Biology subjects

Zhao, X.

Publications and source records attributed to Zhao, X..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Chromosomal-level genome of the Pinus massoniana 'Minlin WY36'

Owing to conifers complex and large genomes, it is challenging to construct a comprehensive reference genome and conduct evolutionary and genomic research. Here, we present the chromosome-level assembly of Pinus massoniana Minlin WY36, a pioneering conifer species used for afforestation, timber production, and oleoresin extraction. The genome size was determined to be 23.41 Gb, with a contig N50 value of 1.15 Mb and a scaffold N50 value of 2.02 Gb. A total of 23.16 Gb of reads (98.93% of the assembled genome) were anchored and oriented onto 12 pseudochromosomes, with chromosome lengths from 1.47 to 2.29 Gb. A total of 32,144 protein-coding genes were predicted, of which 27,173 (84.54%) were functionally annotated. The P. massoniana Minlin WY36 genome consists of 79.41% (18.57 Gb) repetitive sequences, among which long terminal repeat sequences (LTR) were the most abundant. Through comparative genomic analysis, we found that the unique and significantly expanded genes in P. massoniana Minlin WY36 were enriched in the metabolism related to resin synthesis. This study offers valuable insights into conifer evolution and contributes resources for further investigations of conifer adaptation and developmental processes.

genomics↗

bioRxiv2025

Structural insights into type I and type II Lamassu anti-phage systems

Bacteria have developed a variety of immune systems to combat phage infections. The Lamassu system is a prokaryotic immune system with a core conserved Structural Maintenance of Chromosomes (SMC) superfamily protein LmuB and diverse effectors named LmuA, whose mechanism remains unclear. Here, we present a series of cryo-electron microscopy structures of type I Lamassu complex from Bacillus cellulasensis and type II Lamassu complex from Vibrio cholerae, both in apo- and dsDNA-bound states, which reveal an unexpected stoichiometry and topological architecture, distinct from canonical SMC complexes. Combined structural and biochemical analyses show how the nuclease effector LmuA is sequestered in an inactive monomeric form within the Lamassu complex, and upon sensing foreign DNA ends, dissociates and assembles into an active tetramer capable of DNA cleavage. Our findings elucidate the mechanism by which Lamassu systems detect viral replication and implement anti-phage defense, highlighting the unprecedented roles of SMC proteins in prokaryotic immunity.

microbiology↗

bioRxiv2025

Versatile Vasculature Chips for Ultrasound Localization Microscopy

Ultrasound localization microscopy (ULM) has revolutionized microvasculature imaging by surpassing the diffraction limit via microbubbles. ULM demonstrates exceptional potential to resolve micrometer-scale vascular structures in both preclinical and clinical studies. However, its performance evaluation remains challenging primarily due to the lack of reference microvascular phantoms featuring micrometer-scale, hierarchical branches, and realistic vascular structures. Inspired by microfluidic chip techniques, we present an organ-on-a-chip protocol for fabricating agarose-based micro-vessel network phantoms with ground truth. The vasculature pattern offers design versatility, enabling on-demand customization. We experimentally demonstrated the feasibility of the vasculature phantom using two adapted patterns. The first was a leaf pattern, which exhibited intrinsic quasi-two-dimensional venation network with hierarchical and branching channels similar to animal vasculature. The second was a kidney pattern, which was based on a two-dimensional projection of real human vasculature obtained from micro computed tomography. The microbubble solution was perfused into the phantoms by capillary force and gravity. The ULM-reconstructed vasculature maps agreed well with the ground truth. ULM achieved a high sensitivity of 0.97 and 0.95, but a low precision of 0.37 and 0.60, for the leaf and kidney phantom, respectively. The results indicated the capability of ULM to reconstruct vessel structures while making many false positive predictions. The proposed protocol holds significant promise for the development and optimization of ultrasound microvascular imaging techniques.

