Biology subjects

Sharma, A.

Publications and source records attributed to Sharma, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Complement component C4 regulates amyloid pathology and glial reactivity in mouse model of Alzheimer's Disease

The complement system, a proteolytic cascade crucial for innate immune system function, is dysregulated in brain aging and neurodegenerative diseases, including Alzheimer Disease (AD). In models of AD, complement proteins, including C1q and C3, are upregulated and mediate microglial clearance of amyloid plaques and pruning of synapses. Among complement genes, C4b, which in mice encodes complement protein C4, is the most highly upregulated in astrocytes in the setting of aging and amyloid pathology. While C4 plays a key role in the complement cascade, there have been no investigations of the direct role of C4 in regulating AD pathology. To probe the function of C4 in amyloid plaque-related pathology, we crossed a germ line C4b knockout mouse (C4 KO) to the 5XFAD mouse model of AD-related amyloidosis. To our surprise, we observed striking reductions in amyloid plaque pathology across multiple brain regions in 5XFAD-C4 KO mice relative to standard 5XFAD controls. This reduction in plaque burden stands in sharp contrast to previous reports of C3 deletion in AD models, which increases plaques. Additionally, we observed a reduction in neuroinflammation and peri-plaque glial clustering in 5XFAD-C4 KO mice, suggestive of a role for C4 in regulating overall neuroinflammatory tone in AD. Finally, we observed a phenotypic shift of the peri-plaque microglia to a more reactive disease-associated microglia (DAM) phenotype, indicating that C4 could be an important factor in regulating microglial reactivity in AD. Altogether, our results demonstrate that C4 may have functions beyond the classical complement cascade and may serve as a key facilitator of AD-related glial function and pathology and a possible target for therapeutic modification.

neuroscience↗

bioRxiv2026

A negative role for master regulator Bcr1 in Candida albicans hypha-associated gene expression

Filamentation, a central virulence trait of the fungal pathogen Candida albicans, is required for host cell damage, tissue invasion, and biofilm formation. The transcription factor Bcr1 was first found to be required for biofilm formation but not filamentation. Subsequent studies revealed a negative role for Bcr1 in filamentation in opaque cells, a cell type that is required for mating, under hypoxic conditions, and in a wor2del/del mutant background. Here we characterize a new context in which Bcr1 negatively regulates filamentation and present its associated gene expression impact. We compared the wild-type and bcr1del/del mutant cells in the SC5314 reference strain background at 30 degrees C in glucose media, conditions that do not induce filamentation. The bcr1del/del mutant displayed increased invasive growth in a solid medium, and some filamentation ability in a liquid medium. The bcr1del/del effect on filamentation was augmented by overexpression of hyphal cyclin gene HGC1, which caused pseudohyphal growth in wild-type, efg1del/del, or brg1del/del strains, yet caused hyphal growth in the bcr1del/del strain. RNA-sequencing (RNA-seq) analysis of 30 degrees C cells shows that the bcr1del/del mutant has elevated expression of two genes that drive filamentation: HGC1 and UME6. In published data these same two genes have decreased expression in the bcr1del/del mutant at 37 degrees C, the temperature at which biofilm formation is typically assayed. A growing cadre of biofilm/hyphal regulators can have both positive and negative effects on hypha-associated gene expression, including Bcr1, Efg1, Ndt80, and Nrg1.

microbiology↗

bioRxiv2026

Immune-cell depleted diffuse large B-cell lymphomas have reduced expression of MHC class I

Immunotherapy has transformed treatment for many cancers. In the aggressive and genetically heterogeneous diffuse large B-cell lymphoma (DLBCL), CD19 CAR T-cell therapy is highly effective, whereas immune checkpoint blockade has shown limited benefit. Loss of MHC expression is a common mechanism to escape T-cell cytotoxicity, and loss of MHC class I (MHC-I) and II are frequent in DLBCL. We applied imaging mass cytometry to diagnostic biopsies from younger, high-risk DLBCL patients to map the tumor microenvironment (TME) spatial architecture in relation to tumor cell MHC expression, mutational status, transcriptomic and proteomic profiles. Neighborhood analyses identified four TME subtypes: immune-cell depleted and three immune-infiltrated types (mixed, CD4 T cell-rich, CD8 T-cell/macrophage-rich). Depleted cases had shorter overall survival (p = 0.033) and increased expression of proteins involved in DNA replication and proliferation markers compared to infiltrated cases. Tumor cell MHC-I expression was heterogeneous. Cases with low frequency of MHC-I-pos tumor cells were enriched for the depleted TME type. MHC-I-pos tumor cells were surrounded by CD4 and CD8 T cells and M1 macrophages, whereas MHC-I-neg tumor cells were closer to other MHC-I-neg tumor cells. These findings suggest that TME-based classification incorporating tumor cell MHC-I status may improve individualized immunotherapy selection.

