Basic leucine zipper (bZIP) transcription factors are widely involved in plant development and stress responses. Cymbidium goeringii (Rchb.f.) Rchb.f. is a globally important ornamental orchid whose growth is frequently constrained by extreme heat, yet genome-wide information on its bZIP genes and their responses to heat treatment remains limited. In this study, 67 CgbZIP genes were identified from the C. goeringii genome; 63 were assigned to 10 subfamilies based on phylogenetic relationships, while four remained unclassified. RT-qPCR analysis showed that selected CgbZIP genes displayed different transcript-level responses under heat treatment. CgbZIP4 showed increased transcript abundance under heat treatment, whereas CgbZIP49, CgbZIP50, CgbZIP53, and CgbZIP2 showed reduced transcript abundance. CgbZIP25 displayed a fluctuating expression pattern during the 24 h treatment. Yeast two-hybrid assays supported a possible physical interaction between CgbZIP4 and CgbZIP25 in yeast. These results provide candidate CgbZIP genes for further functional studies of heat-stress responses in C. goeringii.

Blastus Lour. is a taxonomically complex genus of Sonerileae (Melastomataceae), with unresolved infrageneric relationships and controversial boundaries among several species and varieties. In this study, we integrated morphological evidence with a broadly sampled internal transcribed spacer (ITS) dataset, an expanded nuclear ribosomal DNA (nrDNA) dataset, plastome data, and genomic single-nucleotide polymorphism (SNP) data to evaluate the phylogenetic relationships and classification within Blastus. The broadly sampled ITS and expanded nrDNA analyses supported the monophyly of the sampled Blastus accessions but provided limited resolution of relationships among closely related taxa. The plastome analysis did not recover the sampled Blastus accessions as monophyletic and revealed marked cytonuclear phylogenetic incongruence. The genomic SNP analysis strongly supported the monophyly of the sampled Blastus accessions and recovered the sampled members of the terminal inflorescence group as a monophyletic clade. However, the sampled members of the traditional axillary inflorescence group were not monophyletic because Blastus borneensis was recovered as sister to the terminal inflorescence clade. Within the terminal inflorescence clade, the sampled members of the B. pauciflorus and B. cavaleriei groups formed two strongly supported sister lineages. Morphological comparisons showed that inflorescence position and architecture, the distribution of yellow glands on the abaxial leaf surfaces, and calyx lobe morphology generally corresponded to the principal lineages recovered in the SNP tree, whereas indumentum characters varied considerably among individuals and populations. We therefore recommend retaining the axillary and terminal inflorescence groups as descriptive morphological categories and treating the B. pauciflorus and B. cavaleriei groups as two informal working subdivisions within the terminal inflorescence group. The broad circumscription of B. pauciflorus adopted in the Flora of China requires reassessment, whereas the boundaries of B. longiflorus var. apricus and B. dunnianus require broader population sampling before formal taxonomic changes are proposed.

Salt stress is a major environmental factor limiting plant growth and productivity. Plants have developed diverse physiological and molecular strategies to adapt to saline conditions. Gardenia jasminoides, a dual-purpose plant with significant economic value in medicine and landscaping, exhibits notable salt tolerance, but the underlying molecular mechanisms remain largely unexplored. Our study aims to elucidate the physiological and molecular adaptive strategies of this plant to salt stress by integrating physiological measurements and transcriptomic analysis. RNA-seq profiling of G. jasminoides leaves, which were subjected to four NaCl concentrations (0, 50, 100, and 200 mmol·L⁻¹) for 15 days, identified 3,883 differentially expressed genes (DEGs). These DEGs were mainly associated with calcium signaling, MAPK–WRKY cascades, antioxidant defense, and phytohormone regulation. Physiological analysis revealed that prolonged stress caused structural damage to the photosynthetic apparatus, evidenced by a significant decline in Fv/Fm and an increase in Fo at Day 15. These changes mirrored transcriptional reprogramming: peroxidase (POD) activity and related genes were strongly induced, catalase (CAT) activity was repressed, and malondialdehyde (MDA) levels increased under severe stress. Osmotic adjustment displayed stress-dependent patterns, with proline accumulation peaking under moderate stress and soluble proteins under severe stress. Network analysis highlighted a hierarchical regulatory system, where calcium signaling and MAPK cascades coordinated antioxidant defense and ion homeostasis. Key salt-responsive regulators, including CaM/CML, CDPK, WRKY22/29, and glutathione S-transferase (GST) family members, were proposed as central nodes integrating Ca²⁺ influx, reactive oxygen species (ROS) production, MAPK activation, and abscisic acid (ABA) signaling. Our findings reveal a hierarchical regulatory network that fine-tunes ROS homeostasis, osmotic balance, and stress signaling in G. jasminoides. Salt-responsive regulators such as WRKY transcription factors and GST family members represent promising targets for functional studies and molecular breeding aimed at enhancing salt tolerance in woody plants for ecological restoration and agricultural production.

Phalaenopsis hybrids are the most popular potted flowers in flower markets worldwide because they exhibit various flower colors, including yellow, green, white and red-purple. A thorough assessment of petal color polymorphism in Phalaenopsis enables the promotion of mechanistic studies on floral coloration regulation. In this study, we collected 156 Phalaenopsis germplasms to assess their chromativity value (L*, a* and b*), and then divided them into six groups according to their petal color: white (21), green (11), yellow-orange (37), pink (40), purplish-red (25) and dark red (22). Significant correlations were detected between petal color chromaticity indices and both the total concentration and the compositional ratio of the two primary anthocyanin components: cyanidin 3,5-O-diglucoside (Cy3G5G) and delphinidin 3,5-O-diglucoside (Dp3G5G). The red petal phenotype was largely determined by high accumulations of Cy3G5G and Dp3G5G, as well as a high Cy3G5G/Dp3G5G ratio. By integrating CIELab color parameters with anthocyanin composition and gene expression analyses, a quantitative regulatory model for Phalaenopsis flower color was established. We have revealed that the phenotypic traits of high a* and low L* values are directly associated with the high expression of key structural genes (PhF3 ' H, PhDFR, PhF3 ' 5 ' H). These results provide molecular markers and a screening basis for screening, enabling directional flower color breeding, and significantly enhancing the predictability and accuracy of breeding programs.

Introgressed genes can significantly influence the ecological fate of recipient species exposed to novel environments. Here, we present a protocol for detecting introgressed genes and assessing their functional impact in recipient species by combining fdM statistics with expression profiling under various stress conditions. We describe procedures for identifying introgressed genes, their paralogs, and their alleles. We also detail steps for analyzing and comparing their responses to abiotic stress in orchids.For complete details on the use and execution of this protocol, please refer to Jiao et al.1

Cupressaceae , a gymnosperm family, draws attention due to its controversial phylogenetic position. Here, we present a comprehensive genome analysis of Chinese fir (Cunninghamia lanceolata), a Cupressaceae species, to enhance our understanding of gymnosperm evolution. The 11.24 Gb assembled genome, shaped by inefficient long terminal repeat removal, offers insights into its phylogenetic position. Phylogenetic analysis refines gymnosperm relationships between Cycads-Ginkgo and their relation to Gnetales-Pinaceae. Whole-genome duplication (WGD) analysis reveals no evidence for an ancient polyploidization event in the lineage of C. lanceolata, and confirms a seed-plant-shared WGD event. We also explore genomic evidence to explain the population history and adaptability of C. lanceolata, including potential glacial refugia, dispersal centers, and unique sterility. Furthermore, the refined (A)B(C) model for reproductive organ development in C. lanceolata has broader applications across gymnosperms. This study provides a valuable genome sequence and contributes to the understanding of gymnosperm evolution.

The labellum, a distinctive floral organ unique to orchids, possesses significant ornamental and research value. Here, wild type plants (W1, W2), a lip-like sepal mutant (MS), a lip-like petal mutant (MP), and a peloric flower mutant (ML) of Cymbidium ensifolium were used to elucidate the molecular mechanisms underlying labellum formation. Morphological and cytological analyses revealed that MS sepals and MP petals acquired labellum-like traits (folded structures, conical papillae), whereas ML labella adopted petal-like features (flat epidermal cells). Transcriptome analysis identified seven key B- and E-class MADS-box genes (including DEF -/ AP3- , SEP-, and AGL6- like genes) potentially involved in labellum development. Subsequent qRT-PCR profiling showed that gene expression dynamics closely reflect organ fate. Expression of CeAP3-3 and CeAP3-4 correlated with the establishment of inner perianth identity (petal/labellum), while CeAGL6-2 activation was specifically associated with labellum specification. Notably, CeAGL6-2 was ectopically expressed in lip-like organs of MS and MP, but absent in the petaloid labellum of ML. Conversely, expression patterns of CeAP3-1 and CeAGL6-1 suggested roles in promoting sepal/petal or non-labellum perianth fates. Protein interaction assays (Y2H, BiFC) demonstrated that CeAP3-3 interacted strongly with CeAGL6-2 and CeSEP2, while CeAP3-4 interacted with CeSEP2. Integrating these results, we propose a model in which heteromeric complexes formed by CeAP3-3, CeAGL6-2, and CeSEP2 are central to specifying labellum identity in C. ensifolium . Overall, these findings highlight the cooperative role of B- and E-class transcription factors in labellum specification through dynamic expression shifts and protein interaction networks, thereby enriching our understanding of the molecular mechanisms driving orchid labellum formation.