bioengineering↗

bioRxiv2025

Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae

Orchidaceae (orchids) is commonly known as one of the largest families of seed plants, and grow in an extensive range of habitats worldwide. In the present study, we generated chromosome-level reference genomes for two orchids using a combination of PacBio, Illumina, and Hi-C sequencing, Cypripedium singchii has the largest genome and chromosomes among the sequenced species so far, with a genome size of 43.19 Gb (1C) with ten chromosomes, and Apostasia fujianica has the smallest known genome and chromosomes in Orchidaceae, with a genome size of 340.90 Mb (1C) with 35 chromosomes. We predicted a total of 32,412 and 21,724 protein-coding genes for C. singchii and A. fujianica, respectively. The overall BUSCO score was 85.01% for C. singchii and 91.80% in A. fujianica. Based on protein-coding sequences from 55 conserved single-copy families across 21 plant species, we constructed a high-confidence phylogenetic tree and estimated the divergence times. The high-quality genomes of super-giga and tiny orchids offer key insight for future evolutionary researches.

genomics↗

bioRxiv2025

Elucidating the Contribution of OVLT Glutamatergic Neurons to Mineralocorticoid Hypertension in TASK-/- Mice

BackgroundAldosterone overactivity intensifies central sodium sensitivity and sympathetic output, driving salt-sensitive hypertension, but specific mechanisms remain incompletely defined. Herein, we aimed to explore the role of organum vasculosum of the lamina terminalis glutamatergic neurons (OVLTGlut) and their hyperexcitability mechanisms in hyperaldosteronism-associated hypertension. MethodsAdult age matched male TASK-/- mice (primary aldosteronism model) and wild-type controls (TASK+/+) mice were used. Neuronal excitability was assessed via patch-clamp techniques. Arterial blood pressure (BP) monitored via telemetry or carotid catheterization. Chronic drug delivery used minipumps. RNA-seq/qPCR profiled gene expression, and intracerebroventricular hypertonic saline tested sodium sensitivity. ResultsIn TASK-/- mice, heightened OVLTGlut activity increased sympathetic outflow and hypertension, mitigated by OVLTGlut neuron ablation. Optogenetic activation of these neurons or their paraventricular nucleus (PVN) / rostral ventrolateral medulla (RVLM) projections acutely elevated BP, with ablation reducing BP selectively in TASK-/- mice. Aldosterone dependence of OVLTGlut-PVN/RVLM neuron hyperactivity was evident in both TASK-/- mice and TASK+/+ mice with chronic aldosterone infusion. Aldosterone chronic infusion enhanced central sodium pressor effects, that were nullified by OVLTGlut-PVN/RVLM neuron lesioning. RNA-seq indicated that aldosterone-induced ion channel expression spectrum changes, including potassium channels and the epithelial sodium channel, underlie the neuronal hyperexcitability. ConclusionOveractivation of OVLTGlut neurons contributes to hypertension in TASK-/- mice through regulation of OVLTGlut-PVN/RVLM circuits. The hyperexcitability of these neurons, possibly due to aldosterone-induced changes in ion channel expression spectrum, contribute to hypertension by amplifying central sodium sensitivity.

neuroscience↗

bioRxiv2025

Scalable expansion and hepatic zone maturation of hepatic progenitor cells from human pluripotent stem cells

Scalable generation of functionally mature hepatocytes from human pluripotent stem cells (hPSCs) is vital for regenerative medicine, disease modeling, and drug screening. We present a modular differentiation platform that enables serial expansion and cryopreservation of hepatic progenitors (hepatoblasts; HBs), supporting efficient downstream maturation. By modulating bile acid signaling with FGF19 and culturing under hypoxia, we preserved HB proliferation and bipotency. Subsequent thyroid hormone treatment induced alpha-fetoprotein-negative, albumin-positive hepatocytes, while WNT pathway modulation promoted zonal identity, mimicking in vivo hepatic metabolic heterogeneity. Zonation was confirmed by differential drug-metabolizing enzyme activity, mitochondrial function, and enhanced engraftment in a liver injury mouse model. To evaluate translational relevance, mature hepatocytes were incorporated into extrusion-based 3D bioprinted constructs, which maintained hepatic viability and function. This integrated strategy of combining progenitor cell banking, zonation control, and tissue engineering offers a scalable and clinically relevant approach for generating functional human liver tissue suitable for therapeutic development.

