Biology subjects

Jiao, Y.

Publications and source records attributed to Jiao, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

DNA-PK enforces the S/G2 checkpoint in ATM-deficient cells to limit ATR inhibitor efficacy

ATR inhibition has been proposed as a strategy for tumors under replication stress or those harboring ATM deficiency. However, anti-tumor activity is limited by DNA-PK and ATM compensation. Here, we have delineated distinct roles for DNA-PK and ATM during ATR inhibitor exposure. Both kinases are activated in a cell cycle-dependent manner at the S/G2 boundary following ATR inhibition. DNA-PK imposes the S/G2 checkpoint and promotes completion of DNA replication, whereas ATM detects persistent aberrant DNA replication structures with associated DNA damage in late S and G2/M to establish a G2/M checkpoint promoting DNA repair. In ATM-deficient cells and patient tumors, DNA-PK is activated following ATR inhibition and assumes greater versatility by not only enforcing the S/G2 checkpoint but also by detecting aberrant replication structures in S phase in place of ATM, allowing cells to tolerate ATR inhibition. Consequently, DNA-PK inhibition synergizes with ATR inhibition in ATM-deficient cells and enhances ATR inhibitor efficacy in ATM-deficient PDX models. These data support clinical evaluation of combined ATR and DNA-PK inhibition in ATM-deficient cancers.

cancer biology↗

bioRxiv2026

A spatial topology atlas of type I myofibers in porcine skeletal muscle reveals local slow-oxidative niches associated with meat quality traits

Skeletal muscle metabolism and meat quality are usually interpreted through myofiber type composition, fiber size, and histochemical state. Whether the spatial topology of myofibers constitutes an independent phenotype layer remains poorly quantified. Here, using succinate dehydrogenase (SDH)-stained cross-sectional images from multiple pig breeds and more than 40 skeletal muscle sites, we established a multiscale spatial phenotyping framework for type I myofibers. To enable scalable instance-level quantification, we developed an improved Mask R-CNN segmentation workflow, trained with SAM-assisted and manually corrected annotations, and optimized for dense, small, irregular, and variably stained muscle fibers. This framework captures single-fiber morphology and staining, local contact, connected-cluster architecture, diffusion-ring neighborhoods, and global tissue configuration. Type I myofiber abundance was separable from spatial organization capacity: some muscles formed stronger-than-expected local connectivity and clustering despite modest type I fiber abundance. Spatial transcriptomic integration further showed that slow-oxidative genes and functional modules were non-randomly organized and formed local high-expression domains in type I fiber-enriched, high-contact neighborhoods. Across muscle sites and breeds, skeletal muscles displayed distinguishable type I fiber spatial topology identities, which were remodeled by breed background in a muscle-specific manner. In samples with matched meat-quality measurements, spatial topology features improved the explanation of pH, meat color, conductivity, and intramuscular fat. These results suggest that skeletal muscle should be modeled as a spatially organized tissue system rather than a simple mixture of fiber types.

bioinformatics↗

bioRxiv2026

Engineered CTLA-4 targeting chimeras for targeted protein degradation and immune synapse reprogramming

Despite the success of immune checkpoint blockade in cancer therapy, overcoming the immunosuppressive tumor microenvironment remains a major barrier to durable responses. Here, we introduce cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4)-targeting chimeras (cTACs), a class of synthetic molecules that harness CTLA-4-mediated trans-endocytosis (TE) for targeted protein degradation across cellular boundaries. The lead candidate, cTAC4.0, is composed of the extracellular domain of CD80 fused to an anti-programmed death-ligand 1 (PD-L1) fragment via a human immunoglobulin G4 (IgG4) heavy chain. Unlike existing protein degraders that function within cancer cells via house-keeping pathways, cTAC4.0 operates in trans between immune and tumor cells. It redirects the natural CD80-CTLA-4 internalization to capture and degrade PD-L1 from tumor cells into T cells, while simultaneously converting PD-L1-mediated suppression into CD28-driven co-stimulation, depending on the relative availability of CTLA-4 or CD28. Mechanistically, we demonstrate that cTAC4.0 promotes CTLA-4-dependent internalization and lysosomal degradation of both membrane-bound and soluble PD-L1, reduces surface PD-L1 levels on target cells, and activates T cells in a CD28-dependent manner. Functionally, cTAC4.0 enhances the cytotoxicity of both bispecific T cell engagers and T cell receptor (TCR)-engineered T cells in vitro, and when combined with these engineered T cells, it suppresses tumor growth in vivo in a glioblastoma xenograft model. By coupling immune checkpoint degradation with T cell activation in an immune synapse-enriched manner, cTACs establish a paradigm for intercellular protein degradation systems that simultaneously deplete suppressive ligands and enhance T cell function to overcome resistance in cancer immunotherapy.

