Molecules. 2025 Apr 30;30(9):2020. doi: 10.3390/molecules30092020.

ABSTRACT

The discovery of bioactive natural products is often challenged by the complexity of isolating and characterizing active compounds within diverse mixtures. Previously, we introduced a ¹H NMR-based weighted gene correlation network analysis (WGCNA) approach to identify spectral features linked to growth inhibitory activity of Piper (Piperaceae) leaf extracts against model plant, fungal, and bacterial organisms. This method enabled us to prioritize specific spectral features linked to bioactivity, offering a targeted approach to natural product discovery. In this study, we validate the predictive capacity of the WGCNA by isolating the compounds responsible for the bioactivity-associated resonances and confirming their antifungal efficacy. Using growth inhibition assays, we verified that the isolated compounds, including three novel antifungal agents, exhibited significant bioactivity. Notably, one of these compounds contains a rare imidazolium heterocyclic motif, marking a new structural class in Piper. These findings substantiate the ¹H NMR-based WGCNA as a reliable tool for identifying structural types associated with biological activity, streamlining the process of discovering bioactive natural products in complex extracts.

PMID:40363825 | PMC:PMC12073215 | DOI:10.3390/molecules30092020

Phytopathology. 2025 Jun 22. doi: 10.1094/PHYTO-03-25-0093-R. Online ahead of print.

ABSTRACT

Phony peach disease (PPD), caused by Xylella fastidiosa subsp. multiplex (Xfm), poses a significant threat to commercial peach orchards in Georgia. Early and accurate detection is essential for effective disease management, yet visual assessment remains the primary approach for diagnosing PPD symptoms due to the high cost and logistical challenges of qPCR-based detection of Xfm. We evaluated the accuracy of visual PPD assessment and examined the factors influencing rater performance, symptom reliability, and optimal survey deployment strategies with CART/Random Forest analyses and simulations. Internode length was the most reliable symptom for PPD identification in two peach cultivars, consistently outperforming other physical traits such as canopy flatness and shape. Primer pair C06Xf-bamA had the greatest relative sensitivity, making it the preferred choice for qPCR confirmation. Principal component analysis suggested that rater experience significantly improved agreement with qPCR results and repeated assessments of the same orchards further enhanced consistency for raters. Simulations results suggested that deploying two experienced raters may provide the highest detection diagnostic accuracy for survey purposes, particularly when qPCR-based pathogen detection is unavailable. Last, PPD-affected trees, through PCR verification and visual identification, exhibited higher mortality rates than Xfm-negative trees, reinforcing the need for early detection and removal to limit disease spread. These findings underscore the importance of strategic rater deployment, targeted symptom selection, and integrating molecular diagnostics when feasible.

PMID:40544457 | DOI:10.1094/PHYTO-03-25-0093-R

Plant Physiol. 2025 Jul 3;198(3):kiaf294. doi: 10.1093/plphys/kiaf294.

ABSTRACT

Minimal native and synthetic Polymerase III promoters enable efficient and customizable CRISPR multiplexing in plants, expanding genome engineering capabilities

PMID:40673482 | PMC:PMC12268498 | DOI:10.1093/plphys/kiaf294

Sci Data. 2025 Aug 5;12(1):1362. doi: 10.1038/s41597-025-05131-4.

ABSTRACT

Biological nitrogen fixation (BNF) is the main natural source of new nitrogen inputs in terrestrial ecosystems, supporting terrestrial productivity, carbon uptake, and other Earth system processes. We assembled a comprehensive global dataset of field measurements of BNF in all major N-fixing niches across natural terrestrial biomes derived from the analysis of 376 BNF studies. The dataset comprises 32 variables, including site location, biome type, N-fixing niche, sampling year, quantification method, BNF rate (kg N ha^-1 y^-1), the percentage of nitrogen derived from the atmosphere (%N_dfa), N fixer or N-fixing substrate abundance, BNF rate per unit of N fixer abundance, and species identity. Overall, the dataset combines 1,207 BNF rates for trees, shrubs, herbs, soil, leaf litter, woody litter, dead wood, mosses, lichens, and biocrusts, 152 herb %N_dfa values, 1,005 measurements of N fixer or N-fixing substrate abundance, and 762 BNF rates per unit of N fixer abundance for a total of 424 species across 66 countries. This dataset facilitates synthesis, meta-analysis, upscaling, and model benchmarking of BNF fluxes at multiple spatial scales.

