Root-knot nematodes establish long-term parasitic relationships with diverse hosts by inducing specialized feeding cells. However, the molecular mechanisms by which nematodes manipulate this developmental reprogramming process remain largely unknown. Here we identify a class of ROOT MERISTEM GROWTH FACTOR (RGF)-like peptide effectors conserved in root-knot nematodes. MgRGF from Meloidogyne graminicola and MiRGF1 from M. incognita are expressed in subventral gland cells during early infection and secreted into the host apoplast. Functional analysis reveals that nematode RGFs are critical for feeding site development. Intriguingly, these peptides elicit host-specific outcomes in Arabidopsis and rice, involving both cell proliferation and expansion-two processes essential for establishing feeding cell identity. Further genetic and biochemical evidence demonstrates that nematode RGF peptides functionally mimic plant endogenous RGFs by hijacking the host RGI-receptor-mediated signalling pathway to regulate root growth and promote parasitism. Beyond PLT transcription factors, PSY peptide genes were identified as key downstream components of this RGF signalling cascade in rice. Functional characterization of OsPSY5 suggests its positive role in promoting cell elongation and facilitating nematode parasitism. Our findings unveil a cross-kingdom mimicry strategy whereby root-knot nematode-secreted RGF peptides co-opt host RGF signalling to orchestrate feeding cell formation, highlighting potential targets for engineering nematode resistance in crops.

Homeostatic regulation of proteolytic activity is fundamental to plant cellular physiology, and dysregulated protease-like activities are frequently associated with cytotoxic or stress-induced cell death. Here, we identify RipBH, a previously uncharacterized type III-secreted protein from Ralstonia solanacearum, as an intracellular self-cleaving protease-like effector with the capacity to perturb host physiological balance. RipBH harbors a papain-like catalytic core and multiple ankyrin repeats; structural mutagenesis showed that conserved catalytic residues (C135, H244, D268, and N117) are indispensable for self-processing and cell death-inducing activity. RipBH undergoes auto-cleavage inside plant cells, producing smaller fragments that are detectable in both the cytoplasm and nucleus. Truncation of ankyrin repeats altered cleavage behavior and abolished cell-death induction, supporting the idea that ankyrin-mediated structural constraints function as a regulatory module required for activation. Importantly, RipBH-induced necrosis occurred largely independently of the tested canonical ETI-related signaling components, suggesting a physiology-centered disruption pathway rather than immune receptor-mediated recognition. We propose that RipBH operates as a pathogen-encoded proteolytic switch that destabilizes intracellular homeostasis, providing a potential mechanistic link between effector auto-processing and necrosis-like physiological collapse under biotic stress. Our findings contribute to the conceptual framework of proteolysis-associated plant cell dysfunction and highlight pathogen-driven interference with core physiological processes.

The experiment aimed to reveal the differences in meat quality and the formation mechanism of flavor compounds in different parts of Qilian Tibetan sheep. The study employed untargeted metabolomics technology to compare and analyze the metabolic profiles of the leg muscle and longissimus dorsi muscle of Qilian Tibetan sheep. Six healthy 12-month-old Qilian Tibetan sheep raised under identical environmental conditions were selected. After slaughter, samples of the longissimus dorsi muscle and leg muscle were collected. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used for metabolite separation and identification, and principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were applied for statistical analysis of the data. The results showed that a total of 20 significantly different metabolic pathways were identified, including the oxidative phosphorylation pathway, pyruvate metabolism pathway, and phosphoinositide metabolism pathway. The differential metabolites between the leg muscle and the longissimus dorsi muscle were mainly involved in pathways such as pyruvate metabolism, phosphoinositide metabolism, the citric acid cycle, tryptophan metabolism, phenylalanine metabolism, and tyrosine metabolism. These pathways played important regulatory roles in the formation of flavor compounds in Qilian Tibetan sheep. A total of 130 significantly different metabolites were identified, among which 61 metabolites were significantly up-regulated (P<0.05), and 69 metabolites were significantly down-regulated (P<0.05). The study shows that there were significant differences in metabolic levels between the leg muscle and the longissimus dorsi muscle, with key differential metabolites, such as phosphoenolpyruvate and glutamate, serving as precursors of flavor compounds, and playing an important role in the formation of mutton flavor.

Qilian sheep are an important local breed of Tibetan sheep with strong adaptation to cold and hypoxic environments. To identify candidate genes related to nutrient metabolism in Qilian sheep, this study compared liver transcriptomes between Qilian sheep and Oula sheep raised under the same grazing and feeding conditions. Six 10-month-old ewes were selected from each breed, and three liver samples with high RNA quality from each group were used for transcriptome sequencing. Differential expression analysis identified 1640 differentially expressed genes under the thresholds of |log2FoldChange| > 1 and false discovery rate < 0.05, including 718 upregulated and 922 downregulated genes. KEGG enrichment analysis showed that these genes were mainly involved in lipid metabolism- and amino acid metabolism-related pathways, especially the peroxisome proliferator-activated receptor signaling pathway, fatty acid synthesis, and fatty acid beta-oxidation. qRT-PCR validation confirmed that RGN, LPGAT1, and BHMT2 were significantly upregulated, whereas SDS, GK, PC, MIOX, HMGCS2, PNPLA3, ACAA2, and HADHA were downregulated in Qilian sheep. These results indicate clear differences in liver nutrient metabolism-related gene expression between Qilian sheep and Oula sheep and provide a molecular basis for understanding the liver metabolic characteristics and adaptive metabolic mechanisms of Qilian sheep.

The Jonah's icefish Neopagetopsis ionah is endemic to the frigid, oxygen-rich waters of the Southern Ocean. This species has evolved remarkable genetic and physiological adaptations, notably the loss of functional hemoglobin, making it an exemplary vertebrate model for studying evolutionary loss is gain and adaptation to extreme environments. In this study, we present a chromosome-level genome assembly of N. ionah (1.27 Gb) integrating Illumina, PacBio HiFi, and Hi-C sequencing data. The assembly comprises 24 chromosomes, with an anchoring efficiency of 96.8%. Genome annotation revealed that 42.14% of the genome consists of repetitive elements and identified 31,777 protein-coding genes. The high genomic collinearity with related species corroborates the assembly's accuracy at the macroscale. This high-quality reference genome provides a crucial resource for elucidating the genetic basis of cold adaptation, trait loss, and the unique cardiovascular innovations in Antarctic icefish.

Extreme temperature fluctuations present substantial challenges to fish survival and reproductive success. Perccottus glenii, a cold-tolerant freshwater species, has emerged as a valuable model for elucidating the molecular mechanisms underlying cold adaptation. Although alternative splicing (AS) is recognized as a crucial post-transcriptional regulatory mechanism, its specific role in cold tolerance remains inadequately characterized. In this study, we conducted a comprehensive transcriptomic analysis of AS events in the brain, liver, and muscle tissues of P. glenii across three physiological states: active, freezing, and recovery. A large number of differentially alternatively spliced genes (DASGs) and differentially expressed genes (DEGs) were identified. Gene Ontology (GO) enrichment analysis revealed distinct tissue-specific functional patterns. Among the three tissues, the enrichment results of DASGs and DEGs revealed both overlapping and distinct functional categories, suggesting that both mechanisms act in concert to facilitate cold adaptation. Notably, splicing variants of key genes such as adgrb1a, baxa, and stat3 were identified as potential contributors to cold adaptation. Collectively, these findings underscore the pivotal role of alternative splicing in the cold adaptation of P. glenii and offer a theoretical foundation for enhancing cold resistance in aquaculture and cryopreservation applications.

