Accepted With the rapid growth in the cultivation area of Selenicereus megalanthus, traditional manual harvesting is inefficient and costly, making automated harvesting a necessary approach. Maturity identification faces challenges such as irregular fruit growth, occlusion and overlap, and nonuniform yellow-green gradient colors. To address this, this paper proposes BMPC-YOLOv8, a lightweight, multi-module collaborative algorithm for maturity detection. The algorithm integrates an improved BAM_ECA mechanism with the efficient HGNetV2 backbone, enhancing feature extraction efficiency and the capability for multi-scale information retention. It introduces the MCA module to enhance the comprehensive understanding of fruit contours, colors, and occlusion relationships. PConv is employed to replace traditional convolution, improving the perception of directional gradients and fine-grained features. Furthermore, it integrates the CBAM module to optimize deep feature maps, reducing confusion between the fruit and the background. Through various experimental validations, BMPC-YOLOv8 demonstrates the best performance in accuracy, speed, and lightweighting. Its mAP@50 increased to 96.5%, model size was reduced by 26.15%, inference speed was boosted by 40.8%, and precision and recall improved by 2.9% and 2.7%, respectively. This research provides an efficient and feasible technical solution for the automated harvesting and quality grading of S. megalanthus, possessing significant practical application value.

Flavonoid content is the core quality indicator of medicinal and edible mulberry (Morus alba L.) leaves. This study investigated the regulatory effects of 100 mu mol/L MEJA, 200 mg/L GABA and 50 mu mol/L MT on flavonoid accumulation, physiological traits, in vitro antioxidant and hypoglycemic activities of mulberry leaves, and elucidated the underlying molecular mechanisms via integrated transcriptomics and metabolomics. All three hormones significantly elevated total flavonoid (TFC), total phenol (TPC) and four characteristic flavonoid contents, with maximum accumulation at 20 d. MEJA showed the optimal effect, increasing TFC and TPC by 89.7% and 191.2% at 20 d, with the strongest DPPH scavenging (97.49% at 0.2 mg/mL) and alpha-amylase inhibitory activity (62.08% at 1.0 mg/mL). MT exhibited superior alpha-glucosidase inhibition, while GABA significantly promoted 1-deoxynojirimycin (DNJ) accumulation. Multi-omics analysis revealed that all three hormones upregulated key flavonoid biosynthetic genes (PAL, 4CL, CHS, CHI) with distinct regulatory patterns. This study systematically clarified the differential regulatory mechanisms of three exogenous hormones on mulberry leaf flavonoid synthesis, providing a theoretical basis for the targeted directional improvement of mulberry leaf functional quality.

Water lilies are among the most basal groups of angiosperms and retain many morphological and physiological traits of early angiosperms, making them invaluable for studying angiosperm evolution, particularly floral organ development. Here we present the most comprehensive phylogeny of the genus Nymphaea to date, alongside gap-free genome assemblies for three species (Nymphaea colorata, Nymphaea thermarum and Nymphaea caerulea). Our analyses resolve 2 major clades, day-flowering (section A) and night-flowering (section B), which diverged approximately 50 million years ago. Comparative genomics reveals an angiosperm-exclusive pectin lyase gene specifically expressed during pollen tube elongation. Regarding floral traits, we identify the transcription factor NcolMYB75-like as a master regulator of blue anthocyanin biosynthesis. Furthermore, the expansion and diversification of the O-methyltransferase gene family drive the synthesis of species-specific floral scent volatiles. These findings deepen our understanding of early angiosperm innovations and provide a genomic framework for plant breeding and ecological conservation.

Global warming has increased the frequency and intensity of extreme heat events, posing a serious threat to crop growth and productivity. Although γ‑aminobutyric acid (GABA) is recognized as a bioactive factor functioning in plant stress adaptation, its specific role and underlying mechanisms under heat stress remain poorly understood in rice. In this study, we demonstrate that exogenous GABA significantly enhances heat tolerance in rice seedlings in a dose‑dependent manner. Application of 0.1 mM GABA effectively alleviated heat-induced growth inhibition and mitigated oxidative damage by suppressing reactive oxygen species (ROS) accumulation, membrane lipid peroxidation, and cell death. This protection was associated with enhanced antioxidant capacity, evidenced by up‑regulation of key antioxidant enzymes and elevated glutathione levels. Moreover, transcriptome and quantitative analysis revealed that GABA supplementation finely reconfigures the heat‑induced accumulation of specific amino acids and carbohydrates, thereby promoting metabolic homeostasis under heat stress. We further show that GABA modulates heat signaling pathway and amplifies the heat-induced expression of heat shock transcription factors (HSFs), which in turn drives stronger induction of downstream heat‑responsive genes, such as heat shock protein (HSP) and antioxidant enzyme genes. Together, these findings indicate that GABA coordinates multiple adaptive mechanisms, including enhancing antioxidant capacity, optimizing metabolic homeostasis, and activating heat‑responsive transcription, thereby enhancing rice heat tolerance. Our study highlights GABA as a promising biostimulant for improving heat resilience in crops and provides a viable strategy for sustainable crop production under climate warming.

