Genome-wide identification, characterization and expression analysis of the HD-Zip gene family in the stem development of the woody plant Prunus mume
Genome-wide identification, characterization and expression analysis of the HD-Zip gene family in the stem development of the woody plant Prunus mume
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HD-Zip基因家族在木本植物梅茎发育中的全基因组鉴定、表征和表达分析
DOI：
10.7717/peerj.7499
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发表时间：
2019-08-08
期刊：
影响因子：
2.7
通讯作者：
Zhang, Qixiang
中科院分区：
文献类型：
--
作者：
Li, Lulu;Zheng, Tangchun;Zhang, Qixiang
同源域亮氨酸拉链（HD-Zip）基因家族是一组植物特异性转录因子（TFs），参与调节植物的生长、发育和环境反应。然而，在冬末春初开花的梅李中HD-Zip基因的特性和生物学功能尚未见报道。本研究鉴定了32个HD-Zip基因，根据其染色体位置命名为PmHB1-PmHB32。这些基因分布在7条染色体中，并在系统发育上聚集成4个主要群体。各组基因结构和基序组成基本保守。Ka/Ks比值表明，净化选择在基因的长期进化中起主导作用，维持了该家族的功能。MicroRNA靶位预测提示HD-Zip III亚家族基因可能受miR165/166调控。表达谱分析表明，32个基因在叶片、花芽、茎、果实和根5个不同组织以及茎和叶芽发育的不同阶段均存在差异表达，表明其中10个基因可能在茎发育中起重要作用。蛋白-蛋白互作预测表明，III亚家族基因可能调控维管发育和茎尖分生组织（SAM）的维持。启动子分析表明，HD-Zip III基因可能参与对光、激素和非生物应激源的反应和茎的发育。综上所述，本研究为木本观赏植物HD-Zip家族的研究提供了综述，并为木本观赏植物的分子育种奠定了基础。
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.