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<title>bioRxiv Subject Collection: Plant Biology</title>
<link>https://biorxiv.org</link>
<description>
This feed contains articles for bioRxiv Subject Collection "Plant Biology"
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<title>bioRxiv</title>
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<link>https://www.biorxiv.org</link>
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<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.10.750615v1?rss=1">
<title>
<![CDATA[
Managing the genetic diversity of Dioscorea yams for adaptation to climate change 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.10.750615v1?rss=1
</link>
<description><![CDATA[
Understanding adaptation to environmental variation is fundamental to climate-resilient agriculture. Here, we analyzed a georeferenced collection of 167 Dioscorea accessions spanning a wide range of bioclimatic and biophysical variation, from dry sahelian environment to rainforest environment. Genome-wide association analyses revealed that the genetic architecture of environmental adaptation is largely driven by large-effect loci, although precipitation-related traits were associated with many small-effect loci. This mixed architecture could lead to multiple breeding strategies, including marker-assisted backcrossing and the targeted use of wild and semi-wild relatives. We identified a core collection of accessions that captures much of the genetic and environmental diversity, and highlighted accessions as potential parents for abiotic stress tolerance. Projections under future climate scenarios using genomic offset identified regions and accessions at elevated risk of maladaptation, as well as others with broad adaptive potentiality. Maximizing the use of available material may facilitate the development of climate-resilient cultivars.
]]></description>
<dc:creator><![CDATA[ Adhikari, B., Akakpo, R., Halpin-McCormick, A., Soto Gomez, M., Scarcelli, N., Alix, K., Vigouroux, y., Kantar, M. B. ]]></dc:creator>
<dc:date>2026-09-13</dc:date>
<dc:identifier>doi:10.64898/2026.09.10.750615</dc:identifier>
<dc:title><![CDATA[Managing the genetic diversity of Dioscorea yams for adaptation to climate change]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.10.750389v1?rss=1">
<title>
<![CDATA[
Plant Acupuncture: a low-cost and open-source device for local mechanical stimulation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.10.750389v1?rss=1
</link>
<description><![CDATA[
Background: Mechanical signals are important regulators of cellular responses in plants. They guide plant development and can activate defense and repair mechanisms. Yet, the molecular mechanisms by which plants perceive, transduce, and interpret mechanical signals are still poorly understood. This is in part due to the lack of methods to apply local, precise and non-damaging mechanical forces to plant cells. Micro-indentation is highly suitable for this purpose, yet available instrumentation is often expensive and difficult to combine with high-resolution microscopy. Results: We designed an open-source and affordable modular indentation device, consisting of 3D printed elements, 3 commercially available piezo motors, and a variety of indentation needles. Due to its modularity, the setup can be readily adapted to meet experimental requirements and works on all microscopes with bespoke adaptors. We show that the setup can be used to explore both rapid and slower touch responses, exemplified by visualizing calcium waves and actin patches induced by touch. We also show that the setup is compatible with various plant species and tissues and can be combined with high-resolution functional imaging. Conclusions: The simple and flexible design of the indentation device presented in this paper ensures that any lab with a 3D printer can build their own setup at low cost and with minimal time investment. The system has a wide range of applications for live plant tissue, making indentation experiments and thereby plant mechanobiology studies, more accessible.
]]></description>
<dc:creator><![CDATA[ Daamen, A., Bellandi, A., Besten, M., Lamers, J., Woudenberg, S., Heijstek, C., Borst, J. W., Borassi, C., Sprakel, J. ]]></dc:creator>
<dc:date>2026-09-13</dc:date>
<dc:identifier>doi:10.64898/2026.09.10.750389</dc:identifier>
<dc:title><![CDATA[Plant Acupuncture: a low-cost and open-source device for local mechanical stimulation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.10.750513v1?rss=1">
<title>
<![CDATA[
Comparative phylogenetic analyses of limestone and non-limestone Begonias in Peninsular Malaysia 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.10.750513v1?rss=1
</link>
<description><![CDATA[
Karsts of Southeast Asia cover ~400,000 km2, with tropical limestone karsts possessing highly biodiverse flora in many, varied microhabitats that are unique from lowland- and hill forests. Begonia L. is a pantropical mega-genus with ~1,550 described species to date, ideal for studying evolutionary patterns and factors driving tropical population- diversity and speciation. Begonias grow on multiple substrates including limestone and granite, sandstone, quartzite, on steep earth slopes and near streams in primary forests. Niche partitioning is commonly observed, resulting in many single-site endemic Begonia species especially on limestone karsts. Molecular phylogenetic analyses were performed on combined chloroplast ndhF-rpl32 and nuclear internal transcribed spacer ITS sequences that included 30 selected Begonia species representing all sections from Peninsular Malaysia (Pen. Msia; ten limestone-, thirteen forest- and seven granite species). Results of Bayesian inference and molecular dating showed evolution of Begonia from continental Asia into Pen. Msia during the mid-late Miocene period of ~ 10.65 mya (9.7 - 12.12 mya), with at least two independent dispersal events observed by the early splitting of the ancestral lineage into two major clades i.e. clades A- and B at 9.85 mya (HPD 9.7-10.36 mya) and 8.85 mya (HPD 7.7-11.23 mya) respectively; followed by multiple speciation events colonizing limestone- as well as non-limestone (forest, granite) habitats. Begonia speciation into limestone habitats occurred three times, with climate indicated as more important factor than substrate in diversification - clade A contained the Indian/Continental Asia (monsoon climate) species, i.e. Sect. Platycentrum and Parvibegonia, resolved slightly older than clade B where Sect. Petermannia, Jackia and Ridleyella formed a Sunda Shelf (equatorial climate) centred group. Strong population structuring by locality, common in Begonias, was also observed (e.g. B. kingiana, B. foxworthyi, B. nurii, B. sinuata), regardless of distribution. However, for widespread species (B. kingiana, B. sinuata) behavioural (physiological) inertia on niche evolution, and/or genome size variation and dynamics (genome evolution) may potentially explain species cohesion. Phylogenetics relationships are mostly concordant with current sectional classifications excepting Sect. Parvibegonia, Sect. Diploclinium and two paraphyletic species complexes. Conservation of Begonias and biodiverse limestone karsts in Malaysia remains concerning due to ongoing threats (large-scale quarrying/mining, human encroachment), and most are still without any legal protection.
]]></description>
<dc:creator><![CDATA[ Kiew, R., Fareed, F. S., FOONG, L. C., Tam, S. M. ]]></dc:creator>
<dc:date>2026-09-13</dc:date>
<dc:identifier>doi:10.64898/2026.09.10.750513</dc:identifier>
<dc:title><![CDATA[Comparative phylogenetic analyses of limestone and non-limestone Begonias in Peninsular Malaysia]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.10.750641v1?rss=1">
<title>
<![CDATA[
Mark-Release-Recapture Experiments in a North Sumatra Oil Palm Plantation: Assessing the Impact of Super-Male Planting Material on Fruit Set and Elaeidobius kamerunicus population size 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.10.750641v1?rss=1
</link>
<description><![CDATA[
Yield improvement is a main issue in the oil palm industry. Several ways to achieve this goal are possible, like, for instance, improving fruit set. Here we explore a planting strategy to increase two major factors influencing pollination; i.e. (1) the number of individuals of its main pollinator, Elaeidobius kamerunicus Faust, and (2) pollen availability, by mixing oil palm planting material, usually highly feminine, with a new oil palm material, the "super-male" (SM) planting material, with a high ratio of male inflorescences. We design and study a field trial comprising extremely feminine planting material mixed with different SM densities. Using Mark-Release-Recapture experiments we estimate the average dispersal of the pollinators over three different periods of the year, from 2017 till 2022. Second, using phenological data recorded over the same period, we studied the impact of the SM planting density on the population size of the pollinators. Finally, we assess the impact over time of different SM planting densities on the fruit set, the fruit-to-bunch, and the number of trapped wild pollinators. The combination of SM material with a highly feminine planting material provides very promising results in terms of fruit set, linked with increased pollinator population and pollen availability, demonstrating its potential for application in oil palm plantations.