Objective To investigate the clinical imaging characteristics of benign and malignant breast calcifications and explore their underlying molecular mechanisms at the transcriptomic level.Methods A retrospective analysis was conducted on the clinical and pathological data of 1 051 breast cancer patients admitted to Nanjing Women and Children's Healthcare Hospital between January 2016 and February 2024.Patients were divided into a calcification group(n=534)and a non-calcification group(n=517)based on mammography findings.Concurrently,3 pairs of benign and malignant breast calcification tissues were collected for high-throughput RNA sequencing(RNA-seq).Differentially expressed genes(DEGs)were identified using DESeq2,followed by Gene Ontology(GO)annotation and Gene Set Enrichment Analysis(GSEA)to uncover key hallmark pathways driving malignant calcification.Results Clinically,the proportions of ductal carcinoma in situ and microinvasive carcinoma were significantly higher in the calcification group(P＜0.05).Molecularly,compared with the non-calcification group,the calcification group had a higher proportion of estrogen receptor(ER)and progesterone receptor(PR)negativity,a higher proportion of human epidermal growth factor receptor 2(HER2)strong positivity,and a higher proportion of intermediate Ki-67 proliferation(P＜0.05).RNA-seq identified 1 686 DEGs,which were significantly enriched in biological processes such as calcium ion binding,angiogenesis,and extracellular matrix organization by GO analysis.GSEA further revealed the robust activation of classical oncogenic pathways-including mTORC1 signaling pathway,E2F target gene,G2/M checkpoint,and MYC target gene—which are closely associated with metabolic reprogramming and cell cycle dysregulation in malignant calcification tissues(false discovery rate q＜0.01).Conclusion Malignant breast calcification is not merely a macroscopic imaging sign of high tumor proliferation,but a consequential by product of extreme tumor cell proliferation and metabolic remodeling driven by pathways such as mTORC1 and MYC in the microenvironment.Integrating macroscopic imaging with microscopic transcriptomic features will facilitate early accurate warning and targeted intervention for breast cancer.

Abstract Since its formulation in 1958, the Central Dogma has provided the organizing framework for molecular biology, describing the informational relationships among DNA, RNA, and protein. Yet, the framework ends at protein synthesis: what proteins do after they are made, how their catalytic specificities determine which molecules actually meet inside the cell, lies beyond its scope. Using a zero-parameter physical model applied to three phylogenetically distant species, we show that physical encounter frequency and metabolic flux are decoupled: raw collision rates predict reaction importance only weakly and show no consistent link to gene essentiality. Enzymatic selectivity bridges this gap through three distinct, species-conserved rescue patterns that persist across more than a billion years of evolution. The cell’s most critical metabolic hubs are, paradoxically, its physically least conspicuous ones— rescued from the collision background by enzymatic precision alone. We term this downstream, measurable layer the Networked Central Dogma: a complement to the classical schema that connects gene expression to the physical organization of cellular chemistry.

Nucleotide sugars serve as the substrates for the biosynthesis of cell wall polysaccharides. Although the enzymes such as uridine diphosphate (UDP)-glucose dehydrogenase (UGD) involved in nucleotide sugar biosynthesis have been biochemically characterized, their biological roles in plants remain largely unexplored. In this study, we identify a rice mutant weakness and root hair defective 1 (wrd1), which exhibits pleiotropic phenotypes including dwarfism, reduced tiller number, and abnormal root architecture. WRD1 encodes a UGD that catalyzes the conversion of UDP-Glc to UDP-GlcA. The WRD1 mutation disrupts this enzymatic function and substantially reduces UGD activity in vivo, resulting in elevated UDP-Glc accumulation, decreased UDP-GlcA levels, and consequently an imbalance in their downstream derivatives. The aberrant UDP-sugar metabolism significantly impairs cell wall architecture and auxin glycosylation in the wrd1 mutant, accompanied by dysregulated reactive oxygen species (ROS) homeostasis and auxin-related gene expression. These combined effects lead to excessive ROS production and abnormal auxin signaling in root cells, resulting in programmed cell death and severe developmental defects. Our findings highlight the critical role of WRD1 in regulating cell wall formation and overall plant growth by modulating nucleotide sugars homeostasis, which provides new insights into the interplay between cell wall biosynthesis, auxin signaling, and ROS metabolism during plant development.

