Biology subjects

Liu, Y.

Publications and source records attributed to Liu, Y..

At least 253 records · Page 14Linked to original sources

bioRxiv2026

Structures of Cas9-Bound Double-Stranded DNA Mini-Circle Reveal Impacts of DNA Shape on Cas9 Target Interrogation

CRISPR-Cas9 is an RNA-guided endonuclease that cleaves double-stranded DNA at specific sites and has been adapted as a powerful tool for genome manipulation. Cas9 recognizes its target through multiple conformational transitions coordinated between the Cas9 ribonucleoprotein and the DNA duplex. Such transitions, and consequently Cas9 targeting specificity, are expected to be significantly influenced by the collective duplex physical properties referred to as DNA shape. To advance our currently limited understanding of the interplay between DNA shape and Cas9 target interrogation, we solved two cryo-EM structures of SpyCas9 bound to a cognate target embedded in a relaxed 95-base-pair DNA double-stranded minicircle. The Cas9-bound DNA segment engages in similar interactions involved in PAM-binding and R-loop initiation as those observed in Cas9-bound linear DNA. However, R-loop is limited to less than three base-pairs, thus interfering with Cas9 cleavage. The minicircle DNA, which is fully resolved, retains its global shape. As Cas9 locally unwinds the protospacer, the closed-ring topology constrains the movement of the paired PAM-distal DNA duplex, thus interfering with R-loop propagation. These data provide detailed insight into the interplay between DNA shape and Cas9 structure and function, and may shed light on genome-editing and manipulation in environments with varied DNA topologies.

biophysics↗

bioRxiv2026

Conserved bacterial genes for biosynthesis of the algal morphogen thallusin span land and sea

Bacterial signals control the development of marine algae, yet the molecular basis of these cross-kingdom interactions remains largely unknown. Thallusin is the paradigmatic case: isolated in 2005, it induces rhizoid and cell wall formation in the green seaweed Ulva at picomolar concentrations, but its biosynthesis has remained elusive for two decades. Comparative genomics across five bacterial phyla identifies a conserved set of genes - the eustigmatophyte bacterial operon (ebo) - as determinants of thallusin biosynthesis. Isotope labeling, heterologous expression, and gene deletion in Stieleria maiorica show that the aromatic scaffold derives from a cyclitol precursor and L-aspartate, with subsequent prenylation and cyclization. Searching 124,295 prokaryotic genomes identifies producers in eleven bacterial lineages, including soil cyanobacteria, establishing thallusin as a widespread cross-kingdom signal reaching beyond the ocean.

microbiology↗

bioRxiv2026

Comprehensive Complete-Genome Analysis of Lactobacillaceae and Bifidobacteriaceae Reveals Strain-Specific Metabolic Interactions in Chinese Gut Microbiota

Bifidobacteriaceae and Lactobacillaceae are key probiotic families and widely used in food production, yet a comprehensive understanding of strain functions and their gut microbial interactions based on complete genomes remain understudied. Here we constructed a complete-genome dataset of 3,300 strains from these two families, including 1,151 newly isolated from China. Compared with draft assemblies, complete genomes substantially recovered a gene functional landscape encompassing stress tolerance, surface exopolysaccharide synthesis, nutrient utilization, and mobile genetic elements. Major species from both families exhibited a prevalence >60% in the Chinese population, far higher than that in US/Dutch cohorts. Notably, as a core probiotic species with remarkable genomic plasticity and gut-adaptive potential, Lactiplantibacillus plantarum stood out in our dataset for its enriched functional profile and was particularly abundant in the Chinese population. Moreover, compared with non-Chinese genomes, our isolates of key species displayed less metabolic complementarity and stronger competition with potentially pathogenic keystone species in the gut, thereby linking strain origin to enhanced probiotic potential and ecological fitness to benefit human gut health.

