Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)

Xin Hu; Lili Zhu; Yi Zhang; Li Xu; Na Li; Xingguo Zhang; Yu Pan

doi:10.7717/peerj.7929

Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)

PeerJ. 2019 Nov 25:7:e7929. doi: 10.7717/peerj.7929. eCollection 2019.

Authors

Xin Hu^{1

2}, Lili Zhu^{1

2}, Yi Zhang^{1

2}, Li Xu^{1

2}, Na Li^{1

2}, Xingguo Zhang^{1

2}, Yu Pan^{1

2}

Affiliations

¹ Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China.
² Academy of Agricultural Sciences, Southwest University, Chongqing, China.

Abstract

The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon-intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.

Keywords: C2H2 zinc finger proteins; Expression pattern; Heat stress; Phylogenetic analysis; Solanum lycopersicum.

Grants and funding

This work was supported by the National Natural Science Foundation of China (NSFC) (No. 31772320), the Chongqing Natural Science Foundation (No. cstc2018jcyjA0947), the Chongqing Social Enterprise and People’s Livelihood Guarantee Science and Technology Innovation Special Project (cstc2017shms-zdyfx0025), and Fundamental Research Funds for the Central Universities (No. XDJK2019C059 and XDJK2017D088). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.