*2.3. Gene Structure and Conserved Motifs of NnDofs*

We investigated the conserved motifs of the genes using MEME to evaluate the diversity and conservation among all 29 *NnDofs* genes. Ten different motifs were predicted and they ranged in size from 16 to 134 amino acids (Figure 3B). The conserved structural domain of Dof consists of Motif 1, and Motif 1 corresponds to the CX2CX21CX2C single zinc finger structure in the Dof structural domain, which is a highly homologous core region of the *Dof* family. NnDofs proteins associated on evolutionary branches of the phylogenetic tree have identical or comparable motif structures. Some motifs, such as Motif 2, Motif 3, Motif 5, and Motif 8, are only found in certain subgroups and may be connected to different functions.

Introns and exons constitute genes, and their numbers and distribution patterns serve as an evolutionary indicator for a gene family. Thus, we completed a comparison of the intron-exon structures of each *NnDofs* (Figure 3C). In general, the number of introns per *NnDof* gene varied very little, ranging from 0 to 1. A total of 11 *NnDof* gene members had no introns (37.9%) and 18 members had only one intron (62.1%). The exon-intron structure pattern of the *NnDofs* gene is similar to that of Arabidopsis, rice, and tomato. Most introns are usually located upstream of the *Dof* structural domain, and only seven genes (*NnDof2*, *NnDof3*, *NnDof8*, *NnDof16*, *NnDof20*, *NnDof26*, and *NnDof28*) have introns located downstream of the *Dof* structural domain. Most of the genes in the same groups showed similar exon and intron patterns. For example, most *Dof* genes in group III do not contain introns. In contrast, groups II, V, VI, and VII almost all contain one intron.

**Figure 1.** Phylogenetic tree of Dof transcription factors in *N. nucifera* and *A. thaliana*. The phylogenetic tree was created using MEGA 6.0, with the neighbor-joining method and bootstrap value set at 1000. Black circles represent the 36 AtDof proteins, and the 29 NnDof proteins are marked with black squares. The resulting phylogenetic tree was clustered into seven main groups, labeled I, II, III, IV, V, VI, and VII.
