Biology subjects

Wu, S.

Publications and source records attributed to Wu, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

WNK kinase regulates plasma membrane levels of the WNT inhibitor RNF43

The E3 ubiquitin ligases RNF43 and ZNRF3 are key negative regulators of canonical WNT signaling, promoting turnover of the WNT receptors FRIZZLED and LRP5/6 at the plasma membrane. While their mechanism of action is well established, how RNF43/ZNRF3 themselves are regulated remains unclear. Here, we identify WNK kinases as novel upstream regulators of RNF43 through proximity labeling proteomics. Using gain- and loss-of-function approaches, we show that WNKs control RNF43 surface localization and thereby its ability to ubiquitinate and downregulate WNT receptors. Pharmacological inhibition of WNKs increases RNF43 membrane abundance and enhances WNT suppression - an effect abolished in RNF43/ZNRF3 double knockout cells and organoids. Mechanistically, WNK inhibition alters RNF43 trafficking and ubiquitination, revealing a role for WNKs in regulating its plasma membrane distribution. These findings define a new regulatory axis linking the pro-WNT activity of WNKs to RNF43/ZNRF3-mediated feedback inhibition. Targeting WNK now offers a novel therapeutic strategy to restore WNT pathway control in cancers with RSPO fusions or RNF43 mutations.

biochemistry↗

bioRxiv2025

Suppressing cortical glutamatergic neurons produces paradoxical interictal discharges and seizures

IntroductionSeizures are traditionally attributed to excessive excitation or deficient inhibition, yet recent clinical and slice data show they can also paradoxically arise when inhibition outweighs excitation. We chemogenetically suppressed neocortical glutamatergic neurons to test whether such suppression elicits epileptic activity in vivo. MethodsCaMKII-driven Gi-coupled hM4Di or Gq-coupled hM3Dq Designer Receptor Exclusively Activated by Designer Drug (DREADDs) were expressed in cortical glutamatergic neurons of Rasgrf2-jGCaMP8m and wildtype C57BL/6J mice. Widefield calcium imaging and 32-channel transparent electrocorticography were performed before and after systemic clozapine-N-oxide (CNO; 1.25-5 mg kg {superscript 1}). ResultsDREADD activation induced intermittent, large-amplitude, synchronized calcium transients confined to the CaMKII-hM4Di focus, accompanied by focal ECoG spikes that persisted for >3 h and sometimes evolved into seizures. By contrast, CNO activation of excitatory neurons via CaMKII-hM3Dq DREADDs desynchronized activity without epileptiform discharges. The same process duplicated in wild-type animals provoked similar epileptiform discharges. ConclusionSelective suppression of excitation can paradoxically drive cortical networks into hypersynchronous, epileptic states, challenging the simple excess-excitation model of ictogenesis. These findings highlight that seizures may result from relative inhibitory dominance, and that considering this excess inhibition mechanism could inspire new therapeutic approaches.

neuroscience↗

bioRxiv2025

Magnesium isoglycyrrhizinate alleviates alcohol-associated liver disease through targeting HSD11B1

While magnesium isoglycyrrhizinate (MgIG) is a clinically approved therapy for alcohol-associated liver disease (ALD), its precise molecular targets and mechanisms remain uncharacterized. This study aimed to define MgIGs hepatoprotective actions in chronic-binge ALD mouse models and ethanol/palmitic acid-exposed AML-12 hepatocytes. Through an integrated strategy encompassing RNA sequencing, molecular docking, and microscale thermophoresis, we discovered that MgIG directly binds to hydroxysteroid 11-beta dehydrogenase 1 (HSD11B1) at residue 187, a finding corroborated by molecular dynamics simulations. In vivo, MgIG markedly attenuated alcohol-induced liver injury, evidenced by ameliorated histological damage, reduced hepatic steatosis, and normalized liver-to-body weight ratios. In vitro, it effectively reduced lipid accumulation, inflammation, and apoptosis. Mechanistically, RNA sequencing identified isopentenyl diphosphate delta isomerase 1 (IDI1) as a key downstream effector. Hepatocyte-specific genetic manipulations confirmed that MgIG modulates the SREBP2-IDI1 axis, thereby suppressing lipogenesis, inflammatory responses, and apoptotic pathways. We reveal HSD11B1 as a novel direct molecular target of MgIG and elucidate its therapeutic mechanism through the HSD11B1-SREBP2-IDI1 signaling axis, which profoundly impacts ALD pathogenesis. These findings not only validate MgIGs clinical utility but also highlight a promising new therapeutic target for ALD.

