Coryphaenoides armatus is a deep-sea species with broad geographic and bathymetric distribution and a highly developed olfactory system, rendering it a potential indicator species for deep-sea mining regions and a model for studying environmental adaptation. Genomic resources for this species are limited, restricting insights into its adaptive evolution. Here, we present a chromosome-level genome assembly of C. armatus, constructed using PacBio HiFi long-read sequencing, Illumina short-read polishing, and Hi-C scaffolding. The final assembly spans 811.1 Mb, achieves a scaffold N50 of 33.3 Mb, and is organized into 24 chromosomes. The complete BUSCO score at the chromosome-level assembly was 90.9%. A total of 24,818 protein-coding genes were annotated in the assembly. This high-quality genome assembly of C. armatus provides a solid foundation for understanding physiological processes, identifying potential indicator species in deep-sea mining regions and exploring adaptive evolution in extreme environments.

The transport of manganese (Mn) from the cytosol into the vacuole is a crucial mechanism for metal and ion tolerance in plants. Mulberry exhibits potential to detoxify Mn via phytoremediation by activating the calcium/proton exchanger 3 (MaCAX3); however, its precise molecular mechanism remains uncharacterised. This study elucidates the molecular mechanisms by which MaCAX3 confers tolerance to Mn toxicity in mulberry, demonstrating its activation via induction by methyl jasmonate (MeJA). Our findings indicate that exposure to Mn toxicity severely impaired mulberry growth and biomass, correlating with a significant decline in the maximal photochemical efficiency of PSII (Fv/Fm) and a reduction in chlorophyll content. Exogenous JA application, however, effectively rescued these growth and physiological parameters by enhancing Mn tolerance. The results further establish that MeJA concentrations up to 200 μM released from the MeJA@ZIF-8 composite are pivotal in alleviating Mn toxicity, significantly boosting the activities of superoxide dismutase, peroxidase and catalase, reducing malondialdehyde content and inducing MaCAX3 expression. Moreover, silencing MaCAX3 compromised mulberry's Mn tolerance, whereas its overexpression in Arabidopsis enhanced Mn tolerance by diminishing reactive oxygen species through the activation of antioxidative enzymes. Collectively, these results underscore MeJA-associated regulation of MaCAX3 and the functional role of MaCAX3 in regulating Mn and ion homoeostasis, presenting a promising target for engineering Mn phytoremediation and for developing Mn-stress-tolerant mulberry varieties.

In gymnosperms such as Ginkgo biloba, the regulatory role of large introns remains unclear. To address this, we conducted integrative multi-omics analyses of chromatin accessibility, three-dimensional chromosomal architecture, histone modifications, DNA methylation, RNA polymerase II occupancy, and gene expression in Ginkgo, complemented by laboratory experiments. We first identified a plant-specific factor, plant-Loop Factor (p-LoopF), which shares ~40% sequence similarity with human CCCTC-binding factor (CTCF). p-LoopF binds specifically to the consensus motif recognized by human CTCF and is significantly associated with chromatin looping, but it lacks canonical CTCF functional features, including motif orientation dependence, chromatin insulation activity, and statistically significant correlations with cohesin subunits. Through integrative multi-omics analyses, we propose a regulatory hypothesis in which p-LoopF-associated chromatin loops are correlated with the recruitment of distal enhancer-like regulatory regions, with large introns serving as a key regulatory context for these interactions. p-LoopF also localizes to promoters and distal intergenic regions, correlating with transcriptional regulation and local chromatin organization. We characterized large introns as regions enriched for chromatin loops, p-LoopF binding sites, and enhancer-like elements, which are strongly associated with the transcriptional regulation of their host genes. Additionally, active histone marks and DNA demethylation were enriched near the boundaries of large introns, particularly around splice sites, suggesting that splicing regulation differs between large and small introns.

