Allopolyploidy can generate rapid phenotypic change, yet its early transcriptomic consequences in a newly generated triploid hybrid remain poorly understood in animals. Here, we establish a sterile triploid hybrid between grass carp (Ctenopharyngodon idella) and yellowcheek (Elopichthys bambusa), designated CCE, using an optimized hydrostatic pressure protocol that achieved 100% triploidy with high embryonic viability. Whole-genome resequencing supported an approximately 2:1 maternal-to-paternal genomic dosage. Transcriptomes from seven tissues revealed that maternal expression-level dominance (ELD-Ci) was the predominant expression-inheritance pattern (63.7–84.2%), consistent with a passive, dosage-dependent mode of regulation. Paternal expression-level dominance (ELD-Eb) was detected in all tissues but with marked tissue specificity: most ELD-Eb genes in the liver and muscle showed expression levels similar to those of the paternal yellowcheek parent before hybridization (96.2% and 72.8%, respectively), whereas the brain and hypothalamus contained more ELD-Eb genes not directly explained by parental differences. Finally, in the gut, CCE had shorter villi than both parents, a thicker muscularis layer than both parents, and fewer goblet cells than Eb. Genes related to digestion, absorption, and nutrient transport were more highly expressed in Eb and retained an Eb-like expression pattern in CCE. By contrast, several smooth muscle-related genes, including myh14 and smtnl1, showed non-additive upregulation beyond the parental range, in parallel with the thickened muscularis layer. Together, these findings provide new insights into how parental genome dosage and tissue-specific regulation shape gene expression divergence in newly formed animal allopolyploids.

Polyploidy frequently originates from meiotic failure, with mis-segregation of homologous chromosomes commonly arising from impaired formation of programmed DNA double-strand breaks (DSBs). Meiotic double-stranded break formation protein 4 (Mei4) is essential for recruiting the Sporulation-specific protein 11 (Spo11) nuclease to chromosome axes to initiate DSB formation in yeast and mice, yet its role in fish remains uncharacterized. In this study, mei4-/- zebrafish mutants were generated and exhibited severe defects in synapsis, DSB formation, homologous recombination, and crossover (CO) formation during meiosis in both male and female germ cells. Notably, pronounced sexual dimorphism in responses to Mei4 deficiency was observed during meiotic prophase I, with males exhibiting complete sterility due to meiotic arrest, while females produced numerous aneuploid oocytes and a minority of unreduced eggs due to defective chromosome segregation. Remarkably, crosses between mei4-/- females and wild-type males yielded a substantial number of viable triploid progeny. These findings demonstrate functional conservation of Mei4 in mediating meiotic DSB formation across vertebrates, reveal sex-specific divergence in meiotic responses to recombination failure in this vertebrate model, and highlight a critical role for DSB-dependent crossover failure in the genesis of polyploidy.

Background Rodent-borne pathogens pose important global health risks, yet national-scale assessments linking host-pathogen ecology with disease dynamics remain limited, particularly in China. Methods We compiled global (>29,000 records) and China-specific (2235 records; 1950–2023) rodent-pathogen datasets to characterize host-pathogen networks, identify hyperreservoirs, and quantify prevalence heterogeneity using hierarchical meta-regression. We applied a two-layer framework integrating 1-km host suitability surfaces (stacking ensemble of boosted regression trees and random forest models) with province-level disease inference using generalized linear models for hemorrhagic fever with renal syndrome (HFRS), leptospirosis, and plague. Human exposure was estimated by overlaying suitability with gridded population data. Results Globally, 116 pathogens of concern were identified across 206 host species, including 30 spillover-risk viruses and 34 hyperreservoirs. Meta-regression identified sample source as the only consistently robust moderator of prevalence heterogeneity; other moderators (e.g., rodent family, region, and habitat type) showed inconsistent or non-robust associations. Host suitability was positively associated with HFRS incidence (incidence rate ratio = 1.36, P < 0.01) but negatively or not significantly associated with leptospirosis and plague. In China, the three diseases showed contrasting suitability patterns, with approximately 404 million people (29.3%) residing in areas with high suitability for at least one disease. Conclusions Our analysis elucidates disease-specific ecological drivers and identifies spatial priorities to inform targeted One Health surveillance and integrated interventions.

Objective:Multidrug-resistant tuberculosis (MDR-TB) remains a major global health challenge. While T cell-mediated immunity in tuberculosis is well characterized, alterations in circulating B-cell subsets during chronic MDR-TB are less well defined. Methods:Peripheral blood mononuclear cells (PBMCs) from healthy controls [interferon gamma release assay negative (IGRA-)], individuals with latent tuberculosis infection (LTBI; IGRA+), and patients with active tuberculosis (ATB) were analyzed using multiparameter flow cytometry panels. Major lymphoid and myeloid populations and detailed B-cell subsets were quantified. Results:Frequencies of major T-cell and natural killer (NK)-cell populations were broadly similar across groups. In contrast, patients with ATB showed a reduction in total CD19+ B cells. Within the B-cell compartment, ATB was characterized by an increased proportion of naïve B cells and a pronounced reduction in antibody-secreting cells (ASCs). Circulating marginal zone-like B cells (MZ B, IgD+IgM+CD27+) were also reduced in ATB compared with non-ATB groups. Receiver operating characteristic (ROC) analysis suggested that reduced MZ B-cell frequency may help discriminate individuals with ATB from those without ATB; however, this observation should be interpreted as exploratory given the cohort size and composition. Conclusion:MDR-TB is associated with broad perturbations of the peripheral B-cell compartment, including reduced ASCs and decreased circulating MZ B cells. These findings highlight B-cell dysregulation as a feature of active disease and identify MZ B cells as a subset of interest for further investigation rather than as a stand-alone diagnostic marker.

Allopolyploids often exhibit enhanced resistance to pathogen stresses. However, our understanding about the patterns that allopolyploids modify homeolog expression upon pathogen invasion remains limited. Since 2012, a disease caused by herpesvirus (CaHV) has posed a severe threat to Carassius auratus aquaculture. Therefore, the synthesis of novel allopolyploids with enhanced resistance has become one of significant priorities for its aquaculture. In this study, we first synthesized and then established a gynogenetic Carassius alloheptaploid clone (CaA7n). It possesses approximately 158 chromosomes of C. gibelio and 24 haploid chromosomes of M. amblycephala. CaHV challenge experiments showed that CaA7n inherited high resistance from its paternal M. amblycephalus, exhibiting a 100% survival rate after CaHV infection. Subsequently, we revealed distinct transcriptional responses among CaA7n and its parents to CaHV infection and identified two key modules. The egiengenes in the module that positively correlated with CaA7n resistance were mainly enriched in chemokine activity GO terms. Finally, we described a profound expression alteration of three homeologs in CaA7n, including additive and non-additive expression patterns. After CaHV infection, three homeologs mainly involved in chemokine activity changed their expression patterns in CaA7n. Moreover, homeologs derived from M. amblycephala associated with chemokine activity, which showed altered expression levels, may enhance the antiviral immune response of CaA7n. This study not only establishes CaA7n as a promising CaHV-resistant candidate for aquaculture but also elucidates how allopolyploids reconfigure parental homeolog expression networks to enhance antiviral defenses, advancing our understanding of allopolyploid adaptation mechanisms under pathogenic pressure.