pharmacology and toxicology↗

bioRxiv2025

A New Aneurysm Rupture-Prone Marfan Mouse Model with FBN1Q2467X Nonsense Mutation Reveals Adventitial Inflammation

Marfan syndrome (MFS) is a genetic disorder caused by mutations in fibrillin-1(FBN1), which encodes FBN1, a key structural component of the extracellular matrix. Mutations in FBN1 influence the severity of aortic disease and therapeutic responses, with aortic aneurysm being the leading cause of mortality in patients with MFS. To investigate the mechanisms driving aneurysm progression, we generated a mouse model (Fbn1Q2469X/+) carrying the FBN1Q2467X nonsense mutation identified in MFS patients. This mutation results in FBN1 deficiency. Although Fbn1Q2469X/+ mice appear normal, showing only mild, nonprogressive dilation of the aortic root and ascending aorta with minor reductions in blood pressure, homozygous Fbn1Q2469X/Q2469X mice develop spontaneous thoracic aortic aneurysms (TAA) that progress to rupture between 10 and 25 days of age, with 100% penetrance. Histopathology shows progressive vessel wall degeneration characterized by disorganized vascular smooth muscle cells, collagen loss, and elastic fiber fragmentation from early to late stages. RNA-seq analysis identifies inflammation as the dominant process in late-stage aneurysms. Immunofluorescence assay reveals inflammatory cells prominently localized to the adventitia near rupture sites, linking adventitial inflammation to aneurysm progression. This genetically modified Fbn1Q2469X/Q2469X mouse model consistently develops progressive aortic aneurysms and provides a reliable, cost-effective platform to investigate the molecular mechanisms of aneurysm progression and to evaluate therapeutic strategies in aneurysm diseases, including Marfan syndrome and related disorders.

genetics↗

bioRxiv2025

Leveraging bioorthogonal conjugation for alpha synuclein fibril surveillance

Alpha synuclein (-syn) amyloid fibrils are associated with various neurodegenerative diseases. To better understand the molecular and cellular basis for -syn fibril persistence and spread, we implemented a fluorophore labeling strategy to surveil pre-formed -syn fibrils in solution and in cells. We leveraged amber codon mediated incorporation of a tetrazine-based artificial amino acid (TetV2.0) to install a cyclooctene-conjugated Janeliaflour, JF549, at four sites on human -syn: residues 4, 60, 96 and 136. Fast coupling occurred under mild buffer conditions and in the presence of the disease-associated cofactor and cytotoxic lipid, psychosine. Labeled fibrils retained their polymorphic features, seeded the growth of new fibrils in vitro, and induced the seeding of positive puncta in -syn FRET biosensor HEK293T cells. This allowed simultaneous tracking of exogenous and endogenous -syn aggregates in biosensor cells, and their localization within the cells. In doing so, our approach facilitates more detailed mechanistic investigation of -syn aggregates.

biochemistry↗

bioRxiv2025

RhoV Promotes Proliferation, Migration, and MAPK Activation in Pancreatic Ductal Adenocarcinoma

Background and AimsPancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy characterized by diagnosis at advanced stages, limited therapeutic options, and frequent resistance to therapies. Although oncogenic KRAS mutations are central drivers of PDAC, alternative pathways indisputably contribute to its tumorigenesis and progression. RhoV, a member of the Rho family of small GTPases, has been implicated in tumor development in other cancer types, such as breast cancer and lung adenocarcinoma; however, its role in PDAC remains unclear. MethodsIn this study, we investigated the expression and functional impact of RhoV on PDAC. Analysis of publicly available datasets and immunohistochemical profiling of 114 PDAC patient specimens were used to evaluate the expression of RhoV in PDAC and its prognostic impact. Overexpression and CRISPR-Cas9-mediated knockout of RhoV were established in three pancreatic cancer cell lines. Functional analyses, such as cell proliferation, migration, invasion, colony formation, spheroid growth, and mouse xenograft, were used to evaluate the role of RhoV in PDAC cells. ResultsRhoV overexpression was associated with reduced overall and recurrence-free survival in public datasets and our own patient cohort. Functional assays demonstrated that RhoV overexpression promoted PDAC cell proliferation, colony formation, and spheroid growth, whereas knockout of RhoV suppressed these changes. Moreover, RhoV enhanced PDAC cell migration and invasion in vitro, accompanied by downregulation of E-cadherin and upregulation of N-cadherin and vimentin, indicating induction of epithelial-mesenchymal transition. Mechanistically, RhoV overexpression activated key MAPK pathway components, including phosphorylation of ERK, JNK, and p38. In vivo, xenograft models confirmed that RhoV drives tumor growth and increases tumor burden. ConclusionThese results establish RhoV as a novel oncogenic factor in PDAC progression and highlight its potential as a biomarker and therapeutic target, warranting further investigation into combinatorial targeting strategies to overcome KRAS inhibitor resistance.