microbiology↗

bioRxiv2026

SnoRNA Expression and RNA 2'-O-Methylation in Drosophila melanogaster S2 Cells

Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that play critical roles in guiding 2-O-methylation (Nm) and pseudouridylation modifications of RNAs. In Drosophila melanogaster, snoRNAs undergo dynamic changes in expression during development. In this study, we identified 239 snoRNAs that are robustly expressed in Drosophila S2 cells, representing 87% of all annotated Drosophila snoRNAs. Given that box C/D snoRNAs guide site-specific 2-O-methylation (Nm) of RNA, we next characterized the Nm landscape of S2 cells using RibOxi-seq2, a high-throughput approach capable of detecting Nm modifications with single-nucleotide resolution. RibOxi-seq2 revealed 17 Nm sites in 18S rRNA with a 94% concordance to previously reported RiboMeth-Seq data. In 28S rRNA, 30 Nm sites were identified, corresponding to an 71.4% overlap with established references. Additionally, we detected both a known Nm site (Gm74) and a novel site (Um66) in 5.8S rRNA, further validating the sensitivity and specificity of the approach. RibOxi-seq2 further identified Nm sites in small nuclear RNAs (snRNAs), expanding the annotation of modified non-coding RNAs. Additionally, the method revealed Nm modifications within internal regions of mRNAs. In total, we detected Nm modifications in 2,057 unique mRNAs, underscoring the widespread presence of this epitranscriptomic modification in coding transcripts. Strikingly, although we could not identify any snoRNAs predicted to guide the mRNA 2-O-methylation modifications by canonical mechanisms, we identified strong consensus sequences surrounding many of these mRNA sites. Together, our findings not only expand the known landscape of Nm-modified RNAs but also highlight the robustness of RibOxi-seq2 for transcriptome-wide RNA modification profiling. Collectively, this study presents a comprehensive atlas of snoRNA expression and 2-O-methylation sites in Drosophila S2 cells, offering valuable insights into the epitranscriptomic landscape orchestrated by snoRNAs.

genomics↗

bioRxiv2026

Heterogeneity-driven adaptive scale graph learning for subcellular spatial transcriptomics

MotivationSpatial transcriptomics enables gene expression profiling within intact tissue sections, providing an important basis for analyzing tissue organization, cellular heterogeneity, and microenvironmental interactions. However, existing spatial structure identification methods often integrate spatial information using fixed neighborhoods or predefined smoothing scales, which limits their ability to adapt to region-specific structural heterogeneity. In homogeneous regions, broader spatial smoothing can help preserve continuous tissue structures, whereas in regions with complex boundaries or mixed cell populations, excessive smoothing may obscure local expression differences and fine-scale structural changes. Therefore, it is necessary to develop an adaptive graph learning framework that can adjust the range of spatial information integration according to tissue structural heterogeneity. ResultsIn this study, we propose HAST, a heterogeneity-driven adaptive-scale graph learning framework for spatial transcriptomics. HAST adaptively determines graph filtering scales according to spatial structural heterogeneity, enabling flexible information aggregation across different tissue regions. It further decomposes gene expression signals into low-frequency structural components and high-frequency residual components, thereby jointly modeling global spatial continuity and local expression variations. Experiments on high-resolution spatial transcriptomics datasets show that HAST improves spatial structure identification and cross-section generalization. Tumor-enriched cluster identification and neighborhood enrichment analysis further demonstrate its ability to characterize tumor-associated spatial regions and microenvironmental organization.

bioinformatics↗

bioRxiv2026

A long-chain heparan sulfate capture mechanism directs paracrine GDNF-GFRα1 signalling through RET

The receptor tyrosine kinase RET is activated by GDNF and GFR1 together as a bipartite ligand, driving receptor activation and signalling in developmental and neuroprotective contexts. Evidence from developmental and cell models has suggested that heparan sulfate (HS) functions as a fourth component in RET signalling by binding to GDNF, but the molecular details remain unclear. Here, we present the cryo-EM structure of the heterohexameric RET:GDNF:GFR1 complex with a fully resolved heparin ligand, revealing an unexpected extended HS binding site spanning all three proteins. The architecture of the complex and binding mode of the HS chain in this complex enables the formation of a higher order 4:4:4 assembly bound to a single 30-saccharide HS chain which bridges two intimately bound complexes. This multi-protein interface selectively binds the highly sulfated domains of HS over other GAG classes, and is essential for RET activation in trans with soluble GFR1, but not in cis when GFR1 is membrane-bound. Our data suggest that HS shapes the dynamics of RET signalling at every stage, from ligand diffusion to signalling complex formation. Thus, GDNF-GFRa1 paracrine signalling reveals a surprising dependence for long-chain GAG function in which the glycan engages in both receptor complex assembly and clustering.

biochemistry↗

bioRxiv2026

Cryo-EM Structure of a 95-Basepair Double-Stranded DNA Minicircle at 5.3 A Resolution