PMID:40764484 | DOI:10.1038/s41597-025-05131-4

Plant Commun. 2025 Jun 3:101393. doi: 10.1016/j.xplc.2025.101393. Online ahead of print.

ABSTRACT

Teucrium chamaedrys, also called wall germander, is a small woody shrub native to the Mediterranean region. Its name is derived from the Greek words meaning ‘ground oak’, since its tiny leaves resemble those of an oak tree. Teucrium species are proliferative producers of diterpenes, which afford them valuable properties widely co-opted in traditional and western medicines. Sequence and assembly of the 3 Gbp tetraploid T. chamaedrys revealed 74 diterpene synthase genes, with the vast representation of these diterpene synthases clustered along four genomic loci. Comparative genomics revealed that this cluster is mirrored in the closely related species, Teucrium marum. Along with the presence of several cytochrome p450 sequences, this region is the one of largest biosynthetic gene clusters identified. Teucrium is well known for accumulating clerodane-type diterpenoids which are produced from a kolavanyl diphosphate precursor. To elucidate the complex biosynthetic pathways of these medicinal compounds, we identified and functionally characterized several kolavanyl diphosphate synthases from T. chamaedrys. Its remarkable chemistry and tetraploidy make T. chamaedrys an interesting and unique model for studying genomic evolution and adaptation in plants.

PMID:40468595 | DOI:10.1016/j.xplc.2025.101393

Front Plant Sci. 2025 Jul 11;16:1607733. doi: 10.3389/fpls.2025.1607733. eCollection 2025.

ABSTRACT

Maize (Zea mays L.) is the most widely produced crop in the world, and conventional production requires significant amounts of synthetic nitrogen fertilizer, which has negative economic and environmental consequences. Maize landraces from Oaxaca, Mexico, can acquire nitrogen from nitrogen-fixing bacteria that live in a mucilage secreted by aerial nodal roots. The development of these nodal roots is a characteristic traditionally associated with the juvenile vegetative stage of maize plants. However, mature Oaxacan landraces develop many more nodes with aerial roots than commercial maize varieties. Our study shows that Oaxacan landraces develop aerial roots during the juvenile and adult vegetative phases and even during early flowering under greenhouse and field conditions. Surprisingly, the development of these roots was only minimally affected by soil nitrogen and ambient humidity. These findings are an essential first step in developing maize varieties to reduce fertilizer needs in maize production across different environmental conditions.

PMID:40718026 | PMC:PMC12289584 | DOI:10.3389/fpls.2025.1607733

Tree Physiol. 2025 Jul 11:tpaf080. doi: 10.1093/treephys/tpaf080. Online ahead of print.

ABSTRACT

Sulfate-proton co-transporters (SULTRs) mediate sulfate uptake, transport, storage, and assimilation in plants. The SULTR family has historically been classified into four groups (SULTR1-SULTR4), with well-characterized roles for SULTR groups 1, 2, and 4. However, the functions of the large and diverse SULTR3 group remain poorly understood. Here, we present an updated phylogenetic analysis of SULTRs across angiosperms, including multiple early-divergent lineages. Our results suggest that the enigmatic SULTR3 group comprises four distinct subfamilies that predate the emergence of angiosperms, providing a basis for reclassifying the SULTR family into seven subfamilies. This expanded classification is supported by subfamily-specific gene structures and amino acid substitutions in the substrate-binding pocket. Structural modeling identified three serine residues uniquely lining the substrate-binding pocket of SULTR3.4, enabling three hydrogen bonds with the phosphate ion. The data support the proposed neofunctionalization of this subfamily for phosphate allocation within vascular tissues. Transcriptome analysis of Populus tremula × alba revealed divergent tissue expression preferences among SULTR subfamilies and between genome duplicates. We observed partitioned expression in vascular tissues among the four SULTR3 subfamilies, with PtaSULTR3.4a and PtaSULTR3.2a preferentially expressed in primary and secondary xylem, respectively. Gene coexpression analysis revealed coordinated expression of PtaSULTR3.4a with genes involved in phosphate starvation responses and nutrient transport, consistent with a potential role in phosphate homeostasis. In contrast, PtaSULTR3.2a was strongly coexpressed with lignification and one-carbon metabolism genes and their upstream transcription regulators. PtaSULTR3.2a belongs to a eudicot-specific branch of the SULTR3.1 subfamily found only in perennial species, suggesting a specialized role in lignifying tissues. Together, our findings provide a refined phylogenetic framework for the SULTR family and suggest that the expanded SULTR3 subfamilies have undergone neofunctionalization during the evolution of vascular and perennial plants.