]]></description>
<dc:creator><![CDATA[ DUMONT, Y., BEAUDOIN-OLLIVIER, L., REY, H., LABEYRIE, A., MADEC, C., DOIZY, A., SYAHPUTRA, I., AFANDI, D., JACOB, F. ]]></dc:creator>
<dc:date>2026-09-13</dc:date>
<dc:identifier>doi:10.64898/2026.09.10.750641</dc:identifier>
<dc:title><![CDATA[Mark-Release-Recapture Experiments in a North Sumatra Oil Palm Plantation: Assessing the Impact of Super-Male Planting Material on Fruit Set and Elaeidobius kamerunicus population size]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750302v1?rss=1">
<title>
<![CDATA[
Sugar metabolism drives shoot branching by repressing BRC1 through miR319-targeted TCP4 in Rosa. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750302v1?rss=1
</link>
<description><![CDATA[
The coupling between sugar availability and shoot branching is well established, yet the underlying molecular mechanisms remain largely unknown. Here, using genome-wide profiling, we characterized the sugar signalling pathways by identifying 10 miRNAs repressed by glycolysis, the tricarboxylic acid (TCA) cycle, and/or the oxidative pentose phosphate pathway (OPPP) in rose buds. Focusing on RhmiR319, a miRNA repressed under active sugar metabolism, we demonstrate that disruption of both glycolysis/the TCA cycle and the OPPP induces the RhmiR319 accumulation, leading to the concomitant repression of its targets, RhTCP4a and RhTCP4b. We additionally reveal that the miR319/TCP4 module regulates shoot branching in Arabidopsis, as miR319 overexpression impairs shoot branching, whereas TCP4 promotes it. Altered branching patterns in Rose and Arabidopsis were associated with the expression of the branching integrator BRC1. Finally, we provide molecular evidence supporting that RhTCP4a/b directly binds to the RhBRC1 promoter and represses its transcription. Together, these results establish the miR319-TCP4-BRC1 regulatory module as a key component in the regulation of shoot branching in response to sugar status. We propose that the miR319-TCP4-BRC1 module is conserved between annual and perennial species and may integrate multiple hormonal and metabolic signals to shape shoot branching in plants.
]]></description>
<dc:creator><![CDATA[ Gouaille, L., Mallet, J., Legrix, J., Porcher, A., Oge, L. a., Perez, T., Kraft, J., Perez-garcia, M.-d., Leduc, N., Barbier, F., Laufs, P., Sakr, S., Le Gourrierec, J. ]]></dc:creator>
<dc:date>2026-09-13</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750302</dc:identifier>
<dc:title><![CDATA[Sugar metabolism drives shoot branching by repressing BRC1 through miR319-targeted TCP4 in Rosa.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.10.750567v1?rss=1">
<title>
<![CDATA[
H3K4me3 recruits the chromatin remodeling DILL-PICKLE-PEPPERCORN complexes to promoters in plants 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.10.750567v1?rss=1
</link>
<description><![CDATA[
The plant CHD chromatin remodeler PICKLE (PKL) is a master regulator of cellular identity and differentiation, controlling developmental, hormonal and stress-response processes. Yet the molecular mechanisms underlying its function remain unclear. Here, we show that PKL forms three complexes, each composed of a protein of previously unknown function and one of three mutually exclusive novel DNAJ proteins that recruit HSP70-1. Simultaneous loss of all three DNAJs phenocopies the pkl mutant, indicating functional redundancy among PKL complexes. In vitro activity assays and cryo-electron microscopy reveal that PKL clamps nucleosomal DNA via its ATPase motor domain and recognizes H3K4me3 through its double chromodomain. Genome-wide profiling shows that H3K4me3 recognition positions PKL complexes at genic promoters to bidirectionally fine-tune gene expression. Together, these results provide structure-function insight into PKL recruitment and its control of developmental gene expression, and reveal a chaperone-coupled complex assembly that offers a broader perspective on how chaperone networks may support chromatin remodeling complexes across eukaryotes.
]]></description>
<dc:creator><![CDATA[ BISCHOF, S., Du, J., Chen, S., Linares, A., Rannou, E., Haerter, N. C., Champeryroux, C., Schwarz, A., Prellion, E., Giraldo-Fonseca, A., Pfammatter, S., Chen, L., Kang, S., Xie, G., Liu, R., Long, J. A. ]]></dc:creator>
<dc:date>2026-09-13</dc:date>
<dc:identifier>doi:10.64898/2026.09.10.750567</dc:identifier>
<dc:title><![CDATA[H3K4me3 recruits the chromatin remodeling DILL-PICKLE-PEPPERCORN complexes to promoters in plants]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750326v1?rss=1">
<title>
<![CDATA[
MYB28 and MYB29 transcription factors regulate iron homeostasis and iron-mobilizing coumarin biosynthesis in Arabidopsis thaliana 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750326v1?rss=1
</link>
<description><![CDATA[
Iron (Fe) deficiency is a major constraint for plant growth and triggers extensive physiological and transcriptional reprogramming to maintain Fe homeostasis. Here, we identify the glucosinolate-associated transcription factors MYB28 and MYB29 as previously unrecognized regulators of Arabidopsis thaliana adaptation to Fe deficiency. Across various growth systems, loss of MYB28 increased sensitivity to Fe deficiency, whereas the myb28myb29 double mutant displayed stronger chlorosis, reduced root growth and impaired biomass accumulation, indicating cooperative but unequal functions of these transcription factors. Despite their enhanced Fe-deficiency phenotype, double mutant plants accumulated higher Fe levels in roots and exhibited stronger induction of canonical Fe-deficiency responses, suggesting impaired Fe utilization or distribution rather than defective Fe uptake. RNA-seq revealed extensive transcriptional reprogramming under Fe deficiency, with pronounced deregulation of genes involved in Fe homeostasis, redox processes and growth, particularly in the double mutant. Among these, SCOPOLETIN 8-HYDROXYLASE (S8H) emerged as a major target gene of MYB28. The expression of S8H was almost abolished in myb28 and myb28myb29 mutants, whereas expression of other coumarin biosynthetic genes remained largely unaffected. Promoter activation assays demonstrated that MYB28 activates the S8H promoter, and metabolic analyses showed accumulation of scopolin together with reduced fraxin levels in the mutants, consistent with impaired S8H activity. Collectively, our results identify MYB28 as a key regulator linking specialized metabolism to Fe homeostasis through control of coumarin biosynthesis, thereby expanding the biological functions of MYB28 and MYB29 transcription factors.