Abstract Genomic selection (GS) has become the core driving force in modern plant and animal breeding. However, state-of-the-art comprehensive GS tools often rely on complex underlying environment configurations and command-line operations, posing significant technical barriers for breeders lacking programming expertise. To address this critical pain point, this study developed a fully “zero-code” graphical user interface (GUI) decision support system for genomic selection. The platform innovatively employs a “portable dual-engine architecture” (R-Portable and Python-Portable) to achieve completely dependency-free, “out-of-the-box” deployment, and integrates a standardized six-step end-to-end workflow from data quality control to result export. Furthermore, the platform comprehensively integrates 33 cutting-edge prediction models across four major paradigms, linear, Bayesian, machine learning, and deep learning, and features an original intelligent parameter configuration system that dynamically renders algorithm parameters to provide a minimalist UI interaction experience. Benchmark testing on the Wheat2000 dataset across six complex agronomic and quality traits, including thousand-kernel weight (TKW) and grain protein content (PROT), demonstrated that classic linear models remain highly robust for polygenic additive traits, while tree-based machine learning and hybrid deep learning architectures exhibit superior predictive potential and noise resilience when resolving complex epistatic effects and low-heritability traits. The successful deployment of this platform fundamentally liberates biologists from the constraints of computational science, providing robust digital infrastructure to accelerate the popularization and practical application of GS technologies in agricultural production.

Plants of the order Nymphaeales are representative tropical and subtropical ornamental aquatic species, valued for their diverse flower colors, distinctive floral scents, and strong environmental adaptability. Although extensive studies have reported their chemical constituents, the roles of secondary metabolites in shaping ornamental traits remain insufficiently integrated. In this review, relevant literature published up to September 2025 was systematically retrieved from PubMed and Web of Science, and the major classes of secondary metabolites reported in representative genera (Nymphaea, Brasenia, and Nuphar) were summarized, with particular emphasis on their contributions to flower color and scent formation. Distinct chemotaxonomic patterns were identified: Nymphaea and Brasenia are predominantly enriched in flavonoids, polyphenols, and polysaccharides, whereas Nuphar is characterized by unique sulfur-containing sesquiterpene alkaloids. Accumulating evidence indicates that differential accumulation of specific anthocyanin derivatives underlies flower color diversification, while the composition and relative abundance of volatile organic compounds (VOCs) determine floral scent profiles among species and cultivars. These metabolite-based insights provide valuable targets for ornamental trait improvement, including flower color modification and fragrance-oriented breeding. In addition, the bioactive metabolites enriched in Nymphaeales support their further development as functional ornamental plants and value-added horticultural resources. This review highlights the integrative potential of linking metabolite diversity with ornamental trait formation to advance the sustainable utilization of tropical ornamental aquatic plants.

Fusarium head blight (FHB), caused by several Fusarium species, among which the most important and widely distributed worldwide is Fusarium graminearum, in the case that the causal agent is F. graminearum, FHB spread is closely linked to the pathogen’s sexual reproduction. The T protein of the glycine cleavage system (GCVT) is a key component of carbon and nitrogen metabolism in organisms, however its biological function in filamentous fungi, particularly F. graminearum, is still unclear. In this study, we characterized two GCVT homologs (FgGCV1 and FgGCV2) to obtain a better understanding of the metabolic processes occurring in F. graminearum. We found that FgGCV1 and FgGCV2 are localized in mitochondria. Deletion of FgGCV2 had no obvious phenotypic alterations, whereas ΔFgGCV1 mutant exhibited severe defects in sexual reproduction. Notably, the sexual reproduction defect in the ΔFgGCV1 mutant was completely restored by exogenous addition of 5,10-methylenetetrahydrofolate (5,10-CH2-THF). Moreover, ΔFgGCV1 accumulated higher intracellular glycine contents and exhibited increased tolerance to calcium stress. Transcriptome analysis identified 1,482 differentially expressed genes (DEGs) in the ΔFgGCV1 mutant, with DEGs enriched in glycine, serine, and threonine metabolism, as well as reproductive and developmental processes. Collectively, our findings demonstrate that FgGCV1 plays a crucial role in regulating glycine metabolism and sexual reproduction in F. graminearum through the glycine cleavage system (GCS) pathway, providing new insights into the molecular mechanisms underlying the pathogen’s metabolic regulation and sexual development.