cell biology↗

bioRxiv2025

Composition of Carotid Plaques Differs Between Chinese and United States Patients: A Histology Study

BackgroundThe clinical manifestations of cerebrovascular disease are known to differ between the Chinese and United States (U.S.) populations as do the plaque features on imaging. ObjectivesThe aim of this study was to investigate and compare the histological features of excised carotid plaques from Chinese and U.S. patients. MethodsCarotid endarterectomy specimens collected from two prospective studies were included. The entire plaque was serially sectioned (10 {micro}m thickness) at 0.5-1 mm intervals. Hematoxylin and eosin staining and Mallorys trichrome staining were performed. The morphology and components of the plaques were measured and compared between the two groups. ResultsA total of 1,152 histological sections from 75 Chinese patients and 1,843 sections from 111 U.S. patients were analyzed. The Chinese group had significantly smaller minimum lumen diameters (median: 1.1 vs. 1.3 mm, p=0.046) and a larger percent wall volume (median: 74% vs. 70%, p=0.018) than the U.S. group. After adjusting for confounding factors, carotid plaques in the Chinese population were more likely to have more lipid pools ({beta}=10.0%, 95%CI: 4.9 to 15.9%), more recent intraplaque hemorrhage (IPH; {beta}=8.4%, 95%CI: 4.5 to 12.7%), and less late IPH ({beta}=-8.2%, 95%CI: -11.3 to -5.4), and fewer fibrous cap disruptions (45% vs. 67%, p=0.061). Chinese plaques were more homogeneous and had a higher percentage of plaques with features of xanthomas than did U.S. plaques (20% vs 2.7%, p<0.001). ConclusionsThe histology of Chinese plaques differs significantly from that of U.S. plaques, suggesting substantial differences in the pathophysiology of atherosclerotic cerebrovascular disease between Chinese and North American populations, which could enhance the gap in racial pathology comparison, indicating a need for a different management approach. Central illustration O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/658993v1_ufig1.gif" ALT="Figure 1"> View larger version (83K): org.highwire.dtl.DTLVardef@14f16corg.highwire.dtl.DTLVardef@f60d66org.highwire.dtl.DTLVardef@1e9a822org.highwire.dtl.DTLVardef@11d7a31_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2025

Selective vulnerability of cerebral vasculature to NOTCH3 variants in small vessel disease and rescue by phosphodiesterase-5 inhibitor

NOTCH3 variants cause CADASIL the most common genetic form of small vessel disease (SVD) and vascular dementia (VaD) and increase the stroke and SVD/VaD risk. CADASIL is a systemic vasculopathy but predominantly manifests in the brain. The molecular mechanisms of CADASIL remain largely unclear with no specific available treatments. NOTCH3 is primarily expressed in vascular smooth muscle cells (VSMCs). Using human induced pluripotent stem cell (iPSC) models and developmental lineage-specific VSMC differentiation, we revealed a selective vulnerability of cerebral but not peripheral VSMC mimics to NOTCH3 variants. Transcriptomic, protein and functional analyses demonstrated a switching of CADASIL iPSC-VSMCs from a contractile to a synthetic phenotype, accompanied with extensive extracellular matrix accumulation and impairment of cell adhesion leading to anoikis. Importantly, we describe an endothelial independent nitric oxide signalling in VSMCs which was dysregulated in the CADASIL iPSC-VSMCs, and posphodiesterase-5 (PDE5) inhibition successfully rescued the abnormal VSMC function, suggesting a novel therapeutic strategy. Our findings offer new mechanistic insights into brain specific phenotype in NOTCH3-associated SVD/VaD and support patient-specific iPSCs to be a valuable model for identifying targeted treatment for NOTCH3-associated SVD/VaD.

neuroscience↗

bioRxiv2025

Adhesive implant interfaces prevent fibrosis by disrupting mechanobiological feedback

