Papaya (Carica papaya L.) is a nutritionally and medicinally important tropical fruit crop, yet its genetic improvement has been limited by insufficient genomic resources. In this study, we constructed chromosome-level genomes for three key varieties (Zhufeng, T3, and T5) and integrated them with three existing assemblies to build a comprehensive pangenome, including graph-based, linear, and syntelog-based representations. The syntelog-based pangenome revealed 24 453 syntelog groups (SGs). Leveraging resequencing data from 222 accessions aligned to the graph-based pangenome, we identified 26 173 structural variations (SVs), including a functionally relevant 94-bp deletion in the RETARDED ROOT GROWTH (RRG) gene in the T3 genome. This deletion affects the expression of the RRG, resulting in a reduction in its expression level in T3. Further phenotypic analysis showed that RRG can influence papaya root length by promoting the proliferation of root meristem cells and inhibiting cell elongation. Additionally, the linear pangenome uncovered 5273 translocations and 1440 inversions, significantly expanding the known SV repertoire in papaya. This study provides a critical genomic resource for deciphering domestication-related traits and accelerating marker-assisted breeding, ultimately advancing the genetic improvement of papaya.

Plant benzylisoquinoline alkaloids (BIAs) are a group of plant-specialized metabolites with significant pharmacological properties. In lotus (Nelumbo nucifera), BIAs accumulate primarily in the leaf blade and plumule organs. The two organs, however, accumulate quite different types of BIAs, within the former primarily aporphine-type BIAs, while the latter predominantly bis-BIAs. Herein, we demonstrate that the spatial regulation of BIA biosynthesis in lotus is coordinately controlled through the NnMYC2-NnMYB14-NnCYP80 modules. Genome-wide screening of lotus CYP80 genes discovered two tandemly arrayed yet tissue-specific NnCYP80s that are identical to the previously reported NnCYP80G and NnCYP80A, respectively. NnCYP80G is expressed primarily in the lotus laminae, while NnCYP80A is expressed particularly in the plumules. Our enzyme assays confirmed the proaporphine synthase activity of NnCYP80G and the bis-BIA synthase activity of NnCYP80A, and revealed the aporphine synthase activity of NnCYP80G by efficiently converting the (R)-reticuline substrate into corytuberine. In addition, we characterized an R2R3 MYB transcription factor (TF) NnMYB14, which binds directly to the NnCYP80G and NnCYP80A promoters and positively regulates their expression. NnMYC2, the core regulator in the JA signaling pathway, acts very upstream of NnMYB14, by binding directly to the NnMYB14 promoter and inducing its expression. Our results resolved that the organ-specific accumulation of BIAs in lotus is attributed to the tissue-specially expressed NnCYP80G and NnCYP80A genes, and the NnMYC2-NnMYB14 TF module could positively regulate the NnCYP80G and NnCYP80A expression and the lotus BIA biosynthesis.

Cucumis sativus L., commonly known as cucumber, is an important vegetable crop worldwide, with China as the largest producer, particularly of the North and South China types. While extensive genomic research has focused on the North China type, especially the Chinese Long 9930, studies on the South China type remain limited. In this study, we assembled high-quality genomes of two widely cultivated and representative parent varieties: S36 (North China type) and H19 (South China type), and conducted mutagenesis analyses. Comparative genome analysis revealed a large number of structural variants between two North China types and two South China types, with many of the affected genes showing strong homology to known functional loci, potentially contributing to phenotypic divergence. We also constructed an EMS mutant library through the mutagenesis of S36 and identified a gene that encodes chlorophyll oxidase, demonstrating the method’s effectiveness for rapid gene discovery. In conclusion, this study provides valuable insights into the classification and evolution of cucumber, highlighting the promising potential of forward genetic approaches in cucumber breeding.

Biological control leveraging endophytic microbes represents a promising eco-friendly strategy to mitigate soil-borne diseases, yet the efficacy and mechanistic underpinnings of synthetic microbial communities (SynComs) derived from plant endophytes remain poorly understood. This study employed a holistic approach—integrating field sampling, microbial profiling, and functional validation—to investigate the dynamics of edible lily (Lilium) microbiomes under continuous cropping and develop targeted SynComs against Fusarium oxysporum. Metacommunity analysis revealed that prolonged monoculture co-enriched both potentially beneficial taxa (e.g. Pseudomonas, Bacillus) and pathogenic Fusarium, reflecting a dynamic equilibrium where naturally recruited antagonists were insufficient to prevent pathogen dominance, while increasing the complexity of endophytic co-occurrence networks. Keystone bacterial lineages, including Burkholderiaceae and Pseudomonas, emerged as critical stabilizers of the endosphere microbiome. Notably, 50% of endogenous bacterial taxa exhibited rhizospheric origins, contrasting with fungal communities where <10% derived from soil—a finding underscoring host-specific filtering mechanisms. Through systematic isolation and combinatorial testing, we engineered SynComs combining core antagonistic strains (Rhizobium, Methylobacterium, Talaromyces) with auxiliary microbes. Fungal-integrated SynComs outperformed bacteria-only consortia in plant growth promotion and pathogen suppression. By bridging fundamental microbial ecology with translational agriculture, our findings establish SynComs as scalable tools for sustainable soil health management, reducing reliance on synthetic fungicides while addressing the yield-limiting challenges in continuous cropping systems.

