Biology subjects

Lu, X.

Publications and source records attributed to Lu, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Characterizing benthic community structure across Western Pacific seamounts to ~5,000 m depth: Implications for conservation

AimSeamounts are key components of deep-sea ecosystems. Yet, their biodiversity patterns and conservation needs remain poorly understood, presenting a critical knowledge gap as they face multiple environmental stressors. Here, we aim to characterize benthic community structure across multiple seamounts along the Kyushu-Palau Ridge (KPR) and identify conservation priorities. LocationPhilippine Sea in the Western Pacific. Major taxa studiedDeep-sea benthos. MethodsWe surveyed six transects (13.3{degrees}N-22.9{degrees}N; 614-5,055 m depth; 165 kilometers in total length) using a towed camera system, yielding 31,342 images and 14,218 identified individuals. Community structure was assessed through species depth-range overlap analysis to distinguish nestedness versus turnover patterns. {beta}-diversity was partitioned into local contributions (LCBD) and species contributions (SCBD) to evaluate site-level uniqueness and species-level influence. Generalized linear mixed models were used to relate LCBD and SCBD to depth, slope, aspect, bathymetric position, and functional traits. ResultsCommunity structures varied among slopes and seamounts. Western, steeper slopes were dominated by nestedness, whereas gentler eastern slopes showed mixed patterns of nestedness and gradual turnover. Sessile species largely exhibited nestedness, while mobile taxa showed mixed structures. LCBD declined with depth overall but increased on north-facing slopes and sites with higher broad-scale bathymetric position. Wide-ranging generalist species, particularly among Echinoidea and Holothuroidea, contributed disproportionately to {beta}-diversity. Main conclusionsSeamount benthic communities along the KPR are structured by interactions between depth, geomorphology, and species ecological breadth. The dominance of nestedness on western slopes suggests that protecting shallow, species-rich habitats could capture much of the biodiversity therein. In contrast, the mixed structures on eastern slopes indicate the need for a hybrid conservation approach that includes both shallow summits and deeper, compositionally distinct zones. Our findings highlight the importance of slope-specific, depth-informed strategies to conserve these vulnerable marine ecosystems.

ecology↗

bioRxiv2026

Genomic alterations enable BRCA1 methylation loss and promoter bypass to drive resistance in high-grade serous ovarian cancer

BRCA1 promoter methylation predicts sensitivity to PARP inhibitors in high-grade serous ovarian cancer, yet therapeutic resistance is common and mechanistically unresolved. Using long-read direct DNA sequencing of patient-derived xenografts and cell lines, we resolved BRCA1 methylation at single-molecule resolution with structural and transcriptomic analyses. We revealed two convergent PARP inhibitor and platinum resistance mechanisms, validated in patient tumors. First, focal, allele-specific loss of BRCA1 methylation arose through local cis-acting genomic alterations, instead of global epigenetic reprogramming. Engineered in cis sequence alterations near the methylated BRCA1 promoter were sufficient to induce methylation loss, restore homologous recombination, and confer resistance. Similar associations were observed across the genome, suggesting this mechanism extends beyond BRCA1. Second, BRCA1 expression was restored despite intact promoter methylation via structural variant-mediated promoter bypass or alternative transcription initiation. Together, these findings redefine BRCA1 methylation loss as a locus-restricted process and reveal multiple routes by which tumors escape PARP inhibitor therapy. Statement of SignificanceWe show that high-grade serous ovarian cancers can restore BRCA1 expression after therapy through multiple genomic mechanisms, including local methylation loss and promoter bypass, thereby re-establishing homologous recombination and driving PARP inhibitor resistance. These findings challenge reliance on BRCA1 methylation alone as a predictive biomarker and support rational combination therapies for more durable responses.

cancer biology↗

bioRxiv2026

Development of GS-441524 Derivatives as Potent SARS-CoV-2 Mac1 Inhibitors via a Direct-to-Biology Approach

