonstrated that ZoNCED01, ZoNCED07 and ZoNCED08 significantly upregulated under salt stress. [Conclusions] This study provided the first comprehensive analysis of the ZoNCED gene family in ginger, uncovering its functional diversity and regulatory networks in abiotic stress responses, thereby offering valuable theoretical insights and candidate gene resources for molecular breeding of stress-resistant ginger varieties.

关键词

生姜 / NCED 基因家族 / 生物信息学 / 盐胁迫 / 基因表达模式 / 调控网络

Key words

Zingiber officinale Roscoe / NCED gene family / bioinformatics / salt stress / gene expression pattern / regulation network

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基金资助

湖北省教育厅科学研究计划青年人才项目(Q20231305)

湖北省国际合作项目(2024EHA011)

长江大学湿地生态与农业利用教育部工程研究中心开放基金项目(KFG202422)