Flower color is an essential biological and ornamental trait in plants. Paeonia rockii (flare tree peony, FTP) exhibits diverse flower colors, characterized by a distinctive basal flare in petals, which enhances its ornamental and ecological value. However, while previous research has mainly focused on flare formation, the regulatory mechanisms controlling the background color of petals remain unclear. This study identifies a novel regulatory module governing petal background coloration in FTP. Within this module, PrMYB75a acts as the central regulator to promote anthocyanin accumulation, as evidenced by stable transformation in Arabidopsis thaliana and tobacco (Nicotiana tabacum), as well as virus-induced gene silencing in FTP. Furthermore, yeast one-hybrid, dual-luciferase reporter, and electrophoretic mobility shift assays collectively demonstrated that PrMYB75a directly activates two key anthocyanin structural genes, PrCHS1 and PrANS, by interacting with MYB-binding sites nearest to the ATG start codon in their promoters. Additionally, we identified an upstream regulator, PrFRS2, which activates both PrMYB75a and PrANS by binding to the FAR1/FHY3-binding sites in their promoters. Modulation of PrFRS2 expression levels through gene silencing and overexpression resulted in alterations in flower pigmentation in both FTP and tobacco. In summary, within the PrFRS2-PrMYB75a module, PrFRS2 indirectly activates PrCHS1 and PrANS by regulating PrMYB75a, or directly activates PrANS, leading to anthocyanin accumulation in FTP purple petals. This module represents a novel regulatory mechanism of petal background coloration in FTP, providing new perspectives on color variation in flowering plants and offering genetic resources for the improvement of the flower color trait in tree peonies.

Chrysanthemum, a globally renowned economic crop, primarily relies on vegetative propagation methods such as cutting for commercial cultivation. However, certain varieties with exceptional ornamental qualities often encounter difficulties in widespread adoption due to poor rooting ability and suboptimal root quality. The genetic underpinnings of rooting ability in chrysanthemum cuttings have remained largely unexplored. This study marks a significant advancement in this field. By evaluating 11 rooting traits across a diverse panel of 188 chrysanthemum genotypes, we found that spray cut chrysanthemums exhibit superior rooting ability compared to other cultivated types and wild species. Selective sweep analysis identified 534 selected genomic regions potentially linked to rooting traits during the domestication and improvement of chrysanthemums. Genome-wide association studies (GWAS) conducted on four key rooting traits - total root length, root surface area, average root diameter, and number of roots, using multiple models discovered 71 significant SNPs and 98 candidate genes, including 21 differentially expressed genes identified via transcriptomic sequencing. A weighted gene co-expression network analysis further revealed two key modules (yellow and lightyellow) related to rooting traits. By integrating GWAS, transcriptomic data, and functional verification, we pinpointed the candidate gene CmNRAMP3 as a negative regulator of rooting ability. These findings substantially enrich our understanding of the genetic mechanisms underlying rooting ability in chrysanthemum cuttings and provide a promising gene pool for improving rooting traits in future breeding programs.

The apple anthocyanin content is an important trait in apple breeding. Auxin, as an important plant hormone, plays significant roles in regulating the biosynthesis of anthocyanins. However, the molecular mechanism of how plants regulate auxin content and activity to affect anthocyanin accumulation remains unclear. In this study, through fruit anthocyanin content analysis and transcriptome sequencing of the hybrids derived from ‘Golden Delicious’ and ‘Fuji Nagafu No. 2’ crosses, a key gene for regulating apple anthocyanin accumulation, indole-3-acetic acid (IAA) methyltransferase (MdIAMT), was identified. Functional analyses showed that the apple calli and peel overexpressing MdIAMT accumulated more anthocyanin than that in Vec by regulating IAA homeostasis. Yeast two-hybrid assays, luciferase complementation imaging assays and co-immunoprecipitation assays revealed that MdCSN5, an important protein in light signal transduction, interacts with MdIAMT. More importantly, further research showed that the MdCSN5-MdIAMT module affected auxin signal transduction pathway by regulating IAA homeostasis, thus promoting anthocyanin accumulation. In summary, our findings elucidate a novel mechanism by which auxin-regulated anthocyanin accumulation via MdCSN5-MdIAMT module, deepening our knowledge of plant hormone signaling in anthocyanin biosynthesis.

Dendrobium officinale, a valuable medicinal plant, contains bioactive mannan polysaccharides that exert significant health-promoting effects in humans and serve as key quality markers for D. officinale products. However, the regulatory mechanisms underlying bioactive polysaccharide biosynthesis in plants remain poorly understood. In this study, we identified an anthocyanin-specific regulator, DoMYB75, as a key transcriptional activator of mannan polysaccharide biosynthesis in D. officinale. We demonstrated that DoMYB75 directly binds to the promoters of CELLULOSE SYNTHASE-LIKE A genes (DoCSLAs) and activate their expression. Genetic evidence showed that DoMYB75 silencing reduced mannose and glucose content of water-soluble polysaccharides (WSPs) and downregulated DoCSLAs expression, whereas DoMYB75 overexpression significantly increased these monosaccharide levels and upregulated DoCSLAs expression. Interestingly, Ubi:DoMYB75 transgenic transformants exhibited enhanced anthocyanin accumulation. Further investigation revealed that DoMYB75 promotes anthocyanin biosynthesis by directly binding to and activating the DoANS promoter. Additionally, DoMYB75 overexpression markedly improved total antioxidant capacity and drought tolerance. Our findings provide novel insights into the dual regulatory role of MYB transcription factors in coordinating polysaccharide and anthocyanin biosynthesis, as well as the adaptive mechanisms of Dendrobium orchids under drought stress.