Targeting viral macrodomains (Mac) has emerged as a promising strategy for antiviral drug development, especially after the outbreak of COVID-19 that claimed millions of lives worldwide. Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Mac1 inhibitors have been reported in the past few years. In the present work, we converted GS-441524 (IC50 of [~]10 M for SARS-CoV-2 Mac1) to KP-S54 (18c), a potent inhibitor of both SARS-CoV-2 Mac1 (IC50: 44 nM) and Middle East respiratory syndrome coronavirus (MERS-CoV) Mac1 (IC50: 91 nM) through an iterative direct-to-biology approach. This approach leverages efficient amide-coupling reaction and the mix-and-read fluorescence polarization (FP) assays where reaction mixtures could be screened directly without purification. Cocrystal structure of a selected derivative (12p) binding to SARS-CoV-2 Mac1 revealed the binding mode, which will guide future drug development against viral macrodomains.

pharmacology and toxicology↗

bioRxiv2026

Energy Metabolizes in Male Bone Marrow Mesenchymal Stem Cells Aging Process

Senescence human bone marrow mesenchymal stem cells (BMSCs), vulnerable to age-related defects, is poor in tissue regeneration. Cells in bone marrow accumulated senescent contributing to the development of metabolic energy regulation hold prospects for therapeutic advances. This study aimed to evaluate energy metabolic changes in male bone marrow mesenchymal stem cells senescence process. Our research established cell specific surface marker and enzymes expression level changes, as well as ECAR and OCR resonance. Notably, CD14, HLA-DRB1 and CD90 upregulated, glycolysis-related genes are increased, tricarboxylic acid cycle-related genes are decreased. We firstly identified links between time-dependent cell aging process and energy metabolism in BMSCs.

cell biology↗

bioRxiv2026

FALCON: Closed-Loop Multi-Objective Optimization of Lipid Nanoparticles for Cell-Selective mRNA Delivery

Efficient, cell type-selective delivery of genetic payloads remains a central challenge in the development of gene and cell therapies. Lipid nanoparticles (LNPs) offer a versatile delivery platform, but their optimization is hindered by reliance on brute-force screening methods that are laborious, resource-intensive, and focus on single targets. Here, we present FALCON (Framework for Active Learning-driven Compositional Optimization of Nanoparticles), a closed-loop pipeline that leverages iterative screening, surrogate modeling, and multi-objective optimization to accelerate LNP compositional design. In B cell-targeted validation experiments, FALCON-optimized LNPs achieved a 1.8-fold increase in splenic B cell transfection in vivo compared with reference compositions. When optimized for selectivity, FALCON LNPs displayed an 84-fold improvement in selective transfection of splenic B cells over off-target liver populations and enabled spleen-tropic behavior across factorial panels of varying ionizable and helper lipid chemistries. In vaccine studies, these LNPs induced higher IgG2c antibody titers and a more Th1-biased immune profile. FALCON was also deployed to optimize LNPs for myeloid cell-selective delivery, achieving enhanced in vivo selectivity following systemic administration both across and within spleen and liver compartments. Our results establish FALCON as a useful tool for data-driven design of LNP compositions for precision gene delivery.

bioengineering↗

bioRxiv2026

Dietary omega-6 arachidonic acid and omega-3 docosahexaenoic acid supplementation differentially impact skeletal muscle inflammaging in mice

