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PLANTS, PEOPLE, PLANET

Wiley

Preprints posted in the last 7 days, ranked by how well they match PLANTS, PEOPLE, PLANET's content profile, based on 27 papers previously published here. The average preprint has a 0.03% match score for this journal, so anything above that is already an above-average fit.

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TreeTOP: Plant experimental platforms in canopy space

Baumeister, J.; Bakhtiari, M. M.; Schreiber, M.; Eisenring, M.; Gossner, M.; Walden, S.; Becker, A.; Bouffaud, M. L.; Cesarz, S.; Dauphin, B.; Eisenhauer, N.; Goldmann, K.; Heidrich, L.; Jurburg, S.; Junker, R. R.; Kreuzwieser, J.; Lampei, C.; Nauss, T.; Peter, M.; Prada-Salcedo, L.; Tarkka, M.; Werner, C.; Zeuss, D.; Herrmann, S.; Buscot, F.; Heer, K.; Opgenoorth, L.

2026-08-31 ecology 10.64898/2026.08.30.748063 medRxiv
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1. Forest canopies harbour strong microclimatic gradients that shape plant performance, species interactions and ecosystem processes. Yet, despite renewed interest sparked by global change, forest canopies remain difficult-to-access experimental spaces. 2. With the goal to expand access to tree canopies as experimental arenas, we designed, built, and tested TreeTOP, a standardized experimental platform that opens canopy space for manipulative ecological experiments, specifically with potted plants. TreeTOP features lightweight aluminum frames placed in mature tree canopies non-invasively, allowing potted plants to be placed in three different heights, ground level, shade canopy, and sun canopy. 3. We implemented TreeTOP using two contrasting infrastructure concepts to demonstrate its applicability in both highly equipped canopy research facilities and forests without permanent canopy infrastructure. One installation relied on a canopy crane, grid power and fully automated irrigation, whereas the second was built by certified tree climbers and was equipped with an autonomous solar-powered, battery-operated irrigation system. At both sites, environmental sensor networks monitor the experiment. 4. TreeTOP successfully reproduced characteristic canopy microclimatic gradients, including increasing light availability, daytime air temperatures and thermal extremes with canopy height. Despite differing infrastructures, both implementations generated comparable microclimatic patterns, demonstrating that standardized canopy experiments are feasible in forests with or without permanent canopy access. By opening canopy space for manipulative experiments, TreeTOP provides a transferable framework for investigating plant performance, phenology, species interactions and microbiome assembly under realistic forest conditions.

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PhenoStream: A Cyberinfrastructure for Automated and AI-Based Crop Trait Extraction from Aerial Imagery

Varela, S.; Ruhter, J.; Sacks, E.; Zheng, X.; Allen, D.; Hale, A.; Landry, C.; Kuang, X.; Long, B.; Zhu, Y.; Proma, S.; Kaur, S.; Jarquin, D.; Morrison, J.; Leakey, A.

2026-08-30 plant biology 10.64898/2026.08.26.747008 medRxiv
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The integration of digital technologies for high-throughput field phenotyping is critical for accelerating crop improvement in agriculture. However, extracting traits from remote sensing data remains constrained by fragmented workflows, manual intervention, and limited interoperability among existing tools, resulting in delays that hinder timely biological insight and decision-making. To address these challenges, we present PhenoStream (Phenotyping Streaming), a scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery-based phenotyping, from data acquisition to plot- and genotype-level inference. The framework integrates automated data ingestion from distributed field sites, geospatial processing, and AI-enabled trait extraction within a unified, user-accessible graphical interface. Its modular and extensible architecture supports adaptable trait modeling and seamless integration of new data sources, enabling deployment across diverse crops, environments, and experimental designs. We demonstrate the system across a large multi-location field trial network of bioenergy crops, where it enables high-throughput characterization of spatiotemporal growth dynamics, genotype-by-environment (GxE) interactions, and predictive modeling of key agronomic traits. By significantly reducing processing latency and manual effort, the platform facilitates near-real-time analysis and reproducible workflows. This work establishes a generalizable and scalable pathway for operationalizing very-high-spatial resolution aerial phenotyping in agricultural research. By bridging data acquisition and analytics, the end-to-end cyberinfrastructure provides a foundation for integrating heterogeneous and unstructured data streams--including remote sensing, environmental, and management data--toward data-driven decision making in agriculture.

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Early-life stage phenomic prediction of field agronomic traits across breeding cycles in intermediate wheatgrass

Harris, Z. N.; Braley, J.; Cassetta, E.; Crain, J.; DeHaan, L.; Van Tassel, D.; Miller, A.; Rubin, M. J.