Plant genomics underpins a foundation for understanding evolution, gene regulation, and fundamental biological processes, subsequently supporting both the conservation and innovative utilization of plant germplasm resources. The Lythraceae family encompasses numerous species of economic and ecological significance, and are valued for their edible, medicinal, and ornamental properties. The family-wide distribution, spanning extreme intertidal zones, semi-deserts and tropical forests, positions Lythraceae as an exemplary model for investigating the genomic mechanisms underlying ecological adaptation. Recent advances in chromosome-level genomes, pan-genomics, genetic mapping, multi-omics integration, and large-scale phenotyping have greatly accelerated research in plant evolution and breeding. Nevertheless, despite the growing genomic and trait-focused studies in Lythraceae, a comprehensive conceptual synthesis linking evolutionary events, structural variation (SV), regulatory networks, and future research directions remain absent. In this review, we present an overview of genomic resources and introduce a unified framework linking whole-genome duplications, lineage-specific SVs, and their functional impacts on species diversification. We also synthesize recent advances in genome evolution, phylogenetic relationships, biotechnology, and molecular mechanisms controlling growth, development, and stress responses. In addition, we address challenges associated with genetic transformation of woody Lythraceae species and discuss strategies to enhance molecular breeding. This review provides a forward-looking perspective on Lythraceae genomics and identifies key scientific questions that will steer future research in evolutionary biology, functional genomics, and crop improvement.

Abstract The genus Zingiber represents an economically important group within Zingiberaceae, distinguished by its aromatic and bioactive rhizomes. Zingiber striolatum Diels is an endemic Chinese medicinal and edible plant highly valued for its flower buds, which are rich in natural red pigments (YRP). Here, we present the first haplotype-resolved, chromosome-scale assembly of ‘Ziyanghe,’ a purplish-red-bud cultivar widely grown in Guizhou Province. The triploid genome was resolved into three haplotypes: subA (2.80 Gb), subB1 (2.66 Gb), and subB2 (2.64 Gb), with the latter two exhibiting strong collinearity. Comparative analysis across five Zingiberaceae genomes revealed a family-specific whole-genome duplication (WGD) approximately 52.5 million years ago (Mya) and lineage-specific bursts of long terminal repeat retrotransposon (LTR-RTs) occurring between 0.5 and 0.66 Mya. These events likely contributed to substantial genome expansion in Z. striolatum. Evolutionary analysis of gene families suggested parallel subgenome adaptation to montane shade environments and rhizome-specific volatile biosynthesis. Metabolomic profiling identified cyanidin-3-O-glucoside, peonidin-3-O-glucoside, delphinidin-3-O-glucoside, and delphinidin-3-O-rutinoside as the major YRP components, with quercetin-3-O-glucoside functioning as a co-pigment. Integrated multi-omics analysis provides a preliminary molecular framework for YRP biosynthesis. This high-quality genomic resource significantly enhances phylogenomic understanding of Zingiberaceae and provides a foundation for the genetic improvement and metabolic engineering of anthocyanin biosynthesis in this species.

