含有保守Su(var)3-9, Enhancer-of-zeste和Trithorax (SET)结构域的蛋白能够催化组蛋白赖氨酸甲基化, 从而调控染色质结构和相关基因的转录, 参与植物多种生理与发育过程。辣椒作为全球重要的蔬菜作物, 其非生物胁迫抗性机制的研究对分子育种具有重要实践意义, 但目前辣椒SET基因家族在胁迫响应中的作用尚不明确。本研究在辣椒基因组中鉴定了39个CaSET基因, 根据保守结构域和系统发育关系可将其划分为六个亚家族(I–VI)。这些基因分布于除第5和9号染色体外的其余10条染色体上, 其中第3号染色体分布最为密集(8个)。大多数CaSETs (89.7%)可能定位于细胞核或细胞质。各分支的CaSETs具有特定的保守结构域, 与系统进化分类结果一致。基因家族扩张分析显示, 串联重复和片段复制事件是CaSET基因扩张的主要驱动力。在CaSET基因启动子中总共鉴定出403个与植物激素及胁迫响应相关的顺式作用元件。CaSET基因在辣椒不同组织中表达存在差异, 多数成员在发育早期果实中的表达水平高于其他组织。多个CaSET基因的表达受盐胁迫和干旱胁迫调控, 且在叶片中的响应比根系更为敏感, 暗示CaSET基因可能参与辣椒对盐和干旱胁迫的应答过程。未来研究将着重阐明关键CaSETs在转录调控和功能蛋白修饰中的作用。总之, 本研究对辣椒CaSET家族进行了全面分析, 为深入揭示其在非生物胁迫耐受性中的分子机制提供了理论基础。

INTRODUCTION: Proteins containing the conserved Su(var)3?9, Enhancer?of?zeste and Trithorax (SET) domain can catalyze histone lysine methylation, thereby modulating chromatin structure and the transcription of related genes, and are involved in various physiological and developmental processes in plants. As an important vegetable crop worldwide, research on the abiotic stress resistance mechanisms in pepper holds significant practical value for molecular breeding. However, the role of the SET gene family in stress responses in pepper remains unclear. RATIONALE: We used the pepper genome as a reference to identify the members of pepper SET gene family, and analyzed their phylogenetic relationships, gene structure, conserved motifs, cis-regulatory elements, gene duplication events, as well as the expression patterns of these genes under salt and drought stress conditions. RESULTS: A total of 39 CaSETs were identified in pepper genome. Based on their conserved domains and phylogenetic relationships, CaSETs were classified into six branches (I, II, III, IV, V, and VI), and each branch's CaSETs were characterized by specific conserved domains. The CaSETs were distributed on the other 10 chromosomes except for chromosomes 5 and 9. Most CaSETs were likely to be in the nucleus or cytoplasm. Tandem duplication and segmental duplication events jointly promoted the expansion of CaSET family. A total of 403 plant hormone and stress response cis-regulatory elements were found in the promoters of CaSETs. Expression analysis indicated differential expression of CaSETs across various pepper tissues, with most members showing higher expression levels in early developmental fruits compared to other tissues. Moreover, the expression of several CaSETs was regulated under salt and drought stress, with leaves exhibiting greater sensitivity to these stresses than roots. CONCLUSION: This study conducted a systematic analysis of the CaSET family in pepper. The results are expected to facilitate the future application of CaSETs-related epigenetic genome engineering in the improvement of pepper crops.

Phylogenetic tree of pepper, Arabidopsis, rice and tomato SET members

The member of Arabidopsis (prefixed by At), rice (Os), tomato (Sl) and pepper (Ca) SET family are used, and the six clades (Class I-VI) are marked by different colors