2026-08-31 plant biology 10.64898/2026.08.28.747871 medRxiv
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Perennial grains represent a promising frontier for sustainable agriculture, but breeding progress is constrained by the accessibility of genotyping and the difficulty of evaluating complex traits expressed for multiple years after establishment across heterogeneous environments. Phenomic selection may help address these challenges by using inexpensive, scalable, high-dimensional phenotypes collected early in development, although the robustness of such predictions across breeding cycles remains uncertain. Here, we compared genomic selection and phenomic selection across two breeding cycles of Thinopyrum intermedium (intermediate wheatgrass; IWG; Kernza(R)), comprising approximately 2,280 individuals from maternal half-sib families evaluated across multiple field sites and years. We constructed relationship matrices from genomic markers and early-life stage phenomic data, including seed and leaf color (HSV), CropReporter multispectral reflectance and indices, and cycle-specific hyperspectral reflectance sensors. Genomic models provided the strongest predictions on average across all field traits in both cycles. Among phenomic predictors, leaf HSV was consistently the most informative, whereas CropReporter and hyperspectral data showed lower and more trait-dependent performance and seed HSV provided little predictive value. Genomic, leaf HSV, and CropReporter models transferred across breeding cycles with little apparent loss of predictive ability relative to within-cycle validation, demonstrating that their predictive signals were not restricted to a single breeding cycle. Early-life stage leaf HSV emerged as a practical, accessible tool for germplasm thinning and early-stage prioritization in perennial breeding programs. Despite limited similarity among relationship matrices, multi-relationship-matrix models rarely improved prediction beyond the stronger constituent single-relationship-matrix model. Together, these results show that early-life stage phenomic data provide reproducible information about agronomic performance expressed years later, but that predictor complexity and data integration do not guarantee improved prediction.

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No evidence for extrafloral nectaries in Erythranthe angulosa

Martin-Eberhardt, S.; Smith, P.; Plunkert, M. L.

2026-08-31 plant biology 10.64898/2026.08.28.747905 medRxiv
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Extrafloral nectaries (EFNs) are a widespread plant defense mutualism trait and are highly convergent, appearing in hundreds of plant lineages worldwide. Here we investigate a report of possible EFNs in Erythranthe angulosa, a recently-described California wildflower. We integrate field observations, insect bioassays, an induction experiment, and microscopy to test for signatures of EFN function, finding no evidence that the distinctive axillary swellings produced by E. angulosa function as EFNs. We also uncovered two distinct morphs at the type locality of E. angulosa that diverge in the number of axillary swellings produced, as well as other shoot architecture traits such as stem thickness, leaf size, and branch number. Although the axillary swellings appear to not function as EFNs, they remain a compelling morphological variant within the yellow monkeyflowers that may perform storage or another unknown function.

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Destructive harvest validation of high-throughput measurements show that water use efficiency is unaffected by moderate drought in tobacco

Stutz, S. S.; Edquilang, R.; Bernacchi, C. J.; Ort, D. R.

2026-08-31 plant biology 10.64898/2026.08.28.747842 medRxiv
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Water-use efficiency (WUE), the ratio of accumulated plant biomass to water lost through transpiration has conventionally been determined using a destructive single-point measurement. Recent advances in high-throughput phenotyping now enable repeated, non-destructive estimation of biomass and WUE. However, these digital measurements must be statistically validated against conventional destructive methods to validate their use as reliable proxies. Therefore, we compared digital biomass determined point clouds produced from multispectral camera scanners with destructive harvests across eight harvests using Samsun tobacco grown under both drought and high-water conditions. WUE efficiency, calculated using the digital biomass estimated from a point cloud and gravimetric water use determinations, were compared to destructive harvest determinations. The coefficient of variation (CV) showed there were no significant differences in digital and destructive measurements for either biomass or WUE. Indicating that digital measurements can be used in place of destructive measurements. Drought plants used significantly less water and were significantly smaller than high-water plants from Harvests 4 through 8. However, there were no significant differences in the ratio of evapotranspiration to leaf area or WUE, indicating that drought plants were simply smaller and used less water than the high-water plants. This work validates that estimating plant biomass from a digital point coupled with continuous gravimetric determination of water use provides a reliable nondestructive measure of WUE in high-throughput measurements across the full plant life cycle.

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Three new species of Thelymitra (Diurideae, Orchidaceae) endemic to Aotearoa New Zealand.

Jones, H. R.; Tate, J. A.; Lehnebach, C. A.