In most fleshy fruit, malate and citrate represent the predominant organic acids, serving as key determinants of flavor and nutritional quality. Their concentrations undergo dynamic changes driven by complex biosynthetic pathways and multilayered genetic regulation. Beyond their impact on taste, these organic acids have pleiotropic effects, influencing secondary metabolism and postharvest performance. This review synthesizes current knowledge on the molecular mechanism governing malate and citrate metabolism, including genes responsible for biosynthesis, catabolism, and transport, as well as regulatory networks orchestrated by transcription factors, environmental factors, and phytohormones such as ethylene, abscisic acid (ABA), auxin, gibberellin (GA), and salicylic acid (SA) during fruit development and ripening. We also explored how the dynamics of citrate and malate interact with critical quality attributes, including starch metabolism, textural properties, and postharvest performance, while highlighting domestication-selected genes that influence acidity. Finally, we propose an integrative model delineates the multifactorial regulation of organic acid metabolism in fleshy fruits.

Grafting in watermelon using traditional methods often causes rootstock regrowth, increasing labor demand and production costs. Although cotyledon-less splice grafting eliminates regrowth by excising meristem tissue, its success rate has consistently been lower. Here, we developed a novel cotyledon-less splice grafting methodology that achieved high survival rates by modulating pre-grafting light intensities from 100 to 300 μmol·m⁻²·s⁻¹ for scion and rootstock, generating four experimental groups: high-light intensity scion/high-light intensity rootstock (HS/HR), high-light intensity scion/low-light intensity rootstock (HS/LR), low-light intensity scion/high-light intensity rootstock (LS/HR), and low-light intensity scion/low-light intensity rootstock (LS/LR). The results demonstrated that HS/HR and LS/HR exhibited the highest survival rates, nearly 98%, and displayed high seedling quality, markedly enhanced graft-union adhesion, and accelerated vascular reconnection. Pretreatment of high light intensity increased starch accumulation in rootstock hypocotyls, enhancing tolerance to carbon starvation after grafting especially in the cotyledon-less grafts. Metabolomic analysis identified elevated levels of key metabolites, including auxins, cytokinins, D-galactose, galactinol, starch, cinnamic acid, M-coumaric acid, and vanilloloside. Transcriptomic profiling revealed significant enrichment of plant hormone signal, starch and sucrose metabolism, and phenylpropanoid biosynthesis pathways in scion and rootstock tissues underpinning hormonal regulation, carbohydrate metabolism, and lignin biosynthesis under high-light conditions. WGCNA identified key co-expression modules associated with graft healing traits and key metabolites. Furthermore, graft healing related genes (PXY, NAC086, CALS7, and TMO6) were upregulated. In conclusion, our findings underscore the critical role of light intensity in orchestrating transcriptional and metabolic networks to optimize graft healing, providing a physiological and molecular foundation for improving cotyledon-less grafting efficiency.

The interaction between plants and pathogens represents a complex evolutionary arms race. Plants employ a sophisticated innate immune system to combat pathogen invasion. However, pathogens inhibit plant immunity by secreting effectors into the host cell. The chloroplast is an indispensable organelle for photosynthesis and metabolism in plants. Notably, increasing evidence has recently revealed the pivotal role of chloroplasts in plant immunity, including reactive oxygen species production, phytohormone biosynthesis, and signal transduction. Accordingly, chloroplasts have emerged as key targets for pathogen effectors. In this review, we summarize the role of chloroplasts in plant immunity and update the identification of pathogen effectors that enhance pathogenicity by targeting chloroplasts. We also discuss the diverse mechanisms by which pathogen effectors hijack chloroplasts to manipulate plant immunity, shedding light on the functional complexity and importance of chloroplasts in plant-pathogen interactions.