Aging is associated with a gradual and progressive decline in skeletal muscle mass and strength known as sarcopenia, which has been attributed to chronic low-grade inflammation. Dietary long-chain polyunsaturated fatty acids (LC-PUFAs), including omega-6 arachidonic acid (ARA) and omega-3 docosahexaenoic acid (DHA), are precursors to bioactive lipid mediators that regulate the initiation, propagation, and active resolution of inflammation. While traditionally considered a pro-inflammatory and catabolic factor, the ARA-derived eicosanoid prostaglandin E2 has recently emerged as a potential anti-sarcopenic molecule. DHA-derived specialized pro-resolving mediators may also act as immunomodulatory pro-regenerative molecules in muscle inflammaging. In the current study, we tested the effects of long-term dietary supplementation with either ARA or DHA on muscle health in aging mice. Twenty-two-month-old C57BL/6N mice were fed a control AIN-93M diet, or an AIN-93M diet supplemented with either ARA (0.48% w/w) or DHA (0.48% w/w) for 12 weeks. Both dietary interventions reduced total body weight, but only ARA reduced absolute fat mass and increased the percentage of lean mass. Despite these changes in body composition, ARA supplementation reduced absolute muscle strength and myofiber size. This functional decline was associated with increased neuromuscular junction fragmentation, elevated expression of pro-inflammatory cytokines/protein degradation markers, and suppressed ribosome biogenesis. In contrast, DHA uniquely reduced chronic inflammation of aged muscle and returned c-Myc expression to young levels but did not affect muscle mass or strength. These data demonstrate that long-term dietary intake of ARA and DHA have overall divergent effects on the structure and function of aging muscle.

physiology↗

bioRxiv2026

Long-read RNA-seq resolves isoform-level and context-specific regulatory architecture of complex traits in cattle

Traditional short-read RNA-seq lacks the resolution to fully capture full-length isoforms and complex alternative splicing, leaving a "missing regulation" gap in existing molecular atlases. Here, we present a population-scale, multi-omics dissection of bovine complex traits using matched deep whole-genome sequencing (30x), long-read (ONT) and short-read RNA-seq, as well as metabolome data from 432 dairy cows across four distinct lactation stages. We expanded the bovine transcript atlas with 13,177 novel isoforms and fine-mapped 1,088,900 regulatory effects across 11 diverse molecular phenotypes. Notably, long-read mapping uncovered 606 genes with isoform expression quantitative trait loci (12.8%, eQTL) and 1,116 genes with detailed splicing QTL (sQTL) (31.8%) that were missed by conventional short-read mapping. We further showed that lactation-specific regulation was profoundly mediated by the metabolic microenvironment (46.8%) and cellular composition (4.3%). Across genome-wide associations (GWAS) of 90 bovine complex traits, isoform-level and context-specific regulatory effects captured GWAS loci missed by short-read eQTL and sQTL analyses, increasing colocalized loci from 35.2% to 60.3%. These regulatory variants also exhibited evolutionary constraints with human immune and metabolic loci. Our study establishes an invaluable resource (https://cattleblr.farmgtex.org) demonstrating that long-read transcriptomics is essential for resolving the complexity of regulatory mechanisms underlying mammalian physiology.

genetics↗

bioRxiv2026

LFCT: A Benchmark Dataset for Low-Frame-Rate Cell Tracking in Long-Term Live-Cell Microscopy

Cell tracking in time-lapse microscopy is essential for studying dynamic biological processes such as migration, proliferation, and lineage formation. Existing benchmarks primarily focus on high-framerate imaging, where short temporal intervals simplify correspondence between cells across consecutive frames. We present the Low Frame-rate Cell Tracking dataset (LCFT), a benchmark dataset designed specifically for evaluating cell tracking methods under low-frame-rate conditions. The dataset contains multi-day live-cell microscopy sequences from four human cell lines (MCF10A, MDA-MB-231, HEK293T, and U87), acquired at 10x and 20x magnifications using phase-contrast and fluorescence imaging (nucleus). Ground-truth annotations include cell identifications, temporal linking, lineage relationships, and mitosis events. To generate reliable annotations, automated segmentation and tracking were combined with extensive manual curation. LCFT provides a comprehensive resource for developing and benchmarking robust cell tracking algorithms capable of handling sparse temporal sampling and large inter-frame motion in long-term live-cell imaging experiments.

