High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar.

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

The enhancing effects of selenomethionine on harmine in attenuating pathological cardiac hypertrophy via glycolysis metabolism.

Pathological cardiac hypertrophy, a common feature in various cardiovascular diseases, can be more effectively managed through combination therapies using natural compounds. Harmine, a ß-carboline alkaloid found in plants, possesses numerous pharmacological functions, including alleviating cardiac hypertrophy. Similarly, Selenomethionine (SE), a primary organic selenium source, has been shown to mitigate cardiac autophagy and alleviate injury. To explores the therapeutic potential of combining Harmine with SE to treat cardiac hypertrophy. The synergistic effects of SE and harmine against cardiac hypertrophy were assessed in vitro with angiotensin II (AngII)-induced hypertrophy and in vivo using a Myh6R404Q mouse model. Co-administration of SE and harmine significantly reduced hypertrophy-related markers, outperforming monotherapies. Transcriptomic and metabolic profiling revealed substantial alterations in key metabolic and signalling pathways, particularly those involved in energy metabolism. Notably, the combination therapy led to a marked reduction in the activity of key glycolytic enzymes. Importantly, the addition of the glycolysis inhibitor 2-deoxy-D-glucose (2-DG) did not further potentiate these effects, suggesting that the antihypertrophic action is predominantly mediated through glycolytic inhibition. These findings highlight the potential of SE and harmine as a promising combination therapy for the treatment of cardiac hypertrophy.

Interfacial Heat and Mass Transfer Effects on Secondary Hydrate Formation under Different Dissociation Conditions.

Secondary hydrate formation or hydrate reformation poses a serious threat to the oil and gas transportation safety and natural gas hydrate exploitation efficiency. The hydrate reformation behaviors in porous media have been widely studied in large simulators due to their importance in traditional industries and new energy resources. However, it is difficult to understand the interfacial effects of hydrate reformation on the surface and in micropores of the porous media via a basic experimental apparatus. In this work, in situ X-ray computed tomography (X-CT) technology is used to detect the period, distribution, volume, and morphology characteristics of secondary hydrate formation during hydrate dissociation under depressurization, thermal stimulation, and the combined conditions. It is found that the secondary hydrate formation is inevitable under any conditions of hydrate dissociation. The secondary hydrate morphology varies among porous, grain-enveloping, grain-cementing, granular, and patchy structures, which are closely correlated to the hydrate reformation region and gas/water saturated conditions during hydrate dissociation. Accordingly, we revealed that the interfacial superheating phenomenon before hydrate dissociation could provide a supercooling condition for hydrate reformation. The gas flow along the interface of pores and inside the liquid water, as well as gas accumulation in noninterconnected pores, would exaggerate the hydrate reformation by increasing the local pore pressure. Meanwhile, the hydrate reformation aggravates the nonuniform distribution of gas hydrates in pores. In order to avoid hydrate reformation during dissociation, we further compared hydrate reformation and dissociation behaviors under three hydrate dissociation conditions. It is revealed that the combination of thermal stimulation and depressurization is an effective method for hydrate dissociation by retarding secondary hydrate formation. This study provides visual evidence and an interaction mechanism between interfacial heat and mass transfer, as well as secondary hydrate formation behaviors, which can be favorable for future quantitative research on secondary hydrate formation in different scales under various dissociation conditions.

Exploring Porous Flow Behavior of the Decomposed Gas from CH4 Hydrate in Clayey Sediments by Molecular Dynamics Simulation.

A fundamental understanding of the fluid flow mechanism during CH4 hydrate dissociation in nanoscale clayey sediments from the molecular perspective can provide invaluable information for macroscale natural gas hydrate (NGH) exploration. In this work, the fluid flow behaviors of the decomposed gas from CH4 hydrate within clayey nanopores under different temperature conditions are revealed by molecular dynamics (MD) simulation. The simulation results indicate that the key influencing factors of gas-water flow in nanoscale clayey sediments include the diffusion and the random migration of gas molecules. The influencing mechanisms of fluid flow in nanopores are closely related with the temperature conditions. Under a low temperature condition, the gas diffusion process is impeded by the secondary hydrate formation, leading to the decline in gas transport velocity within nanopores. However, it is still noteworthy that the gas-water fluid flow channels are not completely blocked by the occurrence of secondary hydrate. Under a high temperature condition, the significant phenomenon of water migration during gas flow is observed, which can be ascribed to the gas-liquid entrainment effect in nanopores of the clayey sediment. These results may provide valuable implications and fundamental evidence for improving gas production efficiency in future field tests of NGH exploitation in marine sediments.