cancer biology↗

bioRxiv2026

Functional Contribution of Multienzyme Glucosome Condensates to Cellular Redox Homeostasis in Cancer Cells

Glucosomes are liquid-liquid phase-separated condensates observed in human cells, formed by phosphofructokinase and other rate-determining enzymes in glycolysis and gluconeogenesis. While glucosomes are spatially formed into small-, medium-, and large-sized assemblies in cancer cells, medium-sized glucosomes are functionally characterized to shunt glucose flux to the pentose phosphate pathway (PPP). As the PPP is the primary pathway responsible for maintaining cytosolic NADPH levels during oxidative stress, we hypothesize that medium-sized glucosomes regulate cellular redox homeostasis through the promotion of the PPP. In this work, we started treating Hs578T cells with hydrogen peroxide (H2O2) to evaluate how glucosomes respond to redox perturbation. High-content imaging demonstrated that H2O2 significantly promotes medium-sized glucosomes at both single-cell and population levels. The extracellular acidification rate by Seahorse extracellular flux analysis then corroborated that H2O2 effectively diverts glycolytic flux to the PPP through the upregulation of medium-sized glucosomes. We then investigated the glutathione redox cycle as a potential mechanistic link between medium-sized glucosomes and H2O2 detoxification. Treatment with oxidized glutathione (GSSG), but not reduced glutathione (GSH), markedly increased the population of cells showing medium-sized glucosomes. Moreover, shRNA-mediated knockdown of glutathione reductase, which converts GSSG to GSH at the expense of NADPH, attenuated H2O2-induced glucosome formation in Hs578T cells. Collectively, we demonstrate that glucosome-mediated metabolic reprogramming couples glucose metabolism to the glutathione redox cycle to facilitate H2O2 detoxification, thereby establishing the functional role of glucosomes in cellular redox homeostasis.

cell biology↗

bioRxiv2026

Macrophage to Myocyte Mitochondrial Transfer in the Myometrium: A Novel Mechanism for the Initiation of Labor

Labor initiation involves influx of peripheral monocytes into uterine tissue, where they differentiate into macrophages (Macs) and polarize toward pro-inflammatory (M1) or anti-inflammatory (M2) phenotypes. Crosstalk between uterine myocytes (MYO) and Macs is implicated in myometrial activation, but the underlying mechanisms remain unclear. Using immunofluorescence and live-cell imaging, we show that M1-Macs (but not M2-Macs) form tunneling nanotubes (TNT) with MYOs, enabling direct, unidirectional mitochondrial transfer. TNT-mediated mitochondrial transfer enhances ATP production and 20-HSD expression in MYO. Functionally, M1-Macs induce intracellular and functional progesterone (P4) withdrawal in MYOs via 20-HSD mediated P4 metabolism and increased PR-A phosphorylation. In vivo, transfer of monocytes, carrying dendra-labelled mitochondria in pregnant mice confirm their myometrial recruitment, differentiation, polarization to M1-Macs, and M1-Mac/MYO mitochondrial transfer. Increased M1-Macs and mitochondrial transfer to MYOs are observed before labor onset, implicating M1-Macs/MYO interaction as key regulator of labor initiation and potentially a therapeutic target to prevent preterm birth.

