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The cuticle constitutes the outermost defensive barrier of most land plants. It comprises a polymeric matrix-cutin, surrounded by soluble waxes. Moreover, the cuticle constitutes the first line of defense against pathogen invasion, while also protecting the plant from many abiotic stresses. Aliphatic monomers in cutin have been suggested to act as immune elicitors in plants. This study analyses the potential of cutin oligomers to activate rapid signaling outputs reminiscent of pattern-triggered immunity in the model plant Arabidopsis. Cutin oligomeric mixtures led to Ca2+ influx and mitogen-activated protein kinase activation. Comparable responses were measured for cutin, which was also able to induce a reactive oxygen species burst. Furthermore, cutin oligomer treatment resulted in a unique transcriptional reprogramming profile, having many archetypal features of pattern-triggered immunity. Targeted spectroscopic and spectrometric analyses of the cutin oligomers suggest that the elicitor compounds consist mostly of two up to three 10,16-dihydroxyhexadecanoic acid monomers linked together through ester bonds. This study demonstrates that cutin breakdown products can act as inducers of early plant immune responses. Further investigation is needed to understand how cutin breakdowns are perceived and to explore their potential use in agriculture.

Natural Rubber (NR)-producing guayule (Parthenium argentatum Gray) has been developed as a new crop to diversify NR production. Guayule NR is mainly synthesized in its stem and is upregulated by cold temperatures. A guayule C-repeat binding factor 4 (PaCBF4) was highly expressed in cold-treated stem tissue, coinciding with active rubber biosynthesis and accumulation. Sequence alignments of PaCBF4 with other CBFs indicated that PaCBF4 contains DNA-binding domains responsible for regulating cold-regulated (COR) gene expression. Spatial gene expression profiling of PaCBF4 revealed that stems had the highest expression level among different organs examined. We further confirmed the function of PaCBF4 as regulator of cold-signaling processes by expressing it in the model plant Arabidopsis under a constitutive ubiquitin promoter from potato. The resulting transgenic Arabidopsis lines expressing PaCBF4 turned on expression of a set of Arabidopsis COR genes under both room (24ºC) and cold (4ºC) temperatures, in contrast to the wild-type Arabidopsis that expressed these COR genes solely upon cold treatment. Furthermore, the transgenic plants displayed enhanced freezing tolerance at −5ºC, exhibiting a survival rate of 88–98% compared with 0% survival rate of wild-type plants. Our results suggest that PaCBF4 is a functional member of the guayule CBF gene family and plays a significant role in cold and freeze tolerance. Interestingly, overexpressing PaCBF4 in Arabidopsis did not affect the normal phenotype of the plant during vegetative and inflorescence growth, but the gene led to more undeveloped siliques after flowering.

Several closely related Myb-like activator proteins are known to have partially redundant functions within the plant circadian clock, but their specific roles are not well understood. To clarify the function of the REVEILLE 4, REVEILLE 6, and REVEILLE 8 transcriptional activators, we characterized the growth and clock phenotypes of CRISPR-Cas9-generated single, double, and triple rve mutants. We found that these genes act synergistically to regulate flowering time, redundantly to regulate leaf growth, and antagonistically to regulate hypocotyl elongation. We previously reported that increasing intensities of monochromatic blue and red light have opposite effects on the period of triple rve468 mutants. Here, we further examined light quality-specific phenotypes of rve mutants and report that rve468 mutants lack the blue light-specific increase in expression of some circadian clock genes observed in wild type. To investigate the basis of these blue light-specific circadian phenotypes, we examined RVE protein abundances and degradation rates in blue and red light and found no significant differences between these conditions. We next examined genetic interactions between RVE genes and ZEITLUPE and ELONGATED HYPOCOTYL5, two factors with blue light-specific functions in the clock. We found that the RVEs interact additively with both ZEITLUPE and ELONGATED HYPOCOTYL5 to regulate circadian period, which suggests that neither of these factors are required for the blue light-specific differences that we observed. Overall, our results suggest that the RVEs have separable functions in plant growth and circadian regulation and that they are involved in blue light-specific circadian signaling via a novel mechanism.

The likelihood that a host will be susceptible to infection is influenced by the interaction of diverse biotic and abiotic factors. As a result, substantial experimental replication and scalability are required to identify the contributions of and interactions between the host, the environment, and biotic factors such as the microbiome. For example, pathogen infection success is known to vary by host genotype, bacterial strain identity and dose, and pathogen dose. Elucidating the interactions between these factors in vivo has been challenging because testing combinations of these variables quickly becomes experimentally intractable. Here, we describe a novel high throughput plant growth system (MYCroplanters) to test how multiple host, non-pathogenic bacteria, and pathogen variables predict host health. Using an Arabidopsis-Pseudomonas host-microbe model, we found that host genotype and bacterial strain order of arrival predict host susceptibility to infection, but pathogen and non-pathogenic bacterial dose can overwhelm these effects. Host susceptibility to infection is therefore driven by complex interactions between multiple factors that can both mask and compensate for each other. However, regardless of host or inoculation conditions, the ratio of pathogen to non-pathogen emerged as a consistent correlate of disease. Our results demonstrate that high-throughput tools like MYCroplanters can isolate interacting drivers of host susceptibility to disease. Increasing the scale at which we can screen drivers of disease, such as microbiome community structure, will facilitate both disease predictions and treatments for medicine and agricultural applications. Author summary: Whether or not hosts are susceptible to pathogen infection depends on complex interactions between the host and the environment. To rapidly and scalably test the contributions of host, non-pathogen, pathogen, and environment in predicting plant disease, we created the MYCroplanter system. MYCroplanters are a high-throughput plant growth platform that allows cultivation of the model plant Arabidopsis thaliana in 96-well arrays. Our tool is compatible with commercially available equipment and consumables, which means it can be used in tandem with high-throughput molecular tools like liquid handling robots and plate readers to design complex experimental set-ups. We use this system to demonstrate how pathogen establishment success is dependent on nuanced interactions between multiple host, non-pathogen, and pathogen variables. The sensitivity and scalability of our system offer the field of host-pathogen interactions an affordable way to conduct large-scale screens. The accessibility and flexibility of this tool will facilitate a new wave of research in predicting host health and disease, which can be leveraged to inform host treatment strategies. [ABSTRACT FROM AUTHOR]

In this study, we investigated the interplay between nitrogen nutrition and the pectin degradation dynamics during Arabidopsis and Botrytis interaction. Our findings revealed that infected detached leaves from nitrogen-sufficient plants released more pectin lyase (PNL)-derived oligogalacturonides compared to nitrogen-deficient ones. We then focused on BcPNL1, the most highly expressed Botrytis PNL upon infection. Using mutant strains lacking BcPNL1, we observed reduced pathogenicity, a delay in germination and a lag in triggering the plant defense response. Additionally, in nitrogen-sufficient detached leaves, the elevated expression of jasmonic acid repressor genes observed upon infection with the wild-type strain was abolished with the mutants. These results linked the increased production of BcPNL-derived products to the increased expression of jasmonic acid repressor genes, contributing partially to the higher susceptibility of nitrogen-sufficient detached leaves. These findings could lay the foundation for new strategies aimed at reconciling both crop resistance to pathogens and the improvement of nitrogen nutrition. The Botrytis cinerea pectin lyase BcPNL1 produces oligogalacturonides that activate expression of jasmonic acid repressor genes, contributing partially to the higher susceptibility of nitrogen-sufficient detached leaves. [ABSTRACT FROM AUTHOR]

We employed hyperspectral imaging to detect chloroplast positioning and assess its influence on common vegetation indices. In low blue light, chloroplasts move to cell walls perpendicular to the direction of the incident light. In high blue light, chloroplasts exhibit the avoidance response, moving to cell walls parallel to the light direction. Irradiation with high light resulted in significant changes in leaf reflectance and the shape of the reflectance spectrum. Using mutants with disrupted chloroplast movements, we found that blue light-induced changes in the reflectance spectrum are mostly due to chloroplast relocations. We trained machine learning methods in the classification of leaves according to the chloroplast positioning, based on the reflectance spectra. The convolutional network showed low levels of misclassification of leaves irradiated with high light even when different species were used for training and testing, suggesting that reflectance spectra may be used to detect chloroplast avoidance in heterogeneous vegetation. We also examined the correlation between chloroplast positioning and values of indices of normalized-difference type for various combinations of wavelengths and identified an index sensitive to chloroplast positioning. We found that values of some of the vegetation indices, including those sensitive to the carotenoid levels, may be altered due to chloroplast rearrangements. [ABSTRACT FROM AUTHOR]

Premature bolting reduces the yield and quality of Chinese cabbage, making bolting resistance gene identification crucial for breeding superior and stable varieties. In this study, we identified an orphan gene BOLTING RESISTANCE 3 (BR3) that positively regulates bolting resistance in Arabidopsis thaliana. The expression of BR3 was developmentally regulated and occurred during the seedling and flowering stages. The BR3 protein was localized to both the plasma membrane and nucleus. Arabidopsis BR3 overexpressing (BR3 OE) plants exhibited delayed bolting and flowering times, an increased number of rosette leaves, reduced plant height, and fewer siliques under long-day (LD) conditions. Key flowering genes were significantly downregulated in BR3 OE plants. BR3 OE plants similarly exhibited delayed bolting and flowering times, and an increased number of rosette leaves under short-day (SD) conditions. BR3 OE plants showed no significant phenotypic differences after vernalization treatment. BR3 OE and WT plants exhibited early flowering after GA3 treatment, and bolting and flowering time remained delayed in BR3 OE plants compared with WT plants. Key DELLA genes BrRGA1 and BrRGL3 exhibited a co-expression pattern consistent with BR3 gene in Chinese cabbage, which suggested that BrRGA1 and BrRGL3 genes may directly or indirectly regulated by BR3 gene. BR3 gene increased bolting resistance perhaps by upregulating the expression of DELLA genes in the GA pathway. This study provides new theoretical insights for addressing premature bolting in Chinese cabbage and offers novel approaches for breeding bolting-resistant varieties. [ABSTRACT FROM AUTHOR]

Coumarins are natural products commonly found in plants and are typical allelopathic substances that strongly affect the growth of plants after being exudated from the root and help plants absorb Fe in cases of iron deficiency. Although coumarins have been found to have multiple effects, this understanding is still relatively limited. Here, we show that coumarin significantly promotes the elongation of the hypocotyl by enhancing cell elongation. Further research has found that coumarin increases the content of BR in plants by enhancing the expression of brassinosteroid (BR) synthesis genes. The effect of coumarin on promoting hypocotyl elongation is completely blocked by the mutation of the BR synthesis gene DEETIOLATED 2 (DET2) or the co-addition of the BR synthesis inhibitor brassinazole (BRZ). Genetic analysis using Arabidopsis mutants showed that coumarin promoting hypocotyl elongation depends on the signaling pathway of the BRs. Overall, coumarin promotes elongation of the hypocotyl by increasing the synthesis of BRs in plants. These results provide us with new insights into the role of coumarins and offer strong theoretical support for the mechanisms of interactions between plants. [ABSTRACT FROM AUTHOR]

Singlet oxygen (1O 2) is a byproduct of photosynthesis whose cytotoxicity is well established. How 1O 2 can trigger specific growth responses is, however, largely unknown. Evidence is accumulating that specific chloroplast-to-nucleus signaling pathways operate. We identified one such pathway in Arabidopsis thaliana (arabidopsis) that requires the transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4). ABI4 confers transcriptional and translational changes that collectively lead to either cell death or halted growth. We review how ABI4 may accomplish these changes in the fluorescent (flu) mutant of arabidopsis. Abscisic acid (ABA) and the AP2/ERF (APETALA 2/ETHYLENE-RESPONSIVE FACTOR)-type transcription factor ABA INSENSITIVE 4 (ABI4) control plant growth and development. We review how singlet oxygen, which is produced in chloroplasts of the fluorescent mutant of Arabidopsis thaliana (arabidopsis) , and ABI4 may cooperate in transcriptional and translational reprogramming to cause plants to halt growth or demise. Key elements of singlet oxygen- and ABI4-dependent chloroplast-to-nucleus retrograde signaling involve the chloroplast EXECUTER (EX) 1 and EX2 proteins as well as nuclear WRKY transcription factors. Mutants designed to study singlet oxygen signaling, that lack either ABI4 or the EX1 and EX2 proteins, do not show most of the growth effects of singlet oxygen. We propose a model that positions ABI4 downstream of WRKY transcription factors and EX1 and EX2. [ABSTRACT FROM AUTHOR]

• This paper proposes a Snakemake pipeline named SV-JIM that combines outputs from multiple structural variant identification tools using several strategies to measure inter-caller variance and identify well supported structural variant results. • SV-JIM was validated using multiple genomes and produced structural variant results for Brassica nigra , Arabidopsis thaliana , and Homo sapiens data. • SV-JIM's experiments revealed that combining the results from three structural variant identification tools provided the optimum balance in precision and recall based on the F1 scores received. • Exploring both the intersection and aggregation of structural variant results between multiple tools revealed that aggregation provided better retention of the less frequently occurring structural variant types, including duplications and inversions. • SV-JIM was evaluated using the Genome In A Bottle benchmark dataset which provided insight into well performing tools and revealed the potential for bias in the precision reported by evaluation software. This paper proposes a detailed process for SV calling that permits a data-driven assessment of multiple SV callers that uses both genome assemblies and long-reads. The process is implemented as a software pipeline named Structural Variant − Jaccard Index Measure, or SVJIM, using the Snakemake [20] workflow management system. Like most state-of-the-art SV callers, SV-JIM detects the presence of variations between pairs of genomes, but it streamlines the numerous SV calling stages into a single process for user convenience and evaluates the multiple SV sets produced using the Jaccard index measure to identify those with the highest consistency among the included SV callers. SV-JIM then produces aggregated SV results based on how many callers supported the reported SVs. For validation, SV-JIM was assessed through three case studies on the Homo sapiens genome and two plant genomes – Brassica nigra and Arabidopsis thaliana. Executing SV-JIM identified a significant amount of inter-caller variance which varied by tens of thousands of results on the larger Brassica nigra and Homo sapiens genomes. Further, aggregating the SV sets helped simplify better retention of the less frequently occurring SV types by requiring a level of minimum support rather than from a specific SV caller combination. Finally, these case studies identified a potential for inflated precision reporting that can occur during evaluation. SV-JIM is available publicly under MIT license at https://github.com/USask-BINFO/SV-JIM. [ABSTRACT FROM AUTHOR]

Bisphenol compounds (BPs) have various industrial uses and can enter the environment through various sources. To evaluate the ecotoxicity of BPs and identify potential gene candidates involved in the plant toxicity, Arabidopsis thaliana was exposed to bisphenol A (BPA), BPB, BPE, BPF, and BPS at 1, 3, 10 mg/L for a duration of 14 days, and their growth status were monitored. At day 14, roots and leaves were collected for internal BPs exposure concentration detection, RNA-seq (only roots), and morphological observations. As shown in the results, exposure to BPs significantly disturbed root elongation, exhibiting a trend of stimulation at low concentration and inhibition at high concentration. Additionally, BPs exhibited pronounced generation of reactive oxygen species, while none of the pollutants caused significant changes in root morphology. Internal exposure concentration analysis indicated that BPs tended to accumulate in the roots, with BPS exhibiting the highest level of accumulation. The results of RNA-seq indicated that the shared 211 differently expressed genes (DEGs) of these 5 exposure groups were enriched in defense response, generation of precursor metabolites, response to organic substance, response to oxygen-containing, response to hormone, oxidation–reduction process and so on. Regarding unique DEGs in each group, BPS was mainly associated with the redox pathway, BPB primarily influenced seed germination, and BPA, BPE and BPF were primarily involved in metabolic signaling pathways. Our results provide new insights for BPs induced adverse effects on Arabidopsis thaliana and suggest that the ecological risks associated with BPA alternatives cannot be ignored. [Display omitted] [ABSTRACT FROM AUTHOR]

Salt stress constrains the development and growth of plants. To tolerate it, mechanisms of endocytosis and vacuolar compartmentalization of Na+ are induced. In this work, the genes that encode a putative activator of vesicular trafficking called MON1/CCZ1 from Solanum chilense, SchMON1 and SchCCZ1, were co‐expressed in roots of Arabidopsis thaliana to determine whether the increase in prevacuolar vesicular trafficking also increases the Na+ compartmentalization capacity and tolerance. Initially, we demonstrated that both SchMON1 and SchCCZ1 genes rescued the dwarf phenotype of both A. thaliana mon1‐1 and ccz1a/b mutants associated with the loss of function, and both proteins colocalized with their functional targets, RabF and RabG, in endosomes. Transgenic A. thaliana plants co‐expressing these genes improved salt stress tolerance compared to wild type plants, with SchMON1 contributing the most. At the sub‐cellular level, co‐expression of SchMON1/SchCCZ1 reduced ROS levels and increased endocytic activity, and number of acidic structures associated with autophagosomes. Notably, greater Na+ accumulation in vacuoles of cortex and endodermis was evidenced in the SchMON1 genotype. Molecular analysis of gene expression in each genotype supported these results. Altogether, our analysis shows that root activation of prevacuolar vesicular trafficking mediated by MON1/CCZ1 emerges as a promising physiological molecular mechanism to increase tolerance to salt stress in crops of economic interest. Summary statement: Our study demonstrates that the roots expression of a Rab7 activator, MON1/CCZ1 from Solanum chilense, a specific regulator for pre‐vacuolar vesicular trafficking, increase the endocytosis and the vacuolar sodium accumulation, improving the tolerance to salt stress in Arabidopsis plants. [ABSTRACT FROM AUTHOR]

Nitrate (NO3−) deficiency decreases root water uptake and root hydraulic conductance. This adaptive response is correlated with reduced abundance and activity of plasma membrane intrinsic protein (PIP) aquaporins. We therefore screened changes in the root architecture of a complete set of Arabidopsis pip loss‐of‐function mutants grown under NO3− deficiency to systematically approach the impact of PIPs under these conditions. NO3− deprivation led to attenuated responses of specific pip single mutants compared to the strongly altered LR parameters of wild‐type plants. In particular, pip1;1 exhibited a lower relative reduction in LR length and LR density, revealing that PIP1;1 represses LR development when NO3− is scarce. Indeed, PIP1;1 compromises root and shoot NO3− accumulation during early developmental stages. A fluorescent VENUS‐PIP1;1 fusion revealed that PIP1;1 is specifically repressed in the pericycle, endodermis and at the flanks of emerging LRs upon NO3− deficiency. Thus, LR plasticity and NO3− uptake are affected by an interactive mechanism involving aquaporins (PIP1;1) and nitrate accumulation during seedling development under NO3−‐deficient conditions. Summary statement: Nitrate deficiency represses Arabidopsis root water uptake and the expression of several PIP‐type aquaporins.Here, the analysis of a complete collection of 15 single pip loss‐of‐function mutants revealed that in turn PIP1;1 suppresses lateral root development and nitrate accumulation under low nitrate availability.Thus, plants employ an interactive mechanism linking root architecture, PIP expression and nutrient uptake in response to low nitrate conditions. [ABSTRACT FROM AUTHOR]

Actin depolymerizing factors (ADFs), like other actin‐binding proteins (ABPs), are modified by phosphorylation to regulate the dynamics of the actin filaments, thereby functioning in various processes throughout the plant lifecycle. In this study, we found that the Arabidopsis thaliana cytoplasmic kinase AGC1.7 interacts with ADF7 in vitro and in vivo. AGC1.7 phosphorylates ADF7 at its Ser‐6, Ser‐103 and Ser‐104 residues in vitro, while replacing these residues with alanine promotes ADF7‐mediated actin depolymerization in vitro. Expression of the phosphorylation‐mimetic mutant protein ADF7S6/103/104D driven by the pollen‐specific LAT52 promoter fully rescues the defects in germination rate, silique length and seeds per silique in both adf7‐2 and agc1.5 agc1.7 (agcdm) mutants. Our data establish a model whereby AGC1.7‐mediated ADF7 phosphorylation plays an important role in pollen germination and pollen tube growth. Summary statement: In the current research article, we found that AGC1.7 phosphorylates ADF7 at Ser‐6/103/04 sites in Arabidopsis. AGC1.7‐mediated phosphorylation of ADF7 regulates pollen germination and elongation, thereby affecting the length of silique and seeds per silique. [ABSTRACT FROM AUTHOR]

Plant waxes, primarily composed of fatty acids and glycerol, serve as vital barriers to minimize water loss and protect pear fruits from pathogen infections. In 'Dangshansuli', the outer pericarp develops a wax layer that peaks in concentration during the later stages of fruit maturation. Conversely, in 'Dangshanjinsu', a russet mutant, the outer epidermis accumulates suberin instead of wax, with suberin content increasing as ripening progresses, accompanied by a decline in wax levels. Long-chain acyl-CoA synthase (LACS), a key enzyme within the acyl-activating enzyme family, contributes to the biosynthesis of ultra-long-chain fatty acids crucial for wax formation. Nevertheless, the role of PbrLACS in the exocarp of 'Dangshanjinsu' remains inadequately understood. In this study, we identified 67 PbrLACS genes in the 'Dangshansuli' genome, categorized into four distinct subfamilies. Our motif analysis showed the presence of seven conserved motifs, which displayed similar lengths and distribution patterns. Notably, several PbrLACS genes were found in close proximity near chromosome ends, suggesting potential tandem duplications that may have contributed to the species' biological diversity and adaptability. During the color transition phase of fruit development, PbrLACS2 expression was markedly lower in the exocarp of 'Dangshanjinsu' than in 'Dangshansuli', with similar patterns observed in other tissues such as flowers, leaves, and pedicels. These findings suggest that PbrLACS2 is involved in wax biosynthesis. Subcellular localization analysis revealed that PbrLACS2 is situated within the cell membrane, indicating a potential role in transporting fatty acids to the endoplasmic reticulum. In transgenic Arabidopsisthaliana lines expressing PbrLACS2, we observed increased surface water retention on leaves, likely resulting from enhanced wax deposition. Gas chromatography-mass spectrometry (GC-MS) analysis confirmed a rise in wax content in stem tissues, accompanied by a reduction in suberin levels, highlighting the unique properties of PbrLACS2. These results underscore the functional significance of PbrLACS2 in the exocarp of 'Dangshanjinsu', contributing to our understanding of its role in wax biosynthesis and its potential effects on water retention in Arabidopsis. [ABSTRACT FROM AUTHOR]

With the rapid advancement of plant phenotyping research, understanding plant genetic information and growth trends has become crucial. Measuring seedling length is a key criterion for assessing seed viability, but traditional ruler-based methods are time-consuming and labor-intensive. To address these limitations, we propose an efficient deep learning approach to enhance plant seedling phenotyping analysis. We improved the DeepLabv3+ model, naming it DFMA, and introduced a novel ASPP structure, PSPA-ASPP. On our self-constructed rice seedling dataset, the model achieved a mean Intersection over Union (mIoU) of 81.72%. On publicly available datasets, including Arabidopsis thaliana, Brachypodium distachyon, and Sinapis alba, detection scores reached 87.69%, 91.07%, and 66.44%, respectively, outperforming existing models. The model generates detailed segmentation masks, capturing structures such as the embryonic shoot, axis, and root, while a seedling length measurement algorithm provides precise parameters for component development. This approach offers a comprehensive, automated solution, improving phenotyping analysis efficiency and addressing the challenges of traditional methods. [ABSTRACT FROM AUTHOR]