Mulberry (Morus alba L.) demonstrates notable tolerance to heavy metals, including excess molybdenum (Mo). However, the metabolic basis of this tolerance remains poorly understood. Our primary objective was to characterize the Mo-induced metabolome alterations and their correlation with physiological changes in M. alba. We conducted a comprehensive analysis of physiological and metabolic responses in M. alba (Yu-711) leaves under four Mo (Na2MoSO4) regimes, viz, deficient (0 mg L−1; T1), normal (0.25 mg L−1; control, CK), and excess (2.5 mg L−1, T2; 12.5 mg L−1, T3) after 20 days of pots experiment and using untargeted LC–MS-based (liquid chromatography-mass spectrometry) metabolomics techniques. Molybdenum deficiency and excess significantly impaired photosynthetic efficiency and reduced chlorophyll content, leading to leaf biomass (dry) reductions of 37.8

Vegetative propagation of mulberry (Morus alba L.) via sapling methods, due to the ability to exponentially multiply lateral buds on stem cuttings to enhance rapid shoot formation, is crucial for sericulture industries. The sprouting of mulberry using stubbles is an emerging method for rapid and mass production of mulberry leaves, but the growth mechanisms associated with its use remain obscure. This study is the first to report how the differential stubble lengths from mulberry plants alter and modulate phytohormones and the associated mechanisms. This study seeks to evaluate the growth mechanisms by elucidating the phytohormone signature modulation in response to differential stubble lengths of 0 cm, 5 cm, 10 cm, 20 cm, and a control via targeted metabolomics analysis in mulberry leaves. The results consistently show that the use of differential stubble lengths of mulberry promoted growth, the number of buds, aboveground biomass, and branch and leaf weights by improving the net photosynthesis, transpiration rate, stomatal conductance, and intercellular CO2 relative to the control. The differential stubble lengths not only caused contrasting responses in the contents of plant hormones, including salicylic acid (SA), abscisic acid (ABA), indole-3-acetic acid (IAA), jasmonic acid (JA), and gibberellin (GA), but also modulated higher elemental contents relative to the control. The results further reveal significant and positive correlations between the phytohormones and all growth, biomass, and photosynthetic parameters, highlighting the role of phytohormones in the sprouting and rejuvenation of mulberry stubbles. Meanwhile, the targeted metabolomics analysis identified a total of 11 differentially accumulated phytohormones in response to the differential stubble lengths, which were significantly implicated and enriched in three major pathways, including the biosynthesis of plant hormones (ko01070), metabolic pathways (ko01100), and the plant hormone signal transduction pathway (ko04575). The use of stubbles for rapid leaf production in mulberry plants is of great importance to improve early sprouting and cutting survival, as well as shortening growth and rooting time, and is highly recommended for the sericulture industries.

This study investigated the mechanisms of cadmium (Cd) tolerance and root exudate-mediated soil activation in mulberry (Morus alba L.), a promising species for phytoremediation. Hydroponic experiments with Cd-tolerant seedlings exposed to 5 and 50 mg/L Cd revealed a biphasic concentration-dependent response. Low Cd induced negligible biological effects, whereas high Cd triggered substantial disturbances across multiple biological levels, including morphological alterations, physiological dysregulation and disrupted elemental accumulation patterns. Metabolomic profiling indicated that Cd stress significantly altered the secretion patterns of 17 root exudate metabolites in mulberry, exemplified by the upregulation of sucrose, lactose and 4-acetylbutyric acid, and the downregulation of β-alanine and myo-inositol. Further pathway enrichment analysis linked these differential metabolites to 17 metabolic pathways, with carbohydrate and amino acid metabolism as the main Cd-responsive pathways, suggesting their core role in mediating mulberry's Cd resistance. Root exudates enhanced soil Cd mobilisation in a positive concentration-dependent yet negative time-dependent manner. Consequently, mulberry adapts to Cd stress via metabolic reprogramming of root exudates-a strategic trade-off that serves a dual role by enhancing plant tolerance while simultaneously increasing Cd bioavailability in the soil. This insight provides a foundational framework for phytoremediation, centred on exudate management and the selection of stress-tolerant varieties.