Cymbidium ensifolium exhibits highly specialized floral structures with considerable morphological diversity, including multi-tepal varieties that are distinguished by unique floral patterning and are of high ornamental value, making them a key breeding target. However, the molecular mechanisms underlying multi-tepal formation in this species remain poorly characterized. To address this, we employed an integrated approach, combining phenotypic observation, cytological examination, transcriptome sequencing, gene expression profiling, functional validation, yeast one-hybrid (Y1H), and dual-luciferase reporter (DLR) assays. The multi-tepal phenotype was characterized by increased numbers of sepals and petals and the absence of a gynostemium. Transcriptome analysis revealed several key regulatory genes, including CeLFY, CeAP1-1, CeAP1-2, CeAG-1, CeAG-2, and CeAG-3. Expression analysis revealed a marked upregulation of CeLFY and CeAP1s during early bud development in the multi-tepal variety, correlating with enhanced perianth organ formation. In contrast, persistent downregulation of CeAGs across floral stages was associated with gynostemium abortion. Transgenic assays confirmed that perturbation of these genes resulted in aberrant floral organ development, and subcellular localization supported the nuclear presence of their protein products. Y1H and DLR experiments indicated that CeLFY activates the promoters of CeAP1s, promoting sepal and petal proliferation. Furthermore, promoter analysis identified structural variations in the CeAGs promoters that reduced CeLFY binding affinity, thereby repressing CeAGs expression and impairing gynostemium development. These findings provide mechanistic insights into the multi-tepal flower formation in C. ensifolium and contribute to the molecular basis for ornamental trait improvement in orchids.

Abstract RK-type ginsenosides are a subgroup of dehydrated dammarane saponins with valuable bioactivities, but they are not naturally produced in cultivated ginseng. The ginseng relative Oplopanax elatus accumulates dammaradienol, the precursor scaffold of RK-type ginsenosides, but does not produce RK-type ginsenosides. Here, we identify OeOSC14 as a specialized dammaradienol synthase that evolved through duplication and neofunctionalization of an ancestral multifunctional triterpene synthase by combining chromosome-level genome assembly, comparative genomics and biochemical analyses. Consistent with this evolutionary transition, a single N260Y substitution converts OeOSC14 from a dammaradienol-specific enzyme back into a multifunctional triterpene synthase. We further show that loss of functional C12 hydroxylase blocks the downstream oxidative step required for RK-type ginsenoside biosynthesis in O. elatus . Reconstitution of the pathway in Nicotiana benthamiana enables de novo production of ginsenosides Rk1, Rk2, and Rk3, providing evolutionary insight into triterpene diversification and establishing a plant-based route for producing these compounds.

The origin and radiation of plant lineages is one of the central topics in evolutionary biology, and the diversification of Orchidaceae is of more concern and still perplexing. In this study, we selected to resolve the origin and radiation of Orchidaceae by focusing on the Calanthe alliance. Using nrITS, plastome sequences, and single-copy SNP data, we systematically reconstructed its phylogeny and spatiotemporal evolution. The monophyly of the six genera was confirmed; however, conflicts between the plastome and single-copy SNPs were observed at both the species and generic levels. In addition, the Calanthe alliance originated in the late Oligocene, during a period of sharp climate cooling, while its three major clades were established in the warmest phase of the Cenozoic. The ancestral area of Calanthe was located in Southeast Asia, and the uplift of the Himalayas and the Tibetan Plateau in the Late Miocene drove the dispersal of Calanthe from tropics to subtropical and temperate areas. The diversification of the Calanthe alliance followed a two-step pattern: an initial steady increase in lineages with adaptation to broader elevational ranges, and a second phase of relative stasis followed by recent speciation. Thus, we deemed that the montane area, as an essential distribution area of Calanthe, functioned as both "museum" and "cradle" in the diversification history of this genus. This work provides new insight into the classification and historical dynamics of complicated taxa in Orchidaceae.

Dendrobium nobile Lindl. is a multifunctional orchid species whose perianth diversity is particularly valued in horticulture, yet the molecular mechanisms underlying perianth coloration remain elusive. Here, we compared wild-type (WT), natural mutant with lip-like petals and a purplish-red blotch at the petal base (SC), and natural mutant with lip-like lateral sepals displaying a purplish-red blotch at the sepal base and a petal-like dorsal sepal (DB) of D. nobile to investigate perianth coloration patterns via pigment analysis, transcriptomics, and functional assays. Qualitative and quantitative analysis of pigments revealed that during development, perianth pigmentation shifted from chlorophyll to anthocyanin dominance. DnMYB1, DnMYB2, DnAGL6-2 and DnSEP3 promoted anthocyanin synthesis, as validated by heterologous transient overexpression and virus-induced gene silencing (VIGS). Transcriptomics, yeast one-hybrid (Y1H), and yeast two-hybrid (Y2H) assays revealed a multi-layered regulatory mechanism: DnAGL6-2 and DnSEP3 can directly activate the anthocyanin biosynthesis pathway (ABP) genes DnF3H, DnFLS, and DnBZ1; the spatially specific distribution of DnMYB1 and DnMYB2, the synergistic interaction between DnAGL6-2 and DnMYB1, and the antagonistic interaction between DnAGL6-2 and DnSEP3 collectively determine the coloration difference between the blotch and non-blotch regions. Our study uncovers a regulatory network for perianth coloration driven by the synergistic and antagonistic interactions among transcription factors (TFs), providing new gene targets and strategies for orchid color breeding.

