Identification, genomic organization, and expression profiles of single C2H2 zinc finger transcription factors in tomato
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PLANT GENETICS • ORIGINAL PAPER
Identification, genomic organization, and expression profiles of single C2H2 zinc finger transcription factors in tomato (Solanum lycopersicum) Xiaoli Liao 1 & Lin Wang 1 & Shunhua Zhu 1 & Fangyan Zheng 1 & Changxian Yang 1,2 Received: 4 March 2020 / Revised: 20 August 2020 / Accepted: 9 September 2020 # Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2020
Abstract C2H2 zinc finger proteins (ZFPs) play essential roles in leaf morphogenesis and floral development, as well as heat stress response and trichome formation, which activate or inhibit gene transcription mainly through interactions with nucleic acids, such as single-strand DNA, RNA binding or RNA/DNA bidirectional binding, and protein interaction. Single C2H2 ZFPs is the subfamily of ZFPs, but little of single C2H2 ZFP family is known in tomato. In this study, we identified 30 single ZFP genes in tomato using bioinformatics-based methods. Gene structures, phylogeny, conserved motifs, cis-element of promoter, chromosomal localization, gene duplication, and expression patterns of these single C2H2 ZFP genes were analyzed. Sequence analysis showed that most single C2H2 ZFP genes possessed only one exon, except for SlC1-liZFP1 and SlC1-liZFP2. These single C2H2 ZFP genes were asymmetrically distributed on 10 chromosomes, excluding 2 and 12 chromosomes. In addition, 24 of these genes were predicated to have experienced segmental duplication. Cis-element prediction indicated that many important elements were located in the putative promoter regions, like light and gibberellic acid (GA)–responsive elements. The expression profiles of these genes in different tissues and various hormones and stress treatment were further analyzed. Many genes were lowly expressed in all tissues, whereas some were specifically expressed in certain tissues, like SlC1-liZFP2 in young leaves, and SlC1-liZFP15 in fruits. Furthermore, these genes could also be induced by several hormones and stresses, including IAA, ETH, GA, cold, and drought. This study sets a good foundation for further characterizing the biological roles of single C2H2 ZFP genes in tomato. Keywords Single C2H2 ZFP genes . Tomato . Expression profiles . Stress . Hormone
Introduction
Xiaoli Liao and Lin Wang contributed equally to this work. Communicated by: Izabela Pawłowicz Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13353-020-00587-z) contains supplementary material, which is available to authorized users. * Changxian Yang [email protected] 1
Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan 430070, China
2
Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
C2H2 type of zinc finger proteins exists extensively in plants, the structures of which were stabilized by a zinc ion surrounded by two cysteine (Cys) and two histidine (His) residues. Zinc finger proteins (ZFPs) were classified into se
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