Seasonal temperature fluctuations following overwintering pose critical challenges to aquaculture by increasing fish susceptibility to opportunistic bacterial infections. Beneficial microorganisms offer sustainable alternatives to antibiotics, yet their viability and efficacy are often limited at low temperatures. This study introduces a novel psychrotolerant strain, CLB_ANTARCTIC_008, isolated from the gut of Dissostichus mawsoni in Antarctica, which shows robust growth in both freshwater and seawater media. Phylogenetic analysis suggests that it represents a novel genus within the family Neisseriaceae, designated as "JAGNPU01" according to GTDB taxonomy. Metabolically, CLB_ANTARCTIC_008 can utilize diverse carbon sources, including amino acids, carboxylic acids, plant oils, and aromatic compounds. Genomic analysis reveals cold adaptation-related genes encoding BCCT family transporters, TMAO biosynthesis enzymes, cold shock proteins, and multiple antioxidant enzymes. In terms of biosafety, the strain is non-hemolytic and does not cause mortality in zebrafish or largemouth bass. Remarkably, it shows strong antimicrobial activity against the highly toxic Aeromonas strain TOXIC001, reducing mortality in largemouth bass by 90 % at 15 degrees C and in zebrafish by 80 % at 28 degrees C. These findings highlight CLB_ANTARCTIC_008 as a promising beneficial bacterium for antibiotic-free disease control in cold-water aquaculture, and underscore the biotechnological value of Antarctic fish-associated microbes.

Metabolic RNA labeling with high-throughput single-cell RNA sequencing (scRNA-seq) enables precise measurement of gene expression dynamics in complex biological processes, such as cell state transitions and embryogenesis. This technique, which tags newly synthesized RNA for detection through induced base conversions, relies on conversion efficiency, RNA integrity, and transcript recovery. These factors are influenced by the chosen chemical conversion method and platform compatibility. Despite its potential, a comprehensive comparison of chemical methods and platform compatibility has been lacking. Here, we benchmark ten chemical conversion methods using the Drop-seq platform, analyzing 52,529 cells. We find that on-beads methods, particularly the meta-chloroperoxy-benzoic acid/2,2,2-trifluoroethylamine combination, outperform in-situ approaches. To assess in vivo applications, we apply these optimized methods to 9883 zebrafish embryonic cells during the maternal-to-zygotic transition, identifying and experimentally validating zygotically activated transcripts, which enhanced zygotic gene detection capabilities. Additionally, we evaluate two commercial platforms with higher capture efficiency and find that on-beads iodoacetamide chemistry is the most effective. Our results provide critical guidance for selecting optimal chemical methods and scRNA-seq platforms, advancing the study of RNA dynamics in complex biological systems.

Multiple seas in East Asia have played distinct roles during the Quaternary climatic cycles, which have repeatedly isolated and reconnected temperate forest species, while it remains unclear whether their roles differ. In this study, we used Smilax sieboldii, a widely distributed species along the eastern coast of East Asia, to simultaneously evaluate the roles of multiple seas, including the East China Sea, the Yellow-Bohai Sea, the Korea-Tsushima Strait, and the Taiwan Strait, as geographic barriers and dispersal corridors during historical sea-level fluctuations. We employed Bayesian clustering analysis and demographic simulations to elucidate the genetic structure and evolutionary history. The effects of spatial or environmental differences on population structure were examined through isolation by distance (IBD) and isolation by environment (IBE) tests. Further, genetic differentiation and gene flow were used as indicators to assess the roles of different seas as barriers or corridors. A pronounced phylogeographic structure was observed in S. sieboldii, with populations divided into three distinct gene pools separated by the East China Sea and the Korea-Tsushima Strait, accompanied by significant genetic admixture at the lineage boundaries. The lineage divergence occurred during the early Quaternary, while secondary contact began in the most recent interglacial period. During population differentiation, the East China Sea and the Korea-Tsushima Strait acted as effective geographic barriers, whereas the Taiwan Strait and the Yellow-Bohai Sea functioned more as dispersal corridors and facilitated greater gene flow. Meanwhile, IBD rather than IBE explained the population structure of S. sieboldii. To conclude, the phylogeographic patterns of S. sieboldii resulted from population isolation and admixture due to sea-level fluctuations since the Pleistocene, and the spatial scale of a sea largely determined its ecological role among the multi-sea systems. These findings improved our understanding of how paleoclimate changes and geological transformations have shaped the speciation and diversification of temperate forest species in East Asia.