Methyl jasmonate (MeJA) has emerged as a promising agent for mitigating chilling injury (CI) in peach fruit (Prunus persica); however, the molecular mechanisms underlying the role of MYC2, a key transcriptional regulator of jasmonic acid (JA) signaling, in mediating cold adaptation remain largely unexplored. In this study, we demonstrated that MeJA treatment effectively alleviated CI in peach fruit, accompanied by enhanced ethylene biosynthesis, elevated accumulation of polyphenols and flavonoids, and a marked reduction in reactive oxygen species levels. Using DNA affinity purification sequencing and transactivation assays, we identified PpMYC2.1 as a central regulator that directly activates key genes involved in ethylene-mediated fruit softening (PpIAA1, PpHB.G7, PpERF61, PpPL1, PpPG2, and PpXTH2) and phenylpropanoid metabolism (PpPAL1, Pp4CL, PpCHI3, and PpCHS). Stable overexpression of PpMYC2.1 in tomato (Solanum lycopersicum) significantly enhanced fruit tolerance to cold stress. Meanwhile, transient overexpression or silencing in peach fruit upregulated or downregulated the expression of its target genes, confirming its positive regulatory role in cold stress response. Mechanistically, MeJA downregulated the expression of transcriptional repressors PpJAZ2 and PpJAZ4, thereby alleviating their suppression of PpMYC2.1-mediated transactivation. Collectively, these findings reveal a previously uncharacterized JA-responsive transcriptional module, PpJAZ2/4-PpMYC2.1, that orchestrates cold stress adaptation in peach fruit, offering novel insights into postharvest preservation strategies for climacteric fruit.

Cyclocarya paliurus is a medicinal plant traditionally used in China to treat hypertension and diabetes. It exhibits heterodichogamy, a dimorphic mating system with protogynous and protandrous morphs, which are based on the maturation sequence of female and male flowers within the same plant. DNA methylation, a crucial epigenetic modification in regulating plant flowering, is poorly characterized in heterodichogamous species. Here, whole-genome bisulfite sequencing and transcriptome analyses were performed on female and male flower buds from two morphs during inflorescence elongation in diploid C. paliurus. Single-base methylation maps revealed higher DNA methylation levels in early-flowering samples, particularly in CHH contexts, which may be dynamically regulated by the interplay between CpDRM-D2 and CpDME-D1. Candidate genes involved in the photoperiod, gibberellin, and trehalose-6-phosphate signaling pathways were identified based on their transcriptional and methylation dynamics across floral buds. Heterologous overexpression of CpHd16, CpTPPD, and CpFTIP3 in Arabidopsis delayed flowering. Furthermore, field application of the DNA methylation inhibitor 5-azacytidine to diploid C. paliurus delayed the flowering of both male and female flowers and altered methylation levels within the CpTPPD promoter and CpFTIP3 gene body. These epigenetic changes, accompanied by downregulated CpTPPD and upregulated CpFTIP3 expression, suggest that these genes may mediate C. paliurus flowering via methylation-dependent regulation. This study provides novel insights into the molecular regulatory mechanisms of heterodichogamous flowering and lays a theoretical foundation for epigenetic research in C. paliurus.

Late blight, caused by the oomycete Phytophthora infestans, is one of the most destructive diseases affecting potato production globally. However, the function of DNA methylation (DNAm) and its association with simultaneous alteration in gene expression in potato’s response to P. infestans infection remain largely unknown. Here, we conducted whole-genome bisulfite sequencing and RNA sequencing on potato cultivar Qingshu No.9 inoculated with P. infestans. Significantly, we identified 18 119 differentially expressed genes (DEGs) across at least one of the four post-inoculation time points. A few pathogenesis-related (PR) genes involved in salicylic acid, ethylene signaling, and DNAm regulation exhibited activation at early infection stages, although they were predominantly downregulated after the onset of necrosis in plants. Hypomethylation changes at 12 h post-inoculation (hpi) were followed by hypermethylation at 24 hpi, with CHH methylation being the primary factor influencing the DNAm pattern. Differentially methylated regions (DMRs) showed significant enrichment at DEGs. Specially, DNAm variations could be associated with subsequent transcriptional changes. This is exemplified by 24 h-hyper-CHG methylation at the gene body that correlates with expression downregulation at 48 hpi, including genes involved in chromatin remodeling pathways. Furthermore, we observed a significant enrichment of hypomethylation changes at the exon of NB-LRR genes, which ultimately resulted in their downregulation. In summary, we have elucidated the DNAm pattern of potato in response to infection by P. infestans, and identified the involvement of epigenetic mechanisms in the reprogramming of the transcriptome, which ultimately contributed to the suppression of immunity and the development of potato late blight.

Brassica juncea var. tumida, commonly known as Zha Cai, is a pickled stem mustard widely cultivated in southern China. Its most distinctive trait is the swollen stem, which serves as the primary economic organ for harvest. However, the origin and domestication history of tumida remain unclear, hindering genetic improvement and molecular breeding efforts. Here, we assembled a chromosome-level genome of the landrace ‘YAXY’ from Chongqing—the center of tumida diversity—totaling 909.1 Mb with a contig N50 of 4.17 Mb. We also collected and resequenced 203 tumida accessions across southern China. By integrating the ‘YAXY’ reference genome with population data, we generated the first comprehensive tumida variation dataset, comprising 1.38 million single-nucleotide polymorphisms (SNPs) and 0.27 million insertions and deletions (InDels). Joint analysis of the newly sequenced tumida population and 504 public B. juncea datasets revealed that tumida and leafy types from southern China share a common origin from local oilseed mustard. Tumida domestication was accompanied by a strong genetic bottleneck. Additionally, we conducted genome-wide association studies (GWAS) for 21 agronomic traits and identified candidate genes linked to key domestication traits in tumida. For the swollen stem trait, selective sweep and GWAS analyses jointly identified candidate genes likely involved in lignification. Transcriptome data showed consistent differential expression of BjuA05g15010, the Arabidopsis SAGL1 ortholog, across all swelling stages, suggesting a key role in stem morphogenesis. Collectively, our findings shed light on tumida evolution and provide valuable genomic resources and candidate genes to support genetic research and breeding in B. juncea.