immunology↗

bioRxiv2026

Hidden genetic diversity in 320 nearly-complete East Asian genome assemblies

East Asian populations, representing over 20% of the global population, remain critically underrepresented in human genomic studies, limiting our understanding of population-stratified genetic variation and its implications for health and disease. Here we present the first phase of the Asian Pan-Genome project (APG), comprising 320 nearly complete, fully phased haploid genome assemblies from 160 East Asian individuals. These assemblies achieve unprecedented quality, with an average contig N50 of 144.3 megabase pairs and an average quality value of 64.5. Leveraging these superior assemblies, we reveal previously uncharacterized diversity in human repeatome, including population-stratified patterns in centromere satellites and rDNA arrays. Compared to existing global human genome assemblies, the newly generated genomes supplement 152 million base pairs of novel sequences, 355 gene gains, 18,300 structural variation loci and 26 large euchromatic inversions missing from current human pangenomes. We perform population stratification analyses of structural variations, and further resolve the structural haplotypes of complex genomic regions such as Major Histocompatibility Complex and Survival Motor Neuron loci across global pangenomes, exemplifying tandem-duplicate and inversion-rich complex locus architectures in the human genome, respectively. This resource provides a critical foundation for human genetic studies, especially for East Asian populations, promoting more accurate variant discovery, reducing bias, and ultimately advancing the equity and efficacy of genomic medicine.

genomics↗

bioRxiv2026

A Novel Hydrogen Polysulfide Donor Alleviates Neuropathic Pain by Enhancing A-Type Potassium Currents via LIMK1-Cofilin Mediated Interaction between Filamin A and Kv4.2

Hydrogen persulfide (H2S2) is an important endogenous signaling molecule, holding significant therapeutic potential across diverse disease models due to its potent antioxidant and redox-regulating properties. Herein, we report the synthesis, characterization, and in vivo evaluation of an esterase responsive H2S2 donor, HPD1. It reduced mechanical and cold allodynia at 14 mg/kg (i.p.) in chronic constriction injury and paclitaxel-induced neuropathic pain models. Moreover, HPD1 exhibited negligible systemic toxicity and behavioral side effects even at 28 mg/kg. Electrophysiological tests showed that HPD1 suppressed PTX-induced hyperexcitability in dorsal root ganglion (DRG) neurons by specifically potentiating A-type potassium currents (IA). Mechanistically, we demonstrate that HPD1 activates LIMK1, which inactivates cofilin and stabilizes F-actin, thereby promoting the interaction between the actin-binding protein Filamin A and Kv4.2. Furthermore, both the HPD1-induced increase in Filamin A-Kv4.2 co-localization and the subsequent restoration of IA density in DRG neurons, as well as the analgesic effect of HPD1 were dampened by pharmacological inhibition of LIMK1 with BMS-5. This work has developed a new generation of H2S2 donors, demonstrated the analgesic efficacy of HPD1, and uncovered the novel LIMK1-cofilin-Filamin A-Kv4.2 dependent mechanism that restores IA, thus providing a reliable therapeutic strategy for neuropathic pain based on H2S2 donors.

pharmacology and toxicology↗

bioRxiv2026

Variable fluid mechanics explain why static efficacy tests overestimate sanitizer performance against Listeria