Fibrotic encapsulation around medical implants affects millions of patients annually. Current approaches targeting inflammation or implant material properties have failed clinically, but the mechanical origins of implant-induced fibrosis remain unexplored. Here, we demonstrate that directional imbalance of mechanical forces ("tension anisotropy") is the primary driver of fibroblast activation at implant-tissue interfaces, and that it can be eliminated through adhesive bonding strategies. Computational modeling reveals a mechanistic basis for successful adhesive anti-fibrotic interfaces: conventional sutured implants generate highly anisotropic stress fields between discrete suture anchor points that activate fibroblasts, while adhesive interfaces distribute forces isotropically, maintaining a mechanical environment that does not activate fibroblasts. In vivo experiments from the literature across multiple animal models confirm these predictions: as predicted, adhesive interfaces completely prevent fibrotic capsule formation for up to 12 weeks across diverse organs, while maintaining identical implant composition and geometry compared to sutured controls. Results establish tension anisotropy as a mechanical regulator of implant fibrosis and provide a mechanistic foundation explaining why adhesive interfaces succeed where all previous anti-fibrotic strategies have failed. By addressing the root mechanical cause of fibrosis, this mechanobiology-driven approach may enable a universal approach for preventing fibrosis across all categories of implantable medical devices. Significance statementMillions of patients suffer from medical device failure due to fibrotic encapsulation, in which a surgically implanted item such as pacemaker leads or a vascular graft loses function by becoming covered with scar tissue. Implants affixed to soft tissues by sutures are especially prone to this form of failure, but implants affixed with a recently invented adhesive are not. We present the discovery that directional imbalance of forces ("tension anisotropy") drives conversion of healing tissue into scar tissue. Conventional sutured implants create highly anisotropic stress fields between anchor points that activate fibroblasts, while adhesive interfaces distribute forces isotropically, attenuating scarring. This mechanistic insight explains why adhesive implant-tissue interfaces successfully prevent fibrotic capsule formation across multiple animal models and organ systems, where all previous anti-fibrotic approaches have failed. By addressing root mechanical causes of fibrotic remodeling, this discovery provides a pathway for clinical remediation of fibrotic encapsulation.

biophysics↗

bioRxiv2025

Ninjurin2 Regulates Vascular Smooth Muscle Cell Phenotypic Switching and Vascular Remodeling through Interacting with PDGF Receptor-β

Vascular smooth muscle cell (VSMC) phenotypic switching from a contractile to synthetic state plays a pivotal role in vascular remodeling. Although genome-wide association studies have linked NINJ2 (encode Ninjurin2) polymorphisms are associated with risk of atherosclerosis and related conditions like ischemic stroke and coronary artery disease, its functional role in regulating VSMC plasticity remains unexplored. Here, using Ninj2 knockout (Ninj2-/-) and smooth muscle-specific overexpressing (Ninj2smcTG) mice subjected to carotid artery ligation, we demonstrate that Ninjurin2 deficiency exacerbates injury-induced intimal hyperplasia, whereas its overexpression attenuates this pathological remodeling. Mechanistically, Ninjurin2 knockdown promoted PDGF-BB-mediated VSMC phenotypic switching, proliferation, and migration, while biochemical studies revealed that Ninjurin2 interacts with PDGFR{beta} to suppress FAK signaling. These findings identify Ninjurin2 as a novel regulator of VSMC phenotypic switching via the PDGFR{beta}/FAK axis, offering new mechanistic insights into vascular remodeling and potential therapeutic avenues for atherosclerosis.

pathology↗

bioRxiv2025

Proteomic analysis of exosomes from lymphatic affluents reveals their implications in developing premetastatic niche in melanoma.