Anthocyanins are vital pigments that play a crucial role in the coloration of various fruits. Our previous study identified a mutant Ppbbx24-del protein in the ‘Red Zaosu’ pear that positively regulates anthocyanin biosynthesis. However, this mutant protein exhibited nucleo-cytoplasmic localization due to the lack of the NLS domain. We hypothesized that a transcription factor in ‘Red Zaosu’ pear interacts with Ppbbx24-del, facilitating its nuclear translocation for regulatory function. In this study, a PpMYB5 was screened by Y2H assay using the Ppbbx24-del as bait, which was an R2R3-MYB transcription factor and significantly up-expressed in ‘Red Zaosu’ compared to ‘Zaosu’. Pull-down, Y2H and BiFC assays confirmed that PpMYB5 could interact with both mutant Ppbbx24-del and common PpBBX24. Notably, co-expression experiments revealed that PpMYB5 facilitated the nuclear translocation of Ppbbx24-del. Transient expression assays in ‘Zaosu’ pear fruits demonstrated that PpMYB5 alone failed to induce anthocyanin accumulation, but its co-expression with Ppbbx24-del significantly enhanced the anthocyanin content of fruit peel compared to Ppbbx24-del alone. This synergistic effect was accompanied by significant upregulation of key anthocyanin biosynthetic genes, including PpCHS and PpCHI. Additionally, dual-luciferase assays demonstrated that PpMYB5 not only enhanced the activation effect on the promoters of PpCHS and PpCHI by Ppbbx24-del but also had the same effect on the promoter of PpMYB5. Our findings indicate that PpMYB5 and Ppbbx24-del form a crucial regulatory module that finely regulates anthocyanin synthesis in pear.

Drastic karyotype changes are a major evolutionary force, potentially involving centromere position, number, distribution, or strength alterations. Yet, the genetic and epigenetic landscape of centromeres, especially in allopolyploid plants during subgenome reshuffling, remains poorly understood. Here, we present a near-complete chromosome-scale genome assembly of the allotetraploid Pennisetum purpureum ‘Purple’, resolving all 14 centromeres. We find that subgenome-biased expansion of six LTR retrotransposons drives architectural divergence between subgenomes. Centromeric satellite repeats (CentPs) show rapid sequence divergence across subgenomes and chromosomes, with CENH3 preferentially binding conserved higher order repeats. Intriguingly, centromeric retrotransposons in Pennisetum (CRPs) are evolutionarily younger compared to their noncentromeric counterparts, coupled with marked subgenome B-biased amplification. Notably, CRP insertions flanking CentP satellites correlate with elevated satellite DNA polymorphism, supporting a model wherein CentP homogenization processes actively purge retrotransposons from centromeric arrays. Despite rapid sequence diversification of centromeric repeats, the epigenetic landscapes remain evolutionarily conserved in the centromeres of two subgenomes. Additionally, comparative analyses across Pennisetum species demonstrate rapid species- and chromosome-level turnover of CentPs and CRPs. Overall, our study illuminates the genetic and epigenetic plasticity of centromeres in allopolyploids, revealing how centromeric repeats adapt post-subgenome reshuffling.

Stress sensitivity and tolerance are the consequences of coordinated regulation by multiple genes. Existing genetic tools can identify key genes that mediate metabolic and physiological processes sensing and perceiving stresses. However, it has become increasingly clear that the end-point phenotype of stress response resulting from these intermediate processes involves intricate but well-coordinated networks constituted by a large array of genes. Here, we describe an emerging functional game-graph theory to coalesce all genes from mapping or association studies into genetic interaction networks. These networks enable geneticists to trace, visualize, and interrogate the precise roadmap of how each gene acts and interacts with every other gene to mediate stress response. By shifting reductionist thinking to a holistic, systems-oriented thinking, this theory overcomes a major challenge of elucidating the detailed genetic architecture of stress response.

The plant hormone salicylic acid (SA) effectively suppresses ethylene biosynthesis in apple (Malus domestica) fruit. However, the underlying molecular mechanism remains unclear. Here, we identified a WRKY transcription factor, MdWRKY40, which was upregulated in response to SA treatment. MdWRKY40 functioned as a transcriptional repressor of the ethylene biosynthesis gene MdACS1 (1-aminocyclopropane-1-carboxylic acid synthase 1). In addition, we found that the expression of U-box-type E3 ubiquitin ligase MdPUB24 was downregulated following SA treatment. MdPUB24 interacted with MdWRKY40 and mediated its ubiquitination, leading to the degradation of MdWRKY40 via the 26S proteasome pathway, which was suppressed by SA. Together, these results suggest that the MdPUB24-MdWRKY40-MdACS1 regulatory module mediates SA-induced suppression of ethylene biosynthesis by post-translational modification during apple fruit ripening. These findings offer new insights into the molecular basis of fruit ripening inhibition and shelf-life extension.