Shanyou oil (SYO), extracted from the seeds of Camellia hainanica in Hainan, is highly valued for its distinctive flavour, compared with that of other camellia seed oils (CSOs). To investigate the chemicals that contribute to its unique aroma, oils from 13 regions across Hainan, Guangdong, and Guangxi were collected. Sensory evaluation revealed that the SYO has intense coffee-like, caramellic, nutty, and potato-like aromas, which are significantly stronger than those of CSOs from other regions. Headspace solid-phase microextraction combined with gas chromatography-mass spectrometry (HS-SPME-GC-MS) revealed the presence of 103 volatile organic compounds (VOCs). Differential analyses of VOCs between samples revealed that acetoin and 2,3-butanediol were markedly abundant in SYO and served as key contributors to its characteristic caramel-like aroma. This study provides critical insights into the flavour chemistry of SYO, facilitating its authentication and quality evaluation.

Osmotic stress, which is mainly caused by water deficiency, is one of the major environmental factors limiting rice productivity. Osmotic stress influences many aspects of plant growth and development, especially flowering. The α subunit of the heterotrimeric G protein complex, IDR1 (also known as RGA1), has been reported to be involved in multiple abiotic-stress responses, while its role in coping with osmotic stress remains unclear. Here, we performed stress stage-based transcriptomic analyses of rice leaves from idr1–1 mutant and wild-type IAPAR9 seedlings that underwent early or middle stage of osmotic stress induced by 20% PEG solution, in order to ascertain the differences in transcriptomes between idr1–1 mutant and IAPAR9 seedlings following early- or middle-stage osmotic stress. Our results showed that 2881 upregulated and 2191 downregulated differentially expressed genes (DEGs) were identified in idr1–1 mutant seedlings relative to wild-type IAPAR9 seedlings under early-stage osmotic stress. Similarly, 2824 upregulated and 2153 downregulated DEGs were also detected in idr1–1 mutant seedlings relative to IAPAR9 seedlings under middle-stage osmotic stress. Overlap analyses revealed that 44 and 325 DEGs were found in idr1–1 mutant seedlings under early and middle stages of osmotic stress, respectively, which were co-regulated by both idr1–1 mutation and osmotic stress. Gene Ontology (GO) analyses of these DEGs demonstrated that in idr1–1 mutant seedlings, GO terms were mainly associated with quick responses to stress (including responses to phytohormones, scavenging of ROS and stomatal movement) following early-stage osmotic stress, while those were associated with operation of photosynthetic systems (including assembly and repair of photosystem complexes, chlorophyll catabolism, and thylakoid) following middle-stage osmotic stress. Interaction assays indicated that IDR1 was able to interact with 5 proteins, OsFLU1, OsHHO3, OsRLIN1, NADPH HC and OsS40-14, with their gene expression being also regulated by idr1–1 mutation. Altogether, our results suggest that idr1–1 mutation contributes to enhanced tolerance to osmotic stress by altering responsiveness to different physiological processes, like responses to water deficit, salt and heat stresses, phytohormone signaling, ROS scavenging, biosynthesis of secondary metabolites, and maintenance and repair of photosynthetic systems, which may play essential roles in enabling idr1–1 mutant seedlings to survive persistent osmotic stress.

This study introduces Nymphaea 'Sirius A' and 'Sirius B', two new interspecific hybrid cultivars that mirror a binary star system. Developed through hybridization between Nymphaea caerulea and the miniature species Nymphaea thermarum, these 'sister' cultivars share distinct stellate flowers and white petals suffused with pale blue-purple tips. Despite their shared origins and similar morphology, they exhibit distinct dimensional variations. 'Sirius A' is larger, featuring 6-7 cm blooms rising 11-13 cm above the water, while 'Sirius B' is significantly more compact (flower diameter 3-4 cm), with darker olivegreen foliage. Both cultivars successfully integrate the dwarf traits of N. thermarum with superior ornamental characteristics, offering novel, compact options for tropical water lily markets.

Water lilies provide a unique blueprint for early angiosperm evolution and aquatic adaptation. Genomic insights into aquatic resilience and ancestral flower models have facilitated modern crop engineering. By leveraging these ancient genetic networks, researchers can develop blue aromatic flowers, implement stolon-mediated expansion in cereal crops, and enhance the flood tolerance of terrestrial crops, thereby building a resilient agricultural future.