cancer biology↗

bioRxiv2025

OmniExtract: An automatic data extraction tool based on Large Language Model and Prompt Engineering

Extracting structured information from documents or scientific papers is crucial for data sharing and retrieval. Recently, Large Language Model (LLM) has shown its impressive ability in text understanding and several tools based on LLM has been developed. However, its still difficult to find a universal and user-friendly tool for various practical extraction tasks. To address this challenge, we propose OmniExtract, an automatic data extraction tool with user-friendly configuration files which can adapt to various data extraction tasks. OmniExtract uses a prompt optimized engineering to improve prompt and obtain high performance, and it can support a comprehensive data extraction including text and tables. Evaluation results show that OmniExtract obtains a high accuracy over 80% for 3 datasets. Furthermore, two additional data extraction applications using OmniExtract have been provided, achieving an accuracy of 92.21% and an average F1 score of 0.83 respectively. The data reliability performance shows that OmniExtract is a valuable tool for database updating.

bioinformatics↗

bioRxiv2025

Polyclonal origins of human premalignant colorectal lesions

Cancer is generally thought to be caused by expansion of a single mutant cell1. However, analyses of early colorectal cancer lesions suggest that tumors may instead originate from multiple, genetically distinct cell populations2,3. Detecting polyclonal tumor initiation is challenging in patients, as it requires profiling early-stage lesions before clonal sweeps obscure diversity. To investigate this, we analyzed normal colorectal mucosa, benign and dysplastic premalignant polyps, and malignant adenocarcinomas (123 samples) from six individuals with familial adenomatous polyposis (FAP). Individuals with FAP have a germline heterozygous APC mutation, predisposing them to colorectal cancer and numerous premalignant polyps by early adulthood4. Whole-genome and/or whole-exome sequencing revealed that many premalignant polyps--40% with benign histology and 28% with dysplasia--were composed of multiple genetic lineages that diverged early, consistent with polyclonal origins. This conclusion was reinforced by whole-genome sequencing of single crypts from multiple polyps in additional patients which showed limited sharing of mutations among crypts within the same lesion. In some cases, multiple distinct APC mutations co-existed in different lineages of a single polyp, consistent with polyclonality. These findings reshape our understanding of early neoplastic events, demonstrating that tumor initiation can arise from the convergence of diverse mutant clones. They also suggest that cell-intrinsic growth advantages alone may not fully explain tumor initiation, highlighting the importance of microenvironmental and tissue-level factors in early cancer evolution.

cancer biology↗

bioRxiv2025

Intrinsic interval timing, not temporal prediction, underlies ramping dynamics in visual and parietal cortex

Ramping neural activity is widely interpreted as a signature of predictive processing, but whether such signals truly reflect predictions or instead emerge from sensory mechanisms remains unclear. To address this question, we used two-photon calcium imaging across multiple cell types in visual and parietal cortex while awake mice passively received repeated audiovisual stimuli presented under distinct temporal structures. Neurons segregated into two broad response classes: stimulus-activated (ramp-down) and stimulus-inhibited (ramp-up) populations with diverse temporal kinetics. Multiple findings argued against a predictive interpretation: ramping activity was present in naive animals, neural responses changed immediately after short/long interval transitions, and unexpected stimulus timings elicited nearly identical responses in predictable and irregular contexts. Population analyses further showed that ramping reflected relaxation from stimulus-evoked activity rather than anticipatory buildup. Heterogeneous kinetics generated a robust population code for elapsed time. Together, these findings show that neural ramps during passive stimulation arise from stimulus-evoked dynamics that intrinsically generate temporal signals, rather than from temporal predictive processing. TeaserRamping activity in visual-parietal cortex during passive stimulation arises from sensory responses, not predictive mechanisms.