This study aims to employ transcriptome sequencing (RNA-Seq) to analyze blood samples from horned and polled populations of Qilian Tibetan sheep in order to identify genes associated with horn development. The results revealed a total of 192 differentially expressed genes (DEGs) between the two groups, among which 140 were upregulated and 52 were downregulated. Gene Ontology (GO) enrichment analysis indicated that these DEGs were significantly enriched in pathways such as cytokine receptor activity, intrinsic component of membrane, and integral component of membrane. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis demonstrated that the genes were prominently enriched in pathways including cytokine-cytokine receptor interaction, and viral protein interaction with cytokines and their receptors. The study indicates that multiple differentially expressed genes may serve as crucial candidate genes influencing the development of the polled trait in Qilian Tibetan sheep. These findings provide a provide reference for revealing the genetic mechanism of horn development in Qilian Tibetan sheep, improving the genetic characteristics of horns and their application, and breeding Tibetan sheep varieties in Qilian region.

Meat quality is a key indicator of meat performance in ruminants, and its mechanism and regulation are also key to ruminant research. Studies have shown that animal meat quality is related to the gut microbiota. In this study, RT-qPCR and 16S omics were employed to assess meat quality and intestinal microbiota. The objective was to investigate the influence of seasonal variations on the meat quality of Tibetan sheep ewes by examining the rumen microflora, meat quality attributes, and associated gene expression profiles over three distinct months: May, August, and December.The results indicate that muscle tenderness was significantly greater (p < 0.001) in the grass period than in the regrowth and dry grass periods and was highest in the longest dorsal muscle. The cooking rate of the foreleg muscle was significantly greater (p < 0.05) than that during the regrowth and dry grass periods, and the pH24h significantly differed (p < 0.05) across the different seasonal periods. The crude protein content of the longest back muscle and the foreleg muscle was significantly greater (p < 0.001) than that of the wither and grass stages during the regrowth period and slightly decreased during the grass stage. The crude fat and crude ash contents of the three groups differed significantly, and the fat content during the grass stage was significantly (p < 0.05) greater than that during the regrowth stage and the wither stage. Expression analysis of genes related to meat quality revealed that the expression of the ADSL gene was significantly greater (p < 0.05) in the anterior and posterior leg muscles during the grass period than during the regrowth and wilting periods, whereas the expression of the FABP3 gene was lower than that during these two periods. Correlation analysis revealed that Rikenellaceae_RC9_gut_group was significantly positively correlated (p < 0.05) with shear forceand cooked meat percentage and significantly negatively correlated (p < 0.05). Ruminococcus and Butyrivibrio were significantly positively correlated (p < 0.05) with CAST and highly significantly positively correlated (p < 0.05). In conclusion, meat quality during different seasons is regulated by the rumen microbiota and their associated genes.

As climate change accelerates, plant species largely rely on genetic variation to adapt and survive when they fail to track their ecological niches through range shifts. Predicted genomic vulnerability is able to identify populations lacking the necessary genetic variation for climate change adaptation. However, the role of introgression in genomic vulnerability remains poorly explored. Here, we used the dove tree (Davidia involucrata), a relict species native to southwestern China, to test whether introgression may reduce genomic vulnerability. By integrating population genomics and environmental data collected from 196 individuals of 18 populations, we identified 747 strictly climate-associated loci across the distribution range of D. involucrata, 138 of which were recovered from the genetically admixed populations. We estimated the genomic vulnerability for three genetic lineages and two admixed groups using the gradient forest approach, and found that eastern populations are likely to be at higher risk. The eastern admixed populations exhibited a significant reduction, with introgression from the southern lineage. Cumulative importance analysis showed moderate importance for introgressive loci along environmental gradients. This indicates that the introduction of novel alleles through introgression provides only a partial and insufficient counterbalance to the maladaptation observed in D. involucrata under climate change. Our study highlights the role of intraspecific introgression in response to climate change and emphasizes the importance of genomic vulnerability studies in informing conservation practices for relict and endangered species.