]]></description>
<dc:creator><![CDATA[ Marin-Pena, A. J., Coleto, I., Urbano-Gamez, J. A., Rossille, A., Tazueco, D., Watanabe, S., Salazar-Gutierrez, D., Santiago, A., Tian, M.-B., Roschzttardtz, H., Medina, J., Matus, J. T., Dubos, C., Marino, D. ]]></dc:creator>
<dc:date>2026-09-13</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750326</dc:identifier>
<dc:title><![CDATA[MYB28 and MYB29 transcription factors regulate iron homeostasis and iron-mobilizing coumarin biosynthesis in Arabidopsis thaliana]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750010v1?rss=1">
<title>
<![CDATA[
Tissue-resolved photosynthetic responses in living leaves revealed by microscopic imaging-pulse-amplitude-modulation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750010v1?rss=1
</link>
<description><![CDATA[
Leaves of terrestrial plants possess heterogeneous anatomical structures composed of multiple cell layers. Although biochemical differences among leaf tissues have been inferred from protein analyses and anatomical studies, direct comparisons of dynamic photochemical responses among tissues while preserving their spatial context remain challenging. Leaves experience intrinsically heterogeneous environments because incident light enters primarily from above and propagates through complex internal leaf structures. Therefore, analyzing photosynthetic activity at the tissue and cellular levels is essential for understanding how photosynthesis operates within structurally heterogeneous leaves. Here, we combined live leaf-section imaging with microscopic Imaging-PAM chlorophyll fluorescence measurements to analyze photochemical responses at the tissue level in living leaf sections. In dorsiventral dicot leaves, palisade tissues exhibited a higher effective PSII quantum yield [Y(II)] and more rapid induction of regulated energy dissipation [Y(NPQ)] than spongy tissues, indicating higher photosynthetic capacity and photoprotective activity. In contrast, rice leaves, which lack palisade-spongy differentiation, showed uniform photochemical responses along the adaxial-abaxial axis. In the C4 plant finger millet, mesophyll and bundle sheath cells displayed distinct photochemical responses consistent with their functional differentiation in C4 photosynthesis. These results demonstrate that photosynthetic responses are spatially organized according to leaf anatomical structure. Although section-based measurements do not reproduce the native optical and gas environments of intact leaves, they enable the comparison of intrinsic tissue-specific photochemical properties under approximately equivalent illumination. The present approach enables tissue-resolved chlorophyll fluorescence analysis in living leaves, providing a new framework for investigating how leaf architecture shapes the spatial organization of photosynthetic activity.
]]></description>
<dc:creator><![CDATA[ Kato, Y., Takeuchi, K., Harimoto, S., Kobayashi, K., Ifuku, K. ]]></dc:creator>
<dc:date>2026-09-13</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750010</dc:identifier>
<dc:title><![CDATA[Tissue-resolved photosynthetic responses in living leaves revealed by microscopic imaging-pulse-amplitude-modulation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.10.750548v1?rss=1">
<title>
<![CDATA[
Live confocal imagining of cellular touch responses upon local quantifiable mechanical stimulation in plant cells 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.10.750548v1?rss=1
</link>
<description><![CDATA[
Plant cells grow and differentiate in an ever-changing environment characterized by transient signals and stimuli. The ability of plant cells to perceive, integrate, and dynamically respond to these stimuli underpins a plant adaptation and survival. Among the plethora of complex stimuli plant cells are exposed to, several stimuli have a mechanical component, for example, wind, touch, contact with insects, penetration of pathogens, and even intrinsic mechanical stresses arising during tissue growth. Despite the presence of a load-bearing cell wall that separates cells from the environment and fixes their location within a tissue, plant cells are responsive to mechanical stimuli. However, several questions remain unanswered around how mechanical stimuli are perceived and translated into cellular responses. Here we establish a system enabling application of quantifiable localized mechanical stress while simultaneously capturing cellular responses with high spatio-temporal resolution using confocal imaging. We show that this system enables estimation of locally applied pressure and provides access to the temporal and spatial details of subcellular events in intact living tissues upon touch. We propose that observing these subcellular events at high spatiotemporal resolution and linking their dynamics to the intensity of mechanical stimuli may uncover the molecular mechanisms underlying plant cell responses to touch.
]]></description>
<dc:creator><![CDATA[ Bellandi, A., Lionnet, C., Arico, D., German, N., Lenz, M. O., Kirchhelle, C., Loisy, I., Hamant, O. ]]></dc:creator>
<dc:date>2026-09-13</dc:date>
<dc:identifier>doi:10.64898/2026.09.10.750548</dc:identifier>
<dc:title><![CDATA[Live confocal imagining of cellular touch responses upon local quantifiable mechanical stimulation in plant cells]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-13</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749878v1?rss=1">
<title>
<![CDATA[
Distinct Temporal Responses to Xanthomonas translucens Strains Shape Bacterial Leaf Streak Development in Triticale 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749878v1?rss=1
</link>
<description><![CDATA[
Bacterial leaf streak caused by Xanthomonas translucens threatens cereal production, however, the temporal coordination of host transcriptional responses during resistant and susceptible interactions in polyploid crops remains partially understood. Here, we used time-resolved transcriptomics to characterize responses of synthetic hexaploid triticale to two X. translucens pv. undulosa strains that produce contrasting disease outcomes. The resistant interaction with non-virulent LB10 showed a strong early transcriptional response that subsequently declined, whereas responses to the virulent strain P3 progressively intensified as water-soaking symptoms developed. Analysis of syntenic A-, B-, and R-subgenome homoeologs revealed extensive regulatory asymmetry, with R-subgenome homoeologs disproportionately represented among transcriptionally suppressed genes. Despite their conserved coding sequences, homoeologs often showed divergent transcriptional responses during infection, whereas greater similarity in upstream regulatory regions was associated with more coordinated responsive trajectories. We next examined pathogen-mediated transcriptional regulation through transcription activator-like (TAL) effectors. Among eight TAL effector templates identified in LB10 and P3, TAL5-associated predicted targets showed the strongest preferential induction during P3 infection. Disruption of TAL5 in P3 predominantly reduced host gene expression, including genes involved in immune signaling, cell wall-associated defense and photosynthetic function, accompanied by reduced maximum photosystem II quantum efficiency at 72 h post-inoculation. Together, our results show that bacterial leaf streak outcomes are shaped by temporally distinct host responses and pathogen effector-associated transcriptional reprogramming, providing insight into the dynamic regulation underlying cereal-Xanthomonas interactions.
]]></description>
<dc:creator><![CDATA[ Hasan, F., Manan, F., Fernandez, E. C., Wu, S., Dhungana, B., Yan, C., Shi, G., Liu, Z., Liang, Z. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749878</dc:identifier>
<dc:title><![CDATA[Distinct Temporal Responses to Xanthomonas translucens Strains Shape Bacterial Leaf Streak Development in Triticale]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750047v1?rss=1">
<title>
<![CDATA[
Emergence of tolerance and avoidance strategies from local and systemic responses to nitrogen: insights from modelling of auxin-mediated root plasticity 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750047v1?rss=1
</link>
<description><![CDATA[
Understanding how root phenotypic plasticity enhances resource-use efficiency can help understand the outcomes of plant competition and identify suitable genotypes for medium- to low-input agricultural systems. Auxin regulates multiple root growth processes, including the root architectural responses to nitrogen (N). We explored the extent to which auxin-mediated local and systemic responses to external and internal N influences plant N uptake and use, using a functional-structural-plant (FSP) modelling approach. A simplified auxin module was developed at the level of the organ and integrated into an FSP model to represent physiological plastic root responses to N. Model performance was evaluated against experimental data. We then ran simulations under various N conditions with local or systemic responses enabled or disabled, to quantify their contribution to N uptake and use. Simulations showed that local auxin responses enhanced N uptake by distributing more roots towards deeper soil layers and increased N forage, thereby avoiding N stress. Systemic auxin responses reduced N uptake by distributing more roots near the top soil layers, which reduced plant size and N demand, thereby enhancing stress tolerance. This points to a trade-off in N uptake between the tolerance and avoidance strategies, which can be traced back to biomass and N investment resulting from source-sink relationships in the plant. Representing hormone-mediated root plasticity in an FSP model provides mechanistic insights into plant strategies for resource capture.