Using spike-in standards for RNA-seq experiments is critical to evaluate technical bias introduced during sample preparation, sequencing and analysis. Although some external RNA spike-in standards have been developed, species-specific spike-in standard was not reported yet. Here we developed the human-specific spike-in standards with 65 controls. We first extracted human endogenous RNAs with various lengths and GC contents, introduced random mutations approximately every 75 bp in each RNA, and then synthesized these RNAs as spike-in RNAs. After that, four mixtures of these spike-in RNAs covering a 220 dynamic range were obtained. To ensure the accuracy of RNA concentration, two rounds of ddPCR were conducted for each spike-in RNA and the intraclass correlation coefficient between two ddPCRs ranged from 0.9954 to 0.9971 after removing the two spike-in RNAs with the largest concentration difference. Furthermore, we showed that the sequencing error profiles were distinct between platforms and the library preparation procedures were related with the discrepancies in spike-in RNA read percent, transcript abundance, sequence coverage distribution, and differential gene expression. In addition, two regression models of sequence coverage were built based on RNA second structure and GC content, and 86.62%–91.78% of the variation can be explained. Our study demonstrates the technical performance of the human-specific spike-in standards for RNA-seq experiments and illustrates the biases across different libraries, platforms, and laboratories. ### Competing Interest Statement The authors have declared no competing interest.

As an economically important tree species, mulberry (Morus spp.) has exhibited a remarkable tolerance for salinity, drought and heavy metals. However, the precise mechanism of metabolome-mediated drought adaptation is unclear. In this study, two new mulberry varieties-'drought-sensitive guisangyou62 (GSY62) and highly drought-tolerant guiyou2024 (GY2024)'-after three days (62F or 2024F) and six days (62B or 2024B) of drought-stress conditions were subjected to transcriptome and metabolome analyses. The enrichment analysis demonstrated that the differentially expressed genes (DEGs) were mainly enriched in carbohydrate metabolism, amino acid metabolism, energy metabolism and secondary metabolite biosynthesis under drought-stress conditions. Notably, compared with the CK group (without drought treatment), 60 and 70 DEGs in GY2024 and GSY62 were involved in sucrose and starch biosynthesis, respectively. The genes encoding sucrose phosphate synthase 2 and 4 were downregulated in GY2024, with a lower expression. The genes encoding key enzymes in starch biosynthesis were upregulated in GY2024 and the transcriptional abundance was significantly higher than in GSY62. These results indicated that drought stress reduced sucrose synthesis but accelerated starch synthesis in mulberry.

Our previous experiments confirmed that two mulberry spermidine synthase (SPDS) genes (MnSPDS1 and MnSPDS2) that encode functional proteins are highly expressed under drought stress. In this study, the functions of MnSPDS1/MnSPDS2 in the drought stress response were further explored by silencing and overexpressing these genes in mulberry and tobacco, respectively. Compared with the wild-type (WT) plants, the MnSPDS1/MnSPDS2-overexpression tobacco plants were more tolerant to drought stress and showed a higher spermidine content (P < 0.05). Moreover, overexpression of MnSPDS1/MnSPDS2 at the physiological level alleviated membrane damage caused by drought and improved osmotic regulation and antioxidant capacity. In addition, correlation analysis showed that the content of spermidine was positively correlated with the expression levels of MnSPDS1 and MnSPDS2, with correlation coefficients of 0.762 and 0.715, respectively. Moreover, drought injury was more serious in the MnSPDS-silenced seedlings than in the WT seedlings after drought treatment. These results suggest that MnSPDS genes play important roles in the drought stress response and are valuable for molecular breeding to enhance the drought tolerance of mulberry.

The commonly-used drug susceptibility testing (DST) relies on bacterial culture and faces shortcomings such as long turnaround time and clonal/subclonal selection biases. Here, we developed a targeted deep amplicon sequencing (DAS) method directly applied to clinical specimens. In this DAS panel, we examined 941 drug-resistant mutations (DRMs) associated with 20 anti-tuberculosis drugs with only 4 pg of initial DNA input, and reduced the clinical testing time from 20 days to 2 days. A prospective study was conducted using 115 clinical specimens, predominantly positive for the Xpert®  Mycobacterium tuberculosis/rifampicin (Xpert MTB/RIF) assay, to evaluate DRM detection. DAS was performed on culture-free specimens, while culture-dependent isolates were used for phenotypic DST, DAS, and whole-genome sequencing (WGS). For in silico molecular DST, our result based on DAS panel revealed the similar accuracy to three published reports based on WGS. For 82 isolates, application of DAS using the resistance-determining mutation method showed better accuracy (93.03% vs. 92.16%), sensitivity (96.10% vs. 95.02%), and specificity (91.33% vs. 90.62%) than WGS using the Mykrobe software. Compared to culture-dependent WGS, culture-free DAS provides a full picture of sequence variation at the population level, exhibiting in detail the gain-and-loss variants caused by bacterial culture. Our study performs a systematic verification of the advantages of DAS in clinical applications and comprehensively illustrates the discrepancies in Mycobacterium tuberculosis before and after culture.