PMID:40643194 | DOI:10.1093/treephys/tpaf080

Insects. 2025 Jun 24;16(7):653. doi: 10.3390/insects16070653.

ABSTRACT

Blueberry is a high-value fruit crop in the United States, with Georgia and Florida serving as important early-season production regions. In these areas, several thrips species (Thysanoptera: Thripidae), including Frankliniella tritici (Fitch), Frankliniella bispinosa (Morgan), and Scirtothrips dorsalis (Hood), have emerged as economically significant pests. While F. tritici and F. bispinosa primarily damage floral tissues, S. dorsalis targets young foliage. Their rapid reproduction, high mobility, and broad host range contribute to rapid population buildup and complicate the management programs. Species identification is often difficult due to overlapping morphological features and requires the use of molecular diagnostic tools for accurate identification. Although action thresholds, such as 2-6 F. tritici per flower cluster, are used to guide management decisions, robust economic thresholds based on yield loss remain undeveloped. Integrated pest management (IPM) practices include regular monitoring, cultural control (e.g., pruning, reflective mulch), biological control using Orius insidiosus (Say) and predatory mites, and chemical control. Reduced-risk insecticides like spinetoram and spinosad offer effective suppression while minimizing harm to pollinators and beneficial insects. However, the brief flowering period limits the establishment of biological control agents. Developing species-specific economic thresholds and phenology-based IPM strategies is critical for effective and sustainable thrips management in blueberry cropping systems.

PMID:40725285 | DOI:10.3390/insects16070653

Fungal Biol. 2025 Aug;129(5):101590. doi: 10.1016/j.funbio.2025.101590. Epub 2025 May 6.

ABSTRACT

The Fifth International Symposium on Fungal Stress (ISFUS) brought together in Brazil many of the leaders in the field of fungal stress responses, from fourteen countries, for four days of outstanding science ranging from basic research to studies with agricultural, medical, industrial, and environmental significance. In addition to the excellent oral and poster presentations, the Symposium organisers ensured that all participants had ample opportunity to engage, socialise, and network to exchange ideas and share research. The conference was enhanced by the world-class venue near Iguazu Falls, probably the greatest natural phenomenon in South America.

PMID:40707112 | DOI:10.1016/j.funbio.2025.101590

Mol Ecol Resour. 2025 Jul 22:e70012. doi: 10.1111/1755-0998.70012. Online ahead of print.

ABSTRACT

Yellow monkeyflowers (Mimulus guttatus complex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan-genomics in this group, we present four chromosome-scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a single M. guttatus population, one from the closely related selfing species M. nasutus, and one from a more divergent species M. tilingii. All assemblies are highly complete and resolve centromeric and repetitive regions. Comparative analyses reveal such extensive structural variation in repeat-rich, gene-poor regions that large portions of the genome are unalignable across accessions. As a result, this Mimulus pan-genome is primarily informative in genic regions, underscoring limitations of resequencing approaches in such polymorphic taxa. We document gene presence-absence, investigate the recombination landscape using high-resolution linkage data, and quantify nucleotide diversity. Surprisingly, pairwise differences at fourfold synonymous sites are exceptionally high-even in regions of very low recombination-reaching ~3.2% within a single M. guttatus population, ~7% within the interfertile M. guttatus species complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolated M. tilingii. Genome-wide patterns of nucleotide variation show little evidence of linked selection, and instead suggest that the concentration of genes (and likely selected sites) in high-recombination regions may buffer diversity loss. These assemblies, annotations, and comparative analyses provide a robust genomic foundation for Mimulus research and offer new insights into the interplay of recombination, structural variation, and molecular evolution in highly diverse plant genomes.

PMID:40693537 | DOI:10.1111/1755-0998.70012

Phytopathology. 2025 Jun 11. doi: 10.1094/PHYTO-04-25-0143-SC. Online ahead of print.