]]></description>
<dc:creator><![CDATA[ Lu, J., Wang, J., Morales, A., Evers, J. B. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750047</dc:identifier>
<dc:title><![CDATA[Emergence of tolerance and avoidance strategies from local and systemic responses to nitrogen: insights from modelling of auxin-mediated root plasticity]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749782v1?rss=1">
<title>
<![CDATA[
First case of three-way multiple herbicide resistance in Amaranthus palmeri outside the Americas: Resistance mechanisms and alternative management strategies 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749782v1?rss=1
</link>
<description><![CDATA[
The rapid spread of herbicide-resistant Amaranthus palmeri S. Watson across the Mediterranean region poses a severe threat to crop production. This study characterizes the resistance profile of an A. palmeri population from Gonen, Israel, which survived multiple post-emergence herbicide applications in maize. Greenhouse dose-response and screening trials were conducted across four modes of action (MOAs). The Gonen population exhibited three-way multiple resistance to acetolactate synthase (ALS), photosystem II (PSII) and 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors, marking the first confirmed case outside the Americas. High-level resistance was demonstrated for the ALS inhibitor foramsulfuron and the PSII inhibitor metribuzin, maintaining 40-70% and 80-100% survival, respectively, at double the labelled field rate. Sequencing of the ALS gene revealed a Trp574 to Leu substitution in resistant plants. The population showed differential PSII sensitivity, as atrazine provided complete control despite high metribuzin survival. Sequencing revealed no known psbA mutations, and malathion pre-treatment caused only a slight reduction in metribuzin survival. Partial resistance was observed for the HPPD inhibitor tembotrione (30-50% survival), where malathion pre-treatment reduced survival by 20-30%. In contrast, pre-mergence applications of S-metolachlor (very long chain fatty acid inhibitor), isoxaflutole (HPPD inhibitor), and a fomesafen + terbutryn mixture [protoporphyrinogen oxidase (PPO) + PSII inhibitors] significantly reduced emergence. These findings confirm multiple-resistant A. palmeri in the region and highlight the urgent need for integrated weed management incorporating effective pre-emergence herbicides rather than relying solely on post-emergence chemical control in summer cereal rotations.
]]></description>
<dc:creator><![CDATA[ Matzrafi, M., Abu-Nassar, J., Paporisch, A. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749782</dc:identifier>
<dc:title><![CDATA[First case of three-way multiple herbicide resistance in Amaranthus palmeri outside the Americas: Resistance mechanisms and alternative management strategies]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.744716v1?rss=1">
<title>
<![CDATA[
The transcription factor ESR2/DRNL/BOL differentially regulates de novo organogenesis, regeneration, and lateral root development in Arabidopsis thaliana 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.744716v1?rss=1
</link>
<description><![CDATA[
Plant regeneration requires coordinated transcriptional and hormonal regulation to re-establish organ identity. The AP2/ERF transcription factor ENHANCER OF SHOOT REGENERATION 2 /DORNROESCHEN-LIKE / BOLITA (ESR2/DRNL/BOL) expressed in aerial organ founder cells promotes shoot formation, but its broader role across organogenic contexts remains unclear. Here, using loss-of-function and inducible overexpression lines of Arabidopsis thaliana, we demonstrate that ESR2 exerts context-dependent and antagonistic effects on shoot and root development. ESR2 activation promotes shoot and aerial-like tissue formation and enhances callus proliferation, particularly under cytokinin-rich conditions. Conversely, ESR2 suppresses or delays multiple de novo root formation programs, including adventitious, basal, and regenerated roots, while its loss enhances root initiation and growth. Expression analyses reveal that ESR2 promoter activity is found at de novo formed basal and adventitious root primordia and emerged root apical meristems, suggesting a role in conferring regenerative competence while restricting their developmental progression. Moreover, it is expressed in newly established quiescent centers of lateral roots in intact plants and the loss of ESR2 function strongly and negatively affects lateral root initiation, revealing an unanticipated developmental role of ESR2 and its requirement for lateral root formation. Together, these findings identify ESR2 as a shared molecular regulator governing early organogenesis in intact plants and plant explants; it establishes an aerial organ fate bias while maintaining the competence for -and limiting the progression of- de novo root development in explants.
]]></description>
<dc:creator><![CDATA[ Guerrero-Largo, H., Ruiz-Cortes, B., Elizarraraz-Anaya, M. I. C., Martinez-Perez, C. M., Jimenez-Jimenez, H., Dubrovsky, J. G., Marsch-Martinez, N. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.744716</dc:identifier>
<dc:title><![CDATA[The transcription factor ESR2/DRNL/BOL differentially regulates de novo organogenesis, regeneration, and lateral root development in Arabidopsis thaliana]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750243v1?rss=1">
<title>
<![CDATA[
Plant-adapted OTO staining improves ultrastructural imaging by transmission electron microscopy 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750243v1?rss=1
</link>
<description><![CDATA[
Transmission electron microscopy (TEM) is widely used to examine plant cellular ultrastructure, but sample preparation remains challenging because polysaccharide-rich cell walls, large vacuoles and complex membrane systems compromise staining and structural preservation. Here, we developed a plant-adapted TEM preparation method based on a modified osmium-thiocarbohydrazide-osmium (OTO) staining workflow combined with optimized washing, dehydration and resin infiltration. Using tomato roots and leaves, we show that the optimized method produces cleaner backgrounds, better-defined cellular boundaries and improved preservation of cellular morphology compared with conventional preparation. Fine membrane-associated structures, including mitochondrial cristae, chloroplast grana and stroma lamellae, nuclear membranes and other endomembrane structures, were more clearly resolved, while staining-related precipitates and diffuse background artifacts were reduced. This method provides a practical approach for high-contrast TEM imaging of plant tissues and ultrastructural analysis of plant cells and organelles.