Double-stranded DNA minicircles have been observed in a variety of biological settings and are also widely employed in biotechnology, therapeutic applications, and basic research. Here, we report a cryo-EM structure of a 95-basepair minicircle (dsMC95) at a 5.3 [A] resolution. dsMC95 forms a closed ring as designed and no local deformation is observed. The two DNA strands are fully resolved, with the major and minor grooves clearly distinguishable. Analysis reveals a nine-fold periodicity in the helical twist, which corresponds to approximately 10.56 base pairs per turn. Together with groove width analysis, the data indicate that dsMC95 maintains a B-DNA configuration. The dsMC95 ring exhibits an in-plane ellipticity of 1.13 and an out-of-plane displacement of 15{degrees}, with differences in out-of-plane displacements observed between the two half-segments. The dsMC95 structure, which is the only free DNA cryo-EM structure with a resolution better than 6 [A] to date, allows comparison to other structures to better understand DNA physical features such as bending. The findings advance our understanding of DNA structure under topological constraints and may inform studies of naturally occurring small circular DNA as well as the manipulation of DNA in nanotechnology applications.

biophysics↗

bioRxiv2026

Targeting THOC2-Mediated mRNA Export Induces PARP Inhibitor Vulnerability in DNA Repair-Competent Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) remains a lethal malignancy with limited therapeutic options. While Poly (ADP-ribose) polymerase inhibitors (PARPi) exploit synthetic lethality in tumors with DNA repair defects, their clinical utility in HCC is hindered by the low prevalence of canonical repair gene mutations and the enhancing DNA repair capacity. Through proteomic analysis of two independent cohorts (n=260), we identified the THO complex component THOC2 as a master regulator of DNA damage response (DDR) via mRNA nuclear export control. Clinically, THOC2 overexpression predicted poor survival (HR=2.68-6.84, P<0.001) and correlated with enhanced DDR gene expression. Mechanistically, THOC2 chaperones mRNA nuclear export of DDR effectors (MDC1, PRKDC, MSH6) and proliferation drivers (TOP2A), thereby establishing a dual pro-repair/pro-growth program. Targeting this vulnerability, THOC2 knockdown induced synthetic lethality with PARPi, reducing Olaparib IC50 by up to 61% and suppressing tumor growth by 76% (P<0.001). Our study illuminates mRNA transport as a druggable DDR modulator and establishes THOC2 as both a prognostic biomarker and a therapeutic target to overcome PARPi resistance in HCC. This work pioneers a strategy to expand synthetic lethality beyond genetic defects by targeting post-transcriptional regulation.

cancer biology↗

bioRxiv2026

Estimating Daily Taxon-specific Tree Pollen at a 1-km Resolution in Atlanta, GA from 2020 to 2024

While tree pollen is a major trigger of allergic respiratory conditions and different taxa exhibit varying allergenic potentials, the lack of high-resolution, taxon-specific exposure metrics have limited our ability to identify which local pollen taxa are primarily responsible for respiratory illness. Traditional pollen monitoring networks, which have an intermittent sampling schedule, are not ideal for examining the delayed effects of pollen exposure due to the missing days. In this study, we developed a modeling framework integrating atmospheric dispersion effects, taxa-specific phenology, and machine learning to predict daily counts of 13 tree taxa in the five-county Metro Atlanta area, Georgia at a 1-km resolution from 2020 to 2024. Machine learning model performance was validated with daily pollen counts collected by a multi-site monitoring network equipped with automated pollen sensors. Findings showed that Betula and Quercus pollens exhibited higher predictive performance than other taxa, with R2 values ranging from 0.69 to 0.92 and from 0.71 to 0.89, respectively. Our 1-kilometer prediction data provides gapless exposure metrics to understand the spatial and temporal variability in pollen exposure, can facilitate investigation of urban pollen hotspots and support epidemiologic studies of pollen-related respiratory outcomes.

plant biology↗

bioRxiv2026

Orally Bioavailable SARS-CoV-2 Protease Inhibitors Bearing a Hydroxymethyl Ketone Warhead