Nuclear factor Y (NF-Y), evolutionarily conserved heterotrimeric transcription factors (TFs), are found throughout eukaryotic organisms. Comprising the NF-YA, NF-YB, and NF-YC subfamilies, this family is established as playing critical roles in plant growth and development. While earlier research has mainly centered on the functional and evolutionary characteristics of NF-Y within individual plant species, large-scale analyses and evolutionary patterns of these genes across major plant lineages remain largely unexplored. Here, we systematically identified 15 392 nonredundant genes of NF-Y family from 320 horticultural and representative plant species. Our findings showed that this gene family originated from charophytes. In bryophytes, pteridophytes, and gymnosperms, dispersed duplication served as the predominant mode of NF-Y gene expansion, whereas in angiosperms, their expansion was driven by whole genome duplication/segmental, dispersed, and tandem duplication. Conserved motif analysis revealed that highly conserved motifs are present within each NF-Y subfamily across eight representative plant species. However, some NF-Y genes in higher plants exhibited motif loss, indicating sequence variations during their evolutionary history. Transcriptomic profiling analysis of NF-Y genes in Arabidopsis thaliana under various conditions, including hormonal treatments, abiotic/biotic stresses, as well as various developmental stages, revealed their functional versatility. Furthermore, an interaction network comprising 36 NF-Y genes along with 2473 downstream and 261 upstream genes was constructed in A. thaliana. Enrichment analysis revealed interactions between NF-Y genes and other TFs, particularly those from the Myb_DNA-binding and APETALA2 (AP2) families, which were consistently enriched among both upstream and downstream regulatory genes. This work provides the first comprehensive and large-scale investigation into the evolutionary dynamics of NF-Y genes, encompassing taxa from basal algae to advanced horticultural plants, thereby offering novel insights into their evolutionary and lineage-specific expansion.

Alfalfa (Medicago sativa L.) is a globally pivotal legume forage. Selenium (Se), an essential trace element for humans and animals, can significantly enhance the growth and development of alfalfa. Chlorophyll is the central pigment of plant photosynthesis. Previous research on chlorophyll synthesis in alfalfa has mainly focused on transcriptional regulation, environmental factors (light, nutrient availability), and phytohormone signaling, while fewer studies have been conducted at the post-transcriptional level. Through whole transcriptome sequencing analysis, microRNAs (miRNAs) were identified as positively responsive to Se. This study focused on the regulation of chlorophyll synthesis by the miR171-SCL6 module in alfalfa. β-glucuronidase staining and dual-luciferase assays revealed that MsmiR171 negatively regulated the transcript levels of the SCARECROW-LIKE 6 transcription factor MsSCL6. Subcellular localization analysis revealed that MsSCL6 was mainly in the cell nucleus. Functional analyses demonstrated that MsmiR171 promoted chlorophyll synthesis and photosynthesis in alfalfa, while MsSCL6 negatively regulated chlorophyll synthesis. Notably, Se treatment upregulated MsmiR171 expression, downregulated MsSCL6 expression, and enhanced chlorophyll accumulation. qRT-PCR analysis revealed differential expression of MsPOR in MsmiR171 and MsSCL6 overexpression or silencing plants. Combined yeast one-hybrid and dual-luciferase assays demonstrated that MsSCL6 transcriptionally represses MsPOR through direct promoter binding, suppressing chlorophyll accumulation. In summary, this study for the first time revealed the mechanism of the MsmiR171-MsSCL6-MsPOR module mediating Se-regulated chlorophyll biosynthesis in alfalfa. These findings provide a theoretical foundation and technical guidance for alfalfa breeding and the production of Se-enriched forage.

Flavonoids are important secondary metabolites that regulate plant growth and development and confer resistance against biotic and abiotic stress. As natural polyphenol substances, flavonoids determine the quality traits of commercial fruits, such as color, flavor, and nutrition. In the past few decades, research on the regulation of flavonoid biosynthesis in plants has made significant progress. However, a deep understanding of this aspect in flavonoid-rich horticultural crops is lacking. This review aims to systematically summarize the current knowledge in the regulation of flavonoid biosynthesis in fruits, including the transcriptional, post-transcriptional, epigenetic, and post-translational regulation mechanisms as well as the composite regulation cascades. Our analysis shows that direct transcriptional regulation involves the actions of different transcription factor families, such as MYB, WRKY, bZIP, AP2/ERF, and MADS, by directly targeting the key synthase genes in flavonoid biosynthetic pathway. Indirect regulation involves specific transcription factors and microRNAs that target the downstream regulators, as well as the regulation modules triggered for degradation of activators or repressors in response to environmental signals or plant hormones. In addition, epigenetic regulation, associated with methylation level in the gene promoter regions or the insertion or deletion of specific sequences therein, plays an important role in controlling anthocyanin accumulation. Based on the diverse regulation mechanisms of the flavonoid biosynthetic pathway, more molecular design targets can be applied in the future, facilitating the production of more stress-tolerant and quality-elevated crop varieties.