]]></description>
<dc:creator><![CDATA[ Yao, H., Jin, X., Sun, M., Cheng, H., Liao, Y., Jiang, Y., Zhao, H., Zhou, H. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750243</dc:identifier>
<dc:title><![CDATA[Plant-adapted OTO staining improves ultrastructural imaging by transmission electron microscopy]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749967v1?rss=1">
<title>
<![CDATA[
Lysine biosynthesis impairment shapes heat-stress acclimation through metabolic and transcriptional reprogramming in Arabidopsis thaliana 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749967v1?rss=1
</link>
<description><![CDATA[
Global warming is increasing the frequency and intensity of high-temperature episodes, limiting plant productivity. However, the molecular mechanisms integrating primary metabolism with the heat stress response remains poorly understood. Here, we show that lysine biosynthesis contributes to the coordination of physiological, metabolic and transcriptional responses to heat stress in Arabidopsis thaliana. We compared wild-type, the lysine-biosynthesis mutant dapat, and the salicylic acid (SA)-biosynthesis and signaling mutants sid2-1 and npr1-3 under prolonged warming (6C above control for 7 days) and heat shock (38C for 6 h), followed by recovery. We assessed growth, gas exchange, photosynthetic performance, free SA, salicylic acid glucoside (SAG), salicylic acid glucose ester (SGE), and total SA content, primary metabolite profiles, heat-stress-responsive gene expression and transcriptome-wide changes by RNA sequencing. Before heat stress, dapat mutant presented a distinct metabolic state, marked by amino-acid accumulation, altered organic-acid profiles, reduced soluble sugars and elevated endogenous SA. This metabolic configuration persisted during prolonged warming, whereas WT and SA-pathway mutants underwent more dynamic reprogramming. Heat shock, by contrast, elicited a more convergent response across genotypes. Despite reduced basal PSII efficiency, dapat maintained photosynthetic performance during prolonged warming and recovered. Its transcriptional response, however, differed from that of WT and SA-pathway mutants: selected heat-responsive genes were constitutively or more strongly expressed, whereas some canonical heat-stress regulators showed weaker induction after heat shock. RNA-seq further revealed a largely conserved core heat-shock response but genotype-dependent regulation of defense, hormone and amino-acid-metabolism programs, particularly during recovery. Together, these findings indicate that impaired DAPAT activity establishes a metabolically primed but energetically constrained state that reshapes gas exchange, photosynthetic acclimation and heat-responsive transcription. Lysine homeostasis therefore emerges as a regulatory node linking primary metabolism and SA accumulation with SA-dependent and SA-independent components of heat-stress acclimation.
]]></description>
<dc:creator><![CDATA[ Gouveia, D. G., Westhoff, P., Barrios, W. E. B., Perrar, M., Flachbart, S., Martins, A. O., dos Reis, P. B., Nunes-Nesi, A., Zeier, J., Weber, A. P. M., Araujo, W. L. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749967</dc:identifier>
<dc:title><![CDATA[Lysine biosynthesis impairment shapes heat-stress acclimation through metabolic and transcriptional reprogramming in Arabidopsis thaliana]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750043v1?rss=1">
<title>
<![CDATA[
The miR319-targeted TCP transcription factors play crucial roles in the establishment of Arabidopsis thaliana shoot architecture in response to carbon and nitrogen availability. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750043v1?rss=1
</link>
<description><![CDATA[
Shoot branching is a highly plastic developmental process that allows plants to adjust their architecture to environmental conditions, such as carbon and nitrogen availability. Although the class II TCP transcription factor BRANCHED1 is a well-established repressor of shoot branching, the contribution of other TCP factors during this process remains less well understood. Here, we show that the miR319-targeted TCP module promotes shoot branching in Arabidopsis thaliana. Overexpression of miR319 reduced rosette branch production, whereas repression of TCP3 activity or triple knockout (KO) mutation in TCP3, TCP4 and TCP10 inhibited branching. Conversely, expression of a miR319-resistant TCP3 triggered a highly branched phenotype, indicating that TCP3 and related miR319 targets act as positive regulators of shoot branching. Genetic analysis with the strigolactone-deficient max4 mutant showed that strigolactones mediate, at least partly, the reduced branching observed in the miR319 overexpressing line and in the tcp3,4,10 triple mutant. Transcriptomic and DNA-binding analyses indicated indirect effect of TCP3 on strigolactone biosynthesis genes. Instead, miR319 overexpression increased the sensitivity of branching to nitrogen limitation and reduced nitrate uptake, thereby increasing the expression of strigolactone synthesis genes. We further show that carbon starvation reduced the transcription levels of miR319-targeted TCPs, independently of miR319 accumulation, and that TCP3 may connect carbon availability to sugar signalling via HEXOKINASE1. Together, our results identify the miR319-targeted TCP module as a positive regulator of shoot branching that links plant architecture to carbon and nitrogen availability.
]]></description>
<dc:creator><![CDATA[ Barbier, F., Amor, I., Pham, T. D., Perez, T., Luo, B., Tang, L., Silvestri, A., Rubio Somoza, I., Nicolas, M., Cubas, P., Alvarez, J. P., Fichtner, F., Beveridge, C. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750043</dc:identifier>
<dc:title><![CDATA[The miR319-targeted TCP transcription factors play crucial roles in the establishment of Arabidopsis thaliana shoot architecture in response to carbon and nitrogen availability.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.05.749627v1?rss=1">
<title>
<![CDATA[
An indirect organogenesis-based citrus transformation system monitored using visible reporter markers 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.05.749627v1?rss=1
</link>
<description><![CDATA[
Genetic transformation of citrus is essential for functional genomics and trait improvement, yet remains limited by prolonged regeneration cycles, genotype-dependent responses, and inefficient screening of transformed tissues. Here, we established an Agrobacterium-mediated indirect organogenesis-based transformation system for Carrizo citrange and evaluated two visible reporter systems, the anthocyanin regulator ROSEA1 and the betalain biosynthetic cassette RUBY, for monitoring transformed tissues throughout regeneration. An optimized regeneration protocol enabled visible callus ini-tiation within 7 days following a 5-day pre-culture treatment and recovery of PCR-confirmed transgenic plantlets within 5 months. Both visible reporters were compatible with callus development and shoot regeneration throughout the indirect organogenesis workflow. During callus proliferation, visible pigmentation closely corresponded with GFP fluorescence, enabling rapid, non-destructive identification of transformed tissues. However, reporter performance diverged during shoot regeneration: RUBY maintained stable pigmentation throughout regeneration, whereas ROSEA1-associated pigmentation progressively declined despite continued GFP fluorescence. Consequently, RUBY exhibited a 4.7-fold higher pigmenta-tion-based detection rate than ROSEA1 at the shoot stage and showed closer agreement with GFP-based detection. Putative transgenic events were confirmed by PCR in independent lines of both constructs, together with GFP fluorescence in leaves and root tips. Together, these findings establish an efficient indirect organogenesis-based transformation platform for citrus and demonstrate that both ROSEA1 and RUBY are effective visual reporters during callus proliferation, whereas RUBY provides more reliable visual identification during shoot regeneration and plant recovery.
]]></description>
<dc:creator><![CDATA[ Tanwir, S. E., Jiang, T., Karn, A., Messina, C., Huo, H. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.05.749627</dc:identifier>
<dc:title><![CDATA[An indirect organogenesis-based citrus transformation system monitored using visible reporter markers]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.06.749702v1?rss=1">
<title>
<![CDATA[
Environmental factors and microbe-microbe interactions drive the structure of the core microbiota of terrestrial microalgae 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.06.749702v1?rss=1
</link>
<description><![CDATA[
Plants and other photosynthetic organisms interact with their environment and surrounding microbiota through specialized associations. A global core microbiota has been proposed at high taxonomic levels, such as the order level. However, it remains unclear which environmental factors and how microbe-microbe interactions drive variation of this core microbiota at lower taxonomic resolution. Here, we leveraged the environmental diversity of 141 sites across the southwest of France to characterize algal populations, and their associated bacterial and fungal microbiota. We then performed a meta-analysis, combining these data with published datasets to formally identify the global core microbiota of terrestrial photosynthetic organisms, which comprises seven bacterial and five fungal orders. We next investigated diversity within this core microbiota and the environmental drivers shaping site-specific community composition. While environmental factors have a low impact on the total relative abundance of core orders, the core microbiota at the ASV-level is impacted by climatic factors, edaphic factors, and plant community descriptors. Using interaction network analysis, we finally explored how microbe-microbe interactions contribute to the assembly of stable core communities. Our results show that core ASVs occupy central positions in algal-associated microbial networks and that distinct core orders drive site-specific variation in core microbiota structure. Together, these findings highlight the importance of both environmental context and microbial interactions in shaping the composition and stability of the core microbiota associated with photosynthetic organisms.
