Biology subjects

Zhang, Z.

Publications and source records attributed to Zhang, Z..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Combinatorial docking and molecular generation to navigate over 100-billion molecules for prospective ligand discovery

Commercially available make-on-demand libraries now exceed 100 billion compounds, requiring over 50 years to screen on 2,000 CPU cores using conventional docking. We present two complementary approaches to address this challenge. CombiDOCK, a combinatorial docking framework, enables exhaustive screening at the 100-billion scale within 40 days. MINT-Dock, a generative framework, accelerates navigation of this space by integrating CombiDOCK with Monte Carlo Tree Search. Benchmarked on 46 diverse targets, CombiDOCK matched full-molecule docking accuracy, and MINT-Dock achieved a 4,800-fold enrichment over random selection. Compared with prior billion-scale brute-force campaigns against {sigma}2, VMAT2, and VAChT, prospective CombiDOCK screens of the 100-billion-molecule library yielded higher hit rates and more potent ligands, while MINT-Dock achieved comparable outcomes across single- and multi-target objectives with >20-fold computational cost reductions. Docking-predicted poses of the best VAChT-binding compounds were confirmed by cryo-EM structures. These methods provide exhaustive and generative paths for navigating the trillion-molecule frontier of drug discovery.

bioinformatics↗

bioRxiv2026

Structural basis for loop-dependent inhibition by AcrIIC1 anti-CRISPR proteins

Most known anti-CRISPR proteins exert inhibition via solitary functional pathways, and few natural Acr homologs have been reported to possess coupled inhibitory mechanisms. Here, we demonstrate that AcrIIC1Boe represses Nme1Cas9 activity through loop-coupled inhibitory effects. Beyond canonical occlusion of the HNH catalytic site, the unique extended loop of AcrIIC1Boe further perturbs sgRNA binding and restricts R-loop maturation to reinforce inhibition. Strikingly, loop deletion completely abrogated this layered inhibitory capacity, confirming that the loop is indispensable for full anti-CRISPR function. Consistently, transplantation of this functional loop into the weakly active AcrIIC1Nme1 markedly upgraded its inhibitory performance. Our findings reveal an unprecedented loop-governed coupled inhibition mode, clarify the structural basis for functional divergence within the AcrIIC1 family, and provide a modular engineering strategy for the rational design and optimization of high-potency anti-CRISPR proteins.

Molecular Biology↗

bioRxiv2026

Architecture of a portal complex embedded in the poxvirus core

Gene transcription within the viral core is a unique feature of poxvirus replication. Following entry into the cytoplasm, the poxvirus core dissociates from the lateral bodies and undergoes expansion, functioning as a compartment for early transcription. However, the mechanisms governing molecular exchange between the viral core and the host cytoplasm remain poorly understood. Here, we determine the structures of the portal complex and its pore on the poxvirus core at 7.1 [A] and 4.9 [A] resolution, respectively, using cryo-electron tomography and sub-tomogram averaging. The pore is assembled from three viral proteins, E8, E6, and L3, for which we constructed an atomic model. Structural and channel analyses reveal that the pore satisfies the geometric and electrostatic requirements for the transport of RNA and smaller negatively charged molecules, while excluding double-stranded DNA and cytosolic DNA sensors. Together, our findings establish a structural framework for understanding the assembly and function of the poxvirus portal complex and identify potential targets for antiviral intervention.

biophysics↗

bioRxiv2026

Chaperonin recognition of protein dynamics drives drug resistance

The emergence of drug resistance is typically driven by mutations that alter drug-target affinity, yet the role of host cellular machinery regulating these processes remains unclear. Here, we reveal that the chaperonin GroEL/S promotes drug resistance through recognition of protein dynamics. Using directed evolution of E. coli DHFR under antibiotic stress and varying GroEL/S expression, we identify a well-folded resistance variant whose fitness, despite tight inhibitor binding, is critically potentiated by GroEL/S engagement. X-ray crystallography, NMR, molecular dynamics and kinetic modeling reveal that millisecond-timescale flipping of the M20 loop generates steric accessibility and a kinetic window for chaperonin interaction that forcibly displaces tightly bound inhibitors, thereby overriding thermodynamic equilibrium of inhibitor binding to restore the active enzyme pool and preserve metabolic flux. Our findings not only reveal a novel paradigm of "dynamic recognition" where both conformational kinetics and distribution govern chaperonin recognition but also establish chaperonins as "deligandases" that actively modulate in vivo drug binding, suggesting that chaperone surveillance of the cellular proteome extends beyond quality control to govern native protein function. This mechanism defines a previously unrecognized route for the rapid development of drug resistance, with implications for understanding therapeutics of microbial infections and human malignancies.

