Introduction Phyllosphere microorganisms play essential roles in plant health and disease resistance, yet their responses to pathogen infections remain poorly understood. Panax ginseng is susceptible to multiple fungal diseases, which threaten its quality and yield. This study aimed to clarify the underlying disease resistance mechanisms of Panax ginseng by analyzing the phyllosphere fungal communities associated with fungal infections.Methods Phyllosphere fungal communities of healthy Panax ginseng plants and those with three fungal infections (gray mold, damping-off and root rot) were compared to explore the disease resistance mechanisms related to fungal community changes.Results Results revealed distinct niche differentiation: leaves were dominated by Basidiomycota (82.0%), while stems harbored more Ascomycota (94.2%), including pathogens like Monilinia laxa (35.73%). Fungal infection significantly reduced microbial alpha diversity, altered community structure (PERMANOVA, p = 0.001), and destabilized co-occurrence networks (modularity decreased from 0.8501 to 0.8116). Functional prediction indicated downregulation of key metabolic pathways (e.g., NAD/NADP interconversion, phospholipid biosynthesis). Disease stress induced an enrichment of potentially beneficial taxa (e.g., Rhodotorula) in leaves, indicative of a limited antagonistic response, while the overall community was ultimately dominated and disrupted by pathogens.Discussion Elucidating these compositional shifts of phyllosphere fungal communities advances the understanding of plant-microbe-pathogen interactions and provides a critical theoretical groundwork for development of microbiome-driven early disease diagnosis, resistance breeding, and eco-friendly disease control strategies for Panax ginseng.

Ejiao, the traditional Chinese medicinal gelatin derived from donkey hide, faces sustainability challenges due to declining donkey populations and constraints on large-scale harvesting. We isolated primary dermal fibroblasts from donkey skin and generated an immortalized line by SV40 large T antigen transduction with puromycin selection. The immortalized cells preserved characteristic fibroblastic morphology while exhibiting enhanced proliferation, delayed senescence, and increased cell-cycle activity relative to primary fibroblasts. Transcriptomic profiling demonstrated enrichment of cell-cycle-related pathways after immortalization, whereas expression of collagen and other extracellular matrix-related genes remained largely consistent. Targeted LC-MS/MS analysis detected Ejiao-related collagen peptide fragments in culture supernatants from both primary and immortalized cells, supporting retention of relevant secretory functions. This study reports the first establishment of an immortalized donkey dermal fibroblast line that preserves fibroblastic features and provide a stable in vitro model for studying fibroblast biology, extracellular matrix metabolism, and skin-associated diseases. Detection of Ejiao-specific peptides further supports their potential as a proof-of-concept system for cell culture-based production of donkey-hide gelatin, addressing raw material scarcity and enabling sustainable applications in veterinary and pharmacological research.

INTRODUCTION:Panax ginseng C. A. Mey., a precious traditional medicinal herb, demonstrates diverse pharmacological activities, including immunomodulation and anti-fatigue effects. However, prolonged cultivation has led to germplasm admixture and cultivar degeneration, resulting in inconsistent quality that severely compromises its medicinal value and industrial standardization. Therefore, establishing accurate and efficient germplasm evaluation tools is critical for ensuring the quality of P. ginseng medicinal materials. OBJECTIVES:To integrate whole-genome sequencing and chemical fingerprinting for ginseng germplasm identification and quality consistency assessment. METHODS:Chromosome-level genomes of ginseng from Jilin (JA) and Liaoning (FC) were assembled using PacBio HiFi, Illumina, and Hi-C technologies. Gene family identification and phylogenetic analysis were performed across 13 representative species. Using the JA genome as the reference, we constructed a pan-genome incorporating 7 ginseng genomes to dissect gene repertoire composition and structural variation distribution across ginseng populations. Population structure analysis with 76 individual ginseng samples revealed genetic diversity, and its integration with HPLC chemical fingerprints provided a joint assessment of quality consistency. RESULTS:We assembled two chromosome-level genomes and, through comparative genomics, revealed significant expansion of ginsenoside biosynthesis-related gene families and subgenome divergence. The core gene set accounted for 54.1% of the pan-genome, indicating high genetic conservation. SNP distribution patterns from population resequencing enabled the development of germplasm-specific molecular markers and a genetic-chemical integrated evaluation model. CONCLUSION:The molecular marker system and genetic-chemical joint assessment developed here provide reliable novel tools for germplasm identification and quality control, advancing standardization in the ginseng industry.