neuroscience↗

bioRxiv2025

SAM-DTI: A Spatial Attention Model for Drug-Target Interaction Prediction

Drug-target protein interaction (DTI) prediction is an important area of research in drug repurposing and discovery. Laboratory experiments for exploring DTI space need a lot of time and money due to the high volume of potential compounds. The past decades advancements in deep learning have made progress in efficient prediction of DTIs. This paper proposes a spatial attention model for predicting drug-target interactions (SAM-DTI) from labeled SMILES strings and protein sequences. SAM-DTI (i) tries to encapsulate the input features with more relevance to the biological binding of drug-target interactions, rather than models that solely extract features from individual inputs, and (ii) emphasizes giving dynamic importance to each pair of drug-target interactions. The model follows a knowledgeinspired sub-structure vocabulary to preprocess the inputs. It predicts accurate DTI values from the interactions between each SMILES sub-structure and protein substructure pair. SAM-DTI achieves competitive performance compared to state-of-the-art methods.

bioinformatics↗

bioRxiv2025

Targeting the TEA DNA binding Domain of TEAD with a Peptide Inhibitor TEAi Suppresses Oncogenic Transcription and Tumor Growth

The Hippo pathway is a critical regulator of organ size and tumorigenesis, with the TEAD-YAP/TAZ transcriptional complex serving as a key effector frequently hyperactivated in cancers. Targeting this complex has emerged as a promising anticancer strategy. Here, we develop TEAi, a 64-amino acid peptide derived from Drosophila Nerfin-1, which directly binds the TEA DNA-binding domain of TEAD. TEAi potently suppressed TEAD-YAP-driven transcriptional activity, as evidenced by luciferase reporter and qPCR assays targeting canonical downstream genes CTGF and CYR61. Mechanistically, TEAi inhibited the DNA-binding capacity of TEAD2 without direct DNA interaction, thereby abolishing promoter recruitment of the TEAD-YAP complex. unexpectedly, TEAi induced nuclear export and cytoplasmic accumulation of TEAD2, suggesting a non-canonical mechanism distinct from native Nerfin-1 function. Functionally, TEAi significantly suppressed cancer cell proliferation in vitro and tumor growth in vivo. Unlike inhibitors targeting the YAP-binding interface, TEAi directly blocks the DNA-binding activity of TEAD, offering a potential advantage by comprehensively inhibiting all TEAD-dependent oncogenic transcription. Our findings establish TEAi as a promising prototype for therapeutics targeting TEAD, with implications for treating cancers driven by Hippo pathway dysregulation.

cell biology↗

bioRxiv2025

Identification and quantification of alternative polyadenylation sites in single cell RNA-seq data using scPAISO

AbstractsAlternative polyadenylation (APA) is a critical posttranscriptional mechanism that generates transcriptomic diversity through the production of mRNA isoforms with distinct 3 UTRs or coding sequences. Current APA analysis based on single-cell RNA sequencing (scRNA-seq) for establishing cell type-specific APA landscapes primarily rely on Read2 data, which lacks precise cleavage site (CS) information. This limitation restricts their ability to achieve precise de novo mapping of polyadenylation sites (PASs). Here, we present single-cell PolyAdenylation ISOform quantification (scPAISO), a computational pipeline designed for de novo identification of PAS and quantification of PAS isoforms in scRNA-seq data, by leveraging the often-discarded Read1 from 3 tag-based scRNA-seq protocols. Unlike existing tools, scPAISO directly captures mRNA 3 end cleavage sites, enabling superior performance in motif enrichment (stronger AAUAAA signal) and peak precision (sharper PAS peaks). Moreover, the smaller peak widths enhance the spatial resolution, enabling more accurate detection of closely spaced PASs in the genome. By integrating Read1 and Read2 data, scPAISO achieves isoform-level quantification with an assignment accuracy exceeding 95%. We demonstrate the robustness of scPAISO in identifying PASs and quantifying APA events across diverse biological contexts, including hematopoiesis, systemic sclerosis (SSc), and mouse tissues. We identified stage-specific 3 UTR lengthening in hematopoietic progenitors, global 3 UTR remodeling in SSc and tissue-specific polyadenylation (PA) preference along with RNA-binding proteins in mice. Overall, scPAISO represents a significant advancement in the analysis of APA at single-cell resolution and provides a powerful tool for exploring the regulatory landscape of APA, offering new insights into transcriptome complexity and gene regulation in both health and disease.