biophysics↗

bioRxiv2026

PAG-Agent: a biologist-oriented research assistant for context-aware pathway-level analysis and interpretation

Pathway analysis is a critical step for translating gene-level omics results into biological mechanisms, yet existing workflows often leave researchers with long lists of statistically significant pathways that are difficult to interpret, validate, and connect to experimental context. We developed PAG-Agent, a biologist-oriented virtual research assistant that integrates pathway-level statistical analysis, context-aware biological interpretation, literature-supported reasoning, and scientific writing support within a unified workflow. PAG-Agent supports bulk and single-cell transcriptomic data and enables users to perform data preprocessing, differential expression analysis, pathway analysis, pathway-level consensus analysis, and pathway-level meta-analysis through click-based and chat-based interactions. Unlike conventional pathway-analysis tools that analyze gene sets largely in isolation, PAG-Agent incorporates experimental conditions and research objectives to prioritize biologically relevant pathways and generate interpretable hypotheses. The system also provides gene and pathway annotation, citation retrieval, visualization, and writing refinement functions. In Alzheimers disease case studies using three transcriptomic datasets, PAG-Agent consistently identified neurodegeneration-related pathways across multiple analysis methods and datasets. In citation-retrieval benchmarking, PAG-Agent outperformed six competing LLMs across five common literature-support scenarios, demonstrating improved ability to provide contextually relevant and valid references. Overall, PAG-Agent lowers technical barriers for pathway-level analysis and helps researchers move from transcriptomic data to biologically grounded interpretation, hypothesis generation, and scientific communication.

bioinformatics↗

bioRxiv2026

Desert hedgehog enhances endothelial resilience and prevents atherosclerosis by mitigating PAI-1 signaling