Background Panax ginseng C. A. Meyer is a medicinally and economically important perennial herb valued for its diverse pharmacologically active compounds. However, the genetic basis of phenotypic variation in ginseng remains poorly understood because of its large, highly repetitive, and allotetraploid genome. Berry colour variation is a conspicuous trait in ginseng and may reflect differences in specialized metabolites such as flavonoids, yet its genetic basis has remained unclear. To investigate the genomic basis of this trait and capture broader genetic diversity, we constructed a chromosome-scale pangenome using sixteen diverse accessions, including cultivated varieties, wild-simulated ginseng, and approximately 50-year-old wild ginseng from Korea and Russia. Results We generated a chromosome-scale pangenome with multiple near telomere-to-telomere assemblies, providing highly contiguous and near-complete reference genomes for diverse ginseng accessions. Comparative analyses identified dihydroflavonol 4-reductase ( DFR ), a key enzyme in the anthocyanin biosynthesis pathway, as the major genetic determinant of berry colour. Two independent loss-of-function alleles were identified: a missense mutation (Gly17Arg) affecting a conserved NADPH-binding residue and a ~ 20 kb deletion removing the entire gene. Metabolite profiling and population-scale analyses further supported the central role of DFR in regulating flavonoid accumulation in ginseng berries. Conclusion Our findings demonstrate that pangenome analysis can effectively uncover structural variants underlying metabolic trait diversity in complex plant genomes. This study advances understanding of berry colour variation in ginseng and provides a valuable genomic framework for trait discovery and molecular breeding in this genetically and experimentally challenging medicinal crop.

BackgroundParkinson’s disease (PD) is a progressive neurodegeneration disease characterized by dopaminergic (DA) neuron loss, with chronic neuroinflammation. Subthalamic nucleus deep brain stimulation (STN-DBS) is clinically effective for the relief of parkinsonism motor symptoms. Here, we used a homemade device to investigate the effect of STN-DBS on neuroprotection and chronic neuroinflammation in a unilateral 6-hydroxydopamine (6-OHDA)-induced PD rat model.MethodMale Sprague–Dawley rats received 6-OHDA injections into the striatum, followed by ipsilateral STN electrode implantation and high-frequency stimulation. Motor function was assessed by open-field and apomorphine-induced rotation tests. DA neuron survival, glial phenotype changes, and nuclear factor (NF)-κB pathway activity in the nigrostriatal system were evaluated using Western blotting, immunofluorescence, and RT-qPCR.ResultsSTN-DBS improved motor deficits and decreased the loss of tyrosine hydroxylase-positive neurons. It promoted astrocytes presented a neuroprotective phenotype and increased expression of brain-derived neurotrophic factor, and microglia mainly presented an anti-inflammatory M2 phenotype instead of a pro-inflammatory M1 phenotype. These effects may be associated with IκB-α stabilization, the suppression of NF-κB hyperactivation, and the consequent reduction in the release of downstream pro-inflammatory cytokines.ConclusionOur findings highlight that our homemade device for STN-DBS is capable of inhibiting NF-κB, modulating glial phenotypes, mitigating neuroinflammation, and ultimately ameliorating parkinsonism deficits.

Temperature constrains stable mycelial growth and production of Oudemansiella raphanipes, but its molecular response to heat stress followed by recovery remains insufficiently resolved. We integrated untargeted LC-MS metabolomics and RNA sequencing to compare control mycelia maintained at 28 °C (HPJZ28) with mycelia exposed to 42 °C for 6 h and then allowed to recover at 28 °C for 2 h (HPJZ42-R). Metabolomic and transcriptomic profiles separated clearly between the two conditions, indicating broad post-heat recovery-associated molecular remodeling. Most differential metabolites were lower in HPJZ42-R, whereas a smaller subset accumulated, suggesting selective metabolic reorganization rather than generalized activation. Transcriptome analysis identified extensive gene-expression remodeling, with 1081 upregulated and 1878 downregulated genes in the HPJZ28 versus HPJZ42-R comparison. Pathway-level analyses implicated central carbon metabolism, lipid metabolism, amino acid metabolism, peroxisome-related processes, and calcium signaling. Because the sampling design included a recovery period and a single post-stress time point, integrated gene–metabolite correlations are interpreted as exploratory associations rather than evidence of direct regulatory coupling. These results provide species-level multi-omics evidence for the post-heat recovery state of O. raphanipes and identify candidate pathways for future functional and physiological validation.

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.

Background: Mucosal healing is a major clinical challenge and a critical prognostic factor in inflammatory bowel disease (IBD). Achieving mucosal healing requires the functional reprogramming of macrophages to facilitate intestinal stem cells (ISCs)-mediated repair, a process impaired in IBD due to dysregulated macrophage activity. Dihydroartemisinin (DHA), a derivative of artemisinin, shows promise in treating IBD, but its therapeutic potential remains underexplored due to its common classification as an anti-inflammatory agent. Purpose: This study aims to evaluate the efficacy of DHA in promoting mucosal healing in IBD and to elucidate the underlying mechanisms of macrophage reprogramming, thereby expanding the therapeutic potential of DHA beyond its conventional anti-inflammatory actions. Methods: The therapeutic efficacy of DHA and its underlying mechanisms were systematically investigated using a DSS-induced colitis mouse model, with a focus on the repair phase. Mucosal healing was assessed through comprehensive histopathological and functional evaluations. DHA's role in macrophage metabolic reprogramming was explored through transcriptomic and metabolic analyses, and its effect on epithelial regeneration was examined using macrophage-organoid co-cultures. A molecular target discovery approach, integrating Mendelian randomization, molecular docking, and direct binding assays, identified 11(3HSD-1 as a molecular target of DHA, which was subsequently confirmed through genetic and pharmacological loss-of-function studies in macrophages. Results: Our findings demonstrated that DHA significantly promoted mucosal healing in a DSS-induced colitis model during the repair phase, as evidenced by reduced disease activity scores, increased colon length, and decreased histological damage. DHA also facilitated the recovery of gut functions, including barrier integrity, absorption, secretion, and motility. Macrophages were found to be essential for therapeutic effects of DHA. Specifically, DHA reprogrammed macrophage metabolism from glycolysis to oxidative phosphorylation, inducing a pro-repair phenotype characterized by enhanced secretion of Relm alpha and Wnt3a, which promoted the proliferation and differentiation of intestinal organoids. Mechanistically, we found that DHA directly bound to and activated 11 beta HSD-1, a key metabolic regulator in macrophages. This activation triggered STAT3/6 signaling, establishing a positive feedback loop that reinforced metabolic remodeling and facilitated the release of repair-promoting factors. Conclusion: Our findings demonstrate that DHA promotes intestinal mucosal healing by reprogramming macrophage metabolism, thereby enhancing ISC proliferation and differentiation. These results provide new insights into the potential of DHA in reshaping immune homeostasis, offering promising therapeutic strategies for IBD.

Ginseng (Panax ginseng) is a medicinal plant of considerable medical and economic interest. However, preserving its genetic stability and targeted selection pose challenges that limit the effective conservation and use of its genetic resources. This study aims to systematically elucidate the structural characteristics, evolutionary patterns, and phylogenetic relationships of the ginseng mitochondrial genome, in order to create a theoretical basis for the conservation of ginseng genetic resources and the acceleration of molecular selection processes. Using PacBio HiFi and DNBSEQ-T7 short-read sequencing, we assembled the complete mitochondrial genome of the BT cultivar (~ 465 kb, 55% A + T, encoding 80 functional genes). Repetitive sequences and codon usage patterns (preference for G/C at third codon positions) were characterized. Selective pressure analysis showed that most genes underwent purifying selection, but respiratory chain genes (nad4, cox2) exhibited positive selection signals. Phylogenetic analysis confirmed close relationships between ginseng and P. quinquefolius, with P. notoginseng forming a distinct clade. A mitochondrial genome variation map was constructed by integrating data from six ginseng populations. Analysis of this comparative mitochondrial genome revealed high genetic stability across populations, with SNPs, InDels, and structural variations identified. These findings not only clarify the structural features, evolutionary dynamics, and population variation patterns of the P. ginseng mitochondrial genome but also provide key genetic resources and molecular markers for high-resolution phylogenetic analysis of Araliaceae, functional research on mitochondrial genomes of medicinal plants, and targeted breeding of P. ginseng varieties, which is of great significance for promoting the conservation and sustainable utilization of ginseng germplasm resources.

Natural components, evolved to help organisms adapt and defend against threats, are also vital sources for drug discovery due to their diverse and potent bioactivities. In the present work, we proposed the Gene-encoded Natural Diverse Components Repository (GNDC, https://cbcb.cdutcm.edu.cn/gndc/), a primary and most extensive database dedicated to cataloging diverse natural components. GNDC currently catalogs over 234 million natural components that are organized into four specialized sub-databases: HerbalMDB for 2.32 million secondary metabolites, HerbalPDB for 229 million small peptides, HerbalRDB for 2.38 million small RNAs, and HerbalCDB for 0.26 million carbohydrates. By leveraging customized pipelines for high-throughput multi-omics data and AI technologies, the GNDC enables large-scale discovery and annotation of natural products from nuclear and organellar genomes of species listed in eight global pharmacopoeias and multi-resource data. Compared to existing resources, GNDC achieves a 10-fold increase in component yield and introduces over 200 million previously unreported components. To support this unprecedented data volume and complexity, state-of-the-art AI tools are seamlessly integrated to decipher and annotate vast data collections, such as classification and gene expression signature generation of millions of secondary metabolites. We envision that the GNDC will drive the transformation of drug discovery from an “experience-driven” approach to a “big data-driven” paradigm.

Nothapodytes nimmoniana is known to produce the highest content of the anticancer compound camptothecin (CPT) in the plant kingdom. We present the chromosome-level allotetraploid genome of N. nimmoniana, marking the first genome sequence from the order Icacinales. This 5-Gb genome encodes 92,630 genes, with subgenome B exhibiting dominant gene expression. Through genome mining, we identified and characterized four key enzymes involved in CPT biosynthesis, revealing that N. nimmoniana shares a similar prestrictosidine pathway with most monoterpene indole alkaloid-producing plants. Notably, homoeologous pairs of all characterized enzymes maintained their functions across both subgenomes, suggesting that gene duplication from allotetraploidization likely enhances CPT production in this species. Phylogenetic and syntenic analyses revealed that strictosidine synthase and strictosamide epoxidase were independently recruited in N. nimmoniana, Camptotheca acuminata, and Ophiorrhiza pumila, supporting the hypothesis that CPT biosynthesis evolved independently at least three times within the asterid clade.

Quality control remains a challenge in traditional Chinese medicine (TCM). This study introduced a novel genetic-based quality control method for TCM. Genetic variations in ginseng were evaluated across whole-genome, chloroplast genome, and ITS2 DNA barcode dimensions. Significant genetic variations were found in whole-genome comparison, leading to the use of inter-simple sequence repeat markers to assess the genetic diversity of ginseng decoction pieces (PG), garden ginseng (GG), and ginseng under forest (FG). Fingerprints of ginseng samples revealed instability within some batches. These evaluations were transformed into information entropy to calculate the size of Hardy–Weinberg equilibrium population (HWEP). FG had significantly higher genetic and chemical minimum HWEP than GG (p < 0.05). Notably, a significant positive correlation was observed between the minimum HWEP for genetics and for chemistry (r = 0.857, p = 0.014). Genetic polymorphism analysis of ginseng has the potential to evaluate chemical quality consistency, offering a new method to ensure quality consistency in TCM.

Artemisia annua, the source of artemisinin production, is a traditional herb used for treating malaria for thousand years. The genetic background is of high heterozygosity and traits (plant height, biomass, artemisinin content, etc.) are diverse across different germplasms. Unraveling the key genes associated with growth and secondary metabolism is essential for the efficient production of artemisinin. The 12-oxo-phytodienoic acid reductase (OPR) genes, crucial for plant growth and development and stress resistance, remain unexplored in A. annua. In this study, nine OPR genes (named as AaOPR1 to AaOPR9) were identified in A. annua, including two pairs of genes formed from recent tandem duplications. The number of OPRs varied among different haplotype genomes, and each OPR gene exhibiting distinct expression pattern. Moreover, the OPR family displayed evolutionarily activity with significant variations in numbers and gene structures observed across different plant species. Widespread gene duplication of OPRs, observed in the majority of analyzed plant genomes, brought evolutionary potential. DBR2, a member of AaOPRs involved in artemisinin biosynthesis, had two copies (AaOPR1/DBR2.1 and AaOPR2/DBR2.2) with different expression patterns, one of which was a recently generated copy with a significant 7-amino acids truncation. Heterologous protein expression and functional characterization of the two copies of DBR2 yielded multiple isomers with identical molecular weights but different arrangements, indicating neofunctionalization of the newly generated copy. The polymorphism within the OPR gene family merely scratches the surface of the genetic diversity in A. annua, and further investigation of genetic features is needed for the screening of elite germplasm resources.

Ginseng (Panax ginseng) renowned as the king of medicinal plants. Ginseng grows slowly under shade conditions, requiring at least 4 years to produce a limited number of seeds. Molecular breeding of ginseng faces challenges due to its the tetraploid genome and the absence of an efficient molecular marker system. To overcome these obstacles, we adopted genotyping-by-sequencing to delve into genetic mapping and survey genetic diversity. We constructed a comprehensive genetic map comprising 24 linkage groups, each corresponding to one of the 24 chromosomes in the ginseng genome, based on 1216 nonredundant SNPs obtained from an F2 mapping population. Additionally, 431 103 SNPs were identified from 119 diverse ginseng genotypes. From these, 192 informative subgenome-specific single copy SNPs were selected to develop a SNP chip. The SNP chip was used to genotype a large ginseng collection, encompassing registered cultivars, breeding lines, wild-simulated ginseng, and wild ginseng from various countries and regions. We evaluated the utility of the assay for molecular breeding with 919 ginseng genotypes. This breeder-friendly SNP chip promises versatility, enabling purity assessments of seeds and products, the authentication of species and cultivars, and the determination of homozygosity and homogeneity rates for breeding lines. Genotype data for 1200 ginseng genotypes are now stored in our database. This SNP chip lays the foundation for a molecular breeding in ginseng and will facilitate the breeding process in this medicinal crop.

Ginseng is a perennial herb of the genus Panax in the family Araliaceae as one of the most important traditional medicine. Genomic studies of ginseng assist in the systematic discovery of genes related to bioactive ginsenosides biosynthesis and resistance to stress, which are of great significance in the conservation of genetic resources and variety improvement. The transcriptome reflects the difference and consistency of gene expression, and transcriptomics studies of ginseng assist in screening ginseng differentially expressed genes to further explore the powerful gene source of ginseng. Protein is the ultimate bearer of ginseng life activities, and proteomic studies of ginseng assist in exploring the biosynthesis and regulation of secondary metabolites like ginsenosides and the molecular mechanism of ginseng adversity adaptation at the overall level. In this review, we summarize the current status of ginseng research in genomics, transcriptomics and proteomics, respectively. We also discuss and look forward to the development of ginseng genome allele mapping, ginseng spatiotemporal, single-cell transcriptome, as well as ginseng post-translational modification proteome. We hope that this review will contribute to the in-depth study of ginseng and provide a reference for future analysis of ginseng from a systems biology perspective.

Abstract As an important natural medicinal resource for humans, Ephedra sinica Stapf often suffers from various biological stresses during its growth process. One of the pests that pose a threat to Ephedra is the Ephedra seed pest. Its primary mode of damage is laying eggs inside the Ephedra seeds, where they develop and eventually emerge as adult wasps, causing significant damage to the seeds. This study aimed to investigate the effectiveness of X-ray for Ephedra seed pest detection, the impact on the use value of Ephedra seeds infested by pests, and the further confirmation of pest species information. The mature Ephedra seeds from the Inner Mongolia Autonomous Region were taken as the teste object. The results showed that the germination rates of three different batches of seeds were 46%, 40%, and 38%, while the seedling emergence rates were only 36%, 30%, and 32%, respectively, significantly lower than that of control healthy seeds 66% and 52%. The phylogenetic tree Neighbor-Joining (NJ) was constructed by extracting the COI sequences of the pest samples, and was identified as a new species of Eurytoma genus based on morphological characteristics. X-ray detection is a commonly used, non-invasive method. Based on non-destructive X-ray testing, the quality of Ephedra seeds could be classified into three types: healthy plump seeds, seeds infested by pests, and underdeveloped hollow seeds. In conclusion, the combined use of X-ray and DNA barcoding methods can achieve rapid and accurate detection and identification of E. sinica seed pests, which is of great significance for the management and control of Ephedra seed production.

Mesotrione is a herbicide used in agricultural production; however, its stability and long-term residues pose ecological risks to soil health and subsequent crops. In this research, the strain Amycolatopsis nivea La24 was identified as capable of completely degrading 50 mg∙L-1 mesotrione within 48 h. It exhibited a broad adaptability to various environment and could degrade three sulfonylurea herbicides (nicosulfuron, chlorimuron-methyl, and cinosulfuron). Non-target metabonomic and mass spectrometry demonstrated that La24 strain broke down the mesotrione parent molecule by targeting the β-diketone bond and nitro group, resulting in the production of five possible degradation products. The differentially expressed genes were significantly enriched in fatty acid degradation, amino acid metabolism, and other pathways, and the differentially metabolites in glutathione metabolism, arginine/proline metabolism, cysteine/methionine metabolism, and other pathways. Additionally, it was confirmed by heterologous expression that nitroreductase was directly involved in the mesotrione degradation, and NDMA-dependent methanol dehydrogenase would increase the resistance to mesotrione. Finally, the intracellular response of La24 during mesotrione degradation was proposed. This work provides insight for a comprehensive understanding of the mesotrione biodegradation mechanism, significantly expands the resources for pollutant degradation, and offers the potential for a more sustainable solution to address herbicide pollution in soil.

BackgroundIt is generally accepted that nuclear genes in eukaryotes are located independently on chromosomes and expressed in a monocistronic manner. However, accumulating evidence suggests a more complex landscape of gene structure and transcription. Ganoderma lingzhi, a model medicinal fungus, currently lacks high-quality genome annotation, hindering genetic studies.ResultsHere, we reported a golden annotation of G. lingzhi, featuring 14,147 high-confidence genes derived from extensive manual corrections. Novel characteristics of gene structure and transcription were identified accordingly. Notably, non-canonical splicing sites accounted for 1.99% of the whole genome, with the predominant types being GC-AG (1.85%), GT-AC (0.05%), and GT-GG (0.04%). 1165 pairs of genes were found to have overlapped transcribed regions, and 92.19% of which showed opposite directions of gene transcription. A total of 5,412,158 genetic variations were identified among 13 G. lingzhi strains, and the manually corrected gene sets resulted in enhanced functional annotation of these variations. More than 60% of G. lingzhi genes were alternatively spliced. In addition, we found that two or more protein-coding genes (PCGs) can be transcribed into a single RNA molecule, referred to as polycistronic genes. In total, 1272 polycistronic genes associated with 2815 PCGs were identified.ConclusionsThe widespread presence of polycistronic genes in G. lingzhi strongly complements the theory that polycistron is also present in eukaryotic genomes. The extraordinary gene structure and transcriptional activity uncovered through this golden annotation provide implications for the study of genes, genomes, and related studies in G. lingzhi and other eukaryotes.

Here, we report a new multi-optical maps scaffolder (MOMS) aiming at utilizing complementary information among optical maps labelled by distinct enzymes. This pipeline was designed for data structure organization, scaffolding by path traversal, gap-filling and molecule reuse of optical maps. Our testing showed that this pipeline has uncapped enzyme tolerance in scaffolding. This means that there are no inbuilt limits as to the number of maps generated by different enzymes that can be utilized by MOMS. For the genome assembly of the human GM12878 cell line, MOMS significantly improved the contiguity and completeness with an up to 144-fold increase of scaffold N50 compared with initial assemblies. Benchmarking on the genomes of human and O. sativa showed that MOMS is more effective and robust compared with other optical-map-based scaffolders. We believe this pipeline will contribute to high-fidelity chromosome assembly and chromosome-level evolutionary analysis.