Genome-wide analysis and identification of stress-responsive genes of the CCCH zinc finger family in Capsicum annuum L

Wenchen Tang; Yupeng Hao; Xinyu Ma; Yiqi Shi; Yongmeng Dang; Zeyu Dong; Yongyan Zhao; Tianlun Zhao; Shuijin Zhu; Zhiyuan Zhang; Fenglin Gu; Ziji Liu; Jinhong Chen

doi:10.3389/fpls.2023.1189038

Genome-wide analysis and identification of stress-responsive genes of the CCCH zinc finger family in Capsicum annuum L

Front Plant Sci. 2023 May 30:14:1189038. doi: 10.3389/fpls.2023.1189038. eCollection 2023.

Authors

Wenchen Tang^{1

2}, Yupeng Hao^{1

2}, Xinyu Ma^{1

2}, Yiqi Shi^{1

2}, Yongmeng Dang^{1

2}, Zeyu Dong^{1

2}, Yongyan Zhao^{1

2}, Tianlun Zhao^{1

2}, Shuijin Zhu^{1

2}, Zhiyuan Zhang^{1

2}, Fenglin Gu³, Ziji Liu⁴, Jinhong Chen^{1

2}

Affiliations

¹ Hainan Institute, Zhejiang University, Sanya, China.
² College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
³ Spice and Beverage Research Institute, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, China.
⁴ Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Haikou, China.

Abstract

The CCCH zinc finger gene family encodes a class of proteins that can bind to both DNA and RNA, and an increasing number of studies have demonstrated that the CCCH gene family plays a key role in growth and development and responses to environmental stress. Here, we identified 57 CCCH genes in the pepper (Capsicum annuum L.) genome and explored the evolution and function of the CCCH gene family in C. annuum. Substantial variation was observed in the structure of these CCCH genes, and the number of exons ranged from one to fourteen. Analysis of gene duplication events revealed that segmental duplication was the main driver of gene expansion in the CCCH gene family in pepper. We found that the expression of CCCH genes was significantly up-regulated during the response to biotic and abiotic stress, especially cold and heat stress, indicating that CCCH genes play key roles in stress responses. Our results provide new information on CCCH genes in pepper and will aid future studies of the evolution, inheritance, and function of CCCH zinc finger genes in pepper.

Keywords: CCCH; Capsicum annuum; gene family; phylogenetic analysis; stress.

Grants and funding

The research was supported by the Project of Central Public-interest Scientific Institution Basal Research Fund, Grant No: 1630032022009, Project of Sanya Yazhou Bay Science and Technology City, Grant No: SCKJ-JYRC-2022-05 and SCKJ-JYRC-2022-25, and Hainan Provincial Natural Science Foundation of China (No. 322MS132).