Ciliated protozoans such as Ichthyophthirius multifiliis and Chilodonella uncinata pose severe threats to freshwater aquaculture, yet the antigenic relationships and cross-protective potential among different ciliate species remain poorly understood. This study systematically evaluated the immune responses and protective efficacy induced by inactivated whole-ciliate vaccines prepared from three ciliates - I. multifiliis (I.M), C. uncinata (C.U) and Tetrahymena thermophila (T.T)-in koi carp (Cyprinus carpio). Fish were intraperitoneally immunized with four doses (1×104-6×104 inactivated ciliates/fish) and boosted at 14 days post-primary vaccination. Results showed that all three vaccines significantly elevated serum levels of IgM, complement C3/C5 and hepatic antioxidant enzymes (SOD, CAT) (P < 0.05). Transcriptional upregulation of key immune genes (IgM, MHC IIβ, IL-1β, IFN-γ, TNF-α, IL-8) was observed in head kidney, spleen and skin, accompanied by increased proportions of IgM+ B cells in primary and secondary lymphoid organs. Challenge trials at 28 days post-immunization revealed strong dose-dependent protection against both I. multifiliis and C. uncinata. Notably, the I.M and C.U vaccines conferred robust homologous protection and exhibited substantial bidirectional cross-protection, while the T.T vaccine provided moderate, dose-dependent cross-protection. Overall, vaccines derived from parasitic ciliates elicited stronger immune responses than those derived from the free-living ciliate, likely reflecting differences in host-parasite coevolution and antigenic compatibility. These findings demonstrate that inactivated whole-ciliate vaccines coordinately activate innate and adaptive immunity and induce cross-protective responses, highlighting their potential as candidates for broad-spectrum antiparasitic vaccine development in aquaculture.

Zipf's law of brevity and Menzerath's law are linguistic principles, predicting that coding length is minimized for optimal coding efficiency. We tested whether two linguistic laws apply to vocal communication of white-headed langurs inhabiting karst forests. Adult male white-headed langurs produce three loud call types in long-distance sequences. Frequent call types were shorter in duration, supporting Zipf's law of brevity. Patterns related to Menzerath's law were more nuanced. Inter-call intervals shortened in longer sequences, but only wahoo calls showed duration compression. Physiological constraints caused calls to shorten and intervals to lengthen later in sequences. Longer sequences contained proportionally more short snorts and fewer long roars and wahoos. Signal compression reflects a trade-off between energy cost and communication efficiency. Constant durations of snorts and roars may aid long-distance transmission and caller recognition. These findings provide evidence for signal brevity and compression under physiological limits, offering insights into vocal communication evolution in non-human primates.

Antibiotic resistance represents a growing threat to human, animal, and ecosystem health, yet its dynamics in wildlife remain poorly understood. We conducted a systematic analysis of the gut resistomes in non-human primates (NHPs) and environmental soils in Guizhou Province, China, a biodiversity hotspot. Metagenomic analyses reveal that human activities and horizontal gene transfer (HGT) influence primate resistome landscapes and enhance their dissemination potential. A total of 1927 antibiotic resistance ontologies (AROs) distributed across 1477 species-level genome bins (SGBs), providing a comprehensive genomic catalog of the NHPs resistome. Bacterial genera such as Pseudomonas, Stenotrophomonas, and Comamonas drive ARG mobilization, with a core subset of ARGs that reliably predict overall resistance burdens. Notably, widely distributed primate species, with large habitat ranges and frequent interspecies interactions exhibit the most potential for ARG dissemination. Ecological modeling identifies current and future hotspot regions requiring prioritized monitoring amid ongoing human disturbance and climate change. These findings provide a molecular-indicator-based framework for environmental antibiotic resistance (AR) monitoring and conservation strategies for endangered species. Despite limitations in temporal and spatial coverage, our study highlights the need to integrate wildlife, particularly NHPs, as sentinel species into "One Health" AR surveillance and policy. This approach will strengthen our understanding of ARG transmission dynamics and their long-term impacts on host adaptation, ecosystem stability, and public health.

