The basic leucine zipper (bZIP) transcription factor family plays crucial roles in plant development and stress responses, yet its evolutionary dynamics and functional diversification across green plants remain poorly understood. Here, we conducted a comprehensive analysis of the bZIP family across 114 green plant taxa, from algae to angiosperms, with emphasis on Rosaceae species and Malus accessions. Phylogenetic analysis showed that most bZIP subfamilies formed stable monophyletic clades across green plants, except for two atypical evolutionary patterns. An intertwined E-M-E-I complex suggested that the core domain of subfamily M originated from the group E lineage, whereas the highly divergent subclades, S1 and I1, highlighted the uneven evolutionary rates within the family. In Rosaceae, lineage-specific whole genome duplication (WGD) events, especially in Malinae subtribe and Potentilla, markedly expanded bZIP repertoires with asymmetric retention among subfamilies. Furthermore, lineage-specific pangenome in Malus identified 1251 core and 18 unique bZIP members across diverse accessions. Pan-transcriptome identified tissue-specific expression and stress-responsive co-expression modules. And functional characterization of MP_bZIP77, a gene derived from wild apple, provides a concrete example of this regulatory mechanism by demonstrating that its overexpression enhances salt tolerance through the activation of antioxidant enzyme activities. This study provides novel insights into the evolutionary origin, expansion pattern, and functional divergence of the bZIP family in green plants and Rosaceae, while laying a theoretical and genetic foundation for future molecular breeding aimed at improving stress resistance in fruit trees.
Xuejing Cao, Cheng Chen, Weifeng Ma et al.· Horticulture Research· 0 citations
The calcium ion-transporting ATPase (Ca2+-ATPase) gene family maintains plant intracellular Ca2+ homeostasis and regulates growth, development and stress immunity; however, its functions remain poorly characterized in Malus domestica. Here, we performed a genome-wide identification of apple Ca2+-ATPase genes and obtained 45 members, which were classified into MdACA (39) and MdECA (6) subfamilies and unevenly distributed on 14 chromosomes. Phylogenetic analysis of Ca2+-ATPase genes from Malus domestica, Arabidopsis thaliana, and Oryza sativa classified these proteins into five subgroups. The ACA and ECA subfamilies were highly conserved across species, whereas Group D was apple-specific. Collinearity and Ka/Ks analyses indicated that segmental duplication and purifying selection dominated the evolution of apple Ca2+-ATPase genes. Promoter cis-element prediction uncovered numerous regulatory elements related to phytohormone signaling, growth, development and stress defense. Codon usage bias analysis indicated that AUG (methionine) was the dominant codon. Tissue expression profiles showed differential expression of apple Ca2+-ATPase genes in various organs. Quantitative real-time PCR (qRT-PCR) assays demonstrated widespread responses of Ca2+-ATPase genes to Alternaria alternata infection, exogenous CaCl2, salicylic acid (SA) and methyl jasmonate (MeJA), among which MdACA39 was strongly induced under all treatments. Subcellular localization verified that MdACA39 resides on the plasma membrane. Moreover, transient overexpression of MdACA39 significantly enhanced apple resistance to A. alternata, likely due to the activation of SA, MeJA and Ca2+ signaling-mediated immune pathways, the induction of disease resistance-related genes, and elevated antioxidant enzyme activity. Collectively, this study systematically characterizes the apple Ca2+-ATPase family and identifies MdACA39 as a key regulator of fungal resistance, providing valuable gene resources for dissecting Ca2+ signaling-mediated disease resistance in apple.
Yingjun Hou, Ming-Zhi Guan, Wenhui Wang et al.· Plants· 0 citations