cell biology↗

bioRxiv2026

A red-emitting, genetically encoded indicator for two-photon voltage recording in vivo

Genetically encoded voltage indicators (GEVIs) enable minimally invasive, cell-type-specific optical measurements of neuronal membrane potential with millisecond temporal resolution. Red-shifted GEVIs are especially advantageous because they permit spectral multiplexing with complementary sensors and enable all-optical circuit interrogation in combination with blue-light-activated opsins. Despite these advantages, existing red GEVIs remain poorly suited for in vivo use due to limited performance under two-photon (2P) excitation, the predominant modality for deep-tissue imaging. Here, we introduce VADER1, a red GEVI that overcomes this limitation and enables reliable spike detection in vivo under 2P illumination. Under 2P excitation, VADER1 supports extended voltage imaging with both random-access and resonant-scanning microscopy, enables recordings from neurons as deep as cortical layer 5, and allows dual-color imaging with calcium indicators. By filling a critical spectral gap, VADER1 enables integrated optical measurements of fast electrical activity alongside other neural signals and establishes a foundation for two-photon all-optical electrophysiology.

neuroscience↗

bioRxiv2026

Rapid vaccine induction of macaque HIV-1 V2 Apex broadly neutralizing antibodies with immunogenetic signatures that are potentially translatable to humans

Due to the complex biology of HIV-1 broadly neutralizing antibodies (bnAbs), HIV-1 vaccines must target unmutated germline precursor antibodies with B cell receptors that have the appropriate specificity and genetic features to develop neutralization breadth. Previous work has shown that immunization or infection in macaques primes unmutated precursor antibodies that target the broadly neutralizing epitope composed of the second variable region and proximal glycans (termed V2-apex site) of HIV-1 envelope (Env). Macaque V2-apex bnAb precursors elicited thus far have homogeneous usage of the second reading frame of a diversity (D) gene found only in macaques, calling into question whether HIV-1 Env immunogens can elicit only this canonical, macaque-specific V2-apex antibody response, limiting human vaccination success. Here, we show that vaccination of rhesus macaques with Env conjugated to a ferritin nanoparticle (OPT4-scNP) rapidly elicited V2-apex bnAbs with distinct D gene segment usage and motifs that are not restricted only to macaques. After two priming immunizations, V2-apex antibodies with non-canonical HCDR3s exhibited greater neutralization potency and breadth than V2-apex antibodies with previously observed HCDR3 motifs. Following sequential boosting immunizations, a V2-apex bnAb lineage with a novel HCDR3-encoded EDGED motif increased its neutralization breadth, including neutralization of viral isolates bearing the N130 glycan, which shields the V2-apex from recognition. High-resolution structures of two members of this V2-apex bnAb lineage, called DH2050, defined a novel binding mode in which it used its EDGED motif to contact the C-strand peptide and the N160 glycan within the V2-apex site. Altogether, we define a novel bnAb binding mode to the V2 Apex and demonstrate that HIV-1 Env sequential vaccination elicits V2-apex bnAbs with immunogenetic signatures that are potentially translatable to the human immune system.

immunology↗

bioRxiv2026

Human hindbrain organoids with segment-specific 5-HT neurons for motor modulation

The serotonergic system regulates human mood, reward, and motor control, and its impairment contributes to debilitating psychiatric disorders. Serotonergic neurons (SNs) arise predominantly in the hindbrain and acquire segment-specific identities and functions; however, the lack of human models remains a challenge to understanding the human serotonergic system. Here, we generate human serotonergic-enriched rostral and caudal hindbrain organoids (hsrHOs and hscHOs) that produce segment-specific SNs with regional identities corresponding to rhombomeres r2-r3 and r5-r8, respectively. hsrHOs and hscHOs produce SNs that recapitulate their in vivo counterparts in transcriptomic profiles, function, and ascending or descending projection preferences. Assembly with human neuromusculoskeletal organoids enables modeling of serotonergic modulation of motor control. This system further reveals that deficiency of the schizophrenia risk gene DISC1 disrupts human serotonergic development and impairs motor modulation. Together, our study establishes a human organoid platform for modeling development, circuit function and disease-associated dysfunction of the serotonergic modulatory system.

