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

Abstract

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.

Identification and analysis of Chrysanthemum nankingense NAC transcription factors and an expression analysis of OsNAC7 subfamily members

“…The CnNAC protein sequences were identified and screened using the SMART tool ( ) and Pfam ( ), and the predicted CnNAC TF members were obtained. The CnNAC TFs were used for subsequent analyses based on this comprehensive screening ( Li et al, 2019 ).…”

Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

“…For example, PLINC is distinguished from other zinc finger classes by the substitution of the usually conserved homeodomain residue F49, with a methionine residue and the insertion of one amino acid between helix 1 and helix 2 [9]. The members of HD-ZIP classes have been shown to play important roles in regulating plant growth, development, and environmental responses [10][11][12][13][14][15][16][17][18]. The members of the WOX class have a derived function of stem cell control besides embryonic patterning, stem cell maintenance, and organ formation, indicating that gene amplification followed by functional diversification is a major force in their evolution [19,20].…”

Wood development regulators involved in apical growth in Pinus canariensis

“…A close homologue of ATHB14 in Populus trichocarpa x P. deltoides is mainly expressed in the apical shoot (Côté et al 2010), while PmHB11, homologue of ATHB14 in Prunus mume , is expressed preferentially in xylem and cambium (Li et al. 2019). We also found a putative KAN2 coding transcript (Contig22823) in Cluster D, overexpressed at stage I.…”