BACKGROUNDAtherosclerotic cardiovascular disease remains the leading cause of death worldwide. Most current pharmacotherapies target conventional risk factors that promote atherosclerosis (e.g., hyperlipidemia) rather than intrinsic resilience factors that protect against atherosclerosis in the face of risk factors. Here, we investigated the role of desert hedgehog (DHH), a canonical ligand of the hedgehog signaling pathway, as a novel resilience factor that restrains endothelial mesenchymal transition (EndoMT) and protects against atherosclerosis. METHODSSingle-cell RNA sequencing (scRNA-seq) was performed on atheroprone and atheroprotective regions of the ApoE knockout mouse aorta to identify mechanoresponsive genes associated with atherosclerosis. Endothelial cell-specific Dhh knockout mice were subjected to partial carotid ligation and hypercholesterolemic conditions to investigate the role of endothelial Dhh in atherosclerosis progression. scRNA-seq, bulk RNA sequencing, endothelial lineage tracing, immunoprecipitation-coupled mass spectrometry, and surface plasmon resonance were used to in-vestigate the role and mechanism of DHH in EndoMT. Pharmacological interventions and recombinant DHH administration were performed in vivo to evaluate therapeutic potential of DHH targeting. DHH expression was also examined in human atherosclerotic arteries and serum samples from patients with coronary artery disease. RESULTSDHH protein expression was enriched in arterial endothelium from mice, porcine, and humans. However, DHH expression was significantly reduced in atherosclerotic arteries and serum from patients with coronary artery disease. scRNA-seq of atheroprone and atheroresistant region of mouse aorta identified Dhh as a novel mechanoresponsive gene enriched in aortic regions exposed to unidirectional laminar flow. Endothelial cell-specific Dhh knockout (DhhecKO) mice exhibited increased atherosclerotic lesion area, large necrotic cores, and reduced collagen content following partial carotid ligation. Similarly, under hypercholesterolemic conditions, both male and female DhhecKO mice showed aggravated atherosclerosis progression. scRNA-seq of DhhecKO mouse aortas revealed an increased proportion of endothelial cells undergoing mesenchymal transition, indicating enhanced EndoMT. These findings were corroborated by bulk RNA-sequencing of DHH depleted HUVECs and endothelial lineage tracing in inducible DhhecKO mice. Mechanistically, DHH directly interacted with plasminogen activator inhibitor type 1 (PAI-1) and suppressed PAI-1-induced EndoMT. PAI-1 promoted EndoMT in ECs through activation of canonical TGF-{beta} signaling (SMAD2/3) and noncanonical AKT/ERK1/2 signaling via interaction with low-density lipoprotein receptor-related protein (LRP1). Neutralization of PAI-1 or inhibition of LRP1, AKT/ERK1/2, or SMAD3 signaling abolished DHH deficiency-induced EndoMT. DHH competitively inhibited PAI-1 binding to LRP1, thereby attenuating downstream pro-EndoMT signaling. Intriguingly, treatment with PAI-1 inhibitor TM5275 mitigated endothelial Dhh deficiency induced EndoMT in vivo. Of translational relevance, recombinant mouse DHH protein administration reduced atherosclerosis progression, stabilized plaque, and decreased the expression of EndoMT markers in ApoE knockout mice. CONCLUSIONSDesert hedgehog (DHH) is an intrinsic endothelial cell-enriched resilience factor that protects against EndoMT and atherosclerosis by preventing PAI-1 signaling. The present study implicates endothelial DHH as a potential therapeutic target for atherosclerotic cardiovascular disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/729715v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@194c8a3org.highwire.dtl.DTLVardef@1004d52org.highwire.dtl.DTLVardef@d47c73org.highwire.dtl.DTLVardef@368866_HPS_FORMAT_FIGEXP M_FIG C_FIG Desert hedgehog (DHH) is an intrinsic endothelial cell-enriched resilience factor that protects against EndoMT and atherosclerosis by preventing PAI-1 binding to LRP1 and downstream AKT/ERK, as well as SMAD2/3 signaling. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIDHH was identified as a flow-responsive resilience gene that is downregulated by disturbed flow in endothelial cells. C_LIO_LIEndothelial-specific deletion of Dhh promoted endothelial-to-mesenchymal transition (En-doMT) and atherosclerosis. C_LIO_LIDHH directly interacts with PAI-1 and preclude PAI-1 mediated pro-EndoMT signaling. C_LI What Are the Clinical Implications?O_LIDHH maintains endothelial homeostasis during atherosclerosis. C_LIO_LITargeting endothelial DHH-PAI-1 axis may represent a potential therapeutic strategy to reduce EndoMT and limit plaque progression. C_LIO_LILower circulating DHH level may serve as a potential biomarker of endothelial dysfunction and plaque vulnerability in atherosclerotic disease. C_LI

biochemistry↗

bioRxiv2026

Inherited input and local transformations shape the spatiotemporal organization of pathway specific striatal signals for motivated behavior

Adaptive behavior requires neural circuits to link sensory events with their location, predictive value, and temporal relationship to outcomes. Although striatal circuits are implicated in this process, it remains unclear how motivationally relevant signals are organized across striatal regions and direct- and indirect-pathway spiny projection neurons, and which components reflect afferent input versus local transformations. Using striatum-wide calcium recordings during visual conditioning in mice, we found that learned cue value, reward proximity, cue location, and lick-related behavior were encoded in distinct regions and time windows. These signals included both pathway-convergent representations and pathway-opponent dynamics. Striatum-wide measurements of glutamatergic input targeted to each SPN subtype revealed that rapid cue-location and lick-related signals were present in afferent input to both pathways, consistent with inherited representations. In contrast, pathway-opponent pDMS value signals and dSPN-selective pVLS ramping were absent from corresponding glutamatergic input dynamics, indicating local striatal transformations. These findings reveal region-specific input-output transformations that organize striatal signals for distinct components of motivated behavior.