Pathogen cross-contamination during food production is primarily controlled through environmental sanitation. However, sanitizer efficacy is often studied in bench-scale experiments that poorly approximate the fluid dynamics of sanitization and limits our understanding of commercial sanitization efficacy. This study paired computational fluid dynamics (CFD) estimates of shear stress with experimental measurements of Listeria innocua reduction on stainless steel following treatment with 100 ppm hypochlorite sanitizer. At the pilot-scale, sanitizer spray manually applied by researchers achieved a 2.6 {+/-} 0.4 log CFU/surface reduction; however, microbial reduction from manual operation of sanitizer spray equipment differed significantly between researchers (p < 0.05). Microbial reduction varied by location following stationary, bench-scale spray application of sanitizer for 3 s. The greatest reduction was at the point of sanitizer spray impingement (7.5 {+/-} 0.5 log CFU/surface) and directly adjacent to the impingement point (6.4 {+/-} 0.7 log CFU/surface) where shear stress was the highest. Significantly less microbial reduction (0.4 {+/-} 0.1 log CFU/surface) occurred where shear stress was lowest in the fluid-film of sanitizer running down from the impingement point (p < 0.05). Static submersion of inoculated coupons in sanitizer for 3 s resulted in a log reduction of 2.3 {+/-} 0.1 log CFU/surface. Discrepancies between bench-scale spraying, pilot-scale spraying, and submerged coupons demonstrate the need for sanitizer efficacy testing under realistic conditions to better estimate the risk reduction achieved through sanitation programs. IMPORTANCESanitation is critical for controlling pathogen cross-contamination during food production. These findings highlight the limitations of traditional approaches to sanitizer efficacy testing, not because they are invalid, but because they do not reflect the level of microbial reduction typically achieved in application. We demonstrate that these differences in outcomes are attributable to fluid dynamics and exposure, which are not well approximated in submerged coupon experiments. Accurate estimation of microbial reduction from sanitizer application is needed to guide food safety policy decisions. For example, overestimation of the risk reduction conferred by sanitizer treatment may result in food safety policies that neglect other sources of microbial reduction within sanitation programs.

microbiology↗

bioRxiv2026

Optogenetic Analysis of Behavior in the Mosquito Aedes aegypti

The mosquito Aedes aegypti is an important vector of viral pathogens and serves as a model for other vector species. Pathogens are transmitted when a mosquito bites a host animal, but the neural circuits that control seeking and biting behavior are not known. Here, we detail methods for the manipulation of neural activity in the mosquito using optogenetics, a key technique to determine the causal relationship between neural circuits and behavior. These methods include rearing mosquitoes for optogenetics and three assays that are designed to measure different steps in the sequence of arousal, attraction, proboscis probing, and engorgement on the blood of host animals. These behaviors occur at different spatial scales and in response to different sensory stimuli. Each behavioral assay is outfitted with red (~625 nm) LEDs for optogenetic activation. To detect arousal in response to olfactory stimuli, flight and walking are quantified. To assay attraction or landing, mosquitoes are presented with a heated blood meal in a large arena. Proboscis probing and engorgement are assayed with video resolution that enables measurement of appendages and abdomen size. The protocol describes machine vision models to enable high-resolution temporal quantification of behavior as well as endpoint measurements of feeding. These methods can be used to test the role of any genetically accessible population of neurons in mosquito biting behavior and can be extended to additional behaviors.

neuroscience↗

bioRxiv2026

Deciphering the Genetic Architecture of Sorghum Grain Oil Content via Lipidome-Integrated Genome-Wide Association Analysis

