六倍体普通油茶 CoCHS 基因家族的全基因组鉴定及表达分析

Genome-wide identification and expression analysis of CoCHS gene family in Camellia oleifera

摘要

【目的】查尔酮合酶（CHS）是黄酮类化合物合成的关键酶，本研究旨在通过鉴定六倍体普通油茶 CHS 基因家族并进行表达分析和互作蛋白预测，为解析 CHS 调控油茶黄酮合成的分子机制提供理论依据。【方法】在六倍体普通油茶‘长林40号’基因组数据中鉴定 CoCHS 基因，对其基因家族进行理化性质、系统进化、基因结构、启动子顺式作用元件、共线性、组织表达等分析，并通过 AlphaFold3 预测与 CoCHS 互作的转录因子。【结果】（1）在六倍体普通油茶中鉴定到 45 个 CoCHS 基因，CoCHS 蛋白主要聚类为 CHS 亚家族和 CHS-like 亚家族两大类；CHS 亚家族均含有 PLN03173 保守结构域，CHS-like 亚家族均含有 PLN03169 保守结构域。（2）顺式作用元件分析表明油茶 CoCHS 基因启动子区含有大量与植物生长发育、植物激素响应及逆境胁迫响应相关的元件，推测油茶 CoCHS 基因家族受到植物激素的调控，且在植物的胁迫响应和生长发育过程中发挥着重要作用。（3）共线性分析表明片段重复是基因家族扩张的主要驱动力，且 CoCHS 基因家族的共线性均存在于同一亚家族之间。种间共线性分析表明四倍体油茶和六倍体普通油茶的共线性基因对最多。（4）转录组分析表明， CoCHS 基因在不同组织和不同发育时期的胚中均有表达， CoCHS16、 CoCHS17、 CoCHS18、 CoCHS19、 CoCHS20 和 CoCHS21 在种仁发育中后期表达量相对较高，推测其可能在油茶种仁黄酮的合成调控过程中扮演着重要角色。（5）对种仁中后期优势表达的 CoCHS16 蛋白构建 CoCHS16-MYB 转录因子蛋白复合物模型，筛选到 5 个潜在的 MYB 互作转录因子。【结论】普通油茶的 45 个 CoCHS 蛋白在进化上相对保守，其成员在黄酮合成及相关逆境响应中可能发挥不同作用。该研究为解析油茶黄酮合成的分子机制提供了核心靶点，也为通过分子育种定向改良油茶品质奠定了理论基础。

Abstract

[Objective] Chalcone synthase is a key enzyme in flavonoid biosynthesis. In this study, we identified the CHS gene family in hexaploid Camellia oleifera, performed expression analysis, and predicted its interacting proteins, aiming to provide a theoretical foundation for elucidating the molecular mechanisms underlying CHS regulation of flavonoid biosynthesis in C. oleifera. [Method] Based on the genomic data of hexaploid C. oleifera ‘Changlin 40’, CoCHS genes were identified, and a comprehensive analysis of the gene family was performed, including physicochemical properties, phylogenetic evolution, gene structure, cis-acting regulatory elements in promoters, collinearity, tissue-specific expression patterns. And interacting proteins of CoCHS were predicted using AlphaFold3. [Result] (1) A total of 45 CoCHS genes were identified from the hexaploid oil- Camellia genome. CoCHS proteins were clustered into two major subfamilies, the CHS subfamily and CHS-like subfamily. All members of the CHS subfamily contained the PLN03173 conserved domain, while those in the CHS-like subfamily contained the PLN03169 conserved domain. (2) Cis-acting element analysis showed that the promoters of the CoCHS genes contained a large number of elements related to plant growth and development, plant hormone response, as well as adversity stress response, which suggests that the CoCHS gene family is likely regulated by phytohormones and plays important roles in both stress responses and developmental processes in oil-tea plants. (3) Collinearity analysis revealed that segmental duplication was the primary driver of gene family expansion, and all hexaploid CoCHS genes exhibited collinearity strictly within the same subfamily. Interspecific collinearity analysis showed that tetraploid C. oleifera and hexaploid C. oleifera shared the highest number of collinear gene pairs. (4) Transcriptome analysis indicated that ubiquitous expression of CoCHS genes in multiple tissues and seed developmental phases, while CoCHS16, CoCHS17, CoCHS18, CoCHS19, CoCHS20, CoCHS21 exhibited significantly elevated expression specifically in mid-to-late embryogenesis, implying their involvement in modulating flavonoid accumulation in oil-tea camellia seeds. (5) CoCHS16-MYB transcription factor protein complex was modeled based on the dominantly expressed CoCHS16 protein during mid-to-late seed development and identified five potential MYB-interacting transcription factors. [Conclusion] 45 CoCHS proteins are evolutionarily conserved, and their members are likely to play distinct roles in flavonoid synthesis and associated stress responses. This study provides key targets for elucidating the molecular mechanisms of flavonoid biosynthesis and lays a theoretical foundation for molecular breeding aimed at improving oil tea quality in C. oleifera.

关键词

油茶 / 查尔酮合成酶 / 黄酮合成 / 全基因组分析 / 表达分析 / 蛋白互作预测 / 分子育种

Key words

Camellia oleifera / chalcone synthase / flavonoid biosynthesis / genome-wide analysis / expression analysis / protein-protein interaction prediction / molecular breeding

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基金资助

湖北省高等学校优秀中青年科技创新团队(T2023025)

湖北省自然科学基金联合基金项目(2025AFD333)