Both unisexuality and polyploidy are significant in agriculture, exhibiting revolutionary biotechnology potential, as their coupling has been demonstrated to enable the design of polyploid genomes in crops. However, their applicability to animals has remained a challenge. Herein, the first case of engineering polyploid genomes with desirable traits via unisexual-sexual reproduction transition is provided. First, a group of genome-reconstructed amphitriploids (GR-A3n) is generated involving unisexual gynogenetic Carassius gibelio, sexual C. auratus, and sexual C. cuvieri. Then, we found that the gynogenesis ability have transferred from C. gibelio to some of the GR-A3n females. This study subsequently established three GR-A3n clones with distinct herpesvirus resistance and in which differential transcriptome profiles are characterized in two main hematopoietic organs. Most genes of the hemoglobin metabolism pathway is found to exhibit high expression levels, as in C. cuvieri, which led to efficient hemoglobin biosynthesis and blood oxygen homeostasis during infection, thereby resulting in strong herpesvirus resistance. Furthermore, this study determined the resistant and susceptible haplotypes derived from chromosome 12B of C. cuvieri, which should be responsible for resistance differences between GR-A3n clones. Overall, this study establishes an approach for genetic improvement through polyploid genome design in animals.

BACKGROUND:Gallbladder cancer (GBC) is the most common and lethal malignancy of the biliary tract that lacks effective therapy. In many GBC cases, infiltration into adjacent organs or distant metastasis happened long before the diagnosis, especially the direct liver invasion, which is the most common and unfavorable way of spreading. METHODS:Single-cell RNA sequencing (scRNA-seq), spatial transcriptomics (ST), proteomics, and multiplexed immunohistochemistry (mIHC) were performed on GBC across multiple tumor stages to characterize the tumor microenvironment (TME), focusing specifically on the preferential enrichment of neutrophils in GBC liver invasion (GBC-LI). RESULTS:Multi-model Analysis reveals the immunosuppressive TME of GBC-LI that was characterized by the enrichment of neutrophils at the invasive front. We identified the context-dependent transcriptional states of neutrophils, with the Tumor-Modifying state being associated with oxidized low-density lipoprotein (oxLDL) metabolism. In vitro assays showed that the direct cell-cell contact between GBC cells and neutrophils led to the drastic increase in oxLDL uptake of neutrophils, which was primarily mediated by the elevated OLR1 on neutrophils. The oxLDL-absorbing neutrophils displayed a higher potential to promote tumor invasion while demonstrating lower cancer cytotoxicity. Finally, we identified a neutrophil-promoting niche at the invasive front of GBC-LI that constituted of KRT17+ GBC cells, neutrophils, and surrounding fibroblasts, which may help cultivate the oxLDL-absorbing neutrophils. CONCLUSIONS:Our study reveals the existence of a subset of pro-tumoral neutrophils with a unique ability to absorb oxLDL via OLR1, a phenomenon induced through cell-cell contact with KRT17+ GBC cells in GBC-LI.

The amh (anti-Müllerian hormone) gene, residing on the sex chromosomes, has been hypothesized to be a potential master sex gene in amphidiploid Carassius auratus (crucian carp/goldfish). However, its role in male determination or differentiation remains unclear. Here, we identified the heteromorphic X and Y chromosomes and confirmed the localization of amh on the sex chromosome by fluorescence in situ hybridization in amphidiploid C. auratus. The transcriptional expressions of X-linked and Y-linked amh alleles showed no significant difference during the period of sex determination and differentiation. The mutation of either the X-linked or Y-linked amh allele did not result in sex reversal, while the disruption of both amh alleles resulted in male-to-female sex reversal in a proportion of genotypic males. This finding suggests that neither the X-linked nor the Y-linked amh allele is responsible for male determination, but rather, amh alleles contribute to male differentiation in amphidiploid C. auratus. Subsequent research found that Amh could repress cyp19a1a (cytochrome P450, family 19, subfamily A, polypeptide 1a) transcription in vitro, and the inhibition of cyp19a1a partially rescued the sex reversal phenotype caused by amh knockout. Besides, the amh null mutation in artificial amphitriploid C. auratus, which possesses an XXX/XXY sex determination system, also led to male-to-female sex reversal in some genotypic males. This study illustrates that the sex chromosome-residing amh is not a male-determining gene but regulates male differentiation in C. auratus, confirming the conserved function of amh in male differentiation in vertebrates.