ABSTRACT

Root-knot nematodes (Meloidogyne spp.) are a continuing threat to soybean production, with M. incognita being the predominant species. The deployment of Mi-resistant soybean cultivars is a primary management strategy, but the underlying molecular mechanisms contributing to resistance remain unknown. A single, additive gene for resistance to M. incognita, Rmi1, was previously identified in soybean cv. Forrest and associated with the emigration of second-stage juveniles from the roots. To better understand the Rmi1-mediated resistance response, we used Forrest-derived F₅ RILs differing for Rmi1 to analyze global changes in gene expression in response to M. incognita infection at 2- and 4-days post inoculation. We identified 1,471 differentially expressed (DE) genes in the compatible interaction and 1,037 DE genes in the incompatible interaction. Forty-five percent of DE genes were DE in both interactions, 42% (856) were unique to the compatible interaction, and 13% (261) were unique to the incompatible interaction. Genes uniquely DE in the incompatible interaction included genes involved in cell wall modification, hormone signaling, endomembrane trafficking, and redox reactions providing new insights into the resistance mechanism mediated by Rmi1 in soybean to root-knot nematodes.

PMID:40498525 | DOI:10.1094/PHYTO-04-25-0143-SC

Genetics. 2025 May 14:iyaf091. doi: 10.1093/genetics/iyaf091. Online ahead of print.

ABSTRACT

In maize, there are two meiotic drive systems that target large heterochromatic knobs composed of tandem repeats known as knob180 and TR-1. The first meiotic drive haplotype, Abnormal chromosome 10 (Ab10) confers strong meiotic drive (∼75% transmission as a heterozygote) and encodes two kinesins: KINDR, which associates with knob180 repeats and TRKIN, which associates with TR-1 repeats. Prior data show that meiotic drive is conferred primarily by the KINDR/knob180 system while the TRKIN/TR-1 system seems to have little or no role, making it unclear why Trkin has been maintained in Ab10 haplotypes. The second meiotic drive haplotype, K10L2, confers a low level of meiotic drive (∼51-52%) and only encodes the TRKIN/TR-1 system. Here we used long-read sequencing to assemble the K10L2 haplotype and showed that it has strong homology to an internal portion of the Ab10 haplotype. We also carried out CRISPR mutagenesis to test the role of Trkin on Ab10 and K10L2. The data indicate that the Trkin gene on Ab10 does not improve drive or fitness but instead has a weak deleterious effect when paired with a normal chromosome 10. The deleterious effect is more severe when Ab10 is paired with K10L2: in this context functional Trkin on either chromosome nearly abolishes Ab10 drive. Mathematical modeling based on the empirical data suggest that Trkin is unlikely to persist on Ab10. We conclude that Trkin either confers an advantage to Ab10 in untested circumstances or that it is in the process of being purged from the Ab10 population.

PMID:40365704 | DOI:10.1093/genetics/iyaf091

BMC Microbiol. 2025 Jul 28;25(1):456. doi: 10.1186/s12866-025-04175-1.

ABSTRACT

BACKGROUND: The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates.

RESULTS: Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110 bp and at 370 bp, while strains only displaying the 110 bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification.

CONCLUSIONS: The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.

PMID:40722002 | DOI:10.1186/s12866-025-04175-1

Plant Dis. 2025 Aug 6. doi: 10.1094/PDIS-12-24-2589-SR. Online ahead of print.

ABSTRACT

Gummy stem blight (GSB), caused by three Stagonosporopsis species, S. citrulli, S. cucurbitacearum and S. caricae, is one of the most economically important diseases hindering watermelon production worldwide. Since there is no commercial resistance to GSB in watermelon cultivars, its management depends on cultural practices and preventative fungicides. Therefore, efficient methods for the detection of Stagonosporopsis species that could aid management decisions are required. To help achieve this, a loop-mediated isothermal amplification (LAMP) assay specific to S. citrulli (SCIT850) was developed under two detection formats: fluorescence quantification and endpoint colorimetric detection. The SCIT850 assay was determined to be specific to its target species and exhibited a consistent sensitivity of 1 pg of genomic DNA under both formats. The assay can be combined with a previously reported LAMP assay for the collective detection of the three Stagonosporopsis spp. (STAGY), which have comparable sensitivity to SCIT850 and can aid in species discrimination. A field diagnostic system for GSB-causing Stagonosporopsis was developed by coupling the SCIT850 and STAGY assays to quick DNA extraction protocols. Two DNA extraction methods were tested: one from leaves using cellulose dipsticks, and one from steel rods (typical of spore traps) using Chelex100. With the dipstick method, we detected pathogen DNA in inoculated asymptomatic, mildly infected, and severely infected plants, while with the Chelex100 we detected pathogen DNA from rods infested with as few as 500 spores. The SCIT850 and STAGY assays coupled with these quick sample processing methods could be adapted for field deployment, which would allow growers to make efficient and timely management decisions based on detection of the actual Stagonosporopsis species present in the field.