immunology↗

bioRxiv2026

Evolutionary divergence V-ATPase function in macropinocytic cup remodeling

Macropinocytosis is an evolutionarily conserved process from unicellular eukaryotes to mammals. This process relies on actin-rich protrusions beneath the plasma membrane to form a macropinocytic cup. Traditionally, V ATPase has been best studied for its role in late endosomal acidification. However, the specific roles of V-ATPase interaction with cytoskeletal machinery and its crosstalk with lipids in the formation of macropinocytic cups have not been investigated. Here, we uncover an unprecedented role of V-ATPase in shaping the macropinocytic cup in the pathogenic amoeba Entamoeba histolytica. Our results showed that the Entamoeba V-ATPase complex is associated with F-actin at macropinocytic cups. Moreover, we found that the V-ATPase complex is dynamically recruited to the macropinocytic cup and dissociates from the macropinosome. We further demonstrated that the V-ATPase V1B subunit directly binds to actin and uniquely promotes actin polymerization. The pH biosensor phosphatidic acid, revealed abundant V-ATPase complex and cytoskeleton associated proteins in its interactome. Surprisingly, the V1B subunit showed reproducible binding to phosphatidic acid and this interaction modulates actin polymerization. Collectively, our work highlights the novel role of V-ATPase in directly driving actin polymerization, in conjunction with phosphatidic acid, to shape the macropinocytic cup.

cell biology↗

bioRxiv2026

Allelic Diversity and Core Conservation of Type III Effectors Across Xanthomonads Causing Bacterial Spot of Pepper and Tomato

Bacterial spot of tomato and pepper (BST/P) is an economically devastating disease caused by four distinct Xanthomonas pathogens: X. euvesicatoria pv. euvesicatoria (Xe), X. euvesicatoria pv. perforans (Xp), X. hortorum pv. gardneri (Xg), and X. vesicatoria (Xv). A key component of virulence in these pathogens is the type III secretion system (T3SS), which delivers type III effector (T3E) proteins into host plant cells. To comprehensively characterize T3E repertoires and assess the stability of core effectors at a population scale, we evaluated a global dataset comprising 1,037 quality-filtered genomes, including 585 Xp, 350 Xe, 69 Xg, and 33 Xv strains. Across this collection, genes for six effectors were present in 100% of the examined genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1) and an additional four effectors in [≥]95% of genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1). Xp and Xe populations maintained large total effector repertoires with extensive allelic variation, displaying exceptional polymorphism within XopD and XopAD. In contrast, Xg and Xv exhibited highly stable effector profiles with markedly reduced allelic diversification across geographic regions and decades. Disruptive mutations, including early stop codons and frameshifts mutations, in genes for XopAZ, XopAF, and XopAR were prevalent across specific pathogens pointing to ongoing pseudogenization and targeted gene loss. These findings provide a high-resolution characterization of the conserved and variable components of the BST/P pathogen effector arsenal and serve as a foundation for monitoring population evolution and breeding durable disease resistance to multiple pathogens.

genomics↗

bioRxiv2026

Sequential HIV-1 fusion protein gates control the initiation of host cell entry

HIV-1 fusion with host cells is initiated upon engagement of the viral envelope (Env) protein by its receptors and co-receptors. Receptor-induced conformational changes in the Env ectodomain expose the fusion machinery and position the HIV-1 fusion peptide for release and transit to the host membrane. However, no allosteric rearrangements in the envelope receptor/co-receptor binding domain that could induce fusion peptide release have been identified, and the trigger for the structural cascade that brings the viral and host membranes together remains unknown. Here, we identified two sequential conformational gates that control fusion peptide release, thereby facilitating its transition to the host membrane. We show that destabilizing a clasp holding the fusion peptide proximal motif enhances fusion peptide release, and that a coupled downstream gate controls the release of the receptor-binding gp120 subunit. Single-particle cryo-EM structures, biased and unbiased atomistic simulations, and functional experiments reveal that this process is controlled by shifts in the angular orientation of the gp120 subunits, induced by the geometries required for receptor and co-receptor binding. These results show how HIV-1 senses contact with the host cell to initiate fusion, thereby permitting viral entry.

