文献类型： 外文期刊

作者： Yang, Hongji ¹ ; Yu, Guorong ¹ ; Lv, Zhidong ¹ ; Li, Tonghui ¹ ; Wang, Xi ³ ; Fu, Ying ¹ ; Zhu, Zhangsheng ¹ ; Guo, Guangjun ⁵ ; He, Hang ¹ ; Wang, Ming ⁶ ; Qin, Guochen ¹ ; Liu, Feng ³ ; Zhong, Zhenhui ⁷ ; Xue, Yan ¹ ;

作者机构： 1.Peking Univ, State Key Lab Wheat Improvement, Shandong Lab Adv Agr Sci Weifang, Inst Adv Agr Sci, Weifang, Shandong, Peoples R China

2.Tel Aviv Univ, Sch Plant Sci & Food Secur, Tel Aviv, Israel

3.Hunan Agr Univ, Coll Hort, Engn Res Ctr Germplasm Innovat & New Varieties Bre, Key Lab Vegetable Biol Hunan Prov, Changsha, Hunan, Peoples R China

4.Yuelushan Lab, Changsha, Hunan, Peoples R China

5.Jiangsu Acad Agr Sci, Inst Vegetable Crops, Jiangsu Key Lab Hort Crop Genet Improvement, Nanjing, Peoples R China

6.Chinese Acad Sci, Inst Zool, State Key Lab Integrated Management Pest Insects &, Beijing, Peoples R China

7.Sichuan Univ, Coll Life Sci, Minist Educ, State Key Lab Hydraul & Mt River Engn,Key Lab Bior, Chengdu, Peoples R China

关键词： Epigenome; Pepper (Capsicum spp.); Cis-regulatory element; Promoter; Enhancer; Proteome; Development; Heat stress; Disease; Transcriptional regulation

期刊名称：GENOME BIOLOGY （ 影响因子：9.4； 五年影响因子：16.3 ）

ISSN： 1474-760X

年卷期： 2025 年 26 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundPepper (Capsicum annuum) is one of the earliest and most widely cultivated vegetable crops worldwide. While the large and complex genome of pepper severely hampered the understanding of its functional genome, it also indicates a rich yet unexplored reservoir of regulatory elements (REs). In fact, variations in the REs represent a major driving force in evolution and domestication in both plants and animals. However, identification of the REs remains difficult especially for plants with complex genomes.ResultsHere, we present a comprehensive epigenomic landscape of Capsicum annuum, Zhangshugang (ST-8), including chromatin accessibility, histone modifications, DNA methylation, and transcriptome. We also develop comparative crosslinked immunoprecipitation mass spectrometry to reveal the proteome associated with certain chromatin features. Through integrated analysis of these epigenetic features, we profile promoters and enhancers involved in development, heat stress and cucumber mosaic virus challenges. We generate stress responsive expression networks composed of potential transcription activators and their target genes. Through population genetics analysis, we demonstrate that some regulatory elements show lower nucleotide diversity compare to other genomic regions during evolution.ConclusionsWe demonstrate that variations in the REs may contribute to more diversified and agronomically desired phenotypes. Our study provides a foundation not only for studying gene regulation, but also for targeted genetic and epigenetic manipulation for pepper improvement.