The use of covalent warheads targeting the catalytic cysteine has been a cornerstone in coronavirus main protease (Mpro) inhibitor development, where various electrophilic motifs have been used including aldehydes, nitriles, ketoamides, and hydroxymethyl ketones (HMKs). Recent efforts have been mostly centered around nitrile warheads, given the success of compounds like Nirmatrelvir and Ensitrelvir in the clinic. However, finding and advancing alternative chemotypes with differentiating chemical and pharmacological profiles is essential for future pandemic preparedness. Among such alternatives, HMKs hold special interest because they balance reduced intrinsic electrophilicity with an excellent selectivity profile. Nevertheless, early HMK-based compounds, such as the clinical-stage Mpro inhibitor PF-00835231, suffered from poor oral bioavailability and therefore required intravenous administration, with or without prodrug derivatization of the hydroxyl group. Here, we describe our efforts in advancing the HMK field via the discovery of mCMX110, a lead that has superior potency, increased unbound exposure in vivo, and favorable oral bioavailability in preclinical studies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/725542v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@40222aorg.highwire.dtl.DTLVardef@831b88org.highwire.dtl.DTLVardef@184a910org.highwire.dtl.DTLVardef@779095_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

CAD rewires nucleotide metabolism to drive oxidative stress in myocardial ischemia/reperfusion injury

Myocardial ischemia/reperfusion (I/R) injury is a major determinant of infarct size and clinical outcome, yet effective therapies remain limited. Although metabolic remodeling is central to I/R pathology, the contribution of nucleotide biosynthesis remains unclear. Here, we identify CAD, the multifunctional rate-limiting enzyme of de novo pyrimidine biosynthesis, as a previously unrecognized regulator of myocardial reperfusion injury. CAD activation exacerbated cardiomyocyte death during simulated I/R, whereas CAD knockdown or pharmacological inhibition was protective in vitro. Mechanistically, CAD enhanced dihydroorotate dehydrogenase (DHODH)-dependent electron transfer, increased the CoQH2/CoQ ratio, and promoted complex I reverse electron transport (RET), thereby amplifying mitochondrial ROS. In parallel, CAD suppressed de novo purine synthesis, causing purine insufficiency, DIS3L-dependent RNA decay, and cytosolic ROS. Importantly, cardiomyocyte-specific CAD deletion protected against cardiac I/R injury in vivo. Together, these findings establish CAD as a metabolic hub linking nucleotide flux to dual-compartment ROS signaling and identify nucleotide metabolism as a therapeutic vulnerability in myocardial I/R injury. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/725578v1_ufig1.gif" ALT="Figure 1"> View larger version (87K): org.highwire.dtl.DTLVardef@14c4fedorg.highwire.dtl.DTLVardef@1138ed2org.highwire.dtl.DTLVardef@1057d8borg.highwire.dtl.DTLVardef@17546bd_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Identification of Reductases Catalyzing Benzyl Alcohol Formation during Salicylic Acid Biosynthesis in Plants

Salicylic acid (SA), a central hormone in plant immunity, is biosynthesized via a recently elucidated phenylalanine-derived pathway in most seed plants. This pathway requires benzyl alcohol as a key substrate for the formation of the SA precursor benzyl benzoate. However, how benzyl alcohol is produced in plants was unclear. Here, we identify a two-step conversion of benzoyl-CoA to benzyl alcohol via benzaldehyde in Nicotiana (N.) benthamiana. From a forward genetic screen for SA-deficient mutants, the and {beta} subunits of heterodimeric benzaldehyde synthase (BalS) involved in the conversion of benzoyl-CoA to benzaldehyde were found to be required for SA biosynthesis in N. benthamiana. Further reverse genetic analysis revealed that the NADPH-dependent benzaldehyde reductase (BalR1) acts downstream of BalS to convert benzaldehyde to benzyl alcohol. Interestingly, OsBalR1, but not OsBalS or OsBalS{beta}, is required for maintaining high basal SA levels in rice, suggesting the presence of redundant benzoyl-CoA-reducing activities or alternative biosynthesis routes for benzyl alcohol production. Together, this work defines the missing enzymatic steps in phenylalanine-derived SA pathway and provides insights into the evolutionary diversification of SA production strategies in plants.

plant biology↗

bioRxiv2026

Patient-specific "Physical Twin" artery-on-chip platform reveals complex flow-dependent VWF mechanobiology and guides personalized antithrombotic therapy

Ischemic stroke triggered by carotid atherosclerosis remains unpredictable because the thrombosis embolization is governed by patient-specific vascular geometry and hemodynamics that cannot be recapitulated in conventional models. Here, we engineered "Physical Twin" artery-on-chip platforms that reproduce individualized carotid anatomy with humanized subendothelial matrix composition and arterial endothelial phenotype under physiological flow patterns. We then established thrombotic microenvironments following laser-induced injury. Computational fluid dynamics-guided experiments across distinct patient geometries reveal that local shear dictates a mechanobiological hierarchy: high-shear bifurcations ([~]3,000 s-{superscript 1}) produce von Willebrand factor (VWF) A1-dependent thrombi suppressible by conformationally sensitive inhibitors, whereas low-shear stenoses generate fragile aggregates where VWF-integrin IIb{beta} coupling governs embolization overgrowth. Pulsatile flow suppresses thrombotic growth independent of mean shear. Molecular dynamics simulations reveal why conformationally sensitive nanobodies (caplacizumab) outperform shear-independent aptamers (ARC1172) in high-shear bifurcation flow zones. This Physical Twin platform provides a mechanistic blueprint for geometry-informed, personalized antithrombotic therapy selection.

bioengineering↗

bioRxiv2026

Neuronal secretome from bipolar patient-derived neurons alters network function and contains candidate biomarkers for diagnosis and lithium response

Delayed diagnosis and treatment are a major burden to patients with bipolar disorder. While lithium is the most effective treatment against mania, depressive episodes, and suicide, only 30% of patients respond to it fully. Currently there are no reliable methods to predict lithium responsiveness. To address these challenges, we aimed to identify potential diagnostic and treatment response biomarkers for BD, in addition furthering understanding of BD pathophysiology. Here, we leveraged human induced pluripotent stem cell (hiPSC) derived neurons from lithium responsive (LR), lithium non-responsive (LNR), and healthy age-matched controls (CTL). We found extracellular vesicle (EV) cargos from hiPSC-derived neurons are indicative of disease state and treatment-response. Unbiased proteomic and miRNA profiling identified 10 proteins and 13 miRNAs that were differentially expressed in BD EVs relative to CTL, as well as distinct molecular signatures separating LR ad LNR groups. These differences converged on pathways related to synaptic function, neurotrophic signalling, and cellular stress responses. Additionally, we found the BD neuronal secretome alters activity in non-BD neuronal networks. Chronic treatment of CTL cultures with BD neuron-conditioned media modified the proportion of active neurons and the frequency and amplitude of calcium transients in individual neurons. We demonstrate that neuronal EVs contain molecular signatures of disease state and treatment response in BD and identify the BD secretome as an active regulator of neuronal network homeostasis. This study provides novel insights into the pathophysiology of BD and candidate biomarkers for personalized BD diagnosis and treatment selection.

neuroscience↗

bioRxiv2026

GatorDuo: Global-Consistency Dual-Graph Refinement With Pseudo-Label Agreement for Spatial Transcriptomics

Spatial transcriptomics (ST) measures gene expression together with spatial coordinates, enabling spatial domain identification of coherent tissue regions. Many recent approaches rely on graph-based modeling to combine spatial neighborhoods and transcriptomic (gene-expression) similarity, yet neighborhood construction is often unreliable under sparsity and technical noise. As a result, spurious cross-domain shortcut edges can persist in static graphs and propagate misleading signals during message passing, ultimately blurring domain boundaries and weakening cluster separability. In this paper, we propose GatorDuo, a topology-aware dual-graph contrastive self-supervised framework for robust spatial domain identification that couples gene-expression similarity with spatial proximity through complementary neighborhood graphs. GatorDuo introduces global-consistency-based graph refinement that uses a pseudo-label agreement mask to suppress cross-domain shortcut edges in both views, thus stabilizing neighborhood topology for representation learning. To avoid manual tuning of domain resolution, GatorDuo further employs a contextual bandit reinforcement-learning strategy to adaptively select the clustering granularity (the number of clusters) used for refinement. The refined view-specific embeddings are integrated via a hybrid-routing Mixture-of-Experts (MoE) module to generate a unified embedding, optimized with contrastive objectives augmented by an MoE-alignment term. Across eight public benchmarks spanning sequencing- and imaging-based ST at spot and single-cell resolution, and compared with ten representative baselines, GatorDuo consistently delivers strong and robust spatial domain identification performance across multiple clustering metrics, while yielding informative unified embeddings that can support downstream biological analyses.

bioinformatics↗

bioRxiv2026

Causally validated phase-amplitude coupling enables high-fidelity motor decoding for next-generation brain-computer interfaces