There are abundant mulberry germplasm resources in China. Generally, in order to better utilize these resources, a comprehensive evaluation is conducted, among which the evaluation of photosynthetic capacity is an important aspect. To evaluate the photosynthetic characteristics of mulberry trees with different ploidy levels, which determine the number of chromosome sets in a cell or organism, we compared the microstructural features and transcriptomes of triploid and diploid mulberry trees. Haploid (n) means having one set of chromosomes, diploid (2n) has two sets, triploid (3n) has three sets, and so on. We compared the microstructural features and transcriptomes of triploid and diploid mulberry trees. In this study, the photosynthetic rates (Pn) of ‘guisang6hao’ (hereinafter referred to as GS6, 2n = 3x = 42) were 1.2 times that of ‘guisangyou12’(hereinafter referred to as GSY12, 2n = 2x = 28). Here, GS6 and GSY12 are abbreviations for the two mulberry varieties. The leaf thickness, main vein thickness, epidermal thickness, palisade tissue thickness, spongy tissue thickness and lower epidermal stomatal density of GS6 were greater than those of GSY12. Additionally, the transcriptome characteristics of GS6 and GSY12 were characterised by Illumina Novaseq 6000 and the differentially expressed genes (DEGs) were significantly enriched in photosynthesis. Four differentially expressed metabolites (DEMs) related to photosynthesis were identified, playing key roles in chlorophyll metabolism and carbon fixation in photosynthetic organisms. The above results indicated that an increase in the ploidy level enhanced the photosynthetic capacity and utilisation of light energy, as well as the accumulation of chlorophyll content, of triploid mulberry trees. This study provides a technical and theoretical basis for germplasm innovation and the genetic improvement of mulberry.

BackgroundTuberculosis (TB) remains a serious global public health problem. The Mycobacterium tuberculosis (MTB) is responsible for approximately 10 million new TB cases globally each year. This study aimed to investigate transmission pattern and drug resistance of MTB in Shenzhen, China.MethodsA retrospective study on 286 samples from 184 TB patients collected between 2015 and 2018 in Shenzhen Third People’s Hospital was conducted using whole-genome sequencing. Drug susceptibility testing (DST) was performed using both phenotypic DST (pDST) and molecular DST (mDST). Sample diversity was evaluated by SNPs and transmission clusters were identified based on SNP differences of 12 or fewer in genetic clusters.ResultsExcept four samples identified as non-tuberculous mycobacteria, 282 MTB samples (181 patients) underwent mDST, with 244 samples (162 patients) undergoing pDST. The overall multidrug-resistant rate in patients was 22.31% in pDST (12.00% for new patients and 40.82% for retreatment patients) and 34.48% in mDST (20.41% for new patients and 58.21% for retreatment patients). Totally 92 transmission clusters were identified, encompassing 70.21% samples (57.46% patients), with 5 clusters containing samples (15, 5.32%) from different patients (9, 4.97%), indicating recent transmission. The drug-resistant mutations in 36 of 45 transmission clusters (80.00%) were identical in all samples, suggesting the transmission of drug resistance. Patients with multiple samples were categorized into simultaneous sampling (SS) and continuous sampling (CS) groups, revealing significant differences in treatment types, treatment outcomes, residential addresses, and drug resistance types. mDST showed greater accuracy than pDST in SS and CS groups. A novel method based on heterozygous SNPs and two-sample Kolmogorov–Smirnov test were developed and identified 12 (4.26%) samples as mixed infection samples. Six of 12 patients had mixed and pure samples together, and major strains of mixed samples were closer to corresponding pure strains than minor strains.ConclusionsThis retrospective study, conducted at the only municipal hospital specializing in infectious diseases in Shenzhen, provides the opportunity to understand drug resistance of TB patients, which mainly are refractory patients. The study revealed transmission patterns of MTB, analyzed mixed infections, and tracked changes in MTB strains during short/long-term treatment.

