Genome-wide identification, characterisation, and expression of C3HC4-type RING finger gene family in Capsicum annuum L

Abstract

ABSTRACT C3HC4-type RING finger gene family is one of the largest, ubiquitous, and diverse proteins, involved in positive regulation of stress response, and enhances drought and salt stress tolerance. The genome-wide characterisation and biological functions of this family protein are well characterised in several plants and animals. However, their characterisation and functions in Capsicum and its related species are unknown. In this study, we identified 16 C3HC4-type RING finger family genes in pepper (Capsicum annuum L). Moreover, chromosome localisation, gene structure, phylogenetic relationships, conserved domain analysis, and cis-element analysis were carried out. In silico expression analysis was carried out to determine the level of expression of these genes in different tissues of pepper. Moreover, RT-qPCR analysis validated that CaRHC1, CaRHC7, and CaRHC13 are upregulated, while CaRHC3, CaRHC4, and CaRHC6 are downregulated in various tissues of pepper. Upregulation and downregulation of few candidate C3HC4-type RING finger genes in the placenta and pericarp of pepper indicates their possible role in capsaicin biosynthesis and pungency, which needs to be investigated further. Thus, the genome-wide analysis provides a comprehensive understanding of C3HC4-type RING finger gene family in Capsicum genome and it shall help to design effective strategies for functional analysis of these genes.