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PeerJ. 2019 Aug 8;7:e7499. doi: 10.7717/peerj.7499. eCollection 2019.

Genome-wide identification, characterization and expression analysis of the HD-Zip gene family in the stem development of the woody plant Prunus mume.

Li L#1,2,3,4,5,6, Zheng T#1,2,3,4,5, Zhuo X1,2,3,4,5,6, Li S1,2,3,4,5,6, Qiu L1,2,3,4,5,6, Wang J1,2,3,4,5, Cheng T1,2,3,4,5, Zhang Q1,2,3,4,5,6.

Author information

Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.
National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.
Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.
Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.
Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.
Contributed equally


The homeodomain-leucine zipper (HD-Zip) gene family, a group of plant-specific transcriptional factors (TFs), participates in regulating growth, development, and environmental responses. However, the characteristics and biological functions of HD-Zip genes in Prunus mume, which blooms in late winter or early spring, have not been reported. In this study, 32 HD-Zip genes, named PmHB1-PmHB32 based on their chromosomal positions, were identified in the genome of P. mume. These genes are distributed among seven chromosomes and are phylogenetically clustered into four major groups. Gene structure and motif composition were mostly conserved in each group. The Ka/Ks ratios showed that purifying selection has played a leading role in the long-term evolution of the genes, which maintained the function of this family. MicroRNA target site prediction indicated that the genes of the HD-Zip III subfamily may be regulated by miR165/166. Expression pattern analysis showed that the 32 genes were differentially expressed across five different tissues (leaf, flower bud, stem, fruit, and root) and at different stages of stem and leaf-bud development, suggesting that 10 of the genes may play important roles in stem development. Protein-protein interaction predictions showed that the subfamily III genes may regulate vascular development and shoot apical meristem (SAM) maintenance. Promoter analysis showed that the HD-Zip III genes might be involved in responses to light, hormones, and abiotic stressors and stem development. Taken together, our results provide an overview of the HD-Zip family in P. mume and lay the foundation for the molecular breeding of woody ornamental plants.


Expression pattern; Genetic evolution; HD-Zip TFs; Prunus mume; Stem development

Conflict of interest statement

The authors declare there are no competing interests.

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