Autochthonous microorganisms play critical roles in shaping the quality of Chinese sausages and may be influenced by local climate and/or processing conditions. The present study aimed to reveal the interprovincial differences in microbial community between Sichuan and Guizhou sausages, as well as driving factors based on high-throughput sequencing and bioinformatic analysis. The results indicated that Cobetia, Debaryomycetaceae, Kurtzmaniella, and Candida zeylanoides served as biomarkers for Sichuan sausages. In contrast, Enterococcus, unclassified Cyanobacteriales, Lactobacillales, Aspergillus vitricola, Mortierella, Fusarium, and Penicillium were identified as biomarkers for Guizhou sausages. Furthermore, salt content and moisture level showed positive correlations with Cobetia, Staphylococcus, Debaryomyces, and Kurtzmaniella, mainly found in Sichuan sausages. Conversely, pH and water activity (Aw) were positively associated with potential pathogenic bacteria (e.g., Vibrio, Cyanobacteria, Enterococcus, and Aeromonas) and fungi (e.g., Aspergillus, Fusarium, and Penicillium), which were mainly distributed in Guizhou sausages. Notably, microbial composition discrepancies between Sichuan and Guizhou sausages were primarily driven by processing conditions rather than regional climate factors. Collectively, these findings provide valuable insight for developing novel specific starters.

Dipteran insects include numerous harmful species that cause significant agricultural damage. However, assembly of genomes for species in this order has been difficult due to their small body size, poor conservation of telomere and centromere structures, high levels of heterozygosity, and complex genetic backgrounds. In this study, we assemble a high-quality 596 Mb telomere-to-telomere genome for Bactrocera dorsalis, a fruit crop pest, using a strategy with a low-input HiFi CCS library from a male individual and an ONT sequence from pooled inbred individuals. The assembly includes complete structural organization information for centromeres and telomeres, providing insights into the evolution of chromosome structure in insects. Comparative genomic analysis reveals the polyphyletic origin of sex chromosomes across Diptera. Furthermore, we identify a homolog of ATPsynβ as a Y chromosome-specific gene that is highly expressed across multiple male tissues and may provide critical support for male-specific physiological activities. Additionally, we discover several tandem duplications of odorant receptor genes, including a triplet of the OR88a family, which was validated to be involved in the behavioral response to methyl eugenol. In summary, this complete reference genome provides a foundation for future genomic research in Diptera and offers genetic insights for the control of B. dorsalis. Insect genomics is entering a telomere-to-telomere (T2T) era. This study presents a 596-Mb T2T genome of an individual male Bactrocera dorsalis—a species with atypical telomeres, centromeres, and sex-chromosome architecture—advancing genetics, chromosome biology, and pest management.

Manganese (Mn) deficiency and toxicity are major constraints on crop production in soil. Plants have evolved cascade strategies and specific mechanisms to tolerate these stresses. Understanding the molecular mechanisms of tolerance to Mn stress is crucial for improving the efficiency of conferring Mn tolerance and phytoremediation, which is intriguing for evolutionary research on plant adaptation to abiotic stresses. In this study, the responses of mulberry to varied concentration levels of Mn (MnSO4), ranging from deficiency (0 mM and 0.03 mM), sufficiency (0.15 mM), and toxicity regimes (1.5 mM and 3 mM) were compared by elucidating the physiological, transcriptome profiling, and functional characterization of the MaCAX3 gene in mulberry leaves. The results show that Mn-induced deficiency and toxicity not only trigger an increase in oxidation and antioxidant parameters, including hydrogen peroxide (H2O2), lipid peroxidase (LPO), polyphenol oxidase (PPO), and reactive oxygen species (ROS) but also concomitantly improved the activities of total antioxidant capacity (TAC) and hydroxyl radical (•OH) scavenging levels in mulberry. Results of the cell wall structural components show that cellulose, hemicellulose, and lignin contents were significantly higher, except for pectin, in the control (CK) compared to the deficiency and toxicity. Functional validation of the MaCAX3 gene via gene silencing revealed that the heterologous expression of the MaCAX3 gene increased the transport of Mn in yeast, thus inhibiting the toxic effect of Mn relative to the silenced Macax3-VIGS. Additionally, transcriptome analysis identified a total of 811 differentially expressed genes (DEGs), with 189 and 622 being up- and downregulated, respectively. These DEGs were significantly involved in Mn transport, detoxification, oxidation, antioxidant defense, and cell wall and protein processing, which conferred tolerance to Mn in mulberry plants. The study sheds substantial light on key molecular mechanisms and the functional characterization and validation of crucial Mn tolerance genes in mulberry leaves.

