**5. Conclusions**

It is essential to systematically analyze the function of transcription factors (TFs), since these genes can regulate the expression of many others, resulting in deep physiological modifications. Although *WRKY* genes have been identified in many other species, the information of longan *WRKY* is still unknown. In the present study, we conducted a genome-wide identification and analysis of the *WRKY* genes in longan. A total of 55 *DlWRKY* genes were identified in the longan genome. Phylogenetic analysis indicated that these 55 *DlWRKYs* could be divided into seven groups. An RNA-seq-based analysis showed that several of the identified *WRKY* genes may play various roles in the development of longan tissues. In addition, comparative expression analysis revealed that 18 *DlWRKY* genes might have participated in the regulation of longan flowering. Our RNA-seq, qRT-PCR, and promoter analyses revealed the gene expression profiles and implied that the response to different stress or hormonal signaling of some *DlWRKY* may be due to the cis-elements in their promoters. In summary, our results will facilitate further studies into the role of *DlWRKY* genes in response to abiotic stresses and the development of molecular breeding programs to enhance abiotic stress tolerance and increase yield in longans.

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/19/8/ 2169/s1. The following are available online. Table S1. The candidate *WRKY* genes and their protein structure found in the longan genome. Table S2. The information for each motif of DlWRKYs. Table S3. FPKM values of *DlWRKY* genes in nine tissues of longan. Table S4. FPKM values of *DlWRKY* genes in the three flower induction stages of "SJ" and "SX" longan species. The red color indicates the genes which showed down-regulated expression; the blue color indicates the genes which showed up-regulated expression; and the green color indicates the genes that showed an up-regulated expression in the first two stages and a down-regulated expression in the third stage. Table S5. Details of the *cis*-elements identified in this study. Table S6. Predicted *cis*-elements in the promoter of the *DlWRKY* genes. Table S7. The WRKY gene number and genome size of different species. Table S8. Primers used in quantitative RT-PCR of *DlWRKY* genes. Figure S1. Expression patterns of selected *DlWRKY* genes which have no significant difference under various hormonal and abiotic stresses. The x-axis indicates various treatments, and the y-axis indicates the relative expression level. Error bars were obtained from three independent biological replicates.

**Author Contributions:** D.J., X.S., and S.S. conceived the experiments and D.J. performed the experiments. J.X. Additionally, C.L. analyzed the data, D.J. Additionally, S.S. contributed to the writing of the manuscript, L.L. provided the value comments and revised the grammar of the manuscript. B.S. provided help in the analysis of qRT-PCR. Y.W. prepared samples for RNA sequencing.

**Funding:** This work was supported by the Natural Science Foundation of China (31572087), the China Litchi and Longan Industry Technology Research System (CARS-32-02), the Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences (No. 1630062018011) and the Natural Science Foundation of Hainan Province (20163111 and 317243).

**Conflicts of Interest:** The authors declare no conflict of interest.