Rodents represent the most abundant order of mammals, exhibiting remarkable diversity in morphology, habitats, behaviors, and hosted pathogens. Significant attention is currently focused on rodents as experimental animals for biomedical research. However, numerous aspects of rodents remain unexplored, such as their potential in unconventional biomedical models, molecular underpinnings of intriguing complex phenotypes, adaptations to environment or climate change, and host-pathogen interactions and arms race evolution. These challenges require a systematic framework to integrate the genomic variations among rodents with information on rodent-borne pathogens. To address this gap, we have established a comprehensive, freely accessible, and user-friendly atlas named Rodent Genome and Pathogen multi-Omics (RodentGPOmics), which provides comparative analysis of rodent genomes and information on zoonotic pathogen sequences in rodents. The RodentGPOmics Atlas provides: (i) basic information on 2706 rodent species; (ii) chromosome-level visualization of genomes, functional annotations, and genomic comparisons across 121 rodent species; (iii) epidemiological profiles based on 21 852 pathogen sequences reported in rodents and (iv) a few genomic tools for in-depth exploration of rodent multi-omics. This resource aims to advance the development of biomedical models for humans for promoting public health, as well as innovate the genetics, genomics, and molecular evolution in rodents, and offer valuable knowledge on rodent-borne emerging/re-emerging zoonotic infectious diseases. The resources are freely available and easy-to-use at http://RodentGPOmics.njau.edu.cn:8888/Rodent/index/homePage.

Goldfish (Carassius auratus) are renowned as a premier ornamental fish in the world. Especially, the hood, a distinctive cephalic skin protrusion, is a highly sought-after feature for its endearing aesthetics. Despite a longstanding hypothesis that the hood is a type of tumor, the details of their composition, structure, and the mechanism of its formation have remained enigmatic. In this study, we attempted to demystify the morphogenetic mechanism of hood development by providing a detailed analysis of the hood’s architectural and compositional attributes, complemented by multi-omics changes across its developmental stages. Our results were also validated through dual-luciferase reporter assays and cytological evaluations in vitro and in vivo. We uncovered a 4-layered complex structure (stratum compactum, stratum spongiosum, stratum adventitia, and epithelial cell layer), with the hood’s protrusions mainly resulting from marked collagen accumulation in the stratum spongiosum and epithelial cell proliferation, suggesting that the goldfish hood belongs to a cutaneous fibrosis. Furthermore, we found that the down-regulation of arachidonic acid metabolism triggers an inflammatory response, culminating in the dysregulation of the tumor necrosis factor (TNF) pathway, which in turn enhances collagen deposition and epithelial cell proliferation—central to hood morphogenesis. During post-formation process, the aberrant TNF pathway expression and collagen accumulation inhibit osteoclast differentiation, promoting the irregular proliferation of the skull and the formation of bony protrusions that support hood attachment. Our findings not only shed light on the molecular mechanism underlying cutaneous fibrosis in goldfish but also offer potential parallels to analogous conditions in humans.

Finding potent promoters that would enable foreign genes to be expressed at high levels in Mycobacteria would be extremely helpful in the creation of recombinant vaccines and features for Mycobacterial antigens. Recombinant mycobacterial gene expression is commonly carried out using Mycobacterium smegmatis (M. smegmatis) as the host. In this paper, we constructed a promoter library with minimized consensus promoter sequence of mycobacteria. This library was ligated to the upstream of green fluorescent protein (EGFP) and transformed into M. smegmatis. Strength of the promoters was revealed by the green fluorescent of the colonies under a blue LED transilluminator. The strong fluorescent colonies were picked up and the promoter sequence was analyzed by sanger sequencing. Overall, we got plenty of strong promoters less than 100 base pair, which can be cloned into other plasmids easily, and would be a useful tool in Mycobacteria genetics.