neuroscience↗

bioRxiv2026

EEG-Neurofeedback Targeting Gamma Oscillations at the Parieto-Occipital Region Reduces Pain Perception

Pain is closely associated with both spontaneous and stimulus-evoked gamma oscillations, which differ in their phenomenology and their relationship to pain perception. These associations make gamma oscillations a promising target for pain interventions, such as closed-loop real-time neurofeedback (NFB). While modulating stimulus-evoked gamma oscillations is technically challenging due to their concurrent occurrence with pain perception, targeting spontaneous gamma oscillations is both feasible and practical, as it could influence subsequent cortical nociceptive processing and reduce pain. To test this mechanistic hypothesis, we developed a novel NFB training protocol aimed at increasing spontaneous gamma oscillations in the parieto-occipital region to alleviate pain. Eight-eight healthy, right-handed subjects were randomly assigned to either an active or sham NFB group and completed three sessions of NFB training. During each session, subjects underwent EEG recording and received randomized laser stimulation while watching a video. After three training sessions, approximately 52% of subjects in the active group successfully increased the spectral power of spontaneous gamma oscillations in the parieto-occipital region. Crucially, the spectral power of spontaneous gamma oscillations was significantly and negatively correlated with subjective pain intensity after the third NFB session. Additionally, subjects who responded successfully to active NFB showed significant reductions in pain intensity, unpleasantness, and laser-evoked potentials compared to the sham group. Together, these findings establish a causal relationship between spontaneous gamma oscillations in the parieto-occipital region and pain perception, potentially offering a novel NFB-based therapeutic strategy for pain management.

neuroscience↗

bioRxiv2026

Long-chain Polyunsaturated Fatty Acids Mitigate In Vitro Skeletal Muscle Wasting Induced by Colorectal Carcinoma Cells via a 15-LOX-dependent Pathway

Up to 50% of adults with colorectal cancer (CRC) are at risk of progressive involuntary loss of skeletal muscle mass and function known as cachexia. Available options to prevent and treat cachexia in cancer survivors are currently limited. Long-chain polyunsaturated fatty acids (LC-PUFAs) and their bioactive metabolites, termed specialized pro-resolving lipid mediators (SPMs), promote the resolution of inflammation and support muscle growth and repair. However, prior studies of cachexia have mainly focused on fish oil supplements, and it is not fully understood how different individual omega-3 (n-3) and omega-6 (n-6) LC-PUFAs mediate CRC-induced muscle wasting. In addition, the crosstalk between cancer cells, the host immune system, and skeletal muscle cells in response to LC-PUFA treatments remains unclear. This study aimed to examine the effects of n-3 and n-6 LC- PUFAs on CRC-induced muscle wasting and the underlying cellular and molecular mechanisms involved. Using murine C2C12 skeletal muscle cells and CT26 colorectal carcinoma cells, we investigated the impacts of LC- PUFAs including arachidonic acid (ARA, 20:4n-6), eicosapentaenoic acid (EPA, 20:5n-3), docosapentaenoic acid (DPA, 22:5n-3), and docosahexaenoic acid (DHA, 22:6n-3) on CT26-induced muscle cell wasting in the presence or absence of lipoxygenase (LOX) inhibitors such as NDGA or BLX-3887. We also examined the lipidomic profile of C2C12-CT26 co-cultures in response to individual LC-PUFA treatments. Our results suggest that LC- PUFAs including ARA, EPA, DHA, and DPA each individually protect against CRC-induced muscle cell wasting in vitro, and these protective effects are dependent on 15-LOX activity. Furthermore, we found that C2C12-CT26 co-culture produced mature SPMs in response to individual PUFA treatments. Taken together, this study suggests that individual n-3 and n-6 LC-PUFAs can mitigate CRC-associated cachexia primarily by producing 15-LOX- derived bioactive lipid mediators.