In this study, single-cell RNA sequencing reveals dynamic cell differentiation and HSP101-mediated regulation during the wheat floral transition, providing insights into reproductive development and grain yield improvement. The transition from vegetative to reproductive growth of flowering plants represents a key development event in which cells and genes undergo radical changes for reproduction and survival. Using the single-cell RNA sequencing technique, we characterized a comprehensive transcriptional landscape of cell types populating the floral transition in wheat. We revealed the differentiation and coordination between cell groups which shapes a clear boundary through the transition. Two cell groups, enriched for genes related to Anther Specific Protein and Thousand Grain Weight 6, emerged sequentially at the initial section of the reproductive stage and influence the establishing and maintaining of floral organs and grains. Moreover, we delineated the developmental trajectories of both of the cell groups, inferring gene expression signatures associated with cell fate decisions. A Heat Shock Protein (HSP) gene, HSP101, was identified as a signature for the initial segment of floral transition with expression pattern and localization to spikelet meristem, suggesting its critical role in this process. We propose a genetic regulatory model for cell/gene interactions during the floral transition in wheat, which provides a high-resolution cellular landscape with new insights into the plant morphogenesis transition process, cell-fate acquisition, gene expression dynamics, and prospects for cereal improvement.

Despite the widespread distribution of horses and their close interface with human environments, the equine antibiotic resistance gene (ARG) reservoir remains insufficiently characterized. This study aimed to comprehensively elucidate the equine resistome by analyzing 104 equine fecal metagenomes sampled across China, thereby establishing a critical baseline for antimicrobial stewardship in equine husbandry. Through a non-redundant gene catalog approach, we identified 3,264 unique ARG-related coding sequences (CDSs). To detect distant homologs, hidden Markov model (HMM) profiling was applied, revealing 2,420 putatively novel ARG-like sequences. Functional classification indicated that over 90

Ichthyophthirius multifiliis is a common protozoan ciliate parasite with low host specificity among teleost fish, and the white spot disease it causes has led to severe economic losses in global freshwater aquaculture. Nevertheless, Percocypris pingi exhibits natural resistance to I. multifiliis, with rare disease outbreaks caused by this parasite in practical aquaculture. In this study, artificial infection experiments were conducted by exposing P. pingi and Ctenopharyngodon idella (grass carp) to I. multifiliis at a dose of 30,000 theronts per fish. The results showed that the average infection intensity in C. idella was 6.68 times higher than that in P. pingi. Histopathological examination via H&E staining revealed severe inflammatory symptoms in the gills and skin of infected C. idella, whereas P. pingi showed no significant pathological damage. Additionally, AB-PAS staining indicated that the mucus cells in the skin and gills of C. idella were predominantly neutral, whereas those in P. pingi were primarily acidic. Moreover, the number of mucus cells in P. pingi increased after I. multifiliis infection. To investigate the natural resistance mechanism of P. pingi against I. multifiliis, transcriptomic and metabolomic analyses were performed on the caudal fin of P. pingi stimulated by the parasite. A total of 2320 differentially expressed genes (DEGs) and 317 differentially abundant metabolites (DAMs) were identified, primarily involved in biological processes such as Glycerophospholipid metabolism, alpha-Linolenic acid metabolism, Arachidonic acid metabolism, Complement and coagulation cascades, and Chemokine signaling pathway. Integrated analysis suggested that the upregulation of complement components and chemokines in P. pingi may play a critical role in resisting I. multifiliis infection. Furthermore, the caudal fin of P. pingi responded to inflammatory stimulation by modulating lipid metabolism and energy metabolism to balance pro-inflammatory, anti-inflammatory and energy-producing metabolites. This study represents the first systematic investigation into the transcriptomic and metabolomic characteristics of P. pingi in response to I. multifiliis infection, revealing the central roles of complement components and cytokines in anti-parasitic defense. These findings provide new theoretical insights into the mechanisms of fish resistance to parasitic infections.

