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.
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Funding
This work was supported by grants of the Natural Science Foundation of China (31872122), the Fundamental Research Funds for the Central Universities (No. 2662020YLPY009), and the Foundation for the Author of National Excellent Doctoral Dissertation of China (No. 201468).
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CY designed all the experiments and revised the manuscript. XL and LW carried out experiments, analyzed the data, and drafted the manuscript. SZ and FZ designed and performed the hormone experiments, cultured plants, and collected samples for study.
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Communicated by: Izabela Pawłowicz
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Appendix 1
. The nucleotide and amino acid sequences of 30 SlC1-liZFP genes. (DOCX 55 kb)
Table S1
Primers used for RT-qPCR analysis of SlC1-liZFP genes in tomato. (XLSX 11 kb)
Figure S1
Expression profiles of SlC1-liZFP genes in tomato Heinz 1706 and LA1589. The organ-based expression profiles for Heinz 1706 and LA1589 (pimp). Log2-based fold changes were used to create the heat-map. Fully opened flowers (FL), unopened flower buds (B), 1 cm fruits (FR1), 2 cm fruits (FR2), 3 cm fruits (FR3), mature green fruits (MGF), breaker fruits (BR), breaker+10 fruits (B.10F), roots (ROOT), leaves (YL); anthesis flowers (0DPA), 10 days post anthesis fruit (10 DPA1), 10 days post anthesis fruit 2 (10 DPA2), 20 days post anthesis fruit (20DPA), ripening fruit (33DPA), cotyledons (COTYL), hypocotyl (HYPO), vegetative meristems (MERI), mature leaves (ML), whole root (ROOT), young flower buds (YFB), young leaves (YL). (PNG 5853 kb)
Figure S2
Tissue-specific expression profiles of SlC1-liZFP genes. Rt, root; St, stem; YL, young leaf; Fl, flower; Ft, young fruit. Error bars represent standard deviations for three replicates. (PNG 3103 kb)
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Liao, X., Wang, L., Zhu, S. et al. Identification, genomic organization, and expression profiles of single C2H2 zinc finger transcription factors in tomato (Solanum lycopersicum). J Appl Genetics 62, 1–15 (2021). https://doi.org/10.1007/s13353-020-00587-z
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DOI: https://doi.org/10.1007/s13353-020-00587-z