ANKRD49 promotes the invasion and metastasis of lung adenocarcinoma via a P38/ATF-2 signalling pathway.

Lung adenocarcinoma (LUAD) is the most challenging neoplasm to treat in clinical practice. Ankyrin repeat domain 49 protein (ANKRD49) is highly expressed in several carcinomas; however, its pattern of expression and role in LUAD are not known. Tissue microarrays, immunohistochemistry, χ2 test, Spearman correlation analysis, Kaplan-Meier, log-rank test, and Cox's proportional hazard model were used to analyse the clinical cases. The effect of ANKRD49 on the LUAD was investigated using CCK-8, clonal formation, would healing, transwell assays, and nude mice experiment. Expressions of ANKRD49 and its associated downstream protein molecules were verified by real-time PCR, Western blot, immunohistochemistry, and/or immunofluorescence analyses. ANKRD49 expression was highly elevated in LUAD. The survival rate and Cox's modelling analysis indicated that there may be an independent prognostic indicator for LUAD patients. We also found that ANKRD49 promoted the invasion and migration in both in in vitro and in vivo assays, through upregulating matrix metalloproteinase (MMP)-2 and MMP-9 activities via the P38/ATF-2 signalling pathway Our findings suggest that ANKRD49 is a latent biomarker for evaluating LUAD prognosis and promotes the metastasis of A549 cells via upregulation of MMP-2 and MMP-9 in a P38/ATF-2 pathway-dependent manner.

FePO4 embedded in nanofibers consisting of amorphous carbon and reduced graphene oxide as an enzyme mimetic for monitoring superoxide anions released by living cells.

FePO4 is biocompatible and can act as a kind of promising enzyme mimetic. Unfortunately, the electrical conductivity of FePO4 is poor. In order to enhance its conductivity, FePO4 was embedded into nanofibers consisting of amorphous carbon and reduced graphene oxide (rGO) by an electrospinning technique. As a sensing material for monitoring superoxide anion (O2•-) and typically operated at 0.5 V (vs. SCE), it displays high sensitivity (9.6 µA⋅µM-1⋅cm-2), a low detection limit (9.7 nM at S/N = 3), a wide linear response range (10 nM to 10 µM), and fast response (1.6 s). Due to its low detection limit and fast response, the sensor in our perception has a large potential for detecting superoxide anions released by HeLa cancer cells. Graphical abstract Schematic of the microstructure of FePO4/C and FePO4/rGO-C nanofibers, a photograph of cancer cells (HeLa), and the electrochemical response towards O2-• of the sensor.

Figure of Merit Enhancement of a Surface Plasmon Resonance Sensor Using a Low-Refractive-Index Porous Silica Film.

In this paper; the surface plasmon resonance (SPR) sensor with a porous silica film was studied. The effect of the thickness and porosity of the porous silica film on the performance of the sensor was analyzed. The results indicated that the figure of merit (FOM) of an SPR sensor can be enhanced by using a porous silica film with a low-refractive-index. Particularly; the FOM of an SPR sensor with 40 nm thick 90% porosity porous silica film; whose refractive index is 1.04 was improved by 311% when compared with that of a traditional SPR sensor. Furthermore; it was found that the decrease in the refractive index or the increase in the thickness of the low-refractive-index porous silica film can enlarge the FOM enhancement. It is believed that the proposed SPR sensor with a low-refractive-index porous silica film will be helpful for high-performance SPR sensors development.

Molecular Dynamics Simulation of the Crystal Nucleation and Growth Behavior of Methane Hydrate in the Presence of the Surface and Nanopores of Porous Sediment.

The behavior of hydrate formation in porous sediment has been widely studied because of its importance in the investigation of reservoirs and in the drilling of natural gas hydrate. However, it is difficult to understand the hydrate nucleation and growth mechanism on the surface and in the nanopores of porous media by experimental and numerical simulation methods. In this work, molecular dynamics simulations of the nucleation and growth of CH4 hydrate in the presence of the surface and nanopores of clay are carried out. The molecular configurations and microstructure properties are analyzed for systems containing one H2O hydrate layer (System A), three H2O hydrate layers (System B), and six H2O hydrate layers (System C) in both clay and the bulk solution. It is found that hydrate formation is more complex in porous media than in the pure bulk solution and that there is cooperativity between hydrate growth and molecular diffusion in clay nanopores. The hydroxylated edge sites of the clay surface could serve as a source of CH4 molecules to facilitate hydrate nucleation. The diffusion velocity of molecules is influenced by the growth of the hydrate that forms a block in the throats of the clay nanopore. Comparing hydrate growth in different clay pore sizes reveals that the pore size plays an important role in hydrate growth and molecular diffusion in clay. This simulation study provides the microscopic mechanism of hydrate nucleation and growth in porous media, which can be favorable for the investigation of the formation of natural gas hydrate in sediments.