Vine tea (Nekemias grossedentata) is a dual-purpose medicinal and edible liana with a documented history of consumption in China spanning millennia. It has been extensively utilized among ethnic minority groups, including the Tujia, Yao, and Dong communities, for at least 700-1000 years, where it is traditionally revered as the ‘Immortal Herb’ or ‘Longevity Tea’. This study reports the haplotype-resolved chromosome-scale genomes of two major cultivated diploid vine tea accessions (N. grossedentata, 2n = 40). Phylogenetic analysis revealed that N. grossedentata diverged from Cissus rotundifolia ~26.27 million years ago (MYA) and from Vitis vinifera around 17.30 MYA. Comparative genomic analysis within the genus uncovered species-specific evolutionary patterns. Furthermore, we constructed a pan-genome encompassing 39 vine tea cultivars and characterized structural variations among cultivated varieties. Correlation analysis between dihydromyricetin (DMY) content and leaf transcriptomes across these cultivars identified ~1 kb presence/absence variations (PAVs) associated with the expression of F3′5′H, a gene critical for DMY biosynthesis in vine tea. Collectively, this genomic resource provides a valuable foundation for advancing herbal crop breeding and development, while offering insights into the biosynthetic pathways underlying specialized metabolism in Vitaceae.

Extreme heat driven by climate change poses a catastrophic threat to global vegetable production, undermining nutritional security because of the heightened physiological sensitivity and succulent tissues of these crops. This review synthesizes the multistage impacts of heat stress across critical developmental phases—from germination to reproduction—emphasizing morphological impairments (such as leaf wilting and floral abortion) and physiological disruptions (including photosynthetic inhibition and oxidative damage). We systematically dissect thermotolerance mechanisms in vegetables, highlighting transcriptional reprogramming by HSFs, WRKY, and NAC transcription factors; chaperone-mediated proteostasis via HSPs; epigenetic remodeling; Ca²⁺-ROS signaling pathways; and the role of phase separation dynamics. Importantly, we propose six strategic pathways to develop heat-resilient vegetables: harnessing natural variation through pan-genome-driven allele mining; employing biotechnological interventions such as CRISPR-mediated editing and synthetic promoters; engineering multistress tolerance by targeting conserved ‘core response’ pathways; exploiting epigenetic memory to achieve transgenerational resilience; optimizing source-sink dynamics with ‘’Climate-Responsive Carbon Optimization; and applying plant growth regulators and nanotechnology to enhance thermotolerance. Together, these strategies chart a clear roadmap for climate-smart vegetable breeding and call for interdisciplinary collaboration to translate molecular discoveries into practical breeding approaches for sustainable food systems under escalating thermal extremes.

Bud dormancy in temperate perennials is often described as a stereotyped state of developmental repression triggered by environmental signals. Here, we investigate the development of vegetative buds in Prunus persica during the cold season to assess whether, like flower buds, they remain transcriptionally active. An integrated approach combining cytological analysis, hormone profiling, transcriptome sequencing, co-expression and gene regulatory network (GRN) inference, and in vivo interaction assays was used to compare bud types. Despite similar levels of abscisic acid and gibberellins during chilling accumulation, vegetative and flower buds displayed divergent transcriptional responses. Vegetative buds activated jasmonate- and photoperiod-responsive gene modules, while floral buds were marked by chilling-responsive modules regulated by SHORT VEGETATIVE PHASE 1 (SVP1). Bimolecular fluorescence complementation confirmed specific interactions between SVP1 and DORMANCY-ASSOCIATED MADS-box (DAM) proteins DAM3, DAM5, and DAM6. GRN analysis highlighted bud-specific combinations of DAM and SVP proteins, with DAM5 and DAM6 homodimers predominant in vegetative buds and DAM4 and SVP1/2 heterodimers dominant in flower buds. Our data revise the classical dormancy paradigm: flower and vegetative buds share hormonal trends yet deploy distinct MADS-box combinations to coordinate environment-dependent winter development. The organ-specific DAM/SVP circuitry uncovered here provides a new framework for mechanistic studies on cold mediated peach bud development.

MicroRNAs (miRNAs) are noncoding RNAs, ~21-24 nucleotides in length, that play a pivotal role in post-transcriptional gene regulation by inducing cleavage or translational repression of target mRNAs with complementary sequences. In this study, we identified miRNAs expressed during the early developmental stage of mung bean (Vigna radiata), a major legume crop, using small RNA sequencing (sRNA-seq), and analyzed their expression profiles across various mung bean tissues. Mung bean-specific miRNAs were found to be highly expressed in the aerial parts of seedlings, particularly in the leaves. Furthermore, the expression of these miRNAs was effectively validated using Tailed-Hoogsteen triplex DNA-encapsulated silver nanocluster (DNA/AgNC) sensors. The nanosensor enables rapid detection of target miRNAs within 30 min and is easy to apply for field-based assessments. The predicted target mRNAs of the identified miRNAs were associated with a range of biological processes relevant to early-stage development. This study highlights the potential of nanosensor-based approaches for the efficient identification of novel miRNAs in staple crops, offering a promising strategy to reduce the cost, time, and labor required during the transition from laboratory research to field applications.