The objective of this study was to better understand immune failure mechanisms during severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 infection, which are critical for developing targeted vaccines and effective treatments. We collected 34 cases representing different disease severities and performed high-quality single-cell TCR/BCR sequencing to analyze the peripheral immune cell profiles. Additionally, we assessed antibody-neutralizing activity through in vitro experiments. Our integrated multiomics analysis uncovers a profound immune paradox in severe COVID-19: hyperinflammation coexists with immunosuppression, driven by distinct yet interconnected dysregulatory mechanisms. Severe patients develop robust humoral immunity, evidenced by clonally expanded plasma cells producing neutralizing antibodies (e.g., IGHG1-dominated responses) and antigen-specific T cell activation. However, these protective responses are counteracted by myeloid-driven immunosuppression, particularly CD14+ HMGB2+ monocytes exhibiting metabolic reprogramming and HLA-DR downregulation, coupled with progressive T cell exhaustion characterized by IFN-γ/TNF-α hyperactivation and impaired antigen presentation. Importantly, prolonged viral persistence in severe cases arises from a failure to coordinate humoral and cellular immunity-antibody-mediated neutralization cannot compensate for defective cytotoxic T cell function and monocyte-mediated immune suppression. These findings highlight the necessity for therapeutic strategies that simultaneously enhance antibody effector functions (e.g., Fc optimization), restore exhausted T cells, and reverse myeloid suppression. They also highlight the importance of vaccines designed to elicit balanced B cell memory and durable T cell responses, which are critical to preventing severe disease progression. By addressing the dual challenges of hyperinflammation and immunosuppression, such approaches could restore immune coordination and improve outcomes in severe COVID-19.

Qihe gibel carp (Carassius gibelio var. Qihe) is a local population of natural gynogenetic amphitriploid (AAABBB) Carassius gibelio, and has high nutritional and economic value. In this study, we assemble a high-quality chromosome-level genome of Qihe gibel carp through DNBSEQ, PacBio HiFi, and Hi-C sequencing data. The resulting assembly consisted of 350 contigs with the full length of 1.607 Gb and 96.21% (1.515 Gb) of the assembled genome was successfully anchored to 50 chromosomes, with a contig N50 of 28.97 Mb and a scaffold N50 of 29.84 Mb. Repeated sequences accounting for 43.72% (732.494 Mb) of the total were also identified, and gene prediction revealed 46,131 protein-coding genes with an annotation ratio of 96.48%. Furthermore, Benchmarking Universal Single-Copy Orthologue (BUSCO) analysis demonstrated that the genome assembly achieved high completeness, with a score of 97.66%. This high-quality chromosome-level genome lays the foundation for molecular biology research as well as molecular breeding and evolutionary studies of Qihe gibel carp in the future.

Non-traditional farmed and wild mammals are often neglected in pathogen surveillance. Through metagenomic and metatranscriptomic sequencing of fecal and tissue samples from 973 asymptomatic mammals, we identified 128 viruses (30 novel), including a new coronavirus genus, 10,255 bacterial species (over 7,000 undescribed), 201 fungi, and 7 parasites. Farmed and wild mammals shared 13.3% of virus species, including canine coronavirus in Asiatic black bears and Getah virus in rabbits, while the 2.3.4.4b clade of H5N1 avian influenza virus was found in a wild leopard cat. We identified potential bacterial pathogen transmission between farmed and wild mammals and bacterial strains with high genetic similarity to those found in humans. We observed 157 clinically prioritized antibiotic resistance genes (ARGs) in mammalian microbiomes with greater than 99% identity to ARGs from human microbiomes, often co-occurring with mobile genetic elements. Overall, this work highlights cross-species risks at the human-animal interface.