The East China Sea coast (ECS) is characterised by a diverse range of landform types, which influence the physical characteristics of the local waters. The spatio-temporal phytoplankton community structure, and the salinity, transparency, and temperature gradients were examined across six different waters of the ECS coast during four seasons. In total, 118 taxa were identified, including 86 Bacillariophyta, 16 Pyrrhophyta, and 16 other taxa. Cluster and multidimensional scaling analyses classified the six study areas into inner the estuary, outer the estuary, and in a semi-enclosed bay. Notable variations were observed in the abundance and species distribution patterns of phytoplankton across the three water types during four seasons. Oscillatoria spp. was the dominant species inner the estuary during the spring, summer, and winter cruises. Coscinodiscus spp. and Skeletonema costatum were the dominant species in all study areas; however, as the main dominant species, there were no significant differences in Coscinodiscus spp. abundance at different dimensional scales. In addition, the biodiversity index values showed no statistically significant differences among the three types of water, except during the summer cruise. Spearman’s rank correlation and redundancy analyses showed that the distribution of Chlorophyta was primarily influenced by salinity. In contrast, transparency was the primary driver of phytoplankton abundance for most seasons and temperature exerted the most significant effect on phytoplankton abundance during summer. These findings indicate that physical disturbances are significant for the regulation of the phytoplankton community structure along the ECS coast.

Based on a pangenome graph platform, we simultaneously analyzed the impacts of SNPs and SVs in the population structure and phenotypic formation of global cattle using 2,409 individuals from 82 breeds. We demonstrated that SVs, like SNPs, effectively explain the population structure of global cattle. Genomic regions under strong selection, identified using both SNPs and SVs, consistently revealed footprints associated with human-mediated selection of economic traits in European improved cattle or natural selection of geographical adaptations. Notably, we detected that ∼40.14% of SVs were not tagged (LD, r2 < 0.6) by nearby SNPs. These “orphan” SVs may uncover new genetic signals and represent recent mutations associated with specific selection pressures or local environmental adaptation. Selected SVs tagged by SNPs also play causal or dominant roles in regions under selection. For example, our single-cell RNA sequencing has demonstrated that a notable SNP-tagged SV functions as an enhancer of the IGFBP7 gene, regulating fat deposition through IGFBP7+ cells. In conclusion, these SV-related mechanisms likely have caused some differences in economic traits and local adaptability across global cattle populations. Our integrated approaches highlight the unique and indispensable roles of SVs in shaping genetic diversity, offering novel insights into adaptation, selection, and strategies for improving cattle populations.

Alternative splicing (AS) is crucial for gene expression regulation during cold adaptation, yet its role in fish remains unclear. This study revealed tissue-specific AS patterns in zebrafish, with the gill exhibiting the highest AS frequency, followed by the skin, ovary and brain. Cold exposure significantly altered splicing sites across tissues, with exon skipping (SE) being the predominant AS form. Alternative splicing genes (ASGs) displayed strong tissue specificity, and splicing variability correlated with temperature, suggesting AS acts as a temperature-sensitive regulatory mechanism. Splicing factors, such as srsf7a, notably undergo AS, demonstrating their responsiveness to temperature changes. Key genes exhibiting differential splicing, including setd7 and mapta, present temperature-dependent isoforms. Under conditions of cold stress, zebrafish setd7 experiences cold-induced AS, resulting in the exclusion of exon 2 and the production of a truncated protein with a disrupted SET domain. This splicing event enhances zebrafish activity at lower temperatures. Simultaneously, mapta produces a 5R tau isoform via exon 7 skipping, which may dynamically regulate the balance between microtubule stability and plasticity during cold adaptation. Our transcriptome-wide analysis elucidates the AS regulatory mechanisms underlying the zebrafish response to cold stress and identifies key AS-mediated genes involved in cold adaptation, thereby providing a theoretical foundation for the molecular breeding of cold-tolerant aquaculture species.

Qaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low-oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole-genome resequencing technology, along with 192 published sets of whole-genome sequencing data of Indian indicine cattle, Chinese indicine cattle, North Chinese cattle breeds, East Asian taurine cattle, Eurasian taurine cattle and European taurine cattle as controls. It was found that Qaidam cattle have rich genetic diversity in Bos taurus, but the degree of inbreeding is also high, which needs further protection. The phylogenetic analysis, principal component analysis and ancestral component analysis showed that Qaidam cattle mainly originated from East Asian taurine cattle. Qaidam cattle had a closer genetic relationship with the North Chinese cattle breeds and the least differentiation from Mongolian cattle. Annotating the selection signals obtained by composite likelihood ratio, nucleotide diversity analysis, integrated haplotype score, genetic differentiation index, genetic diversity ratio and cross-population extended haplotype homozygosity methods, several genes associated with immunity, reproduction, meat, milk, growth and adaptation showed strong selection signals. In general, this study provides genetic evidence for understanding the germplasm characteristics of Qaidam cattle. At the same time, it lays a foundation for the scientific and reasonable protection and utilization of genetic resources of Chinese local cattle breeds, which has great theoretical and practical significance.