Ancient admixture catalyzes evolutionary innovation, yet its long-term genomic consequences for newly formed lineages remain poorly understood. Here, based on 53 genomes covering 19 species of the Asian langur genus Trachypithecus, we explore admixture's role in shaping a reticulated radiation. Genome-wide analyses of phylogenomic triplet topologies demonstrate that phylogenetic discordance across this radiation is primarily driven by widespread introgression rather than incomplete lineage sorting. To mitigate historical noise and resolve the ancestral species tree, we anchored our phylogenetic analysis on the X-linked recombination desert (XLRD), which exhibits an 84.5% introgression reduction compared to autosomes. We identify Delacour's langur as a clear case of homoploid hybrid speciation, arising from ancient admixture with ~70:30 genomic contributions from ancestral northern and southern limestone langur lineages. This hybrid species fixed key reproductive isolation loci; notably, alternate inheritance of pigmentation genes (SLC45A4, HPS5, ADCY10) systematically coupled with a fixed RNF175 chimeric allele to drive its diagnostic pelage phenotype. This illustrates how introgressed multi-gene networks rapidly establish prezygotic visual barriers and profound phenotypic divergence. However, subsequent spatial isolation within fragmented karst landscapes forced a major conversion of genetic burden into realized load. Genome-wide, over 82% of loss-of-function variants occur in a homozygous state, reflecting the expression of lethal recessive mutations within long runs of homozygosity. Together, our findings demonstrate that ancient admixture can trigger homoploid hybrid speciation, yet subsequent ecological restriction locks derived lineages into severe, long-term genomic erosion, revealing a fundamental trade-off in reticulate evolutionary radiations.

Autoimmune hepatitis (AIH) is an immune-mediated liver disease that can progress to fibrosis, cirrhosis, and hepatocellular carcinoma. However, the pathogenic mechanisms underlying AIH remain poorly understood, limiting the development of effective therapies. Here, using a concanavalin A-induced murine model of experimental autoimmune hepatitis (EAH), proteolytic cleavage of the deubiquitinase cylindromatosis (CYLD) at Asp215 is identified as a critical molecular event that promotes disease progression. Mice harboring a macrophage-specific, cleavage-resistant CyldD215A/D215A mutation are markedly protected from hepatic injury, indicating that CYLD stability is a key regulator of liver inflammation. Mechanistically, TNFα induces CYLD cleavage in macrophages, which enhances alarmin-triggered chemokine production through activation of MEK1/2 signaling. Further analyses reveal that CYLD and the E3 ubiquitin ligase TRIM25 cooperatively regulate MEK1/2 ubiquitination at lysine residues K192/K196. MEK1/2 ubiquitination promotes its activation by strengthening its interaction with RAF1 and drives subsequent chemokine production. Importantly, pharmacological inhibition of MEK1/2 significantly attenuates EAH severity. Together, these findings uncover a previously unrecognized CYLD-MEK1/2 axis in macrophages that orchestrates hepatic inflammation and identify MEK signaling as a potential therapeutic target for AIH.

As an extremely endangered species, the gray snub-nosed monkey (Rhinopithecus brelichi) relies on its gut microbiota for adaptation to environmental changes, particularly in coping with fluctuations in energy and nutrient availability. In this study, we employed metagenomic, metatranscriptomic, and widely targeted metabolomic analyses to characterize the gut microbiota of gray snub-nosed monkeys. Based on metagenome-assembled genomes (MAGs), we recovered 1229 non-redundant MAGs. Among them, a total of 103 MAGs exhibited significant seasonal variation, primarily belonging to the phyla Bacillota_A, Bacteroidota, and Bacillota_I. During winter, metagenomic results indicated that the gut microbiota exhibited an enhanced capacity to produce energy substrates such as amino acids, short-chain fatty acids, pyruvate, and acetyl-CoA, with increased conversion of these substrates. Metatranscriptomic analysis further confirmed that key carbon cycle-related genes and metabolic pathways were significantly upregulated in winter. Additionally, metabolite analysis indicated significantly lower levels of amino acids in winter fecal samples, suggesting that gray snub-nosed monkeys efficiently absorb and utilize metabolites, with the gut microbiota likely contributing to energy compensation. Notably, the gut microbiota may also synergistically support the host's non-shivering thermogenesis, helping maintain physiological functions in extreme cold conditions. This study elucidates the cooperative role of the gut microbiota in helping gray snub-nosed monkeys adapt to seasonal environmental fluctuations, providing new insights into how gut microbiota optimize winter energy utilization-an understanding with important implications for the conservation of endangered wildlife.