cancer biology↗

bioRxiv2026

A shared neural code for gender across faces, bodies, and objects in the human brain

Humans can readily infer gender from diverse visual categories, including faces, bodies, and objects, yet it remains unclear whether the brain constructs a shared, category-general representation of gender. To fill the gap, we measured neural responses using fMRI while participants viewed female and male stimuli across these three categories. Multivoxel pattern analyses revealed that gender information was encoded throughout distributed occipitotemporal regions for all categories. Critically, cross-category decoding and regression-based representational similarity analyses converged on a region of the right middle temporal gyrus (rMTG) that encoded gender independently of stimulus category. This region also carried category information, indicating mixed selectivity. Comparisons between neural representational dissimilarity matrices and those from a fine-tuned convolutional neural network (CNN) showed that rMTG activity most closely resembled intermediate CNN layers, suggesting that shared gender representations rely on mid-level visual features. Finally, functional connectivity analyses revealed that gender-related interactions among occipitotemporal regions were similar for faces and bodies but not for objects. Together, these findings identify a category-general neural hub for gender perception and illuminate how mid-level visual features and distributed networks support the abstraction of gender across heterogeneous visual inputs.

neuroscience↗

bioRxiv2026

Quantitative multi-scale morphodynamic analysis reveals ratchet-like collective DVE migration and epiblast retrograde cell flow during anterior patterning in the mouse embryo

The collective unidirectional migration of distal visceral endoderm (DVE) cells in the early mouse embryo is required to pattern the anterior-posterior (A-P) axis in the epiblast. It is unknown to what extent A-P axial asymmetries exist prior to DVE migration, how migration becomes channeled towards one side of the embryo, and whether the epiblast cells they migrate over have coordinated movements. We developed a quantitative embryo-wide, tissue-tracking approach to analyse visceral endoderm and epiblast tissue morphodynamics in a longitudinal light-sheet imaged, multi-embryo data-set. Here we show that asymmetric morphology of the ectoplacental cone already present prior to DVE migration correlates with the alignment of the A-P axis but not its polarity. DVE cell movements are initiated with a relatively low cell coordination and small net migration, then get channelled in an abrupt transition to a highly coordinated, uni-directional anterior motion. This anteriorwards migration is characterised by a ratchet-like, intermittent motion. Vertex modelling demonstrates that tissue rheology can account for DVE start-stop motion, and suggests that T1-mediated stress relaxation in the surrounding tissue can facilitate intermittent DVE motion without requiring intrinsic fluctuations in DVE velocity. Finally, comparing cell movement of the DVE with the underlying epiblast reveals a previously unknown coordinated motion in the anterior epiblast, opposite to the direction of DVE migration. Together these data provide insights into the origin of embryonic axial asymmetry and a previously unappreciated coordination between VE and epiblast tissue-motion during anterior-posterior patterning. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/720339v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1cfe4fdorg.highwire.dtl.DTLVardef@1c2c3e6org.highwire.dtl.DTLVardef@1cb6a5corg.highwire.dtl.DTLVardef@1b3ed19_HPS_FORMAT_FIGEXP M_FIG C_FIG See supplemental movie: animated abstract

developmental biology↗

bioRxiv2026

Coenzyme A is a redox sensing cofactor for malic enzyme 2 regulating oxidative stress and mitochondrial metabolism