The NUCLEAR FACTOR Y (NF-Y) transcription factor family plays a crucial regulatory role in various aspects of plant development, physiological responses, and light signaling pathways. Nevertheless, there are limited reports on the characteristics and functions of NF-Ys in orchids. This study identified the NF-Y gene family in four orchids (Gastrodia elata, Gastrodia menghaiensis, Platanthera guangdongensis, and Platanthera zijinensis) and analyzed their structural domains, physicochemical properties, phylogenetic relationships, gene collinearity, and the cis-elements in their promoter region. A total of 91 NF-Ys were identified from four orchids, among which NF-Y gene numbers varied among orchid species, with relatively fewer NF-Y genes identified in fully mycoheterotrophic orchids compared with partially mycoheterotrophic taxa. Phylogenetic analysis classified these genes into three subfamilies, and the protein domains and gene structures of the same branch exhibited high similarity. The promoters of these NF-Ys are enriched with photoresponsive cis-elements. During floral organ development in G. elata, GelNFY2, GelNFY6, and GelNFY14 were significantly downregulated at the large bud stage (S2) but significantly upregulated in the lip of flowering stage (S4), suggesting their potential involvement in lip development. In conclusion, this study provides a valuable resource for further investigation into the regulatory functions of the NF-Y gene family in orchids.

Background Anthocyanins are major secondary metabolites that determine tea quality and contribute to plant stress adaptation. However, the transcriptional mechanisms coordinating their biosynthesis in response to environmental cues remain largely unclear. Result In this study, we characterized the R2R3-MYB transcription factor CsMYB5 from tea plant ( Camellia sinensis ) and investigated its role in hormone-responsive secondary metabolism regulation. Expression analyses revealed that CsMYB5 is preferentially expressed in anthocyanin-rich tea cultivars and leaf tissues and is strongly induced by SA, MeJA and multiple abiotic stresses. Genome-wide DNA affinity purification sequencing revealed that CsMYB5 binding sites are enriched in promoter regions of genes associated with transcriptional regulation and secondary metabolism, including flavonoid and caffeine biosynthetic pathways. Notably, CsMYB5 directly targets CsTCP15 , a TCP transcription factor potential regulation of anthocyanin synthesis and accumulation, suggesting the existence of a CsMYB5–CsTCP15 regulatory module.Heterologous overexpression of CsMYB5 in Arabidopsis thaliana resulted in enhanced vegetative growth and pronounced anthocyanin accumulation. Conclusions Based on these findings, we propose that CsMYB5 acts as a central transcriptional hub linking hormone signaling with coordinated regulation of anthocyanin accumulation biosynthesis. This study provides new insights into the transcriptional integration of flavonoid metabolism and offers potential targets and research direction for improving tea quality and stress resilience through molecular breeding.

Orchidaceae, one of the largest and most morphologically diverse angiosperm families, showcases unique evolutionary adaptations in morphology, ecology, and function. Recent advances in molecular and genomic research have greatly reshaped our understanding of orchid evolution, revealing how genome dynamics, ecological interactions, and developmental plasticity jointly shaped their exceptional diversification. Phylogenomic frameworks derived from various genomic datasets have reconstructed the evolutionary history, revealing the influence of geological, climatic, and biotic factors on ancient divergences and global distributions. Comprehensive genomic studies have uncovered substantial variation in genome size, structure, and composition, largely driven by repetitive elements and whole-genome duplication events that facilitated adaptive radiations. Key innovations, including epiphytism, mycoheterotrophy, and deceptive pollination, are linked to gene family evolution and modifications in pathways related to CAM photosynthesis, mycorrhizal symbiosis, and floral morphogenesis. Integrative multi-omics approaches further illuminate mechanisms underlying speciation hotspots, coevolution with pollinators and fungi, and the molecular basis of developmental diversity. Overall, this review synthesizes current genomic, phylogenetic, and functional insights into orchid evolution, providing a theoretical foundation and future research framework for understanding their molecular diversification.