Adaptive thermogenesis is a fundamental physiological process by which mammals maintain their body temperature through shivering and non-shivering thermogenesis to adapt to environmental changes. The activation of brown adipose tissue (BAT) is the core of non-shivering thermogenesis. However, the specific mechanisms by which gut-derived bacteria trigger BAT to activate adaptive thermogenesis remain poorly understood. Environmental variations across different altitudes create unique temperature gradients, providing an ideal condition for identifying bacteria associated with cold adaptation. In this study, we identified Pantoea ananatis, a highland-enriched bacterium, as a key species regulating adaptive thermogenesis and lipid metabolism in Macaca mulatta. Through multi-omics and gavage experiments, we discovered that the gut microbiota of high-altitude macaques can enhance the nutritional absorption capacity of the small intestine of mice, increase the concentration of propionic acid, activate the glycerolipid metabolism and strengthen lipid metabolism. Furthermore, we found that P. ananatis, as one of the main effect bacteria of the high-altitude gut microbiota, can activate BAT, reduce white adipose tissue (WAT) storage, and enhance triglyceride metabolism. Finally, we preliminarily verified that ferulic acid, as one of the potential effector metabolites of P. ananatis, also contributes to the reduction of WAT accumulation. Our work uncovers P. ananatis as a high-altitude-adapted potential probiotic that activates BAT and promotes systemic fat reduction through a gut microbiota-driven mechanism. This breakthrough provides a safe, effective alternative to cold-induced thermogenesis, with profound implications for obesity intervention.

Programmed DNA elimination (PDE)—the targeted loss of germline-restricted chromosomes (GRCs) in somatic lineages—is a hallmark of jawless vertebrates, yet its origin and evolutionary trajectory remain unresolved. Here, we generate high-quality genomes of the inshore hagfish (Eptatretus burgeri) and the Korean lamprey (Lampetra morii), including the first assembly of eight germline-restricted scaffolds (GRSs) in hagfish. Comparative analyses further show that PDE removes the same germline‑specific sequences across different somatic tissues in E. burgeri, supporting a uniform developmental program. Phylogenomic analyses indicate that hagfish GRCs arose through progressive recruitment of sequences from somatically retained chromosomes (SRCs), likely beginning in the cyclostome ancestor and continuing via lineage‑specific events. Germline‑specific genes (GSGs) predominantly originate from SRC paralogs with high gonadal expression and show strong male‑biased expression, especially in E. burgeri, whose SRC counterparts also display pronounced testis bias relative to L. morii. In E. burgeri, GSGs exhibit elevated alternative splicing, but this increase is confined to a subset of spermatogenesis‑related genes (e.g., Hydin), a pattern not observed in L. morii. Despite rapid gene turnover, GSGs consistently converge on functions related to germ cell development in different cyclostomes, revealing a conserved reproductive core function. Together, these results establish PDE as a conserved yet dynamic mechanism that shapes germline genome evolution through coordinated changes in gene content, expression bias, and regulatory architecture.

Palmarosa (Cymbopogon martini) essential oil (EO) has been reported to anthelmintic efficacy against monogeneans, but its active components remain unidentified. This study aimed to identify the specific anthelmintic active components, and compare their anthelmintic efficacy to the whole EO in treatment of Dactylogyrus vastator. By gas chromatography-high resolution mass spectrometry (GC-HRMS) analysis, 50 components with higher than 0.1% relative content were determined in C. martini EO. But the main components were not identical among the samples from three companies (MKL, CMS and HWRK), such as more than 15% phenylethyl alcohol and citronellol from MKL and CMS, while more than 20% p-cymene and β-phellandrene from HWRK. In vitro experiments demonstrated that, among the 14 tested components at a concentration of 10 mg/L, α-pinene, β-pinene, α-phellandrene, benzyl benzoate exhibited the higher anthelmintic efficacy. β-Pinene exhibited the optimal anthelmintic efficacy, completely killing D. vastator within two hours. By contrast, the prominent components, such as β-phellandrene, p-cymene, geraniol, camphor and eucalyptol showed negligible anthelmintic efficacy against the dactylogyrids. After 24 h in vivo exposure, the EC50 of C. martini EO and β-pinene against D. vastator were 3.54 mg/L and 1.48 mg/L, respectively, which suggested better anthelmintic efficacy of the β-pinene. The acute toxicity test of goldfish showed thatC. martini EO was less toxic (88.99 mg/L at 48 h LC50) than β-pinene (69.09 mg/L at 48 h LC50). These results suggested that the active ingredients in C. martini EO against dactylogyrids were not the prominent components, but the minor ones. The β-pinene may be the potential lead compound to develop more efficient derivatives. In addition, the low content of β-pinene in the C. martini EO indicated that other active components played a synergistic anthelmintic efficacy, and the C. martini EO was safer to control monogeneans than single active compound.