]]></description>
<dc:creator><![CDATA[ Garrigues, V., Guan, R., Preteseille, N., Leccia, I., Wagner, E., Roux, F., Duran, P. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.06.749702</dc:identifier>
<dc:title><![CDATA[Environmental factors and microbe-microbe interactions drive the structure of the core microbiota of terrestrial microalgae]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.06.749736v1?rss=1">
<title>
<![CDATA[
Quantitative Morphology of Stump Sprouts Reveals a Common Growth Axis and a Reproducible Basal Longitudinal Cavity in an Ornamental Cherry 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.06.749736v1?rss=1
</link>
<description><![CDATA[
Stump sprouts may originate from pre-existing preventitious buds or adventitious buds, but whether these developmental origins produce distinguishable whole-shoot phenotypes remains unclear. We examined all visible sprouts on a single stump of an ornamental cherry (Prunus sp.) and measured four preselected traits: fresh weight, basal diameter, shoot length, and node number. The initial census comprised 35 sprouts. These traits were strongly correlated and were dominated by a common multivariate growth axis. Unsupervised mixture modelling identified statistical components within the morphological distribution, but these components could not be assigned to preventitious or adventitious developmental origins. During subsequent examination, we identified an unexpected basal longitudinal cavity and recorded its presence and axial length. The cavity occurred in 23 of 31 sectioned sprouts (74%). After complete removal of the initial sprout population, all visible sprouts were collected again seven days later. This second cohort comprised 22 substantially smaller sprouts but reproduced the coordinated whole-shoot growth structure. Remarkably, the basal longitudinal cavity occurred in 16 of 22 sprouts (73%), nearly identical to its initial frequency despite the marked difference in shoot size. Cavity presence was largely independent of overall shoot size, whereas cavity length increased with size among cavity-positive sprouts. Thus, gross quantitative morphology did not discriminate the hypothesized developmental origins, whereas basal anatomy revealed a reproducible feature potentially informative of developmental history. Direct anatomical and ontogenetic analyses are required to determine whether the basal longitudinal cavity is associated with sprout origin.
]]></description>
<dc:creator><![CDATA[ OGATA, N. N., OGATA, N. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.06.749736</dc:identifier>
<dc:title><![CDATA[Quantitative Morphology of Stump Sprouts Reveals a Common Growth Axis and a Reproducible Basal Longitudinal Cavity in an Ornamental Cherry]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750280v1?rss=1">
<title>
<![CDATA[
Genomic and ecological characterization of unclassified tetraploid Echinochloa plants distributed in northern Japan 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750280v1?rss=1
</link>
<description><![CDATA[
Understanding the evolutionary origins of globally noxious weeds provides insights into the genetic background of weediness. Among species of Echinochloa, the hexaploid E. crus-galli was previously thought to have arisen through hybridization and allopolyploidization between tetraploid E. oryzicola and an undiscovered diploid species, although they exhibit marked differences in both ecological and morphological characteristics. Recently, in Japan, unknown tetraploid Echinochloa plants were discovered that exhibit distinct ecological and morphological characteristics from those of E. oryzicola, with some traits showing greater similarity to those of E. crus-galli. In this study, we investigated the relationships between well-known Echinochloa species and these unknown tetraploid plants, hereafter referred to as ''ninja''. Subgenome-based read mapping analysis and phylogenetic analysis revealed that ninja possesses a distinct genomic composition, while showing close relationships to E. oryzicola in both its chloroplast and nuclear genomes. Furthermore, the identification of a very small number of ninja x E. oryzicola hybrids among field-collected individuals suggests that these two species rarely hybridize in the wild. Although ninja and E. oryzicola showed similar genomic compositions, ninja has a broader habitat range, partially overlapping with that of E. oryzicola and extending into areas occupied by E. crus-galli. Our findings indicate the possibility that hexaploid E. crus-galli may have originated from a tetraploid Echinochloa species other than E. oryzicola.
]]></description>
<dc:creator><![CDATA[ Kubo, T., Ikeda, H., Yasuda, K., Kurokawa, S. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750280</dc:identifier>
<dc:title><![CDATA[Genomic and ecological characterization of unclassified tetraploid Echinochloa plants distributed in northern Japan]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750206v1?rss=1">
<title>
<![CDATA[
Protein-independent regulation by transgene-derived small interfering RNAs rewires endogenous regulatory networks to enhance plant growth, architecture, and drought performance 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750206v1?rss=1
</link>
<description><![CDATA[
Plants produce diverse small interfering RNA (siRNA) molecules that modulate development, environmental responses, and immunity. Although transgene-derived siRNAs are traditionally viewed as mediators of gene silencing, whether they can actively regulate endogenous host pathways remains largely unexplored. Previously obtained Arabidopsis, wheat, and soybean plants expressing the sunflower gene encoding the transcription factor HaHB4 exhibited water deficit tolerance. Here, we show that expressing inverted-repeat constructs that generate HaHB4-derived siRNAs without producing the HaHB4 protein bypasses transgenic growth penalties and instead enhances vegetative vigor and reproductive performance. In Arabidopsis, these DCL-dependent siRNA-producing lines exhibited enhanced root growth, increased stem and pith areas, increased cauline branching, and higher seed yield under both optimal and water-limiting conditions. Transcriptomic analysis revealed convergent repression of biotic stress-related genes, accompanied by increased bacterial susceptibility and reduced sensitivity to salicylic acid-mediated growth inhibition, suggesting an altered balance between immunity and growth. Functional characterization of candidate endogenous HD-Zip I targets further showed that athb20 and athb53 mutants recapitulated the increased stem expansion and cauline branching of the RNAi lines, respectively, pointing to endogenous HD-Zip I genes as candidate mediators of these traits. Remarkably, these effects were observed in newly obtained transgenic soybean plants, where expression of HaHB4-derived siRNAs enhanced vegetative vigor under controlled growth conditions. Overall, these findings show that transgene-derived siRNAs act independently of protein function to rewire endogenous regulatory networks, providing a potential strategy to optimize crop architecture and yield.
]]></description>
<dc:creator><![CDATA[ Vannay, G. J., Garcia, J. E., Murguia, J. P., Bruno, M. L., Caraballo, L. N., Welchen, E., Cambiagno, D. A., Chan, R. L., Capella, M. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750206</dc:identifier>
<dc:title><![CDATA[Protein-independent regulation by transgene-derived small interfering RNAs rewires endogenous regulatory networks to enhance plant growth, architecture, and drought performance]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750367v1?rss=1">
<title>
<![CDATA[
Influence of flowering phenology and strobili amount on mating patterns in an Abies nordmanniana clonal seed orchard 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750367v1?rss=1
</link>
<description><![CDATA[
Clonal seed orchards (CSOs) provide improved plant material from forest tree breeding. Mating dynamics of CSOs is therefore interesting, since dysfunctions like selfing, pollen contamination and differences in clonal contributions of gametes may hamper the genetic gain. Skewed paternal contribution can be caused by clonal variation in amount of flowering/pollen production, and clonal differences in flowering phenology. Including trees from different populations in CSOs entails a particular risk that the parents are split into non-overlapping phenological classes with limited gene exchange, so the seed crop will consist of different gene pools. The study objective was to study the influence of flowering amount and flowering phenology on the mating patterns in an Abies nordmanniana CSO combining classic ocular observations of strobili with paternity analysis using DNA markers. Furthermore, we tested whether the two different gene pools from which the trees originated, had limited gene exchange. Phenology observations over three years showed that female strobili in A. nordmanniana often are receptive before the male strobili release pollen (5-7 days). However, despite clonal variation in first pollen release there is a ''great dusting day'', where all clones are contributing pollen. Based on DNA-markers, pollination success among 93 clones varied from 0 to over 5%. Clone variation in male strobili amount explained 29% of the variation in pollination success, while early pollen shedding could explain 13%. Our results support the hypothesis of early pollen shedding having an advantage in pollination success and late pollen shedding a disadvantage. No substantial mating barriers between trees from the two gene pools which are included in the CSO could be observed.