molecular biology↗

bioRxiv2026

A Role for Astrocyte Metabolism in Species-Specific Neuronal Development

Human neurons develop more slowly than non-human primate (NHP) neurons, a phenomenon called neoteny, but research has primarily focused on neuron-intrinsic drivers. We hoped to further elucidate any species-specific divergence in function and the astrocytes role in influencing species-specific neurodevelopment rate. In this study, we identified a delayed onset of gliogenesis in human versus NHP organoid models. Transcriptomic and 13C metabolic flux analyses of iPSC-derived astrocytes revealed distinct metabolic profiles: NHP astrocytes exhibit increased serine and glycine synthesis, whereas human astrocytes show elevated lactate secretion, suggesting a change in the metabolic role of astrocytes across primate evolution. We then assessed the impact of these different species astrocytes on neuronal development. We observed an increase in electrophysiological maturation and a change in transcriptomic neuronal development trajectory in human neurons cultured with rhesus astrocyte conditioned media as opposed to human astrocyte conditioned media. Human astrocyte secretomes were enriched for synaptogenic and axon-growth proteins, which could indicate they play a greater role in supporting structural complexity and dendritic arborization over rapid maturation when compared to NHP astrocytes. Finally, chemical inhibition of PHGDH demonstrated that these changes in neuronal differentiation are partially mediated by the different metabolic roles that astrocytes play in humans versus NHPs. Collectively, our results reveal a cell-extrinsic role for astrocyte metabolism in shaping human-specific neurodevelopmental timing and trajectories. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/737608v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@ad88f4org.highwire.dtl.DTLVardef@fa5cf5org.highwire.dtl.DTLVardef@ecf0eborg.highwire.dtl.DTLVardef@1bcf078_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Site-specific cholesterol depletion therapy for gastric cancer

Altered cholesterol metabolism is a recognized hallmark of cancer, but systemic modulation has not yet delivered significant clinical results. Accumulating evidence shows that cholesterol plays distinct roles across diverse cellular membranes, suggesting that site-specific modulation may produce superior therapeutic outcomes. Cholesterol is associated with gastric cancer (GC), but the mechanistic link is complex and no effective cholesterol-targeted therapy has been developed. Here, we report that cholesterol levels in GC cells are site-specifically elevated in the inner leaflet of the plasma membrane (IPM). This elevated IPM cholesterol constitutively activates Wnt-{beta}-catenin signaling to drive cell survival and proliferation. Mechanistically, Niemann-Pick C1-like 1 (NPC1L1), which is highly expressed in GC patient tissues and cell lines, acts as a cholesterol flippase to raise IPM cholesterol levels, facilitating ligand-independent {beta}-catenin signalosome formation. Ezetimibe, a clinically approved NPC1L1 inhibitor, blocks this flippase activity, lowers IPM cholesterol levels, and suppresses {beta}-catenin signaling. Ezetimibe treatment induces apoptosis in GC cells while sparing normal primary gastric epithelial cells, which exhibit low levels of NPC1L1 and IPM cholesterol. Collectively, these results suggest that site-specific modulation of cellular cholesterol is a viable approach to developing safe and effective therapies for cancers linked to local cholesterol elevation.

biochemistry↗

bioRxiv2026

Device-embedded accelerometry complements neural signals for tracking parkinsonian motor states

Adaptive deep brain stimulation (aDBS) relies on physiological biomarkers to infer motor state and guide therapeutic stimulation in Parkinsons disease. However, neural biomarkers may themselves be altered by stimulation, potentially limiting their utility for closed-loop control. We address this limitation by testing whether DBS device-embedded accelerometers can accurately track Parkinsonian motor state across stimulation conditions. We analysed over 1,900 hours of chronic recordings of subthalamic nucleus (STN), sensorimotor cortical and device-embedded accelerometry signals acquired before and during continuous STN stimulation, alongside continuous wearable assessments of bradykinesia and dyskinesia. Across stimulation conditions, accelerometry-derived features robustly tracked motor symptom severity and outperformed neural features for symptom decoding. Mechanistically, total STN beta power - a widely used biomarker for aDBS - proved less informative because it conflates periodic and aperiodic neural processes with opposing relationships to motor state. Under active stimulation, periodic beta activity showed reduced coupling to symptom severity, whereas STN aperiodic activity, cortical periodic activity and cortico-subthalamic coherence remained comparatively stable. Together, these findings demonstrate that neural and behavioural biomarkers exhibit differential robustness during deep brain stimulation and identify device-embedded accelerometry as a robust behavioural biomarker of motor state, motivating its use in next-generation adaptive DBS systems.