Modern Brain-Computer Interfaces (BCIs) face a fundamental performance plateau due to their reliance on broad spectral power reduction (Event-Related Desynchronization, ERD) as the primary decoding feature. ERD acts as a coarse metabolic proxy for cortical activation, discarding the high-frequency temporal syntax necessary for high-dimensional motor control. Here, we demonstrate that Phase-Amplitude Coupling (PAC)--specifically, the phase-locking of high-gamma (70-150 Hz) firing to residual Beta oscillations--provides a high-fidelity temporal feature for decoding motor intent. Using high-density electrocorticography (HD-ECoG) during motor imagery, we show that incorporating Beta-PAC into machine-learning classifiers (LDA/SVM) significantly outperforms traditional power-based features. To definitively validate the causal robustness of this feature against mathematically-derived artifacts, we leveraged a rare in vivo human structural lesion model. In a patient with focal tumor infiltration of the motor tract, the metabolic gate (ERD) was preserved, yet structural uncoupling completely abolished Beta-PAC, collapsing network topology and reducing single-trial decoding accuracy to chance levels. Our findings causally validate Beta-PAC as a robust, independent control signal, establishing a physiological foundation for next-generation, phase-dependent neuroprostheses.

neuroscience↗

bioRxiv2026

A sensitized model of thrombosis validates known multigenic relationships and suggests novel modifiers of hemostasis

BackgroundVenous thromboembolism is a major cause of morbidity and mortality. Despite identification of risk factors, not all individuals with thrombophilia develop thrombosis. Understanding the multigenic factors modifying this incomplete penetrance would help guide patient care. MethodsThe zebrafish has a conserved hemostatic system and is amenable to large genetic studies. Loss of antithrombin III (At3) in zebrafish leads to an early consumptive coagulopathy and lethality in adulthood. Using this genetic background as a sensitized model we performed a dominant unbiased genome-wide N-ethyl-N-nitrosourea (ENU) mutagenesis screen followed by whole genome sequencing (WGS). We used survival studies, laser-mediated endothelial injury, and ex vivo protein assays to validate hits. ResultsENU-treated at3+/- males were crossed with at3+/- females to produce 4,030 total offspring (1.5x genome coverage). Four permanent lines transmitting a survival benefit beyond 7 months were identified and sequenced. A candidate screen of 63 known coagulation-related loci revealed a missense mutation, C504F, in a highly conserved residue of the prothrombin (F2) heavy chain, which was validated through genetic and biochemical studies. Evaluation of UK Biobank electronic health record (EHR) data was underpowered to detect interactions between F2 and AT3 due to minmal deleterious mutations. Mutations produced through genome editing revealed that heterozygosity for factor X and plasminogen also modified at3-/-, resulting in reduced lethality. The three remaining lines had no coagulation-related variants segregating with survival, suggesting the presence of novel modifier loci. ConclusionsUnbiased genome-wide screening identified a modifier of thrombosis. This demonstrated that re-balancing of hemostasis to mitigate thrombosis is conserved in zebrafish, including an unexpected role for fibrinolysis. This interaction was not detected even in a large human dataset, establishing the continued benefit of the zebrafish model. Finally, we found evidence for novel loci outside of the canonical coagulation cascade that may be new targets for diagnosis or treatment.

cell biology↗

bioRxiv2026

A graph-based pangenome reveals the genetic basis of climate-resilient and horticultural traits in pear

Climate change poses an increasing threat to the cultivation of deciduous fruit trees, placing greater demands on modern pear breeding. Using pear germplasm adapted to diverse environments, we assembled 11 chromosome-level genomes. In combination with 13 publicly accessible pear genomes, we analyzed presence-absence variations (PAVs) and constructed a graph-based pangenome for pear. By performing a PAV-eQTL analysis of the fruit of 123 pear accessions, we identified PAVs significantly associated with expression levels of genes that may be involved in regulating agronomic traits. Population analysis of 268 pear accessions revealed two stop-gained variants in DAM1 of independent origin, which may function in advancing the blooming date and reducing the chilling requirement. We detected complex PAVs at the NOR1 locus, including two copy-number variations and one deletion. These PAVs contributed to the rapid diversification of the NOR1 locus and the fruit development period through regulating ARF5 and other ripening-related genes. We revealed the selection history of the NOR1 locus and developed novel pear individuals that accumulated alleles for low chilling requirement, early blooming date, and short fruit development period. The results provide valuable resources for pear genomics research and offer a guideline for breeding modern pears with climate resilience.

plant biology↗