Heart disease remains the leading cause of death worldwide.Iron imbalance,whether deficiency or overload,contributes to heart failure.However,the molecular mechanisms governing iron homeostasis in the heart are poorly understood.Here,we demonstrate that mutation of bmp10,a heart-born morphogen crucial for embryonic heart development,results in severe anemia and cardiac hypertrophy in zebrafish.Initially,bmp10 deficiency causes cardiac iron deficiency,which later progresses to iron overload due to the dysregulated hepcidin/ferroportin axis in cardiac cells,leading to ferroptosis and heart failure.Early iron supplementation in bmp10-/-mutants rescues erythropoiesis,while iron chelation in juvenile fishes significantly alleviates cardiac hypertrophy.We further demonstrate that the interplay between HIF1α-driven hypoxic signaling and the IL6/p-STAT3 inflammatory pathways is critical for regulating cardiac iron metabolism.Our findings reveal BMP10 as a key regulator of iron homeostasis in the vertebrate heart and highlight the potential of targeting the BMP10-hepcidin-iron axis as a therapeutic strategy for iron-related cardiomyopathy.

Less is known about the interaction of viruses with their prokaryotic host in the gut of wild animal. Here we used fecal DNA metagenomic data (n = 24) from black-necked cranes during the wintering period for virus characterization. The results were found to be consistent with the trend of bacterial community changes, and the black-necked crane gut viruses community structure was conservative during the wintering period. A total of 280 vOTUs (6 complete, 3 HQ, 2 MQ and 269 LQ) were obtained and life history predictions identified 207 virulent viruses. 269 LQ vOTUs contained at least 10 viral genes, hence several of these viruses may be too distinct from viral species in the CheckV database to properly estimate their completeness. Meanwhile, gene-sharing network analysis revealed that the gut viruses of black-necked crane formed 32 unique viral clusters (VCs). Virus taxonomic assignment has revealed that Azeredovirinae is the most abundant family during the wintering period of black-necked cranes. Furthermore. Black-necked crane gut viruses have a complex relationship with their prokaryotic hosts, and virus-encoded auxiliary metabolic genes (AMGs) enhance the potential of infecting bacteria for chitin degradation, methionine and tetrahydrofolate (THF) metabolism. These results imply the presence of a large number of novel viruses in the intestinal tract of black-necked cranes, which may further affect birds by regulating prokaryotic bacterial metabolism including lyse prokaryotic host cells and encodes AMGs related to the degradation of complex carbohydrates and amino acid metabolism.

The escalation of major ion concentrations in freshwater and soil poses diverse effects on ecosystems and the environment. Excessive ions can exhibit toxicity to aquatic organisms and terrestrial plants. Currently, research on ion toxicity primarily focuses on cation toxicity. Notably, there is a noticeable research gap in understanding the impact of chloride ion (Cl-) on plant growth and development, as well as on the defense mechanisms against Cl- toxicity. In the present study, sampling was conducted on major rivers in China to measure Cl- concentrations. The results revealed that certain rivers exhibited excessive levels of Cl-, emphasizing the critical need to address Cl- toxicity issues. Subsequently, when salt-tolerant cotton seedlings were subjected to various chloride treatments, it was observed that excessive Cl- severely hindered plant growth and development. A combined analysis of transcriptomic and metabolomic data shed light on significantly enriched pathways related to galactose metabolism, arginine and proline metabolism, carotenoid metabolism, and alpha-linolenic acid metabolism under chloride stress. In summary, this research provides a scientific foundation and references for environmental management and water resource protection and offers novel insights for mitigating the adverse impacts of Cl-, thereby contributing to the preservation of ecosystem health.