bioengineering↗

bioRxiv2026

HLiCA: An integrated cell atlas of the healthy human liver

The human liver is composed of a heterogeneous mix of cell types. How these distinct populations contribute individually and collectively to liver function remains poorly understood. Although single-cell technologies have advanced our understanding of liver biology, individual studies have often been limited by small donor cohorts and inconsistent cell type annotations. Integrating multiple datasets can overcome these challenges and better capture biological variability. We present the Human Liver Cell Atlas (HLiCA), an integrated reference of non-disease liver cells assembled from eight datasets across six research centers, encompassing more than 525,000 cells from 110 donors. Developed in collaboration with the Human Cell Atlas Liver Bionetwork, the HLiCA incorporates expert-curated cell annotations refined through community feedback and dedicated cell type annotation meetings. The HLiCA classifies cells into six lineages and expands the cell type resolution to include 47 distinct cell types. Starting from raw sequencing reads, we realigned all data and performed rigorous benchmarking to ensure robust integration across technical and biological variables. Genetic ancestry was inferred for all samples to evaluate the range of ancestral backgrounds represented in the atlas. The expanded cell type annotation enabled identification of previously unrecognized liver cell types, including NRXN1+ stromal cells. Their presence was validated using spatial transcriptomics, which localized NRXN1+ stromal cells to periportal regions. With the number of donors included in the HLiCA we were able to examine cell type specific associations with demographic covariates. In hepatocytes, drug metabolism genes showed differential expression between sexes, and in cholangiocytes, mucus-production genes varied with age. As the largest and most genetically diverse human liver cell atlas to date, the HLiCA provides a comprehensive, well-annotated reference for the field, annotated by expert consensus. This resource will enable deeper interrogation of liver cellular diversity, architecture, and function in the healthy human liver and serve as a reference to understand changes that occur with disease.

genomics↗

bioRxiv2026

vDeepInsight: an injective three-dimensional voxel carrier for tabular-feature neighborhood learning

DeepInsight-style methods make tabular feature relationships accessible to convolutional networks by placing each feature at a fixed position on an image carrier. An open design question is how the carrier geometry should be constructed when feature neighborhoods themselves carry part of the signal. We introduce vDeepInsight, an injective three-dimensional (3D) voxel carrier that preserves feature neighborhoods more faithfully than matched two-dimensional (2D) carriers while keeping a one-to-one mapping from each feature to a single voxel. Genes are embedded with t-SNE or UMAP, assigned one-to-one to a sparse voxel grid by linear-sum assignment, and processed by a submanifold sparse 3D convolutional network. We evaluate the carrier on gene expression through four linked analyses. First, representation-quality metrics show that 3D layouts reduce gene-neighborhood distortion relative to matched 2D layouts before any model is trained. Second, controlled synthetic tasks show that a sparse 3D convolution can exploit this preserved locality, but only when the supervised signal is constructed to depend on co-located genes and the receptive field spans adjacent voxels. Third, on real omics tasks the 3D carrier matches or exceeds tuned tabular baselines and consistently exceeds matched 2D carriers; the margin is small on marker-type classification, where individual genes already carry much of the label (tissue, lineage and cancer-type classification), and larger on program-type tasks, where the target depends on coordinated, pathway-level multi-gene activity (drug-response regression, TCGA immunogenomic-context regression and mechanism-of-action classification). Fourth, because the assignment is injective, voxel attribution maps directly back to genes, enabling gene-level attribution and pathway-level functional interpretation without voxel-to-gene deconvolution. Overall, the added carrier dimension improves the fidelity of feature-neighborhood representation and translates this improvement into prediction gains that are largest when the signal is distributed across local gene programs rather than dominated by individual marker genes.

bioinformatics↗

bioRxiv2026

SERCA2b loss of function drives pigmentation by inducing adaptive ER stress and enhancing mitochondrial calcium uptake: significance in pathological hyperpigmentation associated with Darier’s Disease