bioinformatics↗

bioRxiv2025

Using targeted therapy to promote a pro-inflammatory tumour microenvironment and anti-tumour immune response in high grade serous ovarian cancer

BACKGROUNDHigh-grade serous ovarian cancer (HGSOC) is characterized by elevated replication stress and an immunosuppressive microenvironment. A synergistic combination of checkpoint kinase 1 inhibitor (CHK1i) with low-dose hydroxyurea (LDHU) promotes a unique ATR-independent moderate replication stress response with potent anti-tumour effects. The ability of this approach to reprogram the tumour immune microenvironment (TIME) to overcome the immunosuppression and promote an anti-tumour immune response in HGSOC is the focus of this study. METHODSWe investigated the therapeutic potential of CHK1i+LDHU in established HGSOC cell cultures, fresh tumour cell explants from HGSOC patient ascites, and syngeneic mouse models, assessing tumour cell killing, immunogenic cell death, pro-inflammatory cytokine/chemokine expression, and anti-tumour immune responses. RESULTSCHK1i+LDHU effectively killed ovarian cancer cells regardless of chemotherapy resistance, BRCA2 mutation and homologous recombination repair status in vitro. In vivo, treatment significantly reduced tumour burden and ascites accumulation. CHK1i+LDHU enhanced expression of pro-inflammatory cytokines/chemokines and triggered immunogenic cell death in tumour. In syngeneic models, treatment promoted CD8+ cytotoxic T cell-dependent anti-tumour responses and reduced immunosuppressive signalling within the TIME. CONCLUSIONSCHK1i+LDHU is a promising therapy for chemotherapy-resistant HGSOC, combining direct cytotoxic effects with reprogramming the TIME to reduce immunosuppression and activate a CD8+ T cell-dependent anti-tumour response.

cancer biology↗

bioRxiv2025

Targeting the COP9 signalosome overcomes platinum resistance in ovarian cancer through two distinct genome stability mechanisms

Tubo-ovarian high-grade serous carcinoma (HGSC) is a leading cause of gynecologic cancer mortality, largely due to the emergence of platinum resistance, which serves as the mainstay of chemotherapy. Here, we identify COPS5 as a therapeutic target and use an available small molecule inhibitor to overcome platinum resistance. A genetic screen for platinum-induced DNA damage in a platinum resistant ovarian cancer model identified COPS5 and COPS6, two components of the COP9 signalosome. Consistently, high COPS5 expression correlated with poor clinical outcomes in patients with HGSC. In both in vitro and in vivo experiments, COPS5 depletion sensitized ovarian cancer cells to carboplatin. A small molecule COPS5 inhibitor, CSN5i-3, synergized with carboplatin in homologous recombination-deficient and -proficient cells. This combination was also effective in xenografts and in a syngeneic mouse model of carboplatin-resistant HGSC. Importantly, we demonstrate that CSN5i-3 is selective for cancer cells, with patient-derived HGSC cells exhibiting up to 50-fold greater sensitivity to CSN5i-3 than benign cells. Finally, we show that genetic or small molecule inhibition of COPS5 impaired both nucleotide excision repair (NER) and interstrand crosslink (ICL) repair, leading to increased DNA platinum adducts. Mechanistically, this was due to increased ubiquitination and degradation of DNA-specific DNA binding protein 1 (DDB1) and other key NER and ICL repair proteins, consistent with the role of COPS5 in the regulation of these factors. Our findings highlight the importance of NER and ICL regulation in chemotherapy response and indicate that targeting COPS5 can enhance the efficacy of platinum-based chemotherapy in HGSC. One Sentence SummaryCOPS5 depletion or inhibition using a small molecule COPS5 inhibitor CSN5i-3 sensitizes high-grade serous carcinoma to platinum chemotherapy through downregulation of nucleotide excision repair and interstrand crosslink repair.

cancer biology↗

bioRxiv2025

Functional Role of Small Extrachromosomal Circular DNA in Colorectal Cancer

Extrachromosomal circular DNA (eccDNA) are circular DNA molecules that originate from chromosomal DNA but exist independently. While large eccDNA (ecDNA) contributes to tumorigenesis, the role of smaller eccDNA (<100,000 base pairs) in cancer remains unclear. Our analysis of 25 colorectal cancer (CRC) tumors and adjacent non-tumorous tissues revealed that eccDNA is significantly more abundant in tumor tissues, correlating strongly with chromosomal amplifications. The presence of whole intact genes on 1.29% of eccDNA was non-random. We identified 84 genes that recurred across tumors of multiple patients when present on eccDNA with 19% of genes being cancer-associated. eccDNA-borne genes were often accompanied by increased expression, and their contribution to expression was much larger than that from linear amplifications and the larger ecDNA. The cytokine gene CXCL5 exemplified this phenomenon, showing substantial copy-number increase and upregulation when present on eccDNA. Functional validation in cell lines showed that CXCL5 eccDNA enhanced transcriptional output and immune cell recruitment function. The recurrence and overexpression of CRC-related genes on eccDNA indicate their selection in tumors, suggest eccDNA can serve as a novel mechanism for dynamically influencing gene expression and is capable of conferring cancer phenotypes to cells. Analysis of chromatin landscapes revealed that eccDNA preferentially forms at sites of open chromatin and active transcription, with architectural boundaries marked by CTCF protein. Clinically, patients with higher eccDNA levels showed poorer relapse-free survival. These findings suggest that circular DNA elements across the entire size spectrum participate in cancer evolution, positioning eccDNA as a potential therapeutic target and prognostic biomarker.

cancer biology↗

bioRxiv2025

Structural and functional basis of PU.1-BAF interaction enables targeting of lineage-specific transcription

Chromatin remodeling complexes like BAF finely regulate transcriptional programs by working in concert with transcription factors. However, evidence is lacking as to whether TFs interact directly with BAF and if so, what the mechanistic and structural principles governing these critical interactions are. Here, we establish direct engagement between a crucial and therapeutically relevant full-length human TF, PU.1 (SPI1), and BAF. Within this 1MDa+ complex, we precisely map the binding site of PU.1 to a YEATS-like domain on BAF60A and elucidate the structure of the PU.1-BAF60A complex. This work reveals that upon binding to BAF, a disordered region within the TF adopts a helical conformation, and that disruption of this functionally critical interface via knockdown abrogates the ability of PU.1 to rescue cell viability. To explore the druggability of TF-BAF protein-protein interactions (PPIs), we conducted a high-throughput screen that identified small molecules capable of disrupting the PU.1-BAF60A PPI by binding to BAF60A. Co-crystal structures reveal distinct compound binding modes that converge on a critical PU.1-BAF60A interaction hotspot. These findings define, for the first time, the structural interface between a human TF and a chromatin remodeling complex and establish a platform that enables the targeting of these interactions, a novel mechanism in cancer therapeutics.

biochemistry↗

bioRxiv2025

Representation Transfer via Invariant Input-driven Neural Manifolds for Brain-inspired Computations

Domain adaptation is a core challenge for embodied AI deployed in unpredictable, noisy environments. Conventional deep models degrade under domain shifts and require costly retraining. Inspired by biological brains, we propose a modular framework where each module is a recurrent neural network pretrained via a simple, task-agnostic protocol to learn robust, transferable features. This shapes stable yet flexible representations as invariant input-driven continuous attractor manifolds embedded in high-dimensional latent space, supporting robust transfer and resilience to noise. At deployment, only a lightweight adapter needs training, enabling rapid few-shot adaptation. Evaluated on the DVS Gesture benchmark and a custom RGB rehabilitation dataset, our framework matches or surpasses leading C3D and ViViT models while using ten times fewer parameters and only one training epoch. By unifying biologically inspired attractor dynamics with cortical-like modular composition, our approach offers a practical path toward robust, continual adaptation for real-world embodied AI. TeaserInvariant input-driven attractors enable representation transfer and domain adaptation in brain-inspired AI.

neuroscience↗

bioRxiv2025

Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon

Pangenomes are increasingly critical for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here, we report a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated near-gapless genomes representing all seven watermelon species. The super-pangenome captures approximately one million structural variants (SVs), enabling accurate variant genotyping across ~900 watermelon accessions and substantially expanding variant discovery both across and within species. Broader sampling within the pangenome provides insights into genome evolution among watermelon species and sheds light on the origin of cultivated watermelon. SV-inclusive genome-wide association studies enhance trait mapping resolution and identify a copy number variation upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, our findings and genomic resources establish a foundational framework for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crop species.

plant biology↗