Melanoma is an aggressive form of skin cancer that often spreads via lymphatic pathways to regional and distant sites. Melanoma-derived lymphatic exosomes play a crucial role in forming a tumor-supportive environment for metastasis, or premetastatic niche, within the first tumor draining lymph node, also known as the sentinel lymph node (SLN). Therefore, analyzing the proteomic content of tumor-draining lymphatic exosomes that deliver oncogenic molecules to the SLN is important in understanding the premetastatic niche. To reveal the proteomic landscape of lymphatic exosomes, we performed multidimension liquid chromatography-tandem mass spectrometry with multiplexing (18-samples) using tandem mass tag (TMT) labeling to profile the lymphatic exosomal proteomes obtained from afferent lymphatic channels leading to the SLN of patients with melanoma (n=6), control afferent lymphatic channels from prophylactic mastectomy (n=3) and non-cancer post-operative lymphatic fluid (n=9). Lymphatic fluid from postoperative lymphadenectomy drains served as another control to filter out non-melanoma alteration in lymph that may be related to the procedure of surgical resection and wound healing process. Our proteomic analysis identified 3929 proteins in the lymphatic exosomes, of which 968 were unique proteins absent from the current exosomal database. Interestingly, melanoma lymphatic exosomes possess distinctive proteomic cargo, which is significantly associated with cancer-associated and cellular structural remodeling pathways (FDR <0.05). Moreover, proinflammatory wound healing pathways are predominantly present in melanoma and postoperative lymph fluid compared to normal control afferent lymphatic channels. We identified a total of 17 uniquely modulated proteins in melanoma compared to control and postoperative lymph, which are critically involved in the process of melanoma tumorigenesis. At least ten upregulated proteins strongly correlate with each other at the gene expression levels in melanoma tumors compared to controls and may serve as a signature panel for melanoma (p = 2.13 x 10-58). In summary, this study represents the first comparative analysis of the lymphatic exosomal proteome and highlights distinct exosomal proteins that may support premetastatic niche formation in the SLN.

cancer biology↗

bioRxiv2025

Cargo recognition of Nesprin-2 by the dynein adapter Bicaudal D2 for a nuclear positioning pathway that is important for neuronal migration

Nesprin-2 and its paralog Nesprin-1 are subunits of LINC complexes that are essential for brain development. To position the nucleus for neuronal migration, Nesprin-2 interacts with the motors kinesin-1 and dynein, which are recruited by the adapter Bicaudal D2 (BicD2), but the molecular details of these interactions are elusive. Here, structural models of minimal Nesprin-2/BicD2 complexes with 1:2 and 2:2 stoichiometry were predicted using AlphaFold and experimentally validated by mutagenesis, binding assays and single-molecule biophysical studies. The core of the binding site is formed by spectrin repeats of Nesprin-2, which form an alpha-helical bundle with BicD2 that is structurally distinct from the Rab6/BicD2 and Nup358/BicD2 complexes. Such structural differences could fine tune motility of associated dynein and kinesin-1 motors for these transport pathways. Furthermore, the Nesprin-2 fragment interacts with full-length BicD2 and activates dynein/dynactin/BicD2 complexes for processive motility, suggesting that no additional components are required to reconstitute this transport pathway. Interestingly, either one or two Nesprin-2 molecules can bind to a BicD2 dimer and activate BicD2/dynein/dynactin complexes for processive motion, resulting in similar speed and run lengths. The BicD2/dynein-binding site is spatially close but does not overlap with the kinesin-1 recruitment site, thus both motors may interact with Nesprin-2 simultaneously. Several mutations of Nesprin-1 and 2 that cause Emery-Dreifuss muscular dystrophy are found in the motor-recruiting domain and may alter interactions with kinesin-1 and BicD2/dynein, consistent with the abnormally positioned nuclei found in patients with this disease.

biophysics↗

bioRxiv2025

Cryo-EM structure of plant urea transporter DUR3 reveals essential role of C-terminal domain in tetramer assembly and insights into proton-coupled transport

Nitrogen pollution, caused by the overuse of nitrogen-fertilizers such as urea in agricultural production, has become a serious problem that threatens both the environment and human health. Improving the nitrogen use efficiency of crops is an important approach to reduce fertilizer use. DUR3, a high-affinity urea transporter, enables plants to acquire urea from natural or agricultural soils with low urea concentrations and has been proposed as a promising target for engineering crops to improve nitrogen-fertilizer use efficiency. Despite extensive studies for more than 20 years, the structure, substrate recognition and transport mechanism of DUR3 have remained unknown. Here we report the cryo-EM structure of maize DUR3 (ZmDUR3) at 3.41 [A] resolution. ZmDUR3 adopts an amino acid-polyamine-organocation (APC) superfamily fold and is structurally distinct from animal facilitative urea transporters. Our structure provides important insights into urea recognition by DUR3 and suggests that a pair of acidic residues is potentially involved in proton coupling during urea transport. Furthermore, our structural and functional studies indicate that DUR3 assembles into a tetramer and tetramer formation is important for its function. Our results pave the way for engineering plant DUR3 protein for applications in sustainable agricultural production.