Afforestation is regarded as an effective strategy to increase carbon (C) sequestration. Mulberry plantation has both economic and cultural significance. However, the study of its influence on soil C pool stability remains limited. The chemical and physical stability characteristics of soil C in mulberries and control wastelands were determined. The mechanism underlying C pool stability change was analyzed in conjunction with soil physicochemical properties, microbial metagenomic characteristics, and climatic factors. (1) Compared with wastelands, mulberries showed a 26.6

Oilseed crops, which are rich in plant lipids, provide essential fatty acids for human consumption and serve as major sources of biofuels and essential raw materials for the chemical industry. As a result of population growth and ecological changes, the demand for vegetable oil is increasingly outpacing supply. A comprehensive understanding of the genes involved in lipid metabolism in oilseed crops and the regulatory relationships among these genes is essential for improving oil content. However, current studies on lipid metabolism genes rely heavily on a decade-old database of genes involved in lipid metabolism in Arabidopsis thaliana . To address this issue, we mined the literature, integrated data from various databases and studies, and aligned homologs of lipid metabolism genes from nine oilseed crops to construct a comprehensive set of lipid metabolism genes in plants. Using this approach, we identified 221 additional lipid metabolism genes. In addition, we created a user-friendly lipid database called CLAIR (Crop Lipid-Associated Information Resource) by integrating and mining multi-omics data from nine major oil crops. The database is available at http://www.clipair.cn/ . These resources should facilitate further research and exploration of lipid metabolism in oil crops, ultimately contributing to improved oil production.

The inference of gene co-expression module in specific cell types is important for understanding of cell-type-specific biological processes. We have developed DeepCSCN, an unsupervised deep-learning framework, to infer gene co-expression modules from single-cell RNA sequencing (scRNA-seq) data. Utilizing a global-to-local network construction approach, DeepCSCN can infer co-expression at the whole sample level and construct cell-type-specific co-expression networks. Systematic evaluations on eight public scRNA-seq datasets show that DeepCSCN significantly outperforms eight existing methods in co-expression network construction. Furthermore, DeepCSCN effectively identifies cell-type-specific co-expression networks that are more enriched for cell-specific functional pathways compared to current methods. Finally, application of DeepCSCN on public scRNA-seq data revealed 280 cell-specific gene modules across 27 cell types, including epithelial cells, immune cells, and myonuclei, demonstrating its versatility and accuracy in elucidating cell-type-specific gene co-expression regulation. DeepCSCN offers a powerful tool for researchers to dissect the intricate gene co-expression networks within distinct cell types. ### Competing Interest Statement The authors have declared no competing interest.

The para rubber tree (Hevea brasiliensis) is the world's sole commercial source of natural rubber, a vital industrial raw material. However, the narrow genetic diversity of this crop poses challenges for rubber breeding. Here, we generate high-quality de novo genome assemblies for three H. brasiliensis cultivars, two H. brasiliensis wild accessions, and three other Hevea species (H. nitida, H. pauciflora, and H. benthamiana). Through analyzing genomes of 94 Hevea accessions, we identify five distinct lineages that do not align with their previous species delineations. We discover multiple accessions with hybrid origins between these lineages, indicating incomplete reproductive isolation between them. Only two out of four wild lineages have been introduced to commercial rubber cultivars. Furthermore, we reveal that the rubber production traits emerged following the development of a large REF/SRPP gene cluster and its functional specialization in rubber-producing laticifers within this genus. These findings would enhance rubber breeding and benefit research communities.