neuroscience↗

bioRxiv2026

Learning residue-level context for modeling protein-protein interactions

Protein language models (PLMs) enable prediction of protein properties by learning residue-level features from sequence, yet most PLM-based approaches to protein-protein interactions aggregate information across entire proteins, limiting resolution and interpretability. Here we present ReCLIP, a transformer-based framework that learns interaction-specific representations at the level of individual residues by combining intra-protein residue neighborhoods with residue-conditioned representations of interaction partners. We show that residue-centered context provides a general framework for modeling protein interactions across diverse biological settings. ReCLIP accurately predicts mutation-induced perturbations (AUROC = 0.973), generalizes to post-translational modifications that do not alter sequence (AUROC = 0.822), and enables zero-shot prediction of peptide-MHC binding across unseen alleles (AUROC up to 0.972). Analysis of learned residue neighborhoods reveals structurally and functionally coherent patterns aligned with known determinants of binding. Applied to clinically annotated genetic variants, ReCLIP identifies disease-associated interaction perturbations that link pathogenic variants to specific molecular interaction contexts. Our results establish a generalizable and interpretable framework for modeling protein interactions and provide insights into how residue-level context shapes interaction specificity and its perturbation.

bioinformatics↗

bioRxiv2026

Coupled intracellular redox and extracellular respiration sensing for quantitative oxidative stress profiling

Quantitative assessment of cellular oxidative stress requires simultaneous measurement of intracellular redox state and extracellular respiratory activity, yet integrated sensing approaches remain limited. Here, we present a dual-fluorescent sensing platform combining a genetically encoded redox biosensor (roGFP2{square}Tsa2{Delta}CR) with an optical oxygen sensor embedded in microwell plates for parallel, non-invasive quantification of intracellular reactive oxygen species (ROS) and oxygen consumption rates (OCR) in industrial yeast systems. The roGFP2-based sensor was stably expressed in Saccharomyces cerevisiae (S. cerevisiae) and Yarrowia lipolytica (Y. lipolytica), enabling dynamic monitoring of oxidative stress at population, single-cell, and subcellular levels, while oxygen-sensitive films provided real-time respiration measurements. Using this platform, we identified distinct redox-respiration phenotypes between the two yeasts. Crabtree-positive S. cerevisiae exhibited low OCR and mitochondrial ROS during glucose cultivation, whereas growth on glycerol increased OCR and mitochondrial ROS by ~2.5-fold and 12%, respectively. In contrast, the obligate respiratory yeast Y. lipolytica displayed 3-fold higher OCR and 16% lower mitochondrial ROS than respiring S. cerevisiae, indicating differences in respiratory oxidative burden. Antimycin A treatment reduced OCR by 60% in respiring S. cerevisiae while increasing mitochondrial ROS by 35%, whereas Y. lipolytica showed greater resistance to respiratory and oxidative perturbations. By integrating intracellular redox sensing with extracellular oxygen measurements, this platform enables quantitative coupling of redox state and respiration in living cells. The approach provides a scalable framework for evaluating cellular fitness, stress tolerance, and metabolic state in biomanufacturing and synthetic biology.

bioengineering↗

bioRxiv2026

Astrocytic μ-δ opioid receptor heterodimers mediate the antidepressant effects of ketamine's metabolite

A deeper understanding of the targets and mechanisms of fast-acting antidepressants, exemplified by ketamine, remains indispensable for better therapeutic strategies and understanding depression. Beyond the canonical neuron-centric NMDAR inhibition hypothesis, brain opioid system and glia-mediated processes are increasingly implicated in ketamines antidepressant efficacy, yet their precise contributions remain poorly understood. Here, we demonstrate that one major metabolite of ketamine, (2R,6R)-hydroxynorketamine (HNK), selectively targets -{delta} opioid receptor heterodimers (-{delta}-ORs) on astrocytes. By promoting the formation and/or stabilization of -{delta}-ORs, HNK engages Gs-coupled signaling, elevates intracellular cAMP, phosphorylates CREB (p-CREB) levels and Ca{superscript 2} dynamics in astrocytes, and consequently restores key astrocytic proteins and functions in depression models. Disrupting -{delta}-OR assembly or Gs signaling abolishes HNK-mediated antidepressant responses both in vitro and in vivo. Collectively, astrocytic opioid receptor heterodimers are critical to antidepressant responses and HNK may serve as a prototype compound for targeting astrocyte dysfunction across a wide range of brain disorders.