Pigmentation is a critical protective mechanism that safeguards the skin against UV-induced damage, whereas dysregulated pigmentation predisposes to pigmentary disorders and skin malignancies. Although calcium signaling has emerged as an important regulator of melanogenesis, the identity of the calcium-handling proteins and the molecular mechanisms linking calcium dynamics to pigmentation remain poorly understood. Here, we identify the ER calcium pump SERCA2b as a negative regulator of pigmentation through modulation of ER stress and mitochondrial calcium uptake. We demonstrate that SERCA2b expression inversely correlates with pigmentation levels, and gain- and loss-of-function studies establish SERCA2b as a suppressor of melanogenesis. Mechanistically, SERCA2b depletion induces adaptive ER stress, enhances ER-mitochondrial proximity, and promotes mitochondrial calcium uptake. Notably, mutations in SERCA2b are associated with Darier disease, a condition characterized by hyperpigmented skin lesions, although the underlying mechanism remains unknown. To address this, we generated SERCA2b mutants corresponding to variants identified in Indian Dariers disease patients and examined their effects on pigmentation, ER stress, and mitochondrial calcium dynamics. The mutant phenotypes closely recapitulated SERCA2b loss-of-function effects, demonstrating that adaptive ER stress and enhanced mitochondrial calcium signaling underlie hyperpigmentation associated with Dariers disease. Importantly, treatment with 4-phenylbutyrate (4-PBA), an FDA-approved ER stress alleviator, rescued mutant-induced hyperpigmentation, reduced ER stress, and normalized mitochondrial calcium uptake. Collectively, our findings uncover a previously unrecognized role of SERCA2b in skin pigmentation, establish a mechanistic link between SERCA2b mutations and hyperpigmentation, and identify adaptive ER stress pathways as potential therapeutic target for pigmentary disorders.

Cell Biology↗

bioRxiv2026

Prostaglandin E2 facilitates reciprocal crosstalk between intestinal smooth muscle tissue and epithelium in tumor development

Colorectal cancer arises from intestinal epithelial cells and is driven by the accumulation of aberrant signaling events that disrupt intestinal stem cell (ISC) homeostasis. While stromal regulation of the ISC niche is increasingly recognized, the contribution of the underlying/adjacent smooth muscle tissue (SMT) remains poorly characterized. In particular, the potential crosstalk between normal or tumoral epithelium and the SMT is largely unexplored. Here, we investigate the ability of the SMT in modulating normal and tumorigenic epithelial biology, and the impact of the tumoral epithelium on the underlying SMT. Mechanistically, by using imaging analyses, transcriptomics, and mass spectrometry, we identify the SMT-derived factor Prostaglandin E2 (PGE2) as the key driver of epithelial dedifferentiation, promoting YAP transcriptional activation, organoid enlargement, and spheroid morphology in intestinal epithelial organoids following SMT supernatant exposure. Conversely, we show that non-invasive tumoral epithelium induces significant changes in the underlying SMT. Tumor-associated SMT shows structural remodeling, inflammation, and reduced muscle fitness. Furthermore, we detected increased prostaglandin signaling, including upregulation of PGE2 synthase Ptgs1 (COX1), in the SMT underneath the epithelial tumor. Our results reveal a communication between the tumoral epithelium and the underlying SMT prior to metastasis, which could be a facilitating step for tumoral extramural progression. Taken together, these findings highlight a novel tumor-stroma interaction.

Molecular Biology↗

bioRxiv2026

Determining organ size through growth rate dependent negative feedback without sensing size.

Drosophila imaginal discs are the favoured system to study organ size determination. The intrinsic mechanism of organ size determination remains elusive despite decades of research into the cellular nature, mechanics and genetics of growth in the wing imaginal discs. Here we propose a new model whose basis is growth rate dependent-negative feedback without size being sensed. We show that alterations in size before the growth period are not corrected for, but alterations in growth rate during the start of the growth period induce size-restoring feedback.

developmental biology↗

bioRxiv2026

A high-quality chromosome-scale reference genome assembly for Asparagus racemosus var. CIM-Shakti (Shatavari), a medicinal plant of Ayurvedic importance

Asparagus racemosus Wild., commonly known as Shatavari, is an important medicinal plant in Ayurveda and is valued for its steroidal saponins, particularly shatavarin compounds, which contribute to its adaptogenic, galactagogue, immunomodulatory, and therapeutic properties. Despite its medicinal and economic importance, genomic resources for this species have remained limited, restricting molecular breeding, pathway discovery, and comparative evolutionary studies within Asparagaceae. Here, we report a high quality chromosome scale reference genome assembly of A. racemosus var. CIM Shakti generated using PacBio HiFi long read sequencing and Omni C chromatin conformation scaffolding. The pseudo haploid assembly spans 817 Mb across 53 scaffolds, with a scaffold N50 of 98.50 Mb, L50 of 5, and a largest scaffold of 113.80 Mb. Ten major chromosome scale pseudomolecules were resolved, corresponding to the haploid chromosome complement of A. racemosus. The assembly showed high gene space completeness, with BUSCO completeness of 99.8% against the Eukaryota dataset and 98.0% against the Embryophyta dataset. BlobToolKit profiling further supported assembly quality, with GC content of approximately 39 to 40% and no major evidence of contamination. EDTA based repeat annotation identified 580.93 Mb of interspersed repetitive elements, accounting for 71.06% of the 817.57 Mb genome assembly. The repeat landscape was dominated by LTR retrotransposons, particularly Gypsy elements, which accounted for 25.01% of the assembly, followed by unclassified LTR elements at 26.58% and Copia elements at 4.84%. Structural and functional annotation identified 29,199 protein coding genes represented by 29,199 transcript models, 138,433 exons, and 125,201 CDS features. The annotation was structurally robust, with an average gene length of 4,605.1 bp, 4.74 exons per transcript, and 97.80% of transcripts containing multiple exons. The CIM Shakti reference genome provides a foundational genomic resource for investigating steroidal saponin biosynthesis, sex chromosome evolution, repeat driven genome expansion, and comparative genomics in Asparagaceae. This assembly will support future studies on medicinal trait improvement, conservation genomics, and genomics assisted breeding of climate resilient Shatavari cultivars.

bioinformatics↗

bioRxiv2026

Gene duplication and retrotransposition diversify the antiviral repertoire of macaque IFITM proteins

Interferon-induced transmembrane (IFITM) proteins are broad-spectrum antiviral restriction factors that inhibit viral entry of diverse enveloped viruses. Comparative genomic studies have revealed extensive lineage-specific diversification of IFITM genes, yet the functional consequences of this diversification remain poorly understood. We previously identified an expanded IFITM repertoire in macaques consisting of the canonical IFITM proteins, IFITM1 and IFITM3, a duplicated IFITM3 paralog (IFITM3A), and two retrotransposed IFITM3-derived genes (IFITM3-R1 and IFITM3-R2). Here, we thoroughly characterized the antiviral activities, intracellular localization, and mechanisms of regulation of canonical and non-canonical macaque IFITMs against vesicular stomatitis virus (VSV), influenza A virus (IAV), Sendai virus, and HIV-1. IFITM3A exhibited enhanced antiviral activity relative to IFITM3, particularly against VSV and HIV-1. Comparative mutational analyses identified amino acid substitutions in IFITM3 that contribute to the enhanced antiviral phenotype of IFITM3A. In contrast, the retrocopy IFITM3-R1 exhibited markedly reduced expression due to lysosome-dependent protein turnover mediated by a PPxY motif and a unique lysine residue (K51). Alteration of these determinants increased IFITM3-R1 expression and selectively enhanced restriction of VSV and IAV. Although several macaque IFITMs reduced HIV-1 infectivity when expressed in producer cells, none significantly inhibited HIV-1 infection in target cells. Furthermore, differential incorporation of IFITMs into HIV-1 virions did not consistently correlate with antiviral activity, indicating that virion incorporation alone is insufficient to explain HIV-1 restriction. Together, these findings demonstrate that gene duplication and retrotransposition have generated a functionally diverse IFITM repertoire in macaques and provide insight into how evolutionary diversification expands innate antiviral defenses in primates. ImportanceIFITM proteins are broad-spectrum antiviral restriction factors that inhibit infection of numerous enveloped viruses. Although IFITM genes have undergone extensive diversification during mammalian evolution, the functional consequences of this diversification remain poorly understood. Here, we show that expansion of the macaque IFITM locus through gene duplication and retrotransposition generated proteins with distinct antiviral activities, intracellular localization patterns, and regulatory mechanisms. We identify amino acid determinants that contribute to the enhanced antiviral activity of the duplicated paralog IFITM3A and demonstrate that lysosome-dependent turnover mediated by a PPxY motif and a unique lysine residue limits expression and antiviral activity of the retrocopy IFITM3-R1. We further show that macaque IFITMs inhibit HIV-1 predominantly through producer-cell-dependent mechanisms and reveal that IFITM virion incorporation alone does not predict antiviral potency. These findings provide mechanistic insight into how restriction factor diversification expands innate antiviral defenses and shapes host-virus interactions in primates.

microbiology↗