2026-09-01 plant biology 10.64898/2026.08.27.745643 medRxiv
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Three new species of sun orchid (Thelymitra) endemic to Aotearoa New Zealand are here described. These are T. palustris, T. scabrifolia and T. semaphora. The morphological distinctiveness of these three species has been acknowledged for decades; however, their taxonomic status has remained unresolved. Evidence from existing karyological data, recently generated DNA sequence data (LFY and ycf1) and morphological studies from historical and fresh collections are used here to support their formal description. Both, T. palustris and T. semaphora are restricted to wet habitats north of Auckland (North Island). Thelymitra scabrifolia inhabits mostly scrub, and it has a similar northern North Island distribution, but is has been found also in Manawat[a]whi / Three Kings Islands and historically in Otago (South Island). All three species are polyploids and are of conservation concern.

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Soil Microbial and Biochemical Properties under Conservation Agriculture in rice-based cropping systems in lower Indo-Gangetic Plain of West Bengal

Singh, P.; Jaison, M.; Saha, N.; Dutta, S.; Sen, A.; Biswas, T.; Mandal, B.; Mukherjee, S.; Dash, B.; Sahu, B.; Patel, R.; Dasgupta, A.

2026-08-31 microbiology 10.64898/2026.08.31.748290 medRxiv
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Microbial and biochemical properties of soil respond quickly with management practices, than chemical and physical properties. Moreover, impact of conservation agriculture (CA) on soil microbial properties is limited to microbial enumeration, but its effect on soil enzyme and microbial activity is little documented. To address these problems soil enzyme activities [dehydrogenase (DHA), {beta}-glucosidase (BGA), acid phosphatase (AcP) and alkaline phosphatase (AlP) and fluoresceine diacetate (FDA)], microbial activites ((Nitrogen fixation (NFBAct), Phosphate solubilization (PSBAct) & Cellulolytic activities (CDBAct)), microbial biomass ((Soil microbial biomass carbon (SMBC) & soil microbial biomass nitrogen (SMBN)) and available nutrient were studied to evaluate biological soil health in alluvial soil of lower Indo-Gangetic plain (IGP) under CA. Field experiment was conducted in split plot design (SPD), under 3 cropping systems (RMCp: rice-maize-cowpea; RWGg: rice-wheat- green gram; RCfBr; rice-cauliflower- bororice/summer rice). Tillage operations (CT: conventional; MT: minimum and ZT: zero tillage) was main plot and residue application as sub plot treatments [(R0 (no residue), R50 (50% residue) and R100 (100% residue)], treatments were replicated thrice. Biological soil health index (BSHI) indicated that among different degree of CA, ZT (0.464) and (MT=0.441) and R100 (0.464) treatment showed better response. Among different cropping system RMCp (0.359) & RWGg (0.343) outperformed RCfBr (0.609) cropping system with respect to (wrt) microbial and biochemical properties of the soil. Results indicated that for restoring microbial and biochemical properties of soil CA can be used as sustainable practice to restore agro-ecosystem. Keywords: Conservation agriculture, Cropping systems, Soil enzyme, Soil microbial properties, Residue application, Tillage operations.

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High-Molecular-Weight Genomic DNA Extraction from Recalcitrant Australian Plants: An Optimised CTAB Protocol for Anigozanthos

Rajput, R.; Saha, L.; Ahmed, Z.; Naiker, P.; Do, L.; Bisset, A.; Hooper, C.

2026-08-31 plant biology 10.64898/2026.08.29.741951 medRxiv
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High-phenolic plant genera present a major technical limitation in genomic research. Standard extraction approaches that perform reliably across diverse flora often perform poorly when applied to recalcitrant taxa, producing low DNA yield and integrity incompatible with sequencing requirements. The genus Anigozanthos (Kangaroo paws) from the family Haemodoraceae exemplifies this problem. We identified key physicochemical factors governing extraction failure in this genus and resolved them through targeted modifications to lysis chemistry and contaminant management. The resulting protocol achieved a near threefold improvement in DNA purity, substantially reducing contaminant carry over and consistently yielded high-integrity, long DNA fragments (DIN > 7) across a diverse sample set spanning cultivated and wild material across four diverse genera of Haemodoraceae. We also tested a straightforward purity assessment framework that can be implemented in any standard molecular laboratory, enabling rapid pre-submission quality assessment without the need for specialised equipment. Together these advances open a practical path to genomic characterisation of Anigozanthos that establishes a transferable model for genomic research across Australia ' s chemically complex native flora.