neuroscience↗

bioRxiv2026

Integrating Histology with Spatial Molecular Programs Using a Multimodal Foundation Model

Histopathological assessment remains central to cancer diagnosis and stratification, yet its mechanistic interpretation remains limited without molecular context. To address this, we developed SQUALL, a multimodal foundation model integrating histology with spatial molecular programs. For pretraining, we assembled histMol, a large-scale corpus of 1.76 billion paired histology-spatial transcriptomics spots/bins across 33 tissues and 12 platforms from 3,446 tissue sections. Following pretraining, SQUALL enables transcriptome-wide virtual biomarker profiling, prognostically relevant spatial niches discovery, and integrative disease progression modeling. Leveraging its multimodal embeddings, SQUALL identifies niches associated with tertiary lymphoid structure (TLS) maturation and ovarian cancer relapse, reconstructs molecular trajectories of breast cancer invasion across 325,112 spots, and uncovers underlying transcriptional programs. Applied to whole-slide images from 898 patients, SQUALL outperforms existing pathology foundation models in outcome prediction while enabling interpretable risk stratification. Together, these results establish spatially aligned multimodal pretraining as a new paradigm for extending molecular insights into pathology images.

bioinformatics↗

bioRxiv2026

immgenT CD4: a reference landscape of mouse CD4+ T cell

CD4+ T cells are orchestrators of the immune system with diverse effector functions. Their full molecular diversity remains unclear due to the lack of a unified framework. Within the immgenT project, we profiled RNA, surface markers, and TCR clonotypes in conventional CD4+ T cells across >700 samples. Integration with a joint RNA-protein deep generative model revealed an ensemble of 20 CD4 states that account for all cells across tissues and challenges. Small, highly polarized clusters ("tips") that evoke Th1, Th2, Th17, and Tfh states co-exist with a majority of activated cells with mixed programs occupying "midland" states. Unlike CD8+ T cells, memory CD4+ cells largely mapped to the same states as effectors. Resting states proved quite diverse, and we uncovered unexpected similarities between Tfh and chronically stimulated states. Together, immgenT provides a unified molecular reference for CD4+ T cell diversity.

immunology↗

bioRxiv2026

Closed-loop auditory stimulation during sleep shapes cortical responses and memory consolidation depending on spindle timing

Sleep spindles contribute to memory consolidation, and acoustic stimulation during sleep can modulate spindle activity. However, it remains unclear whether these effects depend on the timing of stimulation relative to the spindle cycle. Using closed-loop spindle detection, we delivered four variants of pink noise either during ongoing spindles or shortly after spindle offset. In Experiment 1, stimulation delivered during a spindle prolonged its duration, whereas stimulation applied shortly after spindle offset, i.e., within the refractory period, delayed the onset of the subsequent spindle. This pattern was consistent across all sound variants, indicating that the stimulation timing, rather than acoustic properties, drove the observed effects. Experiment 2 examined whether post-spindle stimulation influences memory consolidation. Relative to a no-stimulation nap, post-spindle stimulation reduced post-nap deterioration in motor sequence accuracy but did not significantly affect word-pair recall. EEG analyses revealed that stimulation elicited widespread slow oscillation activity without triggering new spindles, demonstrating that cortical processing of external input persists even during the refractory period. Notably, the motor benefit was greatest in participants with lower spindle density during the baseline adaptation nap. Together, these findings challenge the notion that the post-spindle refractory period is a functionally silent interval. Instead, this period remains receptive to external input, capable of eliciting cortical activity and supporting motor memory consolidation even in the absence of new spindle generation.

neuroscience↗

bioRxiv2026

Brief illumination of an optoGPCR elicits prolonged inhibition of Drosophila behavior