Methanol electro-oxidation on platinum modified tungsten carbides in direct methanol fuel cells: a DFT study.

In exploration of low-cost electrocatalysts for direct methanol fuel cells (DMFCs), Pt modified tungsten carbide (WC) materials are found to be great potential candidates for decreasing Pt usage whilst exhibiting satisfactory reactivity. In this work, the mechanisms, onset potentials and activity for electrooxidation of methanol were studied on a series of Pt-modified WC catalysts where the bare W-terminated WC(0001) substrate was employed. In the surface energy calculations of a series of Pt-modified WC models, we found that the feasible structures are mono- and bi-layer Pt-modified WCs. The tri-layer Pt-modified WC model is not thermodynamically stable where the top layer Pt atoms tend to accumulate and form particles or clusters rather than being dispersed as a layer. We further calculated the mechanisms of methanol oxidation on the feasible models via methanol dehydrogenation to CO involving C-H and O-H bonds dissociating subsequently, and further CO oxidation with the C-O bond association. The onset potentials for the oxidation reactions over the Pt-modified WC catalysts were determined thermodynamically by water dissociation to surface OH* species. The activities of these Pt-modified WC catalysts were estimated from the calculated kinetic data. It has been found that the bi-layer Pt-modified WC catalysts may provide a good reactivity and an onset oxidation potential comparable to pure Pt and serve as promising electrocatalysts for DMFCs with a significant decrease in Pt usage.

Quantification of confocal fluorescence microscopy for the detection of cervical intraepithelial neoplasia.

BACKGROUND: Cervical cancer remains a major health problem, especially in developing countries. Colposcopic examination is used to detect high-grade lesions in patients with a history of abnormal pap smears. New technologies are needed to improve the sensitivity and specificity of this technique. We propose to test the potential of fluorescence confocal microscopy to identify high-grade lesions. METHODS: We examined the quantification of ex vivo confocal fluorescence microscopy to differentiate among normal cervical tissue, low-grade Cervical Intraepithelial Neoplasia (CIN), and high-grade CIN. We sought to (1) quantify nuclear morphology and tissue architecture features by analyzing images of cervical biopsies; and (2) determine the accuracy of high-grade CIN detection via confocal microscopy relative to the accuracy of detection by colposcopic impression. Forty-six biopsies obtained from colposcopically normal and abnormal cervical sites were evaluated. Confocal images were acquired at different depths from the epithelial surface and histological images were analyzed using in-house software. RESULTS: The features calculated from the confocal images compared well with those features obtained from the histological images and histopathological reviews of the specimens (obtained by a gynecologic pathologist). The correlations between two of these features (the nuclear-cytoplasmic ratio and the average of three nearest Delaunay-neighbors distance) and the grade of dysplasia were higher than that of colposcopic impression. The sensitivity of detecting high-grade dysplasia by analysing images collected at the surface of the epithelium, and at 15 and 30 µm below the epithelial surface were respectively 100, 100, and 92 %. CONCLUSIONS: Quantitative analysis of confocal fluorescence images showed its capacity for discriminating high-grade CIN lesions vs. low-grade CIN lesions and normal tissues, at different depth of imaging. This approach could be used to help clinicians identify high-grade CIN in clinical settings.

Transfemoral Device Occlusion and Minimally Invasive Surgical Repair for Doubly Committed Subarterial Ventricular Septal Defects.

Transfemoral device occlusion and minimally invasive surgical repair are performed for doubly committed subarterial ventricular septal defect (dcVSD) to reduce the invasiveness of the conventional surgical repair through a median sternotomy. However, few studies have compared them in terms of effectiveness and cost. Inpatients with isolated dcVSD who had undergone transfemoral device occlusion or minimally invasive surgical repair from January 2011 to June 2014 were reviewed for a comparative investigation between the two procedures. Procedure success was achieved in 36 transfemoral (75 %) and in 36 surgical (100 %) procedures (p = 0.001). Transfemoral patients were older, with a VSD size similar to that of surgical patients (14.5 ± 11.7 vs 4.4 ± 2.9 years, p < 0.001; 4.5 ± 1.5 vs 4.4 ± 1.3 mm, p = 0.577, respectively). No significant difference was observed in complication rates between the two treatment groups (p = 1). No large residual shunt was observed. Small residual shunt was noted in two transfemoral patients and four surgical patients (p = 0.674). All these small residual shunts closed spontaneously during follow-up. The surgical repair costs 26 % less than the device occlusion (Yuan 22063.2 ± 343.9 vs Yuan 29970.1 ± 1335.2, p < 0.001), where most of the cost was attributed to the occluder in the amount of Yuan 19,500. Compared with device occlusion, minimally invasive surgical repair can provide superior efficacy and comparable complication rates. In addition, it is 26 % cheaper than device occlusion. In low-income countries where healthcare resources are limited, medical resources must be judiciously allocated to the treatment that allows for effective treatment of the largest number of patients.