plant biology↗

bioRxiv2025

Circular RNA profiling revealed an evolutionarily conserved circACACA promotes liver lipid metabolism, oxidative stress, and autophagy disorder in a ceRNA manner

Non-alcoholic fatty liver disease (NAFLD) is a clinical syndrome characterized primarily by hepatocellular steatosis and lipid accumulation, which leads to hepatocyte apoptosis, autophagy, inflammation, and intracellular oxidative stress. NAFLD is recognized as one of the most prevalent and complex chronic liver diseases globally, with its occurrence and associated mortality rates rising swiftly each year. Due to the high similarity between chicken fatty liver syndrome (FLS) and NAFLD, as well as the easy availability of diseased chickens, the chicken is considered an ideal model for studying the pathogenesis of NAFLD. Previous studies have pinpointed several circular RNAs (circRNAs) implicated in the pathogenesis of NAFLD, yet the underlying functions and mechanisms of numerous circRNAs continue to remain elusive. In this experiment, we utilized circRNA sequencing of chicken livers to identify a novel circRNA, named circACACA, and discovered that it disrupts the metabolic homeostasis of lipids within hepatocytes. Consequently, this disruption leads to oxidative stress and the induction of autophagy, ultimately exerting an adverse effect on chicken liver health. Mechanistically, circACACA functions as a molecular sponge for miR-132b-5p and miR-101-2-5p to modulate the expression of the downstream CBFB/PIM1 complex. Consequently, it influenced the activity of the AKT/mTOR and PPAR-{gamma} signaling pathways to perform its physiological functions. Crucially, we noticed substantial sequence similarity of circACACA across diverse species by comprehensively searching databases. Further, our research with a mouse model confirmed that the functional conservation of circACACA across livers of different species. Overall, this study built a mechanistic network for circACACA and confirmed its sequence conservation and functional relevance across various species. Our results not only provide new targets for the prevention and treatment of NAFLD but also present fresh perspectives for progress in healthy production of laying hens.

cell biology↗

bioRxiv2025

Theoretical origins of extreme cell differentiation irreversibility: a dynamic model of organismal size effects

Cell differentiation is a pivotal evolutionary transition underlying multicellular complexity. Irreversible differentiation - a process in which cells permanently lose plasticity to become specialized types - is hypothesized to emerge predominantly in large, cell-rich organisms. However, the causal relationship between organismal size and the evolutionary origins of this extreme developmental commitment remains unclear. By integrating developmental dynamics into a mathematical model, we demonstrate that extreme irreversible differentiation (where all cell types exhibit irreversibility) most robustly evolves in intermediately sized multicellularity. This reveals a non-monotonic dependence of cell fate determinism on an organismal scale. Specifically, increasing organismal size initially promotes extreme irreversible differentiation by enhancing the selective advantages of cellular division of labor. Beyond a critical size threshold, however, further expansion destabilizes this extreme irreversibility due to its decreasing differentiation advantages compared with reversible differentiation. Counterintuitively, smaller organisms establish cellular irreversibility at earlier developmental stages rather than larger organisms. Our framework identifies an evolutionary double-edged sword: while body size expansion initially facilitates extreme differentiation irreversibility, it ultimately leads to its collapse. These results establish quantitative links between organismal dimensions and cell fate determinism, explaining the size-dependent evolution of developmental strategies in simple multicellular systems.

evolutionary biology↗

bioRxiv2025

Microbiota-derived secondary bile acids promote STING activation and antitumor activity

