Genome-wide identification, evolutionary dynamics, and abiotic stress response networks of the magnesium transporter gene family in foxtail millet (Setaria italica L.)

Genome-Wide Identification of the Ca2+-ATPase Gene Family and Functional Analysis of MdACA39 in Resistance to Alternaria alternata in Malus domestica

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.

Genome-Wide Identification and Salt Stress Response Analysis of the COMT Gene Family in Poncirus trifoliata

Caffeic acid O-methyltransferase (COMT) serves as a crucial rate-limiting enzyme within the melatonin biosynthesis pathway and is involved in various primary and secondary metabolic processes, significantly contributing to plant growth, development, and stress response. Nevertheless, a comprehensive characterization of the COMT gene family in citrus species, particularly with regard to its functional roles under salinity stress, remains unavailable. In the current study, we identified 47 COMT loci from the Poncirus trifoliata genome, and these genes were observed to be non-uniformly scattered across seven chromosomes. The majority of these genes are predicted to localize within the Golgi apparatus and nucleus. Each PtrCOMT gene contains between 2 and 19 exons and 1 and 18 introns, and they are categorized into four groups based on phylogenetic analysis. Collinearity analysis uncovered three intraspecific collinear gene pairs in Poncirus trifoliata. Three orthologous collinear pairs were detected between P. trifoliata and Arabidopsis thaliana, and one pair between P. trifoliata and Oryza sativa. Additionally, the promoter regions of PtrCOMT genes were found to contain 23 distinct cis-acting regulatory elements. Expression analysis indicated tissue-specific expression patterns, with higher expression levels observed in roots. Furthermore, qRT-PCR profiling detected increased expression of multiple candidate PtrCOMT genes upon high-salt treatment, hinting that members of this family may be implicated in plant salt stress regulatory processes. Overall, these findings provide a foundation for further investigation into the functional roles of PtrCOMT genes in response to salt stress.

Genome-wide analysis of the plant-specific PLATZ gene family in Taraxacum kok-saghyz and its roles in response to drought and salt tolerance.

It is demonstrated that heterologous expression of TksPLATZ1, TksPLATZ2 and TksPLATZ7 localize to the cell nucleus and act as transcriptional activators and repressors, respectively, which enhances the tolerance of Arabidopsis to salt and osmotic stress.

Genome‑wide analysis of the maize CK1 family and functional characterization of ZmCK1-8 in modulating root architecture and nitrate‑responsive physiological traits under low‑nitrogen conditions

Nitrogen deficiency is a major constraint of global maize production. Although CK1 family members have diverse regulatory functions in eukaryotes, the CK1 family in maize has not yet been systematically identified, and their roles in maize nitrogen metabolism remain poorly understood. In the current study, we sought to identify the ZmCK1 family members and investigate the physiological and molecular roles of ZmCK1s in maize growth under low-nitrogen conditions. We identified 20 maize ZmCK1 family members and characterized them through phylogenetic analysis, motif and domain prediction, gene structure analysis, promoter cis-element annotation, and nitrate-responsive transcriptome profiling. ZmCK1-8 , a nitrate-responsive gene, was selected for functional analysis. B73 and ZmCK1-8 mutants were hydroponically cultured under low-nitrogen conditions to assess root architecture, glutamine synthetase (GS), glutamate synthase (GOGAT), nitrate reductase (NR), and protein and nitrogen contents. The mutants exhibited enhanced root growth, suggesting that ZmCK1-8 plays a role in regulating root growth under low‑nitrogen condition and is associated with altered nitrogen‑related physiological traits. Transcriptomic analysis identified 256 and 660 genotype‑dependent nitrate‑responsive genes in ck1‑8‑1 and ck1‑8‑2 mutants, respectively, enriched in hormone signaling, stimulus responses, and transmembrane transporter activity. Loss of ZmCK1-8 was associated with upregulation of ZmGS1-5 , and altered nitrogen-related physiological traits. Yeast two-hybrid and BiFC assays confirmed that ZmCK1-8 physically interacts with the chromatin remodeler ZmCHB101. RT-qPCR analysis of ZmCHB101 RNAi line further suggested that ZmCK1-8 and ZmCHB101 share several downstream targets, including ZmGS1–5 , GOGAT , and ZmPTR11 . In contrast, other nitrate-responsive genes, such as ZmPTR12 , ZmNPF25 , and ZmNPF34 , showed distinct expression patterns between the two genetic backgrounds. Genome-wide analysis identified 20 ZmCK1 members, of which ZmCK1-8 was found to be associated with nitrate‑induced root growth. Loss of ZmCK1-8 function is associated with altered nitrogen-related physiological traits in roots, while ZmGS1-5 is identified as a candidate downstream responder. Furthermore, ZmCK1-8 physically interacts with ZmCHB101, though the mechanistic link between this interaction and target-gene regulation remains to be established. These results uncover a novel component of the maize nitrogen-signaling network and provide a candidate gene for further functional studies on low‑nitrogen adaptation in maize.

Genome-Wide Characterization of the Sugarcane PIP Gene Family and Functional Validation of ScPIP2-70 in Low-Potassium Stress Tolerance

This study comprehensively elucidates the evolutionary dynamics and spatiotemporal expression profiles of the sugarcane PIP gene family and uncovers the novel pleiotropic function of ScPIP2-70 in mediating low-K+ stress tolerance, providing critical theoretical support and candidate gene resources for breeding “potassium-efficient” sugarcane cultivars via modern biotechnology.

Genome-wide identi fi cation and expression divergence of the NDPK gene family in Brassica juncea under abiotic stress