Stem cells with FGF4-bFGF fused gene enhances the expression of bFGF and improves myocardial repair in rats.

The aim of this study was to investigate whether the modification of bone marrow-derived mesenchymal stem cells (BMSCs) with the fused FGF4 (fibroblast growth factor 4)-bFGF (basic fibroblast growth factor) gene could improve the expression and secretion of BFGF, and increase the efficacies in repairing infarcted myocardium. We used In-Fusion technique to construct recombinant lentiviral vectors containing the individual gene of bFGF, enhanced green fluorescent protein (EGFP), or genes of FGF4-bFGF and EGFP, and then transfected these lentiviruses into rat BMSCs. We conducted an in vitro experiment to compare the secretion of bFGF in BMSCs infected by these lentiviruses and also examined their therapeutic effects in the treatment of myocardial infraction in a rodent study. Sixty rats were tested in the following five conditions: Group-SHAM received only sham operation as controls; Group-AMI received only injection of placebo PBS buffer; Group-BMSC, Group-bFGF and Group-FGF4-bFGF received implantation of BMSCs with empty lentivirus, bFGF lentivirus, and FGF4-bFGF lentivirus, respectively. Our results found out that the transplanted FGF4-bFGF BMSCs had the highest survival rate, and also the highest myocardial expression of bFGF and microvascular density as evidenced by Western blotting and immunohistochemistry, respectively. As compared to other groups, the Group-FGF4-BFGF rats had the lowest myocardial fibrotic fraction, and the highest left ventricular ejection fraction. These results suggest that the modification of BMSCs with the FGF4-bFGF fused gene can not only increase the expression of bFGF but also improve its secretion. The FGF4-bFGF BMSCs thus can enhance the survival of the transplanted cells, diminish myocardial fibrosis, promote myocardial angiogenesis, and improve cardiac functions.

The NEDD8 activating enzyme inhibitor MLN4924 mitigates doxorubicin-induced cardiotoxicity in mice.

Doxorubicin (DOX) is a widely utilized chemotherapeutic agent in clinical oncology for treating various cancers. However, its clinical use is constrained by its significant side effects. Among these, the development of cardiomyopathy, characterized by cardiac remodeling and eventual heart failure, stands as a major concern following DOX chemotherapy. In our current investigation, we have showcased the efficacy of MLN4924 in mitigating doxorubicin-induced cardiotoxicity through direct inhibition of the NEDD8-activating enzyme, NAE. MLN4924 demonstrated the ability to stabilize mitochondrial function post-doxorubicin treatment, diminish cardiomyocyte apoptosis, alleviate oxidative stress-induced damage in the myocardium, enhance cardiac contractile function, mitigate cardiac fibrosis, and impede cardiac remodeling associated with heart failure. At the mechanistic level, MLN4924 intervened in the neddylation process by inhibiting the NEDD8 activating enzyme, NAE, within the murine cardiac tissue subsequent to doxorubicin treatment. This intervention resulted in the suppression of NEDD8 protein expression, reduction in neddylation activity, and consequential manifestation of cardioprotective effects. Collectively, our findings posit MLN4924 as a potential therapeutic avenue for mitigating doxorubicin-induced cardiotoxicity by attenuating heightened neddylation activity through NAE inhibition, thereby offering a viable and promising treatment modality for afflicted patients.

Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification.

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.

UV-Triggered Hydrogel Coating of the Double Network Polyelectrolytes for Enhanced Endothelialization.

