Abstract
Dof (DNA-binding One Zinc Finger) transcription factor family is unique to plants and has diverse roles associated with plant-specific phenomena, such as light, phytohormone and defense responses as well as seed development and germination. Although, genome-wide analysis of this family has been performed in many species, information regarding Dof genes in the pepper, Capsicum annuum L., is extremely limited. In this study, exhaustive searches of pepper genome revealed 33 potential CaDofs that were phylogenetically clustered into four subgroups. Twenty-nine of the 33 Dof genes could be mapped on 11 chromosomes, except for chromosome 7. The intron/exon organizations and conserved motif compositions of these genes were also analyzed. Additionally, phylogenetic analysis and classification of the Dof transcription factor family in eight plant species revealed that S. lycopersicum and C. annuum as well as O. sativa and S. bicolor Dof proteins may have evolved conservatively. Moreover, comprehensive expression analysis of CaDofs using a RNA-seq atlas and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that these genes exhibit a variety of expression patterns. Most of the CaDofs were expressed in at least one of the tissues tested, whereas several genes were identified as being highly responsive to heat and salt stresses. Overall, this study describes the first genome-wide analysis of the pepper Dof family, whose genes exhibited different expression patterns in all primary fruit developmental stages and tissue types, as in response to abiotic stress. In particular, some Dof genes might be used as biomarkers for heat and salt stress. The results could expand our understanding of the roles of Dof genes in pepper.
Highlights
The DNA-binding one zinc finger (Dof) protein is a representative of the plant-specific members of transcription factors (TFs)
Pepper Dof genes were designated as CaDof1-CaDof33 based on the positions of their corresponding genes on chromosomes 1–12 from top to bottom
Most of the research on the functions of the Dof genes has been focused in Arabidopsis (Yanagisawa, 2002; Lijavetzky et al, 2003), while it has been extremely limited in other non-model plants like pepper
Summary
The DNA-binding one zinc finger (Dof) protein is a representative of the plant-specific members of transcription factors (TFs). The C-terminal region of Dof proteins is highly variable This unstable C-terminal domain could act as either a transcriptional activator or repressor in the control of the expression of many structural genes, and execute different regulatory functions (Guo et al, 2009; Cominelli et al, 2011; Corrales et al, 2014). In Arabidopsis, more than 10 Dof proteins, including the OBF BINDING PROTEIN (OBP1, OBP2, and OBP3), Dof Affecting Germination (DAG1 and DAG2), and Cycling Dof Factors (CDF1-5) (Imaizumi et al, 2005; Skirycz et al, 2008; Fornara et al, 2009) have been functionally characterized. Combining loss-of-function mutations in four of these genes (CDF1, 2, 3, and 5) causes photoperiod-insensitive early flowering by increasing the CO mRNA level (Fornara et al, 2009; Corrales et al, 2014)
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