The Fagaceae family, comprising over 900 species, is an essential component of Northern Hemisphere forest ecosystems. However, genomic data for tropical and subtropical genera Castanopsis and Castanea remain limited compared to the well-studied oak. Here, we present chromosome-level genome assemblies of Castanopsis carlesii and Castanea henryi, with assembled genome sizes of 927.24 Mb (N50 = 1.57 Mb) and 780.10 Mb (N50 = 1.07 Mb), respectively, and repetitive sequence contents of 45.79% and 44.88%. Comparative genomic analysis revealed that the estimated divergence time between Castanopsis and Castanea was determined to be 48.3 Mya and provided evidence that both genera experienced only one of the ancient whole genome triplication event (γ event) shared with most eudicots. The development of C. carlesii flower bracts and cupules was controlled by A- and E-class genes, suggesting that the cupules may originate from the bracts. Additionally, genes involved in sucrose and starch metabolism genes played distinct roles during C. carlesii fruit development. The amplification of the nucleotide-binding leucine-rich repeat (NLR) gene family in Fagaceae exhibited similarities, indicating that this expansion may be an adaptation to similar environmental pressures. This study provides valuable genomic resources for Asian Fagaceae and enhances our understanding of Fagaceae evolution.

Danxiaorchis yangii is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus Danxiaorchis in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding genes (PCGs), 16 tRNAs, and 2 rRNAs, and conducted analyses of relative synonymous codon usage (RSCU), repeat sequences, horizontal gene transfers (HGTs), and gene selective pressure (dN/dS). Additionally, we sequenced and assembled its plastome, which has a reduced size of 110,364 bp (GC content: 36.60%), comprising 48 PCGs, 26 tRNAs, and 4 rRNAs. We identified 64 potential chloroplast DNA fragments transferred to the mitogenome. Phylogenomic analysis focusing on 33 mitogenomes, with Vitis vinifera as the outgroup, indicated that D. yangii is grouped as follows: D. yangii + ((Dendrobium wilsonii + Dendrobium wilsonii henanense) + Phalaenopsis aphrodite). Phylogenetic analysis based on 83 plastid PCGs from these species showed that D. yangii is grouped as follows: (D. yangii + Pha. aphrodite) + (Den. wilsonii + Den. henanense). Gene selective pressure analysis revealed that most mitochondrial and plastid genes in D. yangii are under purifying selection, ensuring functional stability, and certain genes may have undergone positive selection or adaptive evolution, reflecting the species’ adaptation to specific ecological environments. Our study provides valuable data on the plastomes and mitogenomes of D. yangii and lays the groundwork for future research on genetic variation, evolutionary relationships, and the breeding of orchids.

Ornamental plants can generate higher economic value per unit area compared with traditional crops. Enhancing market share in the flower industry relies on cultivating varieties with exceptional ornamental traits. Petal size, a critical factor influencing flower shape and ornamental appeal, is a primary focus for horticultural breeding selection. In this article, we review recent advances in understanding the regulation of petal size in ornamental plants through analyzing various patterns of cell division and expansion underlying petal growth and the genes involved in the related regulatory paradigms. We further highlight the intricate network of petal size control affected by multiple phytohormones and discuss several open questions and strategies for breeding ornamental plants with desired petal size traits based on current findings.

Calmodulin (CAMs) and calmodulin-like proteins (CMLs) play pivotal roles in sensing and decoding Ca2+ signals, thereby regulating of various physiological processes. Although CAM/CML genes in numerous plants have been extensively studied, their specific functions and mechanisms in orchids remain unexplored. In order to reveal the characteristics of the CAM/CML family in Cremastra appendiculata, a comprehensive analysis was performed at the genome-wide level, focusing on its physicochemical attributes, phylogenetic associations, gene structure, Cis-acting elements, and qRT-PCR. A total of 78 CAM/CML genes were identified in C. appendiculata, including five CAPPCAM and 73 CAPPCML, divided into ten subgroups (Subgroup I-X). Subgroups I and II contain one to four coding DNA sequences (CDS), while subgroup IX includes 9 genes with only one CDS and the remaining genes possess 4–12 CDS. The collinearity analysis revealed seven collinear CAM/CML gene pairs between C. appendiculata and Arabidopsis thaliana, indicating the homology of CAM/CML genes between these two species. The cis-elements in the CAPPCAMs/CMLs promoter mainly enrich methyl jasmonate (MeJA) elements (202/1120, 18