One significant environmental element influencing the growth and yield of rice (Oryza sativa L.) is high temperature. Nevertheless, the mechanism by which rice responds to high temperature is not fully understood. A rice glycosyltransferase gene, OsDUGT1 , was identified as a heat-responsive gene in this investigation. Its function was studied by overexpression and knockout methods. The results showed that under heat stress, OsDUGT1 overexpression lines (OsDUGT1 -OE) increased the survival rate of rice, while Osdugt1 knockout lines (Osdugt1 -ko) decreased the survival rate compared to wild type (ZH11). In addition to rice, heat stress tolerance was also improved by ectopic expression of OsDUGT1 in transgenic Arabidopsis thaliana plants. We observed that ROS scavenging ability, malondialdehyde accumulation, and the ion leakage are relevant to the expression level of OsDUGT1. Through enzyme activity analysis, we found that OsDUGT1 could glycosylate flavonoid compounds. Correspondingly, the loss of OsDUGT1 function caused a significant decrease in endogenous flavonoid accumulation in rice, which was demonstrated by our metabolomics analysis. Additionally, our transcriptomic analysis of Osdugt1 mutant lines under heat stress condition indicated that mutation of OsDUGT1 can reduce the transcriptional activity of heat response related genes, antioxidant enzyme genes and other genes involved in the flavonoid biosynthetic pathway. In summary, our work revealed that OsDUGT1 plays a crucial role in adjusting and balancing the overall plant metabolism and transcription under heat stress through glycosylation of flavonoids, and offers a key prospect gene for breeding efforts to enhance crop heat tolerance under the trend of climate warming all over the globe. [ABSTRACT FROM AUTHOR]

We test here the prediction capabilities of the new generation of deep learning predictors in the more challenging situation of multistate multidomain proteins by using as a case study a coiled-coil family of Nucleotide-binding Oligomerization Domain-like (NOD-like) receptors from A. thaliana and a few extra examples for reference. Results reveal a truly remarkable ability of these platforms to correctly predict the 3D structure of modules that fold in well-established topologies. A lower performance is noticed in modeling morphing regions of these proteins, such as the coiled coils. Predictors also display a good sensitivity to local sequence drifts upon the modeling solution of the overall modular configuration. In multivalued 1D to 3D mappings, the platforms display a marked tendency to model proteins in the most compact configuration and must be retrained by information filtering to drive modeling toward the sparser ones. Bias toward order and compactness is seen at the secondary structure level as well. All in all, using AI predictors for modeling multidomain multistate proteins when global templates are at hand is fruitful, but the above challenges have to be taken into account. In the absence of global templates, a piecewise modeling approach with experimentally constrained reconstruction of the global architecture might give more realistic results. [ABSTRACT FROM AUTHOR]

Summary: This study investigated the generalizability of Arabidopsis thaliana immune responses across diverse pathogens, including Botrytis cinerea, Sclerotinia sclerotiorum, and Pseudomonas syringae, using a data‐driven, machine learning approach.Machine learning models were trained to predict disease development from early transcriptional responses. Feature selection techniques based on network science and topology were used to train models employing only a fraction of the transcriptome. Machine learning models trained on one pathosystem where then validated by predicting disease development in new pathosystems.The identified feature selection gene sets were enriched for pathways related to biotic, abiotic, and stress responses, though the specific genes involved differed between feature sets. This suggests common immune responses to diverse pathogens that operate via different gene sets.The study demonstrates that machine learning can uncover both established and novel components of the plant's immune response, offering insights into disease resistance mechanisms. These predictive models highlight the potential to advance our understanding of multigenic outcomes in plant immunity and can be further refined for applications in disease prediction. [ABSTRACT FROM AUTHOR]