Annexins (ANNs) are a family of calcium (Ca²⁺)-dependent and phospholipid-binding proteins, which are implicated in the regulation of plant growth and development as well as protection from biotic and abiotic stresses. Corydalis saxicola Bunting, an endangered benzylisoquinoline alkaloid (BIA)-rich herbaceous plant, widely used in traditional Chinese medicine, is endemic to the calciphilic karst region of China. However, whether and how ANNs are involved in the biosynthesis pathway of BIAs and/or help C. saxicola plants cope with abiotic properties, such as calcareous soils, are largely unknown. Here, nine CsANN genes were identified from C. saxicola, and they were divided into three subfamilies, namely subfamilies I, II, and IV, based on the phylogenetic tree. The CsANNs clustered into the same clade, sharing similar gene structures and conserved motifs. The nine CsANN genes were located on five chromosomes, and their expansions were mainly attributed to tandem and whole-genome duplications. The CsANN transcripts displayed organ-specific and Ca²⁺-responsive expression patterns across various tissues. In addition, transient overexpression assays showed that CsANN1 could positively regulate the accumulation of BIA compounds in C. saxicola leaves, probably by directly interacting with key BIA-biosynthetic-pathway enzymes or by interacting with BIA-biosynthetic regulatory factors, such as MYBs. This study sheds light on the profiles and functions of the CsANN gene family and paves the way for unraveling the molecular mechanism of BIA accumulation, which is regulated by Ca²⁺ through CsANNs.

Corydalis ophiocarpa is a medicinally valuable plant, noted for its abundant alkaloid content. Despite its significance, the mitochondrial (mt) genome of this plant has not been characterized, which impedes both the phylogenetic understanding within the Corydalis genus and the comprehension of its full genetic potential. In this research, we successfully assembled the complete mitogenome of C. ophiocarpa by employing a hybrid method that integrates Oxford Nanopore long reads with Illumina short reads. The assembled genome forms a circular structure of 600,064 bp, with a GC content of 46.49%, and includes 63 genes, comprising 40 unique protein-coding genes (PCGs), 20 tRNAs, and three rRNAs. Through assembly and coverage analysis, we identified a 6383 bp forward repeat associated with a contig having approximately double the depth, indicating a repeat-mediated multipartite structure where the main circle may coexist with two smaller subgenomic forms. We discovered 775 C-to-U RNA editing sites across the 40 PCGs, with 95.4% being non-synonymous and favoring hydrophobic amino acid substitutions, particularly in Complex I subunits. Furthermore, we identified sixteen mt plastid DNA fragments constituting 2.43% of the mitogenome, a proportion more than double that found in the closely related C. saxicola. Phylogenetic analysis confirms that C. ophiocarpa is most closely related to C. saxicola, with C. pauciovulata as another close relative. This study presents the first complete mitogenome of C. ophiocarpa, providing a genomic basis for investigating the relationships between mt genome structure, post-transcriptional regulation, and specialized metabolism in the Corydalis genus.

Amomum villosum Lour., a medicinal plant within the Zingiberaceae family, has not yet had its molecular mechanisms governing flowering time investigated. The florigen activation complex (FAC), which include PEBP, FD/bZIP, and GRF proteins, is crucial for controlling flowering time control in model plants. In this study, we identified 13 PEBP, 5 FD, and 19 GRF genes within the A. villosum genome. Our analyses included phylogenetic assessment, conserved motif characterization, gene structure examination, and promoter cis-regulatory element prediction. Protein-protein interactions among these three families were predicted through cross-species analysis and validated using yeast two-hybrid assays. Significantly, an AREB3-like FD protein (AvFD5) and a GRF protein (AvGRF13) were found to directly interact with specific PEBP members, whereas canonical FD-like proteins (AvFD1 and AvFD4) did not exhibit detectable interactions, differing from the classical rice FAC model (Hd3a-14-3-3-OsFD1). This study represents the first systematic characterization of FAC core gene families in A. villosum and, more broadly, within the Zingiberaceae family, thereby laying the groundwork for understanding flowering time regulation in this economically important plant family.

Sophora tonkinensis is a key medicinal plant endemic to the calcium-rich karst regions along the China–Vietnam border. This study investigated how calcium regulates the growth and biosynthesis of bioactive compounds in S. tonkinensis tissue culture seedlings by exposing them to a gradient of calcium concentrations. Our findings demonstrate that a moderate calcium level (T2, 2.99 mmol·L⁻¹) promoted root development, increasing root dry weight, and significantly elevated the content of matrine and oxymatrine. In contrast, a high calcium level (T4, 5.98 mmol·L⁻¹) inhibited root growth, reducing root length, but triggered a distinct metabolic shift, markedly increasing the accumulation of trifolirhizin and maackiain. Integrated transcriptomic, proteomic, and metabolomic analyses revealed that calcium exerts systemic regulation through multiple functional pathways. We identified four key signaling pathways—phytohormone, plant immunity, MAPK, and phospholipid signaling—as central hubs coordinating genetic information processing, vesicular transport, and metabolic reprogramming. These results provide valuable insights into the calcium-mediated regulatory networks and offer valuable targets for optimizing cultivation practices to enhance the yield of bioactive compounds in S. tonkinensis

A detailed understanding of the molecular mechanisms governing the flowering time of Amomum villosum Lour., a medicinal plant within the Zingiberaceae family, is currently lacking. In modern plants, the florigen activation complex (FAC), which includes PEBP, FD/bZIP, and GRF proteins, is known to regulate flowering. In this study, we identified 13 PEBP, 5 FD, and 19 GRF genes within the A. villosum genome and conducted phylogenetic, structural and promoter analysis. Notably, cross-species protein–protein interaction predictions and yeast two-hybrid assays uncovered an unexpected interaction pattern: an AREB3-like FD protein (AvFD5) and a GRF protein (AvGRF13) directly interact with specific PEBP members, whereas canonical FD-like proteins (AvFD1 and AvFD4) did not, which contrasts with the classical rice FAC model (Hd3a-14-3-3-OsFD1). These results imply that FAC assembly in A. villosum may involve alternative components or regulatory mechanisms, potentially indicating lineage-specific divergence within monocots. This research represents the first systematic characterization of FAC core gene families in A. villosum and Zingiberaceae, laying the groundwork for understanding flowering time regulation and facilitating future molecular breeding efforts in this economically significant plant.