]]></description>
<dc:creator><![CDATA[ Hansen, O. K., Xu, J., Nielsen, U. B. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750367</dc:identifier>
<dc:title><![CDATA[Influence of flowering phenology and strobili amount on mating patterns in an Abies nordmanniana clonal seed orchard]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750301v1?rss=1">
<title>
<![CDATA[
Gene repertoire expansion and cis-regulatory diversification shaped 26S proteasome evolution within a proteostasis-centered network 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750301v1?rss=1
</link>
<description><![CDATA[
The 26S proteasome is essential for proteostasis and constitutes one of the most conserved molecular machineries in eukaryotes. Its homeostasis is maintained by a mechanistically conserved feedback loop involving kingdom-specific components. Yet, how the proteasome subunits and associated regulatory feedback loop have evolved to accommodate ever-changing cellular context is poorly understood. Here, we combine gene duplicate analysis, cis-regulatory element identification, functional validation, and protein network inference to investigate the evolution of plant 26S proteasome. Proteasome gene repertoires expanded largely independently across plant lineages, with paralogs showing shifts in post-translational modification sites and pronounced transcriptional divergence in response to environmental cues. Comparative analysis of 26S proteasome gene promoters revealed extensive diversification of proteasome-associated cis-elements across plants, with repeated enrichment of related motifs. These observations led to the identification of telomere repeat-binding proteins (TRBs) as novel transcriptional regulators of proteasome genes in A. thaliana, through association with the previously characterized PRCE motif. Finally, evolutionary rate covariation analysis identified a conserved proteasome-associated network connected through proteasome-associated cis-elements and unifying cellular proteostasis. Together, our results indicate that plant 26S proteasome is controlled by a regulatory architecture that combines conserved cis-regulatory mechanisms, lineage-specific innovation, and stress-responsive paralog specialization at the center of the proteostasis network; offering a new perspective on the evolution of one of the most essential molecular complexes.
]]></description>
<dc:creator><![CDATA[ Langin, G., Wilczek, T., Biermann, D., Rehmann, E. A., Forsythe, E. S., Uestuen, S. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750301</dc:identifier>
<dc:title><![CDATA[Gene repertoire expansion and cis-regulatory diversification shaped 26S proteasome evolution within a proteostasis-centered network]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750133v1?rss=1">
<title>
<![CDATA[
Evolution of an unstable sex determination system in white Guinea yam (Dioscorea rotundata) 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750133v1?rss=1
</link>
<description><![CDATA[
Plants often produce unstable sex phenotypes; however, the underlying evolutionary and molecular mechanisms are unclear. In white Guinea yam (Dioscorea rotundata), the most economically important tuber crop, genetic improvement is critical for food security but remains constrained by dioecy and complex sex phenotypes. White Guinea yam has a ZZ/ZW sex determination system in which ZZ individuals are consistently male, whereas ZW individuals can be female, male, or monoecious. Here we show that chromosome 11 is the sex chromosome, featuring a 1.2-Mb inversion between the Z and W chromosomes. A 170-kb W-specific region carries the microRNA gene dro-MIR432, likely involved in sex switching. The recent emergence of this miRNA-mediated ZZ/ZW system, distinct from the XY/XX system within Dioscorea, underscores the dynamic evolution of plant sex determination.
]]></description>
<dc:creator><![CDATA[ Kudoh, A., Sugihara, Y., Iseki, K., Matsumoto, R., Minoji, K., Onai, K., Abe, A., Natsume, S., Sakai, T., Oikawa, K., Shimizu, M., Itoh, K., Adachi, H., Honda, K., Yamanaka, S., Agre, P. A., Adebola, P., Asfaw, A., Terauchi, R. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750133</dc:identifier>
<dc:title><![CDATA[Evolution of an unstable sex determination system in white Guinea yam (Dioscorea rotundata)]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750143v1?rss=1">
<title>
<![CDATA[
Distinct nanoscale dynamics of growth receptor complexes link hormone perception to rapid cell wall remodeling 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750143v1?rss=1
</link>
<description><![CDATA[
Cell elongation is a fundamental process allowing plants to change size and shape, a process governed by several growth promoting hormones. While hormones such as brassinosteroids (BRs) and phytosulfokines (PSKs) have been shown to play important roles in elongation growth, the early steps of signal perception remains elusive, especially with regard to PSK. Here we report a rapid mechanism by which PSK alter cell wall mechanical properties in elongating hypocotyls. Notably, this mode of action differs from that of BR. Making use of atomic force microscopy and fluorescence lifetime imaging microscopy we demonstrate how hallmarks of growing plant cells such as mechanical wall properties, porosity and apoplastic pH are differentially affected by PSK compared to BR. Using super-resolution microscopy, we show that the receptor complex components for BR and PSK display individual spatiotemporal movement and organization patterns. The BR receptor BRI1 transitions to a faster diffusive state upon ligand perception, while the PSK receptor PSKR1 associates in tighter clusters. The shared co-receptor BAK1 displays a selective decrease in cluster density after PSK treatment. We found that the putative cell wall state sensor RLP44 is required for the observed changes, however the spatiotemporal dynamics of RLP44 are not altered during signaling. We propose a model of how cell walls are specifically tuned by BRI1- and PSKR1-centered signaling hubs as potential prerequisites for and during cell elongation initiation.
]]></description>
<dc:creator><![CDATA[ Rausch, L., Balmes, A., Zoller, D., Singh, J., zur Oven-Krockhaus, S., Bettinger, H. F., Schaeffer, T. E., Harter, K. J. W. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750143</dc:identifier>
<dc:title><![CDATA[Distinct nanoscale dynamics of growth receptor complexes link hormone perception to rapid cell wall remodeling]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.04.748299v1?rss=1">
<title>
<![CDATA[
Vision Transformers Enable Advanced Plant Phenotyping in Controlled Environments 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.04.748299v1?rss=1
</link>
<description><![CDATA[
Reliable plant segmentation in high-throughput phenotyping must transfer across species and imaging conditions without repeated model tuning or extensive reannotation. We compare three segmentation strategies using images from Oak Ridge National Laboratory's Advanced Plant Phenotyping Laboratory: (i) fixed color-based thresholding, (ii) supervised U-Nets trained from scratch, and (iii) pretrained vision transformers fine-tuned for binary segmentation. Models were evaluated on a held-out test set and a generalization set that comprised unseen species. On the held-out test set, thresholding, the best U-Net, and the best vision transformer achieved mean Dice scores of 58.3, 96.6, and 97.3, respectively. On the generalization set, the corresponding Dice scores were 56.5, 86.2, and 95.7. Thresholding remained effective on some datasets but failed when plant appearance changed. Supervised U-Net training resolved within-distribution errors but failed to generalize to novel species and backgrounds. Pretrained vision transformers consistently produced high-accuracy segmentations across the evaluated species, views, soil backgrounds, and tray types. These results benchmark the practical progression from fixed rules to task-specific supervision and pretrained visual representations for controlled-environment plant phenotyping.