Coenzyme A (CoA) is an essential cofactor required for numerous metabolic reactions, yet its ability to bind and regulate proteins remains poorly defined. Using a proteomic approach, we identified malic enzyme 2 (ME2) as a CoA-binding protein. ME2 uses NAD(P)+ to convert malate to pyruvate, generating NAD(P)H to support energy production and redox homeostasis. ME2 binds CoA at an allosteric site previously thought to bind NAD(P)+. Reduced CoA has minimal effect on ME2 activity, but the oxidized form, CoA disulfide, strongly activates ME2 by promoting ME2 tetramerization and a catalytically efficient closed conformation. Under oxidative stress, ME2 facilitates CoA disulfide formation, enhancing NADPH production and cellular defense against reactive oxygen species (ROS). Mice with ME2 mutation that cannot bind CoA show impaired muscle performance, elevated ROS, and mitochondrial dysfunction. These findings establish CoA as a redox-sensing cofactor, allowing cells to respond to ROS and promote mitochondrial metabolism, and expanding the function of this essential cofactor.

biochemistry↗

bioRxiv2026

Cell membrane proteome profiling uncovers molecular signatures and GPCR regulators underlying diet-induced obesity and exercise-mediated adaptation

Cell membrane proteins (CMPs), notably G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs), represent the largest class of druggable targets. Despite their therapeutic importance, how the CMP landscape is systemically remodeled during metabolic disease progression and in response to exercise remains poorly understood. Here, we constructed the most comprehensive CMP proteome atlas to date across 22 male mouse tissues and established the first multi-tissue map of GPCR-associated protein hormones/prohormones. Integrated CMP proteomic and transcriptomic analysis revealed that diet-induced obesity and its progression to type 2 diabetes remodel the CMP repertoire in patterns distinct from those induced by exercise. We found that numerous GPCRs and RTKs critical for energy homeostasis are dysregulated during obesity in a tissue-specific manner, and these alterations are reversed to varying extents by exercise training. Importantly, our CMP-centric omics study identified two parathyroid hormone receptors (PTHRs) in the hypothalamus as negative regulators of feeding and body weight. Genetically silencing these hypothalamic PTHRs led to severe obesity even on a chow diet and markedly blunted exercise-induced weight loss. Collectively, our study provides not only new insights into systematic CMP regulation underlying metabolic deterioration versus exercise adaptation, but also nominates potential receptor targets for obesity management.

biochemistry↗

bioRxiv2026

A telomere-to-telomere (T2T) pig genome assembly reveals Y chromosome diversity and structural variations of Wuzhishan pigs

BackgroudWuzhishan (WZS) pigs are native to Hainan Province of China, and serve as both important agricultural resources and biomedical models. Although the published WZS pig genome (T2T-pig1.0) even achieving telomere-to telomere (T2T) completeness, substantial genetic diversity still exists within the same pig breed, another WZS pig genome named WZS-T2T was assembled in this study. ResultsMultiple sequencing data were used to assemble genome, and finally yielded a [~]2.68 Gb telomere-to-telomere genome, with N50 length [~]142.87 Mb, and annotated protein coding genes of 23,100. Compared to T2T-pig1.0, QV and BUSCO value was higher, and the Y chromosome (ChrY) length was longer in WZS-T2T than that of T2T-pig1.0. ChrY of two WZS pigs shared 11 genes, including sex differentiation-related genes of SHOX, PRKX, and DDX3X, and SRY; however, energy metabolism gene SLC25A4 and the macrophage-related receptor gene CSF2RA of ChrY were specific to WZS-T2T. An inversion SV on chromosome 10 with length [~]33.86 Mb was identified between two WZS pigs, and three proofs were proposed for proving the accuracy sequence orientation of WZS-T2T.The genetic diversity was consistent with LD decay speed in population different analysis. WZS pigs exhibited higher genetic diversity than other four pig populations (Tunchang pigs, Yuxi black pigs, Large White pig, and Duroc pigs) examined in this study, and presented slower LD decay compared to other four breeds. ConclusionsTherefore, WZS-T2T provided a higher-quality assembly, and potential advantages of both agricultural production and biomedical targets for WZS pigs.

genomics↗