PMID:40767855 | DOI:10.1094/PDIS-12-24-2589-SR

Plant Dis. 2025 May 22. doi: 10.1094/PDIS-01-25-0117-SR. Online ahead of print.

ABSTRACT

Alternaria brassicicola is the causal agent typically associated with Alternaria leaf blight and head rot (ABHR) disease in broccoli and related crops in the Eastern United States. Recently a new species, A. japonica, has been reported as causing disease in broccoli and other vegetables in this region. We conducted a multi-state pathogen survey during the growing seasons of 2022 and 2023 to assess the distribution and occurrence of A. japonica in relation to A. brassicicola in five broccoli-producing states. Our approach specifically targeted collection of broccoli leaves with lesions typical of ABHR within commercially grown fields managed using either organic or conventional approaches in Connecticut, Massachusetts, New York, Virginia, and Georgia. Only typical ABHR leaf lesions were selected for pathogen isolation and, subsequently, sequencing of the Alternaria major allergen a1 gene was used to identify Alternaria species. The predominant species isolated was A. brassicicola (88% in 2022 and 94% in 2023) and the second most common was A. alternata (12% in 2022 and 6% in 2023), which was obtained from fields in Connecticut and Massachusetts in 2022, and in Virginia in both years. Alternaria japonica was not found in either year. Symptoms of A. alternata were indistinguishable from A. brassicicola, as were colony morphologies. While A. alternata is considered a generalist and of little consequence for broccoli, it is considered a pathogen of significance on multiple crops (blueberry, citrus, pistachios), but there remains scant information on the disease etiology on broccoli. Therefore, we inoculated broccoli with A. alternata in controlled conditions in order to shed light on possible differences in infectivity of these species on broccoli. Results of our study showed that A. alternata is pathogenic on broccoli, capable of initiating infection and causing lesions typical of ABHR. This indicates that future disease surveys of ABHR should conclusively identify species of Alternaria that are causing disease. Additional research is needed to determine the significance of this finding in relation to yield impacts, epidemiology, fungicide resistance, and management recommendations.

PMID:40403277 | DOI:10.1094/PDIS-01-25-0117-SR

Plant Genome. 2025 Jun;18(2):e70055. doi: 10.1002/tpg2.70055.

ABSTRACT

Leaf rust (LR) and stripe rust (YR), which are caused by Puccinia triticina and Puccinia striiformis, respectively, are among the most devastating wheat rusts worldwide. These diseases can be managed by using genetically resistant cultivars, an economical and environmentally safer alternative to fungicides. Over 100 and 80 Lr and Yr resistance genes have been discovered, respectively; however, rust pathogens are overcoming introduced resistance genes in the southeastern United States. Genome-wide association study has emerged as a valuable tool to identify new LR and YR resistance loci. In this study, a panel of 263 soft red winter wheat genotypes was evaluated for LR and YR severity in Plains, GA, and Williamson, GA, in a randomized complete block design of two replicates during 2019 and 2021-2023. Also, LR and YR infection types were assessed on seedlings at the three leaf stage in three greenhouse trials. A total of 26 significant quantitative trait loci (QTL) explaining 0.6%-30.8% phenotypic variance (PV) was detected by at least two of the five GAPIT models (BLINK, CMLM, FarmCPU, GLM, and MLM) tested. Nine major QTL included QLrYr-2A.1 linked to single-nucleotide polymorphism S2A_20855466, which had the highest overall PV (30.8%) for response to both rust pathogens in the field. Using the Chinese Spring Reference Genome Version 1.0, we detected 16 candidate genes, and four known R genes and QTL overlapped two major QTL. Of these QTL, 16 are likely novel genetic loci with potential for marker-assisted selection.