The left atrial appendage (LAA) occluder is an important medical device for closing the LAA and preventing stroke. The device-related thrombus (DRT) prevents the implantation of the occluder in exerting the desired therapeutic effect, which is primarily caused by the delayed endothelialization of the occluder. Functional coatings are an effective strategy for accelerating the endothelialization of occluders. However, the occluder surface area is particularly large and structurally complex, and the device is subjected to a large shear friction in the sheath during implantation, which poses a significant challenge to the coating. Herein, a hydrogel coating by the in situ UV-triggered polymerization of double-network polyelectrolytes is reported. The findings reveal that the double network and electrostatic interactions between the networks resulted in excellent mechanical properties of the hydrogel coating. The sulfonate and Arg-Gly-Asp (RGD) groups in the coating promoted hemocompatibility and endothelial growth of the occluder, respectively. The coating significantly accelerated the endothelialization of the LAA occluder in a canine model is further demonstrated. This study has potential clinical benefits in reducing both the incidence of DRT and the postoperative anticoagulant course for LAA closure.

Hydrogel Microneedle Patches Loaded with Stem Cell Mitochondria-Enriched Microvesicles Boost the Chronic Wound Healing.

Rescuing or compensating mitochondrial function represents a promising therapeutic avenue for radiation-induced chronic wounds. Adult stem cell efficacies are primarily dependent on the paracrine secretion of mitochondria-containing extracellular vesicles (EVs). However, effective therapeutic strategies addressing the quantity of mitochondria and mitochondria-delivery system are lacking. Thus, in this study, we aimed to design an effective hydrogel microneedle patch (MNP) loaded with stem cell-derived mitochondria-rich EVs to gradually release and deliver mitochondria into the wound tissues and boost wound healing. We, first, used metformin to enhance mitochondrial biogenesis and thereby increasing the secretion of mitochondria-containing EVs (termed "Met-EVs") in adipose-derived stem cells. To verify the therapeutic effects of Met-EVs, we established an in vitro and an in vivo model of X-ray-induced mitochondrial dysfunction. The Met-EVs ameliorated the mitochondrial dysfunction by rescuing mitochondrial membrane potential, increasing adenosine 5'-triphosphate levels, and decreasing reactive oxygen species production by transferring active mitochondria. To sustain the release of EVs into damaged tissues, we constructed a Met-EVs@Decellularized Adipose Matrix (DAM)/Hyaluronic Acid Methacrylic Acid (HAMA)-MNP. Met-EVs@DAM/HAMA-MNP can load and gradually release Met-EVs and their contained mitochondria into wound tissues to alleviate mitochondrial dysfunction. Moreover, we found Met-EVs@DAM/HAMA-MNP can markedly promote macrophage polarization toward the M2 subtype with anti-inflammatory and regenerative functions, which can, in turn, enhance the healing process in mice with skin wounds combined radiation injuries. Collectively, we successfully fabricated a delivery system for EVs, Met-EVs@DAM/HAMA-MNP, to effectively deliver stem cell-derived mitochondria-rich EVs. The effectiveness of this system has been demonstrated, holding great potential for chronic wound treatments in clinic.

Shexiang Baoxin Pill treats acute myocardial infarction by promoting angiogenesis via GDF15-TRPV4 signaling.

Angiogenesis has been considered a pivotal strategy for treating ischemic heart disease. One possible approach, the Shexiang Baoxin Pill (MUSKARDIA), has been noted to promote angiogenesis, but its underlying mechanism is still largely unknown. We aimed to determine the effects of MUSKARDIA on acute myocardial infarction (AMI), as well as the underlying mechanistic bases. AMI was induced in rats, using left anterior descending coronary arterial occlusion, and either 6 (low) or 12 (high-dose) mg/kg/day of MUSKARDIA was administered for 56 days. We found that MUSKARDIA improved cardiac function and counteracted against adverse remodeling among AMI rats, which most likely is due to it promoting angiogenesis. Transcriptome analysis by RNA-sequencing found that MUSKARDIA up-regulated cardiac pro-angiogenic genes, particularly growth differentiation factor 15 (GDF15), which was confirmed by RT-qPCR. This up-regulation was also correlated with elevated serum GDF15 levels. In vitro analyses with human umbilical vein endothelial cells found that increased GDF15, stimulated by MUSKARDIA, resulted in enhanced cell migration, proliferation, and tubular formation, all of which were reversed after GDF15 knockdown using a lentiviral vector. Gene Ontology, as well as Kyoto Genes and Genomes enrichment analyses identified calcium signaling pathway as a major contributor to these outcomes, which was verified by Western blot and Cal-590 AM loading showing that transient receptor potential cation channel subfamily V member 4 protein (TRPV4) and intracellular Ca2+ levels increased in accordance with MUSKARDIA-induced GDF15 up-regulation, and decreased with GDF15 knock-down. Therefore, MUSKARDIA may exert its cardioprotective effects via stimulating the GDF15/TRPV4/calcium signaling/angiogenesis axis.

Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub.

Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.

Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values.

Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.

Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color.

The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.