Divergence in basic chromosome numbers among closely related species is widespread in plants, yet a fundamental question regarding the evolutionary direction of karyotype—whether descending (from higher to lower numbers) or ascending (from lower to higher)—remains contentious. Alfalfa (Medicago sativa L.), a key forage crop, displays two basic chromosome numbers (x = 8 and x = 7) within the genus, and whether this divergence arose through descending evolution from 8 to 7 or the reverse remains unclear. Here, we developed a set of chromosome-specific painting markers capable of tracing chromosomal evolutionary trajectories among Medicago species. Comparative cytological analysis of seven accessions (x = 8) from the M. sativa L. complex revealed conserved chromosomal synteny in both diploid and autotetraploid species, with no detectable interchromosomal rearrangements. In Medicago polymorpha (x = 7), we discovered that the divergence in basic chromosome numbers (x = 7 vs. x = 8) resulted from large-scale fission-fusion events involving chromosomes 3, 5, and 6, rather than the simple fusion of chromosomes 3 and 7 as previously published genomic hypotheses. Further supporting evidence from rDNA remodeling and phylogenetic analysis indicates a descending evolutionary pathway, with the ancestral x = 8 transitioning to x = 7 approximately Mid-Miocene (~12 million years ago). Our results offer new insights into Medicago speciation and evolutionary origins, and instantiate a strategy for studying karyotypic evolutionary direction in other plant taxa with similar chromosomal dynamics.

Polyploidization has occurred throughout the tree of life and is particularly common in plants. Despite its ubiquity, our understanding of the short- and long-term effects and consequences of genome doubling in natural populations remains incomplete. In this study, we identified a novel ploidy-variable species system within the ornamental and industrial oilseed genus Orychophragmus (Brassicaceae), which comprises six species, including diploid and tetraploid cytotypes of Orychophragmus taibaiensis. By integrating population-scale genomic and transcriptomic datasets across the species in this genus, we constructed a robust phylogenetic framework and investigated the divergence and demographic history of O. taibaiensis in comparison to its relatives. Specifically, we characterized the geographical distribution patterns of diploids and tetraploids in natural populations of O. taibaiensis, confirmed the autopolyploid origin of tetraploids, and inferred their origin time relative to diploid counterparts. Our findings further revealed that, following genome doubling, tetraploids accumulated a higher genetic load of deleterious mutations, likely due to relaxed purifying selection facilitated by allelic redundancy. Additionally, genome doubling was associated with pronounced changes in gene expression patterns, with differentially expressed genes evolving under relaxed selective constraints. These results highlight that the initial masking of deleterious mutations, changes in expression regulation, and divergent efficacy of selection likely all contribute to shaping the establishment and evolutionary potential of polyploids.

Somatic embryogenesis (SE) in plants requires the prior formation of embryogenic cells in plants. The remodeling of the cell wall in mature somatic cells is a prerequisite for embryogenic cell formation. However, the mechanism of this process remains unelucidated. In this study, eTM3699, miR3699, and MANNAN7 (MAN7) were identified as key regulators of embryogenic cell formation through whole-transcriptome sequencing. The dual-luciferase reporter assays and GUS histochemical staining assays, were used to identified the regulatory network of eTM3699-miR3699-MdMAN7. The overexpression and CRISPR/Cas9-mediated transgenic assays were used for functional analysis of miR3699 and MdMAN7. MdMAN7 overexpression can enhance the activity of β-mannanase, induce hemicellulose degradation, reshape the cell wall of highly differentiated somatic cells, and relieve the restriction on cell differentiation and division, ultimately positively regulating the embryogenic cell formation. Specifically, the overexpression of MdMAN7 can significantly improve the efficiency and shorten the induction cycle of SE. miR3699 acted by negatively regulating MdMAN7. In addition, eTM3699 were identified as endogenous target mimics of miR3699 that bind to miR3699 to prevent cleavage of MdMAN7 and thereby positively regulate embryogenic cell formation. In conclusion, our results elucidate the mechanism of eTM-miR3699-MAN7 module regulating embryogenic cell formation during the early stage of SE in apple.

Organ abscission is essential for optimal reproduction, yet its regulation in perennial woody plant species is poorly understood. To investigate how abscission is spatially and temporally regulated during reproduction, we analyzed five sequential abscission events in the cherry species Prunus × yedoensis (Cerasus × yedoensis, Somei-Yoshino) and Prunus sargentii var. verecunda (Bunhong-Beot): abscission of the petals, calyces, flower pedicels, fruit pedicels, and peduncles. The abscission zone of the calyx formed de novo upon activation, whereas other abscission zones were pre-formed but developmentally arrested. Localized ethylene responsiveness reactivated these zones, promoting cell division, differentiation of residuum and secession cells on either side of the abscission zone, and lignin deposition in some cases. This progression was accompanied by reactive oxygen species accumulation and pH shifts. We observed species-specific differences during early floral abscission: P. yedoensis shed petals rapidly in a pollination-independent manner, whereas P. sargentii retained petals on unpollinated flowers, which later abscised with the pedicel, potentially extending the fertilization window. Both species employed a post-fertilization developmental gate via fruit pedicel abscission to selectively eliminate small, slow-growing fruits. These findings reveal that Prunus species coordinate a hierarchical abscission program functioning as a multilayered reproductive filter, progressively refining investment decisions to determine the final fruit set.