Genome‐wide identification of HD‐ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum

Abstract Zanthoxylum armatum is an important cash crop for medicinal and food purposes in Asia. However, its stems and leaves are covered with a large number of prickles, which cause many problems in the production process. The homeodomain leucine zipper (HD‐ZIP) gene family is a class of transcription factors unique to plants that play an important role in biological processes such as morphogenesis, signal transduction, and secondary metabolite synthesis. However, little is known about HD‐ZIP gene information that may be involved in prickle development of Z. armatum . Here, we identified 76 ZaHDZ genes from the Z. armatum genome and classified them into four subfamilies (I–IV) based on phylogenetic analysis, a classification further supported by gene structure and conserved motif analysis. Seventy‐six ZaHDZ genes were unevenly distributed on chromosomes. Evolutionary analysis revealed that the expansion of ZaHDZ genes mainly were due to whole‐genome duplication (WGD) or segmental duplication, and they experienced strong purifying selection pressure in the process of evolution. A total of 47 cis ‐elements were identified in the promoter region of ZaHDZ genes. Quantitative real‐time polymerase chain reaction analysis was performed on subfamily IV ZaHDZ gene expression levels in five tissues and under four hormone treatments. Finally, ZaHDZ16 was predicted to be the candidate gene most likely to be involved in prickle development of Z. armatum . These results contribute to a better understanding of the characteristics of HD‐ZIP gene family and lay a foundation for further study on the function of genes related to prickle development of Z. armatum .