]]></description>
<dc:creator><![CDATA[ Milligan, J., Seethepalli, A., Tsaris, A., Wang, X., York, L., Lagergren, J. H. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.04.748299</dc:identifier>
<dc:title><![CDATA[Vision Transformers Enable Advanced Plant Phenotyping in Controlled Environments]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749952v1?rss=1">
<title>
<![CDATA[
Decarboxylation of indoleacetic acid illuminates its evolution into a plant hormone 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749952v1?rss=1
</link>
<description><![CDATA[
The evolution of indoleacetic acid (IAA) into the plant hormone auxin remains unclear. Here, we compared IAA response and metabolism in land plants and their closest living relatives, the streptophyte algae, using chemical treatments, phytohormone profiling, and targeted and untargeted metabolomics. Streptophyte algae showed neither plant-like auxin responses nor canonical IAA metabolism. Here, we demonstrate IAA side-chain decarboxylation as a novel pathway of cellular IAA metabolism, operating in streptophyte algae and land plants alike. Decarboxylation also underpinned IAA's innate photolability and yielded cytotoxic intermediates, which also accumulated endogenously under simulated sunlight. Together, these findings establish IAA decarboxylation as a major, conserved metabolic pathway, and suggest that the metabolic constraints arising from IAA's instability and indirect cytotoxicity contributed to its adoption as a plant hormone.
]]></description>
<dc:creator><![CDATA[ Schmidt, V., Dobrev, P. I., Knirsch, V., Muller, K., Svobodova, B., Lacek, J., Marsik, P., Vosolsobe, S., Coudert, Y., Skokan, R., Petrasek, J. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749952</dc:identifier>
<dc:title><![CDATA[Decarboxylation of indoleacetic acid illuminates its evolution into a plant hormone]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750255v1?rss=1">
<title>
<![CDATA[
A native single-transcript TnpB architecture enables efficient virus-induced genome editing and visual screening of heritable progeny harboring phenotypically silent edits 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750255v1?rss=1
</link>
<description><![CDATA[
TnpB are ultra-compact RNA-guided nucleases, yet most reported systems require separate expression of the nuclease and cognate reRNA, eroding their size advantage and restricting viral delivery in plants. Here we demonstrate that ISDra2 TnpB harnesses its native overlapping architecture in which the reRNA sequence resides within the 3' coding region of TnpB, processing its own mRNA to generate functional reRNA and enabling single-transcript genome editing in plants. Only a 7-bp conserved motif followed by a 16-20 bp spacer directly downstream of the coding sequence suffices for editing, requiring no exogenous ribozymes or independent guide promoters. This ultra-compact design enables simultaneous packaging of the editing system and an NbPDS silencing module into a single TRV vector, achieving robust editing in systemic Nicotiana benthamiana tissues and establishing a dual VIGE-VIGS strategy for direct visual selection of heritable, transgene-free edited progeny via distinct albino phenotypes, reducing laborious large-scale genotyping even for targets lacking inherent visible traits.
]]></description>
<dc:creator><![CDATA[ Wang, R., Liu, H., Jia, S., Bai, S., Cao, X., Li, D., Sun, Y. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750255</dc:identifier>
<dc:title><![CDATA[A native single-transcript TnpB architecture enables efficient virus-induced genome editing and visual screening of heritable progeny harboring phenotypically silent edits]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750075v1?rss=1">
<title>
<![CDATA[
Deoxyribonucleotide dephosphorylation by VENOSA4 supports organellar genome replication in plants 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750075v1?rss=1
</link>
<description><![CDATA[
The replication of the three genomes in plant cells during germination is a complex process, which requires a high degree of coordination between the genome-containing compartments: the nucleus, mitochondria, and chloroplasts. The first committed step for the de novo synthesis of deoxynucleoside triphosphates (dNTPs), the building blocks for DNA replication, occurs exclusively in the cytosol. A major unresolved question is how an adequate supply of dNTPs for the organelles is achieved. Here, we show that VENOSA4 (VEN4), a dNTP triphosphohydrolase, is critical for this process in Arabidopsis thaliana. Using isotope feeding combined with mass spectrometry analysis, we demonstrate that VEN4 converts most de novo-synthesized dNTPs to deoxynucleosides (dNs). Preventing this conversion by VEN4 mutation strongly diminishes both cpDNA and mtDNA amounts, but these can be partially rescued by the application of exogenous dNs. Hence, the dNTP catabolic activity of VEN4 ensures that sufficient DNA precursors in form of dNs reach the chloroplasts and the mitochondria to be salvaged there to dNTPs for DNA synthesis. This seemingly counterintuitive coupling of de novo synthesis, dNTP hydrolysis, and salvage may provide a mechanism to control DNA precursor allocation between cellular compartments through selective transport and metabolic trapping.
]]></description>
<dc:creator><![CDATA[ Fischer, L., Straube, H., Passon, N., Thoelke, H., Witte, C.-P., Herde, M. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750075</dc:identifier>
<dc:title><![CDATA[Deoxyribonucleotide dephosphorylation by VENOSA4 supports organellar genome replication in plants]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749821v1?rss=1">
<title>
<![CDATA[
Phytosulfokine signaling modulates salt stress responses and cell wall remodeling in Arabidopsis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749821v1?rss=1
</link>
<description><![CDATA[
Salinity severely impairs plant growth and development. Increasing evidence suggests that the cell wall (CW) plays a central role in salt stress acclimation, not only as a structural barrier but also as a dynamic sensor that activates downstream stress signaling pathways. To identify extracellular factors involved in cell wall remodeling and integrity signaling during salt stress, we performed a comparative proteomic analysis of the Arabidopsis seedling apoplast. Among the proteins that accumulated under salt stress, we focused on three members of the Subtilisin-Like Protease family (SBT1.1, SBT1.6, and SBT5.3), which have previously been implicated in the processing of signaling peptides and CW-associated proteins. Functional analyses revealed that sbt1.1 and sbt5.3 mutants exhibit enhanced lignin deposition under salt stress, suggesting altered CW remodeling during stress application. Given the established role of SBT1.1 in processing PHYTOSULFOKINE (PSK) peptides, we investigated the involvement of PSK signaling in salt stress responses. Mutants lacking the two PSK RECEPTORS (pskr1 pskr2) displayed reduced growth and increased lignification under salt treatment. Exogenous application of PSK attenuated salt-induced responses, including MITOGEN ACTIVATED PROTEIN KINASE 6 (MPK6) phosphorylation, salt stress marker gene expression, and lignin accumulation, ultimately promoting root elongation under salt stress. Furthermore, PSK treatment mitigated salt-induced changes in CW composition. In cell wall integrity (CWI) mutants, PSK treatment failed to restore wild-type root growth under salt stress and induced a pronounced root bending phenotype in fer-4, indicating that CWI signaling influences PSK-mediated root growth responses. Together, these results support a role for PSK signaling in modulating CW-associated responses to salinity stress in Arabidopsis.
]]></description>
<dc:creator><![CDATA[ Debnath, J., Jiang, Z., van der Meer, T., Roosjen, M., Braun, N., Weijers, D., Testerink, C., Engelsdorf, T., Gigli-Bisceglia, N. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749821</dc:identifier>
<dc:title><![CDATA[Phytosulfokine signaling modulates salt stress responses and cell wall remodeling in Arabidopsis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