Light-actuated G protein-coupled receptors (optoGPCRs) are a class of opsins that act through intracellular signaling cascades. As optogenetic tools, bistable inhibitory optoGPCRs are attractive as they decouple the duration of silencing from the duration of illumination: brief light pulses drive prolonged signaling. Opsin3 from the mosquito Anopheles stephensi (MosOPN3) is a bistable Gi/o-coupled opsin that produces sustained inhibition in mammalian neurons and C. elegans, but its utility in vinegar flies, Drosophila melanogaster, remains untested. Here we tested three optoGPCRs in adult flies; MosOPN3 emerged as the most effective and was benchmarked against an established inhibitor, Guillardia theta anion channelrhodopsin 1 (GtACR1), in walking and memory assays. MosOPN3 inhibitory potency was comparable to that of GtACR1 across most neuronal classes tested, with substantially lower developmental toxicity. Rearing flies on all-trans-retinal-supplemented food throughout development improved both viability and inhibitory efficacy for both opsins. A single pulse of green light (as brief as 5 s) inhibited behavior for minutes, and was sufficient to ablate aversive olfactory learning over a one-minute training epoch. For flies, MosOPN3 is a low-toxicity optogenetic inhibitor for flies that yields minutes of silencing from brief light pulses--especially useful where continuous actuating light would be confounding. Key pointsO_LITo our knowledge, Anopheles stephensi Opsin3 (OPN3) is the first GPCR opsin that inhibits behavior in adult Drosophila melanogaster. C_LIO_LIOPN3 has inhibitory efficacy close to that of GtACR1, with superior viability. C_LIO_LIBrief light pulses drive sustained inhibition lasting minutes, eliminating the need for continuous illumination. C_LIO_LIFor both GtACR1 and OPN3, rearing flies on ATR-supplemented food enhances inhibition efficacy and improves developmental viability. C_LI

neuroscience↗

bioRxiv2026

Chromatin architecture sets origin licensing capacity

Replication origin licensing enables complete and faithful genome duplication, yet how chromatin regulates this process in vivo remains unclear. Using MCM-ChEC-seq to track helicase loading from metaphase through G1 in budding yeast, we find that licensing occurs in a rapid, synchronous burst at mitotic exit and then reaches an early plateau despite continued permissive cell-cycle conditions and persistent ORC binding at origins. Here we show that this plateau is imposed by chromatin architecture at replication origins, which limits the extent of origin licensing. Histone H3K56 acetylation marks newly replicated chromatin and is removed at S-phase exit by the deacetylases Hst3 and Hst4. Persistent H3K56ac severely impairs MCM loading without affecting ORC occupancy, indicating that chromatin limits licensing at the helicase-loading step. Strikingly, deletion or catalytic inactivation of the chromatin remodeler Isw2 increases licensing by approximately 40% in wild-type cells and fully suppresses the licensing defect in hst3{Delta} hst4{Delta} mutants, identifying Isw2 as a physiological inhibitor of origin licensing. Isw2-dependent nucleosome repositioning narrows the origin nucleosome-depleted region and restricts helicase loading. Together, these findings show that chromatin architecture at replication origins sets licensing capacity. Newly replicated chromatin transiently adopts an Isw2-dependent inhibitory configuration that is relieved, but not completely eliminated, by post-replicative chromatin maturation. Genome-wide licensing thus reflects integration of chromatin-imposed licensing capacity with cell cycle-dependent control of licensing timing.

genetics↗

bioRxiv2026

Local control of dopamine release in nucleus accumbens gates opioid withdrawal aversion

The opioid crisis has emphasized the need for more effective treatments for opioid use disorder (OUD)1-3, which is characterized by habitual opioid use to avoid withdrawal symptoms4,5. Both physical and affective symptoms contribute to opioid withdrawal yet whether different neural mechanisms mediate these different symptom domains and contribute distinctly to opioid relapse is unknown. While neurons expressing mu opioid receptors (MORs) gate opioids reinforcing effects6-8 by increasing dopamine (DA) release in nucleus accumbens (NAc), sharp decreases in NAc DA release are associated with withdrawal9-11, the cellular and circuit mechanisms of which are unknown. Here we describe an unusual population of evolutionarily-conserved MOR+ neurons in the NAc expressing the transcription factor Tshz1. Increased activity in these neurons is required for withdrawal aversion learning. Deletion of MORs in Tshz1 neurons prevented withdrawal-induced decreases in DA release and affective aversion, but not physical symptoms associated with withdrawal. Pharmacological activation of mGluR8, which is preferentially expressed in Tshz1 neurons, reduced withdrawal aversion. Thus, by dissociating the circuit mechanisms contributing to the physical and affective components of opioid withdrawal focusing on the critical role of Tshz1 neurons, we have identified a novel druggable target with therapeutic potential for treating key OUD withdrawal symptoms.

