Genome wide identification and expression analysis of pepper C2H2 zinc finger transcription factors in response to anthracnose pathogen Colletotrichum truncatum

Richa Sharma; Bijayalaxmi Mahanty; Rukmini Mishra; Raj Kumar Joshi

doi:10.1007/s13205-020-02601-x

Genome wide identification and expression analysis of pepper C₂H₂ zinc finger transcription factors in response to anthracnose pathogen Colletotrichum truncatum

3 Biotech. 2021 Mar;11(3):118. doi: 10.1007/s13205-020-02601-x. Epub 2021 Feb 8.

Authors

Richa Sharma^#¹, Bijayalaxmi Mahanty^#¹, Rukmini Mishra², Raj Kumar Joshi¹

Affiliations

¹ Department of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar, Odisha 751022 India.
² School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha India.

^# Contributed equally.

Abstract

Although, the C₂H₂ zinc finger (ZF) family of plant transcription factors have been implicated in multiple biological processes, they are yet to be characterized in the economically important chilli pepper (Capsicum annuum). In this study, a total of 79 C₂H₂ ZF genes were identified in the pepper genome. Phylogenetic analysis categorized the pepper C₂H₂ ZF (CaZF) members into five subfamilies each with unique conserved domains and functions. Genomic organization revealed that CaZF genes have variable number of introns consistent with the characteristics defined by the evolutionary analysis. Segmental duplication-based purifying selection contributed to the expansion of CaZF genes in pepper. Additionally, 11 CaZF genes were identified as targets for 38 miRNAs indicating their role in post-transcriptional silencing-mediated genetic regulation. Gene expression analysis revealed that 18 CaZF genes were differentially expressed post-infection with the anthrocnose pathogen Colletotrichum truncatum, uncovering their potential function in pepper response to biotic stresses. Moreover, CaZFs were significantly induced post-treatment with methyl jasmonate and ethylene indicating their role in defense signaling. Notably, the MeJA responsive cis-elements were detected in the promoter regions of majority of CaZF genes, suggesting that CaZFs may be implicated in defense-responsive signal cross talking. Additionally, 18 CaZF genes were differentially expressed under drought and heat treatment, indicating their involvement in plant response to abiotic stresses. Overall, a comprehensive analysis of CaZF gene family in pepper provided significant insights into the understanding of C₂H₂ ZF-mediated stress regulation network, which would benefit the genetic improvement of pepper and other allied plants.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-020-02601-x.

Keywords: C2H2 zinc finger proteins; Capsicum annuum; Colletotrichum truncatum; Genome wide analysis; Pepper anthracnose.