9
Closing the biodiversity observation-to-action loop

Yamaguchi, K.; Uchida, K.; Hiraiwa, M.; Fukano, Y.

2026-08-31 ecology 10.64898/2026.08.27.747669 medRxiv
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Citizen science observations are abundant, but conservation requires turning uneven records into reliable predictions and directing new surveys to where information is missing. We developed a biodiversity platform for Japan that is updated monthly and integrates 2.32 million records to predict 8,297 species across seven taxonomic groups. Shared representation models outperformed species-specific models in four groups and extended predictions to species with few records. Five independent datasets, including structured monitoring, environmental DNA and complete forest inventories, confirmed that the models ranked observed species and occupied sites above alternatives, with median AUCs of 0.724 to 0.894 across sites and 0.650 to 0.841 across species. For any user-selected area, the platform returns candidate species, distribution predictions, a biodiversity map corrected for uneven observation effort, a conservation priority map for native species and a map recommending where to survey next. This map highlights places where species with few records are predicted to occur despite limited sampling. Independent observations showed that areas ranked highly by this predicted potential contained many such species, indicating that model predictions can help direct surveys toward knowledge gaps. New observations are incorporated into monthly updates, creating a national feedback system connecting citizen science, local conservation decisions and future surveys.

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A century of soybean breeding increased photosynthetic capacity but not NPQ relaxation

Pereira de Oliveira, L.; Attri, K.; Doran, L.; Leonelli, L. B.; Long, S. P.; Ainsworth, E.

2026-09-01 plant biology 10.64898/2026.08.28.747836 medRxiv
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Accelerating photoprotective regulation to improve carbon assimilation is a promising strategy to increase crop productivity. Although rapid non-photochemical quenching (NPQ) relaxation has been validated as a target through metabolic engineering, it remains unclear whether conventional breeding has improved this trait. Here, we investigated whether more than a century of soybean breeding enhanced NPQ relaxation alongside light-saturated carbon assimilation and seed traits. We evaluated a historical panel of 24 soybean genotypes across vegetative and reproductive developmental stages by integrating NPQ relaxation, gas exchange parameters, xanthophyll-cycle pigment profiles, expression of key photoprotective genes (VDE, PsbS, and ZEP), seed number and seed weight. NPQ relaxation parameters were not consistently associated with genotype release year, seed number, or seed weight at either developmental stage. The only exception was the amplitude of the rapidly relaxing NPQ component (AqE), which was negatively correlated with all three variables during the reproductive stage. In contrast, genotype release year was positively associated with maximum net CO2 assimilation rate (Amax), maximum carboxylation rate of Rubisco (Vcmax), maximum electron transport rate (Jmax), seed number, and seed weight, while Amax and Vcmax were positively correlated with seed number and seed weight. These findings indicate that the greater photosynthetic capacity of modern genotypes was not accompanied by faster photoprotective response. Thus, photoprotective regulation has not kept pace with gains in photosynthetic capacity under field conditions. We conclude that rapid NPQ relaxation remains an important target for synchronizing photoprotection with the high photosynthetic capacity of modern soybean lines.

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Effect of Mushroom-Bacteria Co-culture on Mushroom Growth and Antimicrobial Properties

Wang, E.; Cavanaugh, N. T.; He, Y.; Chai, Y.

2026-08-31 microbiology 10.64898/2026.08.30.747672 medRxiv
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Edible mushrooms have been reported to have antimicrobial properties and other health benefits. This study aims to test the antimicrobial activities of several edible mushrooms from markets and test if co-culturing them with bacteria could induce stronger anti-bacterial properties. Commercial mushrooms, Hericium erinaceus (lions mane), Pleurotus ostreatus (oyster mushroom), Lentinula edodes (Shiitake) and Agaricus bisporus (button mushroom), were grown from strictly controlled/sterile substrates. Ethanol and water extracts from the mushrooms were prepared and tested against the bacteria Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis, and the fungus Candida albicans for antimicrobial activities. Shiitake water extract (SWE) showed strong antibacterial effects against all tested bacterial species, inhibitory effects on their biofilms, and antifungal activity. The antimicrobials in SWE seem to damage the cell wall and cell membrane of the bacteria, prefer weak acidic conditions, and are heat labile. Some antimicrobials are likely proteins and polysaccharides. In contrast, 3 other mushrooms displayed only weak antimicrobial effects. The fast-growing lions mane and oyster mushroom were co-cultured with different bacteria. The co-cultivation promoted the fruiting body development of lions mane. Co-culturing with S. aureus increased the anti-bacterial effects of lions mane against S. aureus, E. coli and particularly B. subtilis. Co-culturing the oyster mushroom with bacteria, especially B. subtilis and P. aeruginosa, boosted the mushroom growth. All tested bacteria, especially S. aureus, increased oyster mushroom anti-bacterial effect against E. coli and B. subtilis. The findings indicate that mushroom-bacteria co-culturing could have benefits both agriculturally and medicinally.