Grain oil content and composition are complex quantitative traits that shape cereal grain quality and nutritional value. Sorghum (Sorghum bicolor), a heat- and drought-adapted C crop essential for global food and feed security, remains insufficiently characterized with respect to grain lipidome diversity and its genetic architecture. Here, we integrated population-scale whole-grain lipidomics with genome-wide association studies (GWAS) in 266 sorghum accessions. Lipidome profiling revealed extensive natural variation in triacylglycerols (TAGs), accompanied by coordinated shifts in phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs), explaining 87% of population-level differences in total grain oil. Lipidome-wide GWAS identified approximately 1.6 million significant variant-trait associations and resolved 55 loci linked to plastidial fatty acid synthesis, TAG assembly, lipid transport, and membrane remodeling. These loci, many undetected in previous GWAS of bulk oil content, demonstrated the increased mapping resolution achieved through lipidomics. Integration with metabolic gene clusters revealed significant enrichment of lipid-associated variants within terpene and saccharide-terpene biosynthetic clusters, indicating coordinated genetic regulation between central lipid metabolism and specialized metabolic pathways. Variants within these clusters explained more than 50% of the variance in measured grain oil content and exhibited additive effects of favorable alleles. Haplotype analyses further identified 27 elite sorghum accessions and 12 linked markers for marker-assisted improvement of sorghum grain oil. These findings elucidate the multilayered genetic architecture of sorghum grain lipid diversity and showcase the value of large-scale lipidomics integrated with GWAS for accelerating C crop grain quality improvement.

bioinformatics↗

bioRxiv2026

Orthologous synteny provides robust structural evidence for the ancestral angiosperm ε-WGD

The ancestral angiosperm whole-genome duplication ({varepsilon}-WGD) is a pivotal yet contentious event that has long been debated. A recent study refuted its occurrence based on deviations from expected retention patterns of dosage-sensitive genes. Here, we provide both structural (orthologous synteny) and phylogenetic (subgenome-aware) evidence to revisit this debate. With improved annotation of the Ginkgo genome, we uncover a clear 1:2 orthologous synteny ratio between Ginkgo and early-diverging angiosperms (Amborella and Aristolochia), which lack lineage-specific WGDs. Subgenome-aware phylogenomic analyses further demonstrate that the Amborella/Aristolochia subgenomes diverged after the gymnosperm-angiosperm split but before the radiation of extant angiosperms. Together, these findings provide direct structural evidence for an ancestral angiosperm tetraploidization in the early Jurassic, following divergence from gymnosperms. We argue that the recent refutation of the {varepsilon}-WGD relies on restrictive assumptions regarding ploidy level and duplicate retention that may not hold for deep-time polyploidy events. Our results provide a robust resolution to this long-standing debate and reaffirm the {varepsilon}-WGD as a shared synapomorphy of extant angiosperms.

evolutionary biology↗

bioRxiv2026

Colitis-induced visceral pain recruits central neurotensin neurons that modulate colonic sensitivity

Inflammatory bowel disease produces debilitating visceral pain that remains a major clinical challenge. Notably, many patients experience persistent pain even after the inflammation resolves, indicating a sustained sensitization of central neural circuits that drives enduring pain. The brainstem parabrachial nucleus integrates interoceptive signals from the gastrointestinal tract to elicit both pain perception and affective responses. Using activity-dependent mapping and an RNAscope assay, we identified a neurotensin (NT)-expressing neuronal population in the lateral PBN (PBNL) that is selectively activated during dextran sulfate sodium-induced colitis. In vivo neural activity recordings demonstrate that PBNL NT neurons encode colon-derived nociceptive signals in an intensity-dependent manner. Silencing these neurons attenuates colonic reflexes evoked by luminal distension and normalizes aberrant gastrointestinal transit and nociceptive licking behavior in colitic mice. Pharmacological blockade of NT signaling alleviates colitis-associated hypersensitivity. These findings identify a central neural population that encodes visceral inflammation and regulates peripheral organ function, and pinpoints neurotensin as a promising therapeutic target to treat colitis-induced visceral pain.

neuroscience↗

bioRxiv2026

Distributed neural signatures of discomfort induced by transcranial magnetic stimulation

Transcranial magnetic stimulation (TMS) is a cornerstone tool for causal inference in human brain function and an increasingly used neuromodulation therapy, yet it induces well-recognized discomfort that may systematically bias measured outcomes. Despite its ubiquity, a critical gap remains in understanding how TMS-induced discomfort is represented across the brain and to what extent it contributes to TMS-evoked neural responses. Using concurrent TMS-fMRI across 11 cortical targets, we collected an unprecedented dataset (165 participants; 1,535 runs) spanning healthy participants and those with elevated affective symptoms. Cross-validated multivariate modeling revealed that TMS-induced discomfort engages distributed cortical and subcortical regions across sensorimotor, attentional, default mode, and limbic networks, with both shared and group-specific patterns. Discomfort-related activity accounted for approximately 12% and 25% of TMS-evoked responses in healthy and elevated-symptom groups, respectively, and varied systematically across stimulating sites. These findings identify TMS-induced discomfort as a substantial and previously under-characterized component of TMS-evoked neural responses, underscoring the need to explicitly measure and model it. By providing a whole-brain map of regional contributions associated with TMS-induced discomfort and an analytic framework to dissociate direct neuromodulatory effects from discomfort-related responses, this work improves the interpretability of TMS-evoked signals and supports more rigorous causal inference and therapeutic applications.

neuroscience↗

bioRxiv2026

A Grass-Specific Structural Feature of Myosin VIII Regulates Protoxylem Development and Hydraulic Conductance in Sorghum

Sorghum (Sorghum bicolor), a C grass adapted to hot semi-arid environments, depends on reinforced xylem vessels to maintain hydraulic conductance under high evaporative demand. During protoxylem differentiation, coordinated microtubule and actin dynamics guide secondary cell wall (SCW) deposition; however, whether actin-based motors directly regulate vascular architecture and hydraulic performance has remained unknown. Here, we identify HEAT-SENSITIVE 1 (HS1), a previously uncharacterized myosin VIII, as a central regulator of protoxylem integrity and water transport in sorghum. The hs1 mutant exhibited severe leaf scorching under field conditions. The hs1 mutant displayed severe leaf scorching under field conditions, accompanied by pronounced protoxylem defects under controlled environments, including vessel collapse, reduced lumen area, and attenuated lignified SCWs. These structural abnormalities compromised longitudinal hydraulic conductance, diminished whole-plant water use, and rendered expanding leaves unable to meet transpirational demand, resulting in transient water deficit and thermal injury. HS1 encoded a grass-specific myosin VIII with a grass-specific N-terminal extension exhibiting high intrinsic disorder and lineage-specific substitutions in the motor domain. Molecular and single-cell transcriptome analyses positioned HS1 within differentiating protoxylem cells of developing leaves, revealing pronounced temporal and cell-type specificity. Furthermore bulk transcriptome profiling and quantitative lignin measurements indicated that HS1 promoted lignin-associated SCW biosynthesis during protoxylem differentiation, functionally linking actin-based motor activity to wall reinforcement. HS1 encodes a grass-specific myosin VIII distinguished by an extended intrinsically disordered N-terminal region and lineage-specific substitutions within the motor domain, suggesting evolutionary specialization. Consistant with core developmental role, reduced nucleotide diversity at the HS1 locus across diverse sorghum accessions further supported strong evolutionary constraint. Together, these findings established HS1 as the first actin-based motor protein shown to control xylem architecture and hydraulic function in plants.

plant biology↗

bioRxiv2026

Lipid monounsaturation confers cold tolerance and improves tissue viability during hypothermic storage

The rapid loss of tissue viability during hypothermic storage frequently results in organ failure and high discard rates in transplantation. In contrast, ectothermic animals can tolerate prolonged exposure to low temperatures in their natural environments. Elucidating the mechanisms underlying this cold tolerance may therefore inform improved strategies for tissue preservation. Here, we investigate proteomic and metabolomic responses to cold exposure in the livers of two frog species from distinct habitats: the cold-sensitive African clawed frog (Xenopus laevis) and the cold-tolerant Northeastern Asian brown frog (Rana dybowskii). Cold exposure induced lipid mobilization in X. laevis, whereas it promoted phospholipid mono-unsaturation in R. dybowskii. Notably, treatment with monounsaturated fatty acids (MUFAs) or overexpression of stearoyl-CoA desaturase (SCD) reduced cell death during cold storage. Moreover, MUFA infusion significantly improved cell viability in mouse liver tissue under hypothermic conditions. Together, these findings suggest that lipid mono-unsaturation, an adaptive feature of cold-tolerant frogs, can be leveraged to enhance tissue preservation during cold storage.

biochemistry↗

bioRxiv2026

Noncanonical loops regulated by EMF1 and cohesin-associated factors shape the distinct 3D genome architecture in plants

In mammals, cohesin-mediated chromatin loop extrusion is blocked at boundaries, where CTCF, WAPL, and PDS5s co-bind and regulate cohesin, establishing an impermeable barrier with no exceptions. In contrast, our study revealed that in Arabidopsis, some noncanonical contacts have emerged between the boundary flanking regions, which suggest that cohesin is not absolutely blocked but enables sliding beyond boundaries. We identified these interactions as noncanonical loops and clarified their regulatory proteins. Firstly, the plant-specific boundary binding protein EMF1 is essential for noncanonical loops formation. Surprisingly, although both Arabidopsis WAPLs and PDS5s inhibit loop extension as mammals, PDS5s do not co-bind and cooperate with WAPLs at boundaries. Instead, PDS5s bind to boundary-flanking regions enriched with H3K4me1 through their Tudor domains, restricting further extension of noncanonical loops. Consequently, pds5a/b/c mutants lose noncanonical loops, resulting in emergence of larger canonical loops but anchored on boundaries and co-upregulation of anchored gene pairs. Collectively, our findings reveal that the plant-specific noncanonical loop, regulated by plant-specific EMF1 and PDS5 proteins, is the fundamental structure of the distinctive chromatin organization of plants, which provides novel mechanistic insights into eukaryotic chromatin architecture regulation.

plant biology↗

bioRxiv2026

Single Plaque Proteomics Reveals the Composition and Dynamics of the Amyloid Microenvironment in Alzheimer's Disease

Alzheimers disease (AD) is characterized by amyloid plaques that form complex microenvironments in the brain. However, the molecular composition of these plaques and their temporal regulation are not well defined. Here, we developed a sensitive workflow for quantitative proteomic profiling of single plaques using refined laser capture microdissection and data-independent acquisition mass spectrometry (LCM-DIA-MS). From >200 plaques and control regions in AD mouse models (5xFAD and APP-KI) and human brains, we quantified >7,000 proteins, revealing stage-dependent, cell-type-related remodeling of the amyloid proteome (amyloidome). Temporal profiling uncovered early immune and lysosomal activation followed by engagement of RNA processing and synaptic pathways. Cross-model and cross-species analyses determined a conserved amyloidome including APOE, MDK, PTN, and HTRA1, validated by co-localization in imaging analysis. Network analysis highlighted modules in lipid transport, vesicle organization, and autophagy. These findings establish amyloid plaques as conserved, dynamic multicellular hubs that link amyloid accumulation to downstream cellular events.

neuroscience↗

bioRxiv2026

Cell type-resolved proteomics reveals intra- and intercellular signalingin Alzheimers disease

Alzheimers disease (AD) arises from pathological interactions among diverse brain cell types, but cell-specific proteomic changes remain underexplored. Here, we present deep proteomic profiling of sorted or proximity-labeled brain cells from AD mouse models (5xFAD and AppNL-G-F) at multiple ages, quantifying 13,411 proteins in microglia (three subtypes), astrocytes, oligodendrocyte precursor cells, and neurons. We identified 3,028 differentially abundant proteins across these cell types, the majority of which were not detected in bulk proteomic datasets, and constructed cell type-specific networks to define functional modules and hub proteins. Comparison with transcriptomic data revealed that [~]30% of proteomic changes are RNA-independent. Further analyses uncovered cross-cell type signaling proteins conserved in human AD brains, such as pleiotrophin (Ptn), which is transcriptionally enriched in astrocytes but accumulates in microglia. Importantly, recombinant PTN directly activates induced microglia-like (iMG) human cells. Thus, these findings provide a comprehensive cell type-resolved proteomic atlas of AD models, highlighting novel intra- and intercellular signaling events. HighlightsO_LIA high-resolution cell type-resolved proteomic atlas of Alzheimers disease mouse models C_LIO_LI[~]3,000 cell type-specific protein alterations identified beyond bulk tissue analyses C_LIO_LIProteomic profiling of microglial subtypes reveals subtype-specific changes in Alzheimers disease C_LIO_LIAstrocyte-microglia signaling is highlighted and validated through PTN-mediated interactions C_LI

neuroscience↗

bioRxiv2026

Pan-genome and multi-omics analyses reveal the genomic basis of symbiotic evolution in the mycoheterotrophic medicinal orchid Gastrodia elata

Mycoheterotrophy represents an extreme evolutionary strategy in which plants abandon photosynthesis and become obligately dependent on fungal partners for carbon and nutrients. Gastrodia elata, a medicinal orchid forming long-term symbioses with Armillaria and Mycena, provides a compelling system to investigate the genomic basis of obligate plant-fungus mutualism. Here, we generate a chromosome-level genome assembly (1.09 Gb) of a dark-red G. elata accession and construct a pan-genome from 12 Gastrodia accessions to dissect the evolutionary consequences of mycoheterotrophy. Phylogenomic analyses reveal pervasive hybridization across cultivated germplasm and demonstrate that tuber morphology more accurately reflects intraspecific relationships than stem color, challenging the traditional color-based taxonomy. Comparative genomic analyses reveal a pronounced degeneration of photosynthetic capacity. We detect no intact nuclear-encoded rbcS loci, which would preclude assembly of the Rubisco holoenzyme and thus canonical Calvin-Benson carbon fixation. Notably, a subset of photosynthesis-related genes is retained and transcriptionally active, suggesting their co-option into non-photosynthetic regulatory roles. Despite millions of years of intimate association with fungal partners, we detect no evidence of fungal-derived horizontal gene transfer based on a multi-step phylogenomic validation pipeline, indicating that G. elata-fungus mutualism is sustained through metabolic exchange rather than genetic integration. We further identify the Gastrodia antifungal protein (GAFP) gene family as a key molecular innovation underlying symbiotic homeostasis. The recently derived Class 1 GAFP lineage exhibits distinct domain architecture, tandem expansion, and elevated expression, consistent with enhanced regulation of fungal overgrowth. Finally, we delineate a specialized nutrient-acquisition framework adapted to obligate heterotrophy, in which fungal trehalose hydrolysis supplies hexose carbon via an expanded sugar transporter protein (STP) repertoire, while organic nitrogen is assimilated through amino acid and oligopeptide transporters coupled with urease-mediated conversion, compensating for the loss of nitrate uptake and reduction pathways. Together, these results establish a pan-genomic blueprint for symbiotic adaptation and reductive genome evolution in G. elata.

genomics↗

bioRxiv2026

A family portrait of lanmodulin selectivity for enhanced rare-earth separations

Proteins offer a molecular design space to create bespoke ligands for the separation of critical metals, like rare earth elements (REs). However, data-intensive approaches to fine-tune metalloprotein selectivity are bottlenecked by the low-throughput nature of existing characterization methods. Here we invented an assay called SpyTag-Catcher Immobilization of Lanmodulin for Assaying Metal-Binding Selectivity (SpyCI-LAMBS) to measure metalloprotein selectivity en masse. This 96-format workflow was used to study the selectivity of 621 lanmodulin (LanM) orthologs for 15 REs, revealing eight distinct selectivity profiles based on sequence-to-function analyses. We discovered >200 LanMs with dampened selectivity for low-value LaIII relative to the prototypical LanM. This includes a LanM that can perform a challenging one-stage separation of PrIII from LaIII with up to >99.9 mol% purity and 83% yield. SpyCI-LAMBS is a powerful tool that can rapidly collect high-fidelity selectivity data to inform metal ion separations and machine learning-assisted metalloprotein design.

bioengineering↗