Microbiota metabolism generates diverse bile acids that are associated with health and disease, but the molecular targets and mechanisms of action for these metabolites have not been fully elucidated. Using deoxycholic acid (DCA) photoaffinity probes, with cholic acid (CA) probe as a comparator, we found many protein targets of microbiota-derived DCA in mammalian cells. Of note, we discovered that DCA binds the transmembrane domain of stimulator of interferon genes (STING), and enhances agonist-induced accumulation of higher-order STING species, type I interferon signaling and antitumor immunity. Moreover, DCA-producing microbiota species enhanced STING agonist-induced antitumor immunity primarily through the activation of natural killer (NK) cells. This reverse chemical microbiology approach revealed an unpredicted mechanism of action for DCA on STING activation and suggests that specific secondary bile acids and their associated microbiota species may promote NK activation and impact the efficacy of STING-targeted therapeutics.

immunology↗

bioRxiv2025

A biGWAS strategy reveals the genetic architecture of the interaction between wheat and Blumeria graminis f. sp. tritici

BackgroundWheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt) is one of the most significant diseases affecting global wheat production. Breeding for disease resistance (R) genes against Bgt often follows a boom-bust cycles, where cultivars with effective resistance are widely deployed on an expanding area until virulence emerges in the avirulence (Avr) pathogen population. While extensive effort has been devoted to identifying and cloning R genes, Avr genes remain relatively understudied, limiting our understanding of R-Avr interactions. That said, understanding R-Avr interactions is crucial for developing durable resistance strategies. ResultsWe conducted whole genome sequencing on 245 Bgt isolates collected from major wheat-growing regions in China, identifying 120 genetically unique isolates. Each of these unique isolates was inoculated and phenotyped on a diverse panel of wheat germplasm. Through Genome-Wide Association Analysis (GWAS) in both Bgt and wheat, we identified 65 Avr loci and 251 R loci overlapping with nine and eight cloned Avr or R genes, respectively. On average, each isolate carries eight Avr alleles, ranging from one to 17. Little geographical preference for Avr alleles or their combinations was observed, suggesting that disease resistance breeding against this pathogen should be coordinated at the national level. The level of resistance level is positively correlated with the number of R alleles carried by a wheat line, and the average frequency of an R allele is 2% among the wheat panel, indicating the potential for accumulating R alleles in breeding programs. We mapped 212 R-Avr interactions based on joint GWAS using both plant and pathogen genomes and cross-species epistasis, where a network of interactions was formed between wheat and Bgt. These interactions indicate that pyramiding five major R loci has the potential to confer resistance to half of the Avr loci. As a proof of concept, we successfully verified two previously described R-Avr pairs using tobacco experiments. Furthermore, we provided molecular validation evidence for three new Avr genes, including Bgt-50651, BgtE-5826 and BgtE-20009, and two new R-Avr interactions. Among them, Bgt-50651 interacts with Pm1a, Pm2a, and another unidentified R gene located near the Pm6/Pm52 interval. ConclusionOur study provides a framework for understanding the genetic interaction between plants and pathogens. The discovery of novel R/Avr loci and their complex interaction network underscores the need to integrate crop and pathogen genetic background, particularly the R/Avr allele composition, into breeding program design. These findings have significant implications for developing durable resistance strategies in wheat alongside offering valuable insights into the broader dynamics of plant-pathogen interactions.

genomics↗

bioRxiv2025

A transcriptional biosensor reveals mechanisms of α-ketoglutarate signaling to chromatin

Alpha-ketoglutarate (KG) is required for chromatin demethylation but mechanisms controlling KG abundance in the nucleus are poorly defined. Therefore, we designed a biosensor system to monitor this metabolite pool in human cells using an KG-responsive cyanobacterial transcription factor, NtcA. We then coupled this system with a genetic screen to identify genes that regulate KG in the nucleus, defining an inter-organelle pathway in which sequential mitochondrial activities of the GPT2 transaminase and SLC25A11 transporter supply nuclear KG. Using a mouse model of GPT2 deficiency, a human inborn error of metabolism, we found that this pathway controls chromatin methylation in the developing brain. Our work provides a tool to assess KG signaling to chromatin and a framework for leveraging forward genetics to study nuclear metabolite pools.

synthetic biology↗