Sterculia lanceolata, a tree species of the Malvaceae family with notable ornamental and medicinal value, has long been constrained in genetic research and breeding applications due to the lack of genomic resources. In this study, we report for the first time a high-quality, chromosome-level genome assembly of this species, aimed at elucidating its evolutionary history and the genetic basis of key traits. We constructed the genome using PacBio HiFi sequencing and further assembled it into 20 pseudochromosomes with the aid of Hi-C technology, yielding a final genome assembly size of 602.8 Mb with a contig N50 of 29.3 Mb and a BUSCO completeness of 98.7%. The assembly includes the identification of 20 pseudochromosomes and the annotation of 35,873 protein-coding genes, with an annotation rate of 96.4%. By integrating genomic data from other Malvaceae species, we analyzed the karyotype evolution of S. lanceolata and revealed the basal ploidy level of the family. Comparative genomic analyses uncovered significant syntenic relationships and whole-genome duplication (WGD) events among Malvaceae species, thereby clarifying the trajectory of karyotype evolution. Moreover, the study identified key regulatory gene families associated with fruit dehiscence (homologs of SHP1/2, FUL, IND, and ALC) that have undergone extensive expansion in S. lanceolata as a consequence of ancient polyploidy events. The reference genome provided in this study not only serves as a critical resource for evolutionary research in Malvaceae but also establishes a foundational framework for molecular breeding, genetic improvement, and conservation of S. lanceolata and related species.

Phenylalanine ammonia-lyase (PAL) catalyzes the initial committed step in the phenylpropanoid pathway, supplying precursors for a wide range of secondary metabolites, including amphetamine-type alkaloids, the signature bioactive constituents of Ephedra sinica. In this study, a PAL gene (EsPAL) was cloned and characterized from E. sinica, and its sequence features, expression patterns, and catalytic function were investigated. The EsPAL coding sequence is 2,124 bp in length, encoding a 707-amino-acid hydrophilic non-transmembrane protein with α-helices as the predominant structural element. Phylogenetic analysis placed EsPAL within the gymnosperm clade, distinct from angiosperm, bryophyte, and lycophyte PALs. Expression analysis revealed ubiquitous EsPAL expression across tissues, with the highest transcript abundance in roots, followed by mature and young stems. Recombinant EsPAL protein was successfully expressed in E. coli and functional assays demonstrated that the recombinant EsPAL protein catalyzed the deamination of L-phenylalanine to trans-cinnamic acid in vitro, and its catalytic activity was further confirmed in planta via Agrobacterium-mediated transient expression in Nicotiana benthamiana leaves. Collectively, these results establish that EsPAL encodes a functional PAL enzyme involved in phenylpropanoid precursor supply in E. sinica, with predominant root expression suggesting a potential regulatory role in root-specific secondary metabolism, thereby providing a foundational genetic element for dissecting the biosynthetic pathway of amphetamine-type alkaloids.

The evolutionary history of the ANA-grade angiosperms provides a crucial window into the transition of early flowering plants. Within this group, the Nymphaeales (water lilies) are pivotal, yet a lack of gapless genomic resources has hindered research into their complex developmental and adaptive programs. In this study, we present a telomere-to-telomere (T2T), gap-free genome assembly of Nymphaea minuta, a miniature water lily endemic to Madagascar. Utilizing PacBio Revio HiFi and Hi-C technologies, we generated a 382-Mb assembly anchored to 14 chromosomes. Comparative analysis reveals a compact genome with lower levels of ancient polyploidization than other Nymphaeaceae. By integrating a comprehensive transcriptome atlas of 15 organs and developmental stages, we identified seven primary developmental trajectories and 1179 organ-specific genes. Our analysis uncovered two critical regulatory models: Sequential Dual-Module Relay: In leaves, water fluctuation triggers an initial MAPK-signaling stress response, followed by a post-transcriptional 'transcriptome reset' mediated by the RNA degradation pathway (LSM1/2 and ENOC) during severe drought. Energy-Program Coordination: Seed development is governed by a three-phase transition where the glyoxylate cycle (MLS) drives energy mobilization, while an ERF1-centered hub integrates ethylene, ABA, and JA signaling to balance rapid germination with immune defense. These findings provide a definitive genomic reference for basal angiosperms and elucidate the molecular networks enabling the survival and rapid development of these ancient aquatic herbs.