**1. Introduction**

Physic nut (*Jatropha curcas* L.) is a perennial small tree in the spurge family, Euphorbiaceae, with a high seed-oil content (40–50%). It can grow easily in barren soil and endure drought and saline environments, thus, having a broad adaptability in various agro-climatic conditions. Given its great potential for biofuel production, nowadays, Physic nut is attracting much attention due to the gradual depletion and a cost increase of fossil energy resources [1,2]. However, there are still a number of challenges in physic nut industries. For example, most physic nut germplasms are monoecious with very low ratios of female to male flowers (approximately female:male = 1:13–29), which considerably reduces the seed yield in physic nut [3,4]. Another serious drawback to the use of physic nut is the presence of toxic components, such as lectin, trypsin inhibitor, and phorbol esters, in all parts of the plant [5]. Therefore, in-depth understanding of the structure and function of key gene families and metabolic pathways of physic nut is essential for improving its crop productivity and commercialization.

Additionally, physic nut is a potential model organism for functional genomic analysis, particularly in Euphorbiaceae. Physic nut is a diploid species (2*n* = 22) [6], with a relatively small genome size (approximately 416Mbp) compared to other members of the Euphorbiaceae [7,8]. According to the most recently updated version, the assembled genome has a total length of 320.5 Mbp consisting of 27,127 putative protein-coding genes, and most of the scaffolds have been anchored on the genetic linkage map [9]. In addition, high-throughput sequencing has mushroomed over the past decade, stimulating the transcriptome profiling analyses. Gene expression profiles of physic nut from different tissues, developmental stages, and biotic/abiotic stresses were constructed [10,11]. Additionally, more than 170 biosamples of physic nut are publicly available from NCBI (National Coalition Building Institute) (as of 5 February 2018). All these genomic and transcriptional data provided a valuable resource for basic and applied studies in physic nut.

Transcription factors (TFs), also known as trans-acting elements, are DNA-binding proteins that specifically bind cis-acting elements in the eukaryotic promoters to activate or inhibit transcriptional regulation [12,13]. As its important roles in the regulation of plant gene expression [14], the structure and function of TFs are now becoming research hotspots in plant molecular biology. The gene expression involves different classes of TFs, which have evolved to regulate a variety of plant-specific genes or signals [15,16]. The *Dof* gene family is a typical example of such TFs. The Dof proteins typically have 200–400 amino acids and contain two main functional domains. One is the Dof domains in the N-terminal domain includes a highly-conserved single zinc-finger structure formed by a CX2CX21CX2C motif, where one Zn2+ can covalently combine with four Cys residues. The other one is a regulatory *C*-terminal domain [17–19]. For instance, the transcription activation domain of the maize *ZmDof1* gene is formed by 44 amino acid residues located at the C-terminal domain [20]. In spite of high level homology in the Dof domain, the rest of the amino acid sequences in the proteins are divergent, coinciding with their expected diverse functions [19].

Previous studies disclosed a variety of roles of Dof proteins in gene expression regulation when associated with plant-specific phenomena, including metabolism, photoperiodic regulation, phytohormone responses, defense responses, and other aspects of plant development [21–23]. Maize *Dof1* (*ZmDof1*) is the first member of the *Dof* gene family identified in plants which may be involved in novel molecular mechanisms underlying tissue-specific and light-regulated gene expression in plants [24]. In addition, recent studies revealed that two closely-related *Arabidopsis thaliana* L. *Dof* genes, *AtDof3.7* (*DAG1*) and *AtDof2.5* (*DAG2*), are maternal genes involved in the control of seed germination, although their actions are opposite [25]. A rice Dof protein, OsDof3, affected the DNA binding of GAMYB to GARE, which is important for combinational regulation of the transcriptional response to Gibberellic acid (GA), and might be a mediator for GA signaling during germination [19,26]. Although none of roles has been confirmed conclusively, Dof proteins apparently participate in the regulation of various processes.

Until now, the *Dof* genes have been identified and characterized in different plant species, such as *A. thaliana*, *Oryza sativa* L. [27], *Glycine max* L. [28], *Triticuma estivum* L. [29], and *Ricinus communis* L. [30]. However, understanding of the *Dof* gene family members and their evolutionary and functional characteristics in physic nut is limited. Based on the genomic and transcriptional data, we focused on the identification, characterization and functional exploration of the *Dof* genes in physic nut. In total, 33 JcDof proteins (encoded by 24 *JcDof* genes) were identified and characterized. These *JcDof* genes were further divided into three major groups by comparison to their orthologs/paralogs in castor bean (*Ricinus communis* L.) and *A. thaliana*. The gene structure, motif, and phylogenetic analysis revealed that genes within each group exhibited similar gene structure and protein motif arrangements. Segmental duplication probably played crucial roles in the expansion of the *JcDof* gene family, and the gene expansion was mainly subjected to positive selection. The expression profile demonstrated the broad involvement of *JcDof* genes in response to various abiotic stresses and hormonal treatments and their possible functional divergence. Taken together, our results provide valuable information for understanding the *JcDof* genes' evolution, and lay a foundation for future functional analysis of the *JcDof* genes.