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Eucalyptus microRNA Archive (EMA): a multi-study and cross-condition curated database of microRNAs in Eucalyptus grandis

Aires Teixeira, J. V.; Motta Venancio, T.; Quintanilha-Peixoto, G.; Pimenta de Oliveira, K. K.

2026-08-31 plant biology 10.64898/2026.08.29.747619 medRxiv
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MicroRNAs (miRNAs) are key post-transcriptional regulators of development, stress response, and secondary cell wall formation in woody plants, yet annotations for Eucalyptus grandis, the world's most widely planted hardwood, remain fragmented across studies using incompatible discovery pipelines and filtering criteria. Here we present the Eucalyptus MicroRNA Archive (EMA), a curated, locus-resolved database integrating three independent small RNA sequencing datasets spanning vegetative tissue, somatic embryogenesis, and mechanically induced tension wood formation. Applying annotation criteria aligned with current plant miRNA standards, EMA catalogs 99 curated miRNAs (31 previously described, 68 novel) organized into 34 family-level groupings under a three-tier confidence system, known-reference-supported, multi-study replicated, or single-study, that preserves study-of-origin and sample-level evidence for every entry. Cross-study comparison showed that only 9 of 99 entries (9.1%) were independently supported by all three datasets, supporting an evidence-tiered rather than binary annotation scheme. Target prediction against the E. grandis transcriptome yielded 1,773 miRNA-target interactions spanning 764 loci, integrated into a combined miRNA-target and protein-protein interaction network. This network resolved into functionally coherent, mutually isolated clusters, including an miR482-associated NBS-LRR/TIR disease-resistance hub with a substantial translational-repression component, alongside modules enriched for ribosome biogenesis and translation, DNA replication, and nitrogen and carbohydrate metabolism. EMA is publicly accessible through an interactive web dashboard, with all curated data, source code, and analysis scripts openly available, providing a reproducible, extensible framework for E. grandis miRNA research and a template for similarly structured resources in other non-model woody species.

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Seed Microbiome Transfer Mitigates Intergenerational Dysbiosis, Modulates Plant Defenses and Suppresses Foliar Disease

Perina, F. J.; Thomas, V.; Ketehouli, T.; Mudiyanselage, S.; Jain, M.; Schlathoelter, I.; Goss, E.; Martins, S. J.

2026-09-01 plant biology 10.64898/2026.08.31.747941 medRxiv
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Antibiotic-induced disruption of plant-associated microbiomes has the potential to alter host health beyond the directly exposed generation, yet whether the effects of dysbiosis are transmitted through the seed microbiome remains unknown. Here, we investigated the intergenerational impacts of streptomycin-induced dysbiosis in tomato (Solanum lycopersicum), demonstrated that seed microbiome transfer (SMT) restores progeny microbiome function and disease resistance, and characterized the underlying physiological and genetic mechanisms. Parental streptomycin exposure altered the composition of progeny rhizosphere bacterial communities, reduced expression of defense-associated genes, and increased susceptibility to Xanthomonas perforans. Suppression of immune gene expression was strongly associated with increased disease severity, indicating that parental dysbiosis impaired progeny plants ability to mount effective immune responses. Transfer of the seed microbiome from healthy plant donors partially restored rhizosphere community composition, reduced disease severity and recovered defense gene expression of three genes. Together, our findings demonstrated that antibiotic exposure microbiome disturbance generates intergenerational legacy effects that influence plant immunity and disease susceptibility and seed microbiome transfer can counteract this dysbiosis across generations.

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Democratizing three-dimensional surface phenotyping: an open structured-light platform reveals and removes the projection bias in biological imaging

Gentsch, G. J.; Guo, M.; Platz, A.; Brehm, G.; Hennings, J. C.; Huebner, C. A.; Stark, A. W.; Franke, C.

2026-08-31 bioengineering 10.64898/2026.08.30.748077 medRxiv
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Surface phenotyping underpins plant science, preclinical animal research and entomology, yet across all three the measurement is almost always a photograph, which records a projection and not the surface itself. Here we present the Gentschinator3000, an open structured-light platform that brings high-end metric surface measurement within reach of laboratories with no optics expertise, combining documented open hardware, open reconstruction software and analysis workflows for under 4000 Euro in components. It resolves a planar reference to 45 m local flatness, registers full rotations to a loop closure of 156 m, and performs stably across acquisition ranges that we define. Applying one workflow to a leaf before and after desiccation, to murine anatomy and to a spread lepidopteran, we find that projection underestimates surface area by 11 to 41 %. That error grows with the condition under study, with the evaluation scale and with the direction of view, so it can confound phenotype comparisons dramatically. In murine limbs a 15-degree change of viewing direction shifts a projected inter-segment angle by up to 23.2 degrees, while the three-dimensional angle does not move. Projection geometry can therefore contribute as much to a measured phenotype as the biology it is meant to quantify.

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A subgenome-resolved and chromosome-scale reference genome assembly of allotetraploid wheat wild relative Aegilops peregrina

Singh, J.; Gudi, S.; Maughan, P. J.; Gill, U.; Gupta, R.

2026-08-30 genomics 10.64898/2026.08.28.747929 medRxiv
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Aegilops peregrina is a wild allotetraploid wheat wild relative and an important source of genetic diversity for stress tolerance and agronomic traits. Here, we report a subgenome-resolved, chromosome-scale reference genome assembly of a drought tolerant and stem rust resistant Ae. peregrina accession PI 604178 generated using PacBio HiFi and Hi-C sequencing. The 10.13 Gb assembly contains 98.81% of sequence anchored to 14 pseudomolecules representing the seven S and seven U chromosomes, with contig and scaffold N50 values of 25.84 and 746.48 Mb, respectively. The assembly achieved a consensus quality value of 74.61, 97.83% k-mers completeness, and 99.9% BUSCO completeness. LTR Assembly Index values of 20.43 and 18.79 for the S and U subgenomes, respectively, further supported high continuity across repeat-rich regions. Repetitive elements comprise 85.93% of chromosome-anchored assembly. We annotated 59,910 high-confidence protein-coding genes, with comparable gene representation across the two subgenomes. This reference genome provides a high-quality genomic framework for comparative analyses, characterization of important loci regulating agronomic and resilience related traits, and sequence-guided exploitation of Ae. peregrina allelic diversity for wheat improvement.

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The first chromosome-scale genome assembly of Blumeria graminis f. sp. avenae provides insights into genome evolution and host specialization

Ding, Y.; Zhang, P.; Ociepa, T.; Nucia, A.; Guan, H.; Kowalczyk, K.; Park, R. F.; Okon, S.

2026-08-30 genomics 10.64898/2026.08.28.747853 medRxiv
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Blumeria graminis f. sp. avenae (Bga), the causal agent of oat powdery mildew, is one of the most host-specialized members of the B. graminis species complex. Despite its agricultural importance, the lack of a high-quality reference genome has limited studies of host specialization, virulence evolution and comparative genomics in this pathogen. Here, we generated the first chromosome-scale genome assembly of Bga using an integrative approach combining long- and short-read sequencing, Hi-C scaffolding and transcriptome data. The Bga genome exhibits hallmark features of powdery mildew fungi, including extensive repeat content and low gene density. Comparative analyses revealed that genome expansion is primarily associated with historical transposable element proliferation rather than recent transpositional activity. Genome organization is consistent with a functionally stratified "one-speed" model, in which genes associated with pathogenicity, including predicted effectors and infection-responsive genes, are preferentially located in transposable element-rich regions characterized by reduced synteny conservation and extended intergenic spaces. In contrast, conserved genes are concentrated in compact genomic regions and maintain strong syntenic conservation across cereal-infecting formae speciales. Hi-C analyses demonstrated a highly structured chromatin architecture and revealed genome organization patterns associated with infection-related gene expression. Comparative genomic analyses indicated that host specialization in Bga is driven by localized diversification of a relatively small subset of genes rather than large-scale genome restructuring. These results provide the first high-quality genomic resource for Bga and offer new insights into the evolutionary mechanisms underlying host specialization in powdery mildew fungi.

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Two evolutionary histories in one nucleus: genome remodeling and allelic regulation underlying heterosis in hybrid oil palm

Su, X.; Peng, Y.; Yang, X.; Zhang, F.; Xu, Q.; Ma, Z.; Dong, Y.; Zhou, L.; Xue, H.; Cao, X.; Zou, Z.; Wang, Y.; Zhou, Y.; Zeng, X.

2026-08-31 genomics 10.64898/2026.08.27.747553 medRxiv
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Oil palm (Elaeis) is the primary source of global vegetable oil. Interspecific hybrids of Elaeis exhibit pronounced heterosis by integrating two distinct subgenomes into a single nucleus, effectively combining the high yield of African oil palm (E. guineensis) with the high unsaturated fatty acid content and disease resistance of American oil palm (E. oleifera). However, the genetic basis underlying heterosis is still unclear. Here, we combine phased genome assembly, comparative genomics, evolutionary genomics and haplotype-aware transcriptomics to unravel the genetic architecture of heterosis of hybrid oil palm. We assemble the highly heterozygous F1 genome ('Reyou 40', 3.75% heterozygosity) into a complete 1.73 Gb T2T haplotype (HapG) and a 1.84 Gb near-T2T haplotype (HapO with17 gaps). Despite 91.56% sequence identity, HapG and HapO diverged in LTR-RT occurrence and PAV affected genes, showing complementary biases in lipid metabolism and stress responses, respectively. Evolutionary genomics revealed that ancient WGDs preserved the palm family. Whereas lineage-specific lipid-related gene expansions in oil palm. Six ancient introgressed regions (~64 Mb) in HapG were reshaped by transposable elements and tandem duplication, showing an enrichment of genes related to resistance and lipid metabolism. Transcriptomically, 82.2% of allelic gene pairs maintained balanced expression, accompanied by parental functional complementarity and dosage buffering, revealing a potential regulatory basis for coordinating parental genetic differences in the hybrid genome. These haplotype-resolved genomic resources offer vital targets for understanding heterosis and accelerating oil palm molecular breeding.

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An interpretable, formally verified point-of-care ultrasound risk equation for difficult videolaryngoscopy: development and internal validation

Oyarzun-Silva, R. A.; Hernandez-Hernandez, P.; Fernandez-Vaquero, M. A.; De Luis-Cabezon, N.

2026-09-02 anesthesia 10.64898/2026.08.28.26361621 medRxiv
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Background. Videolaryngoscopy still requires adjuncts or hyperangulated rescue in a clinically important minority, and bedside screening discriminates modestly. Point-of-care ultrasound (POCUS) of the anterior airway is a promising alternative, but existing prediction models are opaque or assume a pre-specified functional form. We developed and internally validated a parsimonious, fully disclosed POCUS risk equation whose form is recovered from data and whose structural properties are machine-checked by formal proof - to our knowledge the first formally verified clinical risk predictor - following TRIPOD+AI 2024. Methods. In a prospective single-centre, single-operator cohort of 259 adults undergoing elective videolaryngoscopy (no-Easy airway 68/259, 26.3%), Sequentially Thresholded Least Squares with bootstrap stability selection (B=300) screened a 71-term library of nine POCUS features and retained a seven-term logistic equation; a two-term bootstrap-stable model was pre-specified as robustness analysis. Internal validation used 5x10 repeated cross-validation plus temporal and device hold-outs, with pre-specified overfitting and optimism assessments. Five behavioural properties of the deployed equation were machine-checked in Lean 4. Results. Two interactions met the |c|/sigma_c>2 stability criterion: skin-to-epiglottis x skin-to-hyoid-bone distance and tongue volume x sagittal tongue area. The seven-term equation reached a 5x10 cross-validated C-statistic of 0.966 (optimism-corrected 0.968) and held across temporal and device hold-outs (0.94-0.97). Calibration-in-the-large matched prevalence, with cross-validated slope 0.90 attenuating to 0.625 out-of-time; standard recalibration restored 0.92 without loss of discrimination. The pre-specified two-term robustness model reproduced this performance (C-statistic 0.964-0.968; events-per-parameter 34; shrinkage 0.99), confirming the result is not an artefact of the screening stage. Net benefit over a clinical baseline was positive across 10-50% thresholds. All five Lean 4 theorems compiled without sorry. Conclusions. A sparse, formally verified POCUS equation predicts difficult videolaryngoscopy with high internally validated discrimination and quantified, modest overfitting. Because the equation was developed in a single-operator cohort and its inputs are operator-dependent, external validation requires prior harmonisation of the measurement protocol and operator credentialing.

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GLP-1/GIP Uptake, Indication, and Access Pathways Among US Adults in the Understanding America Study

Chaturvedi, R. R.; Gracner, T.; Perez-Arce, F.; Suen, S.-c.; Jin, J.; Orriens, B.; Pacula, R. L.; Sexton Ward, A.; Haile, R.; Kapteyn, A.

2026-09-02 endocrinology 10.64898/2026.08.28.26361368 medRxiv
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Importance: Evidence on GLP-1/GIP therapies is largely derived from trials enrolling selected populations or medical records that miss utilization outside healthcare channels. No nationally representative cohort has characterized real-world uptake, indications, and access. Objective: To characterize GLP-1/GIP prevalence, indication, clinical profile, and access. Design: Prospective cohort study with three GLP-1/GIP surveillance waves (March 2024, December 2024, October 2025). Setting: The Understanding America Study, an address-based, nationally representative panel of approximately 15,000 US adults aged 18+ years initiated in 2014. Participants: UAS participants responding to at least one surveillance wave (n=9150). Exposures: GLP-1/GIP use status (never vs any use, comprising current and former use), self-reported primary indication (diabetes, weight loss, or other), and access pathway (traditional vs non-traditional). Main Outcomes and Measures: Survey-weighted prevalence of GLP-1/GIP use, overall and by indication and access pathway; sociodemographic, cardiometabolic, treatment, and access characteristics; and smartwatch-derived resting heart rate, heart rate variability, maximum activity heart rate, step count, and sleep duration and variability. Results: Among n=9150 adults (1274 with any use; 60.9% female; median age 53 years), weighted prevalence increased 46%, from 8.2% (March 2024) to 12.0% (October 2025) representing 32 million. Weight-loss indications grew, reaching nearly half of use (4.1% to 5.6%); diabetes-indicated use was stable (5.3% to 5.4%). Users carried high cardiometabolic burden (obesity, 68.2%; diabetes, 53.6%) but diverged by indication: diabetes-indicated users were older (median, 59 vs 49 years), whereas weight-loss-indicated users were more often female (69.9% vs 51.3%) and healthier. One in three users (~9 million) had non-traditional access, especially in weight-loss-indicated users, of whom 33% had no conventional prescription; 41% used compounding, online, or foreign pharmacies; and, 43% lacked coverage. Non-traditional users were five times as likely to report an unlisted, likely compounded formulation (19.8% vs 4.1%). All p<0.05. Conclusions and Relevance: Real-world GLP-1/GIP use has grown rapidly and diversified substantially in indication, access, and population profile. One in 3 users obtained treatment through nontraditional channels largely invisible to claims data, raising long-term safety, efficacy, and coverage questions. GLIMMER provides a public, nationally representative longitudinal evidence base for future payer and provider decisions.

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Burden of fatigue in compensated chronic liver disease: findings from the multinational a:GAP Study

Choudhuri, G.; Akhundova-Unadkat, G.; Naidoo, N.; Morales-Castillo, M.; Guillaume, X.; Duijnhoven, R. G.; Safaei, A.; Swain, M. G.

2026-09-02 gastroenterology 10.64898/2026.08.28.26361618 medRxiv
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Background & Aims: Fatigue is a central symptom of chronic liver disease (CLD), substantially impacting health-related quality of life (HRQoL). This study aimed to further understand CLD symptomatology, including fatigue, and its impact on HRQoL from a patient perspective. Methods: Abbott Global Assessment of Patients unmet needs (aGAP) was a multinational, cross-sectional survey in adults with compensated CLD in China, India and Mexico, conducted between July and November 2024. Adult participants who self-reported that they had physician-diagnosed CLD and were experiencing fatigue completed a quantitative survey to assess symptom burden and included three HRQoL patient-reported outcome (PRO) questionnaires (Patient-Reported Outcomes Measurement Information System [PROMIS]-29+2, Work Productivity and Activity Impairment - Specific Health Problem version 2.0 [WPAI: SHP], Multidimensional Fatigue Inventory [MFI]). Results: Overall, 505 participants (China: 200; Mexico: 105; India: 200) completed the study. Participants reported that their CLD-related fatigue sometimes, often or always affected their self-esteem/confidence (45.1%) and ability to maintain or acquire new employment (38.6%). Most participants reported moderate (51.3%) or serious (26.9%) fatigue, with 33.5% experiencing fatigue every day or almost every day. Many participants felt their social life was negatively impacted by their fatigue (47.3%) and that there were related financial difficulties (53.9%). Use of validated PRO tools demonstrated severe fatigue (MFI: overall mean [SD] 13.9 [3.4] general fatigue and 13.4 [3.6] physical fatigue) as well as substantial levels of work and activity impairment (WPAI: SHP overall mean [SD] 53.0 [26.4]) and high levels of anxiety, pain interference, depression and sleep interference (PROMIS T-scores [&ge;]54). Conclusions: Fatigue has a substantial impact on HRQoL among adults with CLD across several countries, highlighting a global unmet need for targeted interventions to effectively identify and manage the condition.