We report the complete genome sequence of Limnothrix sp. CMB-01, a self-flocculating cyanobacterium isolated from rare earth element wastewater. The assembled genome comprises a single circular chromosome of 4,574,928 bp with a GC content of 55.22%, providing genomic insights into the metabolic potential and adaptive traits of this underexplored cyanobacterium.

Genome sizes across vertebrates are remarkably variable ranging by a factor of approximately 250 from 350 Mb to over 92 Gb. Pufferfish genomes (e.g., Tetraodon nigroviridis and Takifugu rubripes) are notable for their compact size, with T. nigroviridis possessing the smallest known vertebrate genome. Yet they all maintain a similar number of protein-coding genes. Until recently, the lack of high-quality, complete genome assemblies has hindered detailed investigations into the mechanisms of genome size evolution. Here, we present two haplotype-resolved, complete telomere-to-telomere (T2T) genome assemblies of T. nigroviridis. The two haplotype-resolved T2T assemblies each contain 21 gapless chromosomes with total lengths of 342,798,327 bp and 344,013,623 bp, respectively. This diploid genome harbors the canonical vertebrate telomeric repeat and a conserved 118 bp centromeric satellite unit shared across all chromosomes. Our analyses reveal that the compact genome of T. nigroviridis is achieved through the repression of transposable elements and the dramatic reduction of intergenic regions and intron sizes, while protein-coding regions remain highly conserved. The T. nigroviridis genome shows high GC content, especially in the small chromosomes. Comparative analyses highlight synteny conservation across vertebrates, underscoring the evolutionary stability of synteny units in vertebrate genomes despite a more than 250-fold range in genome size. In particular, chromosome 19 showed notable synteny conservation throughout teleost evolution. This work not only enhances our understanding of genome size evolution but also serves as a valuable resource for future evolutionary and comparative genomic studies.

Rapid climate change poses a severe threat to biodiversity, and phylogenetic diversity—a key metric capturing evolutionary uniqueness and adaptive potential—is critical for conservation. Integrating a well-resolved phylogenetic tree of 424 primate species, we combined spatial analysis and climate risk modeling to explore global spatiotemporal patterns of primates and assess their vulnerability under future climate scenarios. The results suggest a pronounced latitudinal pattern in primate distribution, with isothermality and annual mean precipitation as key drivers. Primate species in the American tropics (Mexico, Central, and South America) and southern China showed later divergence times and lower phylogenetic diversity, emerging as neo-hotspots for primates. Under future climate change, species in these neo-hotspots will face higher climate risks than those in paleo-hotspots of primate diversity. In addition, high human pressure, high climate risk, and limited protected area coverage increase species and population survival risks in hotspot regions. Overall, this global study deepens our understanding of biodiversity conservation under current climate change scenarios and synergistically advances the preservation of numerous natural services essential to ecosystem health and human well-being. Our study provides a spatially explicit framework to fulfill Targets 3 and 8 of the Kunming-Montreal Global Biodiversity Framework.