neuroscience↗

bioRxiv2026

Inter-haplotype inversions and repeat expansion in the sexually deceptive orchid Chiloglottis trapeziformis

Chiloglottis trapeziformis is a sexually deceptive Australian orchid that provides a valuable system for studying orchid genome evolution, structural variation, and the molecular basis of specialized pollination. However, high-quality nuclear genome resources remain scarce for most orchids, particularly Australias diverse terrestrial lineages. To address this gap, we integrated PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C chromatin-contact data to generate the first chromosome-scale, haplotype-resolved nuclear genome assembly for an Australian terrestrial orchid, Chiloglottis trapeziformis. Hi-C guided scaffolding resolved two haplotypes into 20 chromosomes each, consistent with the reported karyotype and genome size (2n=40, haplotype sizes of 1.58 Gb and 1.91 Gb). Genome completeness was high for both haplotypes, recovering 95.1% and 95.5% complete BUSCO genes for haplotype 1 and haplotype 2, respectively. De novo repeat annotation revealed a repeat-rich genome (85.79- 88.25% repetitive sequence), dominated by LTR retrotransposons. Evidence-guided annotation identified 16,287 and 16,548 protein-coding genes in Haplotype 1 and Haplotype 2, respectively. Phylogenetically informed comparisons placed C. trapeziformis as sister to Anoectochilus roxburghii among sampled Orchidoideae and showed broad gene-order conservation. Comparing the two haplotypes for structural variation, we identified large inter-haplotype inversions containing functionally annotated genes with detectable RNA expression, with focal examples further supported by local Hi-C contact patterns and breakpoint-level inspection. Inversion-overlapping genes did not show elevated dS relative to collinear background. This assembly and annotation resource provides a foundation for population and conservation genomics, structural and comparative analyses, and genome-enabled hypothesis testing of molecular traits underlying sexual deception in orchids. Significance statementSexually deceptive orchids use remarkable chemical, visual, and tactile mimicry to attract specific pollinators, but the genome resources needed to understand how these complex traits evolved remain scarce. By generating a chromosome-scale, haplotype-resolved genome for Chiloglottis trapeziformis, we provide the first genomic framework for the large and unique Australasian tribe Diurideae. We show extensive structural variation between haplotypes in an otherwise highly collinear genome, with several large inversions potentially impacting expressed genes. The absence of elevated coding divergence in these regions highlights structural variation as a potentially underappreciated driver of orchid genome evolution. This resource fills a major gap for Australian orchids and provides a foundation for linking genome structure with orchid diversification, conservation, and the evolution of sexual deception.

genomics↗

bioRxiv2026

ACLY integrates metabolism and chromatin accessibility to enable B Cell activation and humoral immunity

B cell activation and differentiation into antibody-secreting cells require extensive metabolic and epigenetic remodeling, yet the molecular mechanisms that integrate these programs remain incompletely understood. ATP-citrate lyase (ACLY) links glucose metabolism to acetyl-CoA production, supporting lipid biosynthesis and protein acetylation. However, its role in humoral immunity has not been fully defined. Here, using genetic and integrated multi-omics approaches, we show that B cell activation is accompanied by coordinated metabolic, transcriptional, and epigenetic reprograming. Although ACLY is dispensable for B cell development and homeostasis, it is required to establish chromatin accessibility programs in activated B cells, with a more pronounced impact on the epigenetic landscape than on transcriptional output. ACLY-deficient B cells exhibit profound defects in TLR and BCR elicited activation, survival and metabolic fitness ex vivo. In vivo, B cell-intrinsic loss of ACLY results in impaired antigen-specific antibody production, associated with reduced germinal center and plasmablast formation, but normal homeostatic proliferation. Deletion of ACLY after B cell activation reduces plasmablast generation in vivo, indicating a continued requirement for ACLY beyond the initial activation phase. Together, these findings identify ACLY as a central regulator that links metabolism to epigenetic programing that supports B cell activation and humoral immunity.

immunology↗