Animals such as raccoon dogs, mink and muskrats are farmed for fur and are sometimes used as food or medicinal products1,2, yet they are also potential reservoirs of emerging pathogens3. Here we performed single-sample metatranscriptomic sequencing of internal tissues from 461 individual fur animals that were found dead due to disease. We characterized 125 virus species, including 36 that were novel and 39 at potentially high risk of cross-species transmission, including zoonotic spillover. Notably, we identified seven species of coronaviruses, expanding their known host range, and documented the cross-species transmission of a novel canine respiratory coronavirus to raccoon dogs and of bat HKU5-like coronaviruses to mink, present at a high abundance in lung tissues. Three subtypes of influenza A virus—H1N2, H5N6 and H6N2—were detected in the lungs of guinea pig, mink and muskrat, respectively. Multiple known zoonotic viruses, such as Japanese encephalitis virus and mammalian orthoreovirus4,5, were detected in guinea pigs. Raccoon dogs and mink carried the highest number of potentially high-risk viruses, while viruses from the Coronaviridae, Paramyxoviridae and Sedoreoviridae families commonly infected multiple hosts. These data also reveal potential virus transmission between farmed animals and wild animals, and from humans to farmed animals, indicating that fur farming represents an important transmission hub for viral zoonoses. Fur farming represents an important hub of cross-species transmission for viral zoonoses.

The retransmissions of SARS-CoV-2 from several mammals - primarily mink and white-tailed deer - to humans have raised concerns for the emergence of a new animal-derived SARS-CoV-2 variant to worsen the pandemic. Here, we discuss animal species that are susceptible to natural or experimental infection with SARS-CoV-2 and can transmit the virus to mates or humans. We describe cutting-edge techniques to assess the impact of a mutation in the viral spike (S) protein on its receptor and on antibody binding. Our review of spike sequences of animal-derived viruses identified nine unique amino acid exchanges in the receptor-binding domain (RBD) that are not present in any variant of concern (VOC). These mutations are present in SARS-CoV-2 found in companion animals such as dogs and cats, and they exhibit a higher frequency in SARS-CoV-2 found in mink and white-tailed deer, suggesting that sustained transmissions may contribute to maintaining novel mutations. Four of these exchanges, such as Leu452Met, could undermine acquired immune protection in humans while maintaining high affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor. Finally, we discuss important avenues of future research into animal-derived viruses with public health risks.

Type I interferon (IFN) production is crucial in tuberculosis pathogenesis, yet the bacterial factors initiating this process are incompletely understood. CpsA, protein of Mycobacterium marinum and Mycobacterium tuberculosis , plays a key role in maintaining bacterial virulence and inhibiting host cell LC3-associated phagocytosis. By utilizing CpsA full deletion mutant studies, we re -verified its essential role in infection -induced pathology and revealed its new role in type I IFN expression. CpsA deficiency hindered IFN production in infected macrophages in vitro as well as zebrafish and mice in vivo . This effect was linked to the cGAS-TBK1-IRF3 pathway, as evidenced by decreased TBK1 and IRF3 phosphorylation in CpsA-deficient bacterial strain -infected macrophages. Moreover, we further show that CpsA deficiency cause decreased cytosolic DNA levels, correlating with impaired phagosomal membrane rupture. Our findings reveal a new function of mycobacterial CpsA in type I IFN production and offer insight into the molecular mechanisms underlying mycobacterial infection pathology.

Slc7a5 is an important amino acid transporter that is highly expressed in metabolically active and rapidly proliferating cells. To explore the effect of Slc7a5 on adult B cell development, we conditionally deleted Slc7a5 in murine B cells and observed a significant reduction of B1a cells. In contrast to PI3K-Akt pathway activation, activity of the mTOR pathway was decreased. This may result from intracellular amino acid starvation in Slc7a5 knockdown (Slc7a5 KD) bone marrow B cells, thereby dampening B1a development. RNA-seq analysis demonstrated increased translation and reduced proliferation in Slc7a5 KD bone marrow B cells. Overall, the results of our study highlight the importance of Slc7a5 in peritoneal B1a cell development.