Receptor-interacting protein kinase 1 (RIPK1) is a key regulator of cell death and inflammation, with its activation modulated by diverse posttranslational modifications. While ubiquitination of RIPK1 at lysine 376 (K376) has been shown to inhibit apoptosis and necroptosis both in vitro and in vivo, its role in inflammation remains undefined. In this study, we introduced a kinase-dead D138N mutation into Ripk1K376R/K376R mice. Notably, Ripk1K376R,D138N/K376R,D138N mice rescued the embryonic lethality observed in Ripk1K376R/K376R mice, but developed systemic inflammation. Remarkably, this inflammation was significantly alleviated by codeletion of Caspase-1/11, but not Trif, indicating a critical role for inflammasome activation. Mechanistically, loss of ubiquitination at the K376 residue of RIPK1 promotes kinase activity-dependent cell death, which underlies the lethality of Ripk1K376R/K376R mice. Importantly, the K376R mutation also drives RIPK1 kinase-independent inflammatory responses by triggering intrinsic NLRP3 inflammasome activation and downstream IL-1β secretion. Furthermore, we found that RIPK1 promotes this process through a RIPK3-dependent mechanism. Consistently, deletion of Ripk3-but not Mlkl-ameliorated this inflammation, highlighting a necroptosis-independent inflammatory axis. Together, our findings demonstrate that the RIPK1K376R mutant not only induces kinase activity-dependent cell death during embryogenesis but also promotes kinase-independent, scaffold-driven inflammation in adults via RIPK3-mediated metabolic reprogramming that activates the NLRP3 inflammasome.

ABSTRACT Few nonhuman primates inhabit high‐latitude regions that pose significant adaptive challenges. The Tibetan macaque (Macaca thibetana) represents a rare primate species entirely distributed north of the Tropic of Cancer. To investigate the genetic basis underlying its adaptation to high latitudes, we generated a refined Tibetan macaque reference genome (99.41% completeness). Genomic analyses identified a species‐specific homozygous mutation (Pro71Thr) in the TBX6 gene, which potentially explains their characteristic shortened tail morphology. Functional validation using CRISPR‐Cas9‐edited mice demonstrated that this mutation reduces caudal vertebrae count, providing a mechanistic basis for the shortened tail. Quantitative CT revealed that Tibetan macaques accumulated approximately 9.3‐fold more abdominal fat than rhesus macaques. Genomic analysis uncovered enhanced lipid metabolic capacity supported by multiple sources of evidence: (1) positive selection on genes associated with lipid storage (DGAT2, DYSF, CAV1), adipogenesis (PRKD1), and appetite regulation (LEPR); (2) a 390‐bp deletion in CPE; (3) expansions of gene families on oxidative phosphorylation and gluconeogenesis/glycolysis. These genetic variations may account for the marked differences in adipose tissue gene expression between the two macaque species. The shortened tail and increased fat accumulation represent key adaptations for thermoregulation and energy conservation in high‐latitude habitats. Notably, all Tibetan macaque populations experienced long‐term selection pressures from cold at high latitudes, which have not only shaped distinctive adaptive traits, but may also render the species particularly vulnerable to contemporary climate warming, particularly for the eastern populations.

Human-driven habitat change is forcing nonhuman primates to exploit anthropogenic landscapes, resulting in primate crop feeding, reduced farmer food security, and human-primate conflict. Here, we investigate the crop feeding behavior of a wild group of rhesus macaques in a farm-forest mosaic in central Nepal. Macaque behavioral data were collected over 12 months using scan- and all-occurrence sampling methods, along with monitoring crop availability. We evaluated the relationship between macaque feeding behavior, crop type, availability, damage, and farmers' actions to reduce crop damage. We found that ~49% of the macaque's annual diet was composed of cultivated crops, with three crops-maize, oranges, and potatoes-accounting for ~52% of macaque crop feeding time. There was a significant positive association between monthly crop productivity and macaque feeding time on these crops. Local farmers attempted to deter macaque crop feeding 83.1% of the time, but their efforts failed to reduce crop damage. During the maize cultivation season, total maize damage caused by macaques was estimated at 1647 kg (~50 kg/ha) of dry kernels, resulting in a loss of 1.5% of total maize yield per hectare. Thus, macaque crop feeding had only a limited effect on farmer food security. We propose a set of practical and low-cost actions that can be taken to continue the current balance between the dietary needs of the rhesus macaques and the economic needs of farm families in the local community.