PMID:40495572 | DOI:10.1002/tpg2.70055

Nat Chem Biol. 2025 Jul 16. doi: 10.1038/s41589-025-01970-9. Online ahead of print.

ABSTRACT

Monoterpene indole alkaloids (MIAs) are a large, structurally diverse class of bioactive natural products. These compounds are biosynthetically derived from a stereoselective Pictet-Spengler condensation that generates a tetrahydro-β-carboline scaffold characterized by a 3S stereocenter. However, a subset of MIAs contains a noncanonical 3R stereocenter. Here we report the basis for 3R-MIA biosynthesis in Mitragyna speciosa (kratom). We discover the presence of the iminium species (20S)-3-dehydrocorynantheidine, which supports isomerization of 3S to 3R via oxidation and stereoselective reduction downstream of the initial Pictet-Spengler condensation. Isotopologue feeding experiments identify the sites for downstream MIA pathway biosynthesis as well as the oxidase/reductase pair that catalyzes this epimerization. This oxidase/reductase pair has broad substrate specificity, suggesting that this pathway may be responsible for the formation of many 3R-MIAs and downstream spirooxindole alkaloids in kratom. The elucidation of this epimerization mechanism allows biocatalytic access to a range of pharmacologically active spirooxindole alkaloid compounds.

PMID:40670688 | DOI:10.1038/s41589-025-01970-9

BMC Plant Biol. 2025 Jun 5;25(1):766. doi: 10.1186/s12870-025-06799-x.

ABSTRACT

BACKGROUND: Fruit ripening is a coordinated process that leads to an increase in sugars, decrease in acids and accumulation of pigments. Blueberry fruit exhibit an atypical climacteric ripening behavior. These fruit display an increase in respiration and ethylene production during ripening, however ethylene synthesis is developmentally regulated. In this study, the effect of ethylene on blueberry fruit ripening was investigated via preharvest applications of ethylene-releasing plant growth regulators (PGRs), ethephon and 1-aminocyclopropane 1-carboxylic acid (ACC), in one southern highbush cultivar, Miss Lilly in 2019, and two rabbiteye cultivars, Premier and Powderblue in 2019 and 2020. Further, the effects of these two PGRs on fruit metabolism during ripening in the two rabbiteye cultivars, and postharvest fruit quality in all three cultivars were evaluated.

RESULTS: Both PGRs increased ethylene evolution within 1-3 days after treatment (DAT). Ethephon and ACC applications increased the rate of ripening within 5 DAT in all cultivars, and increased ripe (blue) fruit by up to 35% and 29%, respectively between 7 to 10 DAT compared to the control. Metabolite analysis revealed that PGR treatments resulted in an immediate, but transient increase in sucrose, glucose and fructose, in ‘Premier’ at 3 DAT. Malate decreased at 3 DAT in response to both PGR treatments in ‘Premier’, and at 5 DAT in ethephon treatment in both cultivars. A rapid increase in the concentration of multiple anthocyanins was noted at 3 DAT in response to both PGRs in ‘Premier’ and ‘Powderblue’. Gene expression analysis revealed an increase in transcript abundance of VACUOLAR INVERTASE (vINV) and multiple anthocyanin biosynthesis genes between 1 and 3 DAT after PGR treatments in both cultivars, supporting the metabolite changes. However, the alteration in fruit metabolite concentrations were not sustained, and similar in PGR-treated fruit compared to the control in ripe fruit harvested at 10 DAT. Postharvest fruit quality attributes, such as firmness, total soluble solids, titratable acidity, and visual quality, were not consistently affected by the PGR applications compared to control treatments across all cultivars. A decrease in fruit weight was noted, although not consistently, in response to PGR treatments.

CONCLUSIONS: Overall, this study demonstrates that ethylene plays a crucial role in promoting ripening via rapid and transient stimulation of sugar, acid and anthocyanin metabolism. The promotion of fruit ripening by ethylene-releasing PGRs can lead to minimal but inconsistent changes in fruit quality attributes during postharvest storage.

PMID:40474063 | DOI:10.1186/s12870-025-06799-x

bioRxiv [Preprint]. 2025 May 28:2025.05.23.655667. doi: 10.1101/2025.05.23.655667.

ABSTRACT

Repairing a damaged body part is critical for the survival of any organism. In plants, tissue damage induces rapid responses that activate defense, regeneration and wound healing. While early wound signaling mediated by phytohormones, electrical signals and reactive oxygen species is well-characterized, the mechanisms governing the final stages of wound healing remain poorly understood. Here, we show that wounding in Arabidopsis leaves induces localized cooling, likely due to evaporative water loss, accompanied by the activation of cold-responsive genes. The subsequent disappearance of localized cooling and deactivation of cold-responsive genes serve as a quantitative marker of wound healing. Based on these observations, we developed a workflow by leveraging computer vision and deep learning to monitor the dynamics of wound healing. We found that CBFs transcription factors relay injury-induced cooling signal to wound healing. Thus, our work advances our understanding of tissue repair and provides a tool to quantify wound healing in plants.

PMID:40502075 | PMC:PMC12154623 | DOI:10.1101/2025.05.23.655667

PLoS Genet. 2025 Jul 16;21(7):e1011742. doi: 10.1371/journal.pgen.1011742. Online ahead of print.

ABSTRACT

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used genotype-by-sequencing data to score more than 10,000 maize and teosinte lines for the presence or absence of each driver. Fewer than ~0.5% of modern inbred lines carry chromosomal drivers. In contrast, among individuals from 5331 open-pollinated landraces, 6.32% carried Ab10, 5.16% carried K10L2, and 12.28% carried at least one B chromosome. These frequencies are consistent with those reported in previous studies. Using a GWAS approach we identified unlinked loci that associate with the presence or absence of the selfish genetic elements. Many significant SNPs are positively associated with the drivers, suggesting that there may have been selection for alleles that ameliorate their negative fitness consequences. We then assessed the contributions of population structure, associated loci, and the environment on the distribution of each chromosomal driver. There was no significant relationship between any chromosomal driver and altitude, contrary to conclusions based on smaller studies. Our data suggest that the distribution of the major chromosomal drivers is primarily influenced by neutral processes and the deleterious fitness consequences of the drivers themselves. While each driver has a unique relationship to genetic background and the environment, they are largely unconstrained by either.

PMID:40668866 | DOI:10.1371/journal.pgen.1011742

bioRxiv [Preprint]. 2025 May 27:2025.05.22.655462. doi: 10.1101/2025.05.22.655462.

ABSTRACT

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used genotype-by-sequencing data to score more than 10,000 maize and teosinte lines for the presence or absence of each driver. Less than ~0.5% of modern inbred lines carry chromosomal drivers. Among individuals from 5331 open-pollinated landraces, 6.32% carried Ab10, 5.16% carried K10L2, and 12.28% carried at least one B chromosome. Using a GWAS approach we identified unlinked loci that associate with the presence or absence of the selfish genetic elements. Many genetic modifiers are positively associated with the drivers, suggesting that there may have been selection for alleles that ameliorate their negative fitness consequences. We then assessed the contributions of population structure, associated loci, and the environment on the distribution of each chromosomal driver. There was no significant relationship between any chromosomal driver and altitude, contrary to conclusions based on smaller studies. Our data suggest that the distribution of the major chromosomal drivers is primarily influenced by neutral processes and the deleterious fitness consequences of the drivers themselves. While each driver has a unique relationship to genetic background and the environment, they are largely unconstrained by either.

PMID:40501570 | PMC:PMC12154789 | DOI:10.1101/2025.05.22.655462

Molecules. 2025 Apr 30;30(9):2020. doi: 10.3390/molecules30092020.

ABSTRACT

The discovery of bioactive natural products is often challenged by the complexity of isolating and characterizing active compounds within diverse mixtures. Previously, we introduced a ¹H NMR-based weighted gene correlation network analysis (WGCNA) approach to identify spectral features linked to growth inhibitory activity of Piper (Piperaceae) leaf extracts against model plant, fungal, and bacterial organisms. This method enabled us to prioritize specific spectral features linked to bioactivity, offering a targeted approach to natural product discovery. In this study, we validate the predictive capacity of the WGCNA by isolating the compounds responsible for the bioactivity-associated resonances and confirming their antifungal efficacy. Using growth inhibition assays, we verified that the isolated compounds, including three novel antifungal agents, exhibited significant bioactivity. Notably, one of these compounds contains a rