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AI-summarized plant biology research papers from bioRxiv

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Latest 136 Papers

The functional divergence of two ethylene receptor subfamilies that exhibit Ca2+-permeable channel activity

Authors: Pan, C., Cheng, J., Lin, Z., Hao, D., Xiao, Z., Ming, Y., Song, W., Liu, L., Guo, H.

Date: 2025-11-29 · Version: 1
DOI: 10.1101/2025.11.28.691086

Category: Plant Biology

Model Organism: General

AI Summary

The study demonstrates that subfamily I ethylene receptors form the core ethylene‑sensing module and act epistatically over subfamily II receptors, uniquely possessing Ca2+‑permeable channel activity that drives ethylene‑induced cytosolic calcium influx. This reveals a mechanistic link whereby subfamily I receptors integrate hormone perception with calcium signaling in plants.

ethylene signaling subfamily I receptors Ca2+ influx epistasis hormone‑induced calcium channel

Reconnecting food production and consumption through redesigning food systems to support healthy diets

Authors: De Clerck, C., Desmarez, T., Delandmeter, M., de Faccio Carvalho, P. C., Dumont, B., Bindelle, J.

Date: 2025-11-28 · Version: 1
DOI: 10.1101/2025.11.25.690428

Category: Plant Biology

Model Organism: General

AI Summary

The authors created a decision‑making and optimization model that evaluates how cropping systems can meet the EAT‑Lancet dietary guidelines for vegan, ovo‑lacto vegetarian, and omnivorous diets while minimizing trade flows. Simulations show that longer, more diverse rotations—especially those incorporating grazing animals, rapeseed, legumes, and cereals—best satisfy calorie and food‑group requirements. The model serves as a tool for designing multi‑objective, diet‑aligned crop‑livestock systems to support sustainable food production.

EAT-Lancet diet crop rotation diversity integrated crop‑livestock systems multi‑objective optimization sustainable food systems

Quantitative modelling of biological response dynamics reveals novel patterns in plant volatile signalling

Authors: Waterman, J. M., Moore, G. J., Amdahl-Culleton, L. K., Hoefer, S., Erb, M.

Date: 2025-11-28 · Version: 1
DOI: 10.1101/2025.11.26.690448

Category: Plant Biology

Model Organism: General

AI Summary

The authors present an unbiased mathematical modeling framework that quantitatively characterizes dynamic biological response curves without prior knowledge of underlying mechanisms, and they validate it using stress‑induced plant volatile emission data. The model reliably fits diverse datasets, including incomplete and low‑resolution curves, and reveals novel patterns such as light‑independent timing effects of wounding, modulation by herbivory‑associated molecular patterns, and genotype‑specific regulation of volatile induction strength and duration. This approach enables deeper quantitative analysis of organismal responses across taxa.

dynamic response curves plant volatile emissions unbiased mathematical modeling time‑resolved measurements herbivory‑associated molecular patterns

Synthetic tools to redirect the ubiquitin E3 ligase activity of, PRT1, a plant-specific N-recognin.

Authors: Oldham, K. E. A., Mabbitt, P. D.

Date: 2025-11-28 · Version: 1
DOI: 10.1101/2025.11.27.690864

Category: Plant Biology

Model Organism: General

AI Summary

The study reveals that plant PRT1 recruits the UBC35‑UEV1 complex via its RING1 domain, promoting the synthesis of K63‑linked ubiquitin chains. By engineering a synthetic substrate with an N‑terminal calmodulin‑binding peptide, the authors create a calcium‑regulated off switch for PRT1‑mediated ubiquitination, and they also develop nanobodies that target PRT1 to trigger ubiquitination of a reporter protein, providing new tools to manipulate the Arg/N‑degron pathway.

Arg/N-degron pathway PRT1 K63-linked ubiquitin chains calmodulin‑regulated substrate nanobody‑mediated ubiquitination

Setting priorities for the acquisition of primary plant occurrence data

Authors: Bystriakova, N., De Melo, P. A. H., Antonelli, A., Bachman, S., Bramley, G., Brown, M., Cespedes, G., Cheek, M., Darbyshire, I., Demissew, S., DeEgea, J., Erst, A., Forest, F., Friis, I., Fu, L.-F., Fuentes, A., Gogoi, R., Jennings, L., Jongkind, C. C. H., Klitgaard, B., Larridon, I., Lucas, E., Maldonado, C., Martinez, M., Moat, J., Nic Lughadha, E., Reynel, C., Rustiami, H., Santamaria Aguilar, D., Tello, S., Trethowan, L., Utteridge, T. M. A., Vorontsova, B., Wei, Y.-G., Wells, T., Monro, A. K.

Date: 2025-11-27 · Version: 2
DOI: 10.1101/2025.11.11.683036

Category: Plant Biology

Model Organism: General

AI Summary

The study presents a scalable, TOPSIS‑based framework to prioritize geographic areas for acquiring vascular plant occurrence data, integrating ecosystem service value, floristic threat, and species‑richness uncertainty. Validation by botanical experts across multiple regions showed high concordance between regional and global priority maps, indicating the method’s adaptability for national implementation of the Global Biodiversity Framework.

plant distribution prioritization TOPSIS multi‑criteria analysis ecosystem service value species‑richness uncertainty Global Biodiversity Framework

Achieving Micrometer-Scale 4D X-ray tomography of Living Leaf Tissue in the Laboratory

Authors: Siracusa, F., Kristensen, E. V., Szameitat, A., Tobler, D. J., Ertem, I., Frank, M., Wu, C., Abdurrahmanoglu, R., Pinna, A., Minutello, F., Husted, S., Grivel, J.-C., Mokso, R.

Date: 2025-11-22 · Version: 1
DOI: 10.1101/2025.11.21.689754

Category: Plant Biology

Model Organism: General

AI Summary

The authors developed a laboratory‑based micro‑CT workflow that enables micrometer‑scale 4D imaging of living leaf tissue while minimizing radiation damage and motion artifacts, identifying a horizontal mounting setup as optimal for stability over up to 22 hours of acquisition (~15600 Gy). The method achieves 1 µm pixel resolution and permits tracking of compounds such as iohexol and aggregated nanoparticles, demonstrating in‑vivo monitoring of anatomical and physiological dynamics in plants.

microCT 4D plant imaging leaf tissue radiation dose management nanoparticle tracking

A user-friendly machine-learning program to quantify stomatal features from fluorescence images

Authors: Angres, G. J., Gillert, A., Muroyama, A.

Date: 2025-11-21 · Version: 1
DOI: 10.1101/2025.11.20.689597

Category: Plant Biology

Model Organism: General

AI Summary

The authors introduce QuickSpotter, a lightweight tool for semi‑automated annotation of stomata in fluorescence images, complemented by a fast proofreading utility (StomEdit) and a pair‑calling classifier (PairCaller) to detect stomatal clusters. Using these tools, they quantify stomatal morphological changes during cotyledon development and reveal subtle effects of pharmacological treatments, enabling high‑throughput leaf phenotyping.

stomatal morphology high‑throughput phenotyping image annotation fluorescence microscopy computational analysis

PlantCV v4: Image analysis software for high-throughput plant phenotyping

Authors: Schuhl, H., Brown, K. E., Sheng, H., Bhatt, P. K., Gutierrez, J., Schneider, D., Casto, A. L., Acosta-Gamboa, L., Ballenger, J. G., Barbero, F., Braley, J., Brown, A. M., Chavez, L., Cunningham, S., Dilhara, M., Dimech, A. M., Duenwald, J. G., Fischer, A., Gordon, J. M., Hendrikse, C., Hernandez, G. L., Hodge, J. G., Huber, M., Hurr, B. M., Jarolmasjed, S., Medina Jimenez, K., Kenney, S., Konkel, G., Kutschera, A., Lama, S., Lohbihler, M., Lorence, A., Luebbert, C., Ly, N., Manching, H. K., Marrano, A., Meerdink, S., Miklave, N. M., Mudrageda, P., Murphy, K. M., Peery, J. D., Pierik, R., Polyd

Date: 2025-11-20 · Version: 1
DOI: 10.1101/2025.11.19.689271

Category: Plant Biology

Model Organism: General

AI Summary

PlantCV v4 is an open-source Python framework that simplifies image-based plant phenotyping by providing extensive tutorials and streamlined installation, enabling users with limited coding skills to automate trait extraction. The release adds support for fluorescence, thermal, and hyperspectral imaging and introduces a new subpackage for morphological measurements such as leaf angle, which is validated against manual data collection methods.

PlantCV image-based phenotyping fluorescence imaging thermal imaging hyperspectral imaging

In Vitro Dynamic and Quantitative Monitoring of Strigolactone-signaling Complex Formation by Time-resolved FRET

Authors: Suzuki, T., Nishiyama, K., Kato, Y., Shinkai, C., Ishikawa, T., Robertlee, J., Kuruma, M., Hagihara, S., Marco, B., Fukui, K., Asami, T., Seto, Y.

Date: 2025-11-18 · Version: 1
DOI: 10.1101/2025.11.18.688998

Category: Plant Biology

Model Organism: General

AI Summary

The authors introduced an in vitro Time-Resolved Förster Resonance Energy Transfer (TR‑FRET) assay to dynamically monitor strigolactone‑induced protein‑protein interactions, allowing kinetic and quantitative analysis of signaling complex formation. Using this system they demonstrated distinct kinetic profiles for various strigolactone analogs and showed that the receptor antagonist tolfenamic acid blocks complex formation but cannot dissociate pre‑formed complexes, and they also applied the assay to rapidly detect natural strigolactones in root exudates.

strigolactones TR‑FRET assay protein‑protein interactions SL receptor antagonists root exudate detection

Cytogenetic constraints on hybridization: A meta-analysis investigating the role of chromosome number in monocot hybrid evolution using a newly developed tool, the ploidy deviation index (PDI).

Authors: Scholten, J., Sprenger, A., Perez, A., Hullihen, O., Specht, C. D.

Date: 2025-11-14 · Version: 1
DOI: 10.1101/2025.11.13.688279

Category: Plant Biology

Model Organism: General

AI Summary

The study introduces the Ploidy Deviation Index (PDI) to quantify chromosome-number differences between monocot hybrids and their parents, applying it to ~200 documented hybrid cases. Analyses reveal homoploid hybrids are most common, with growth habit influencing cytogenetic outcomes, and challenge the view that polyploidy predominates in hybrid formation. The PDI framework provides a standardized tool for assessing cytogenetic constraints on hybridization across monocots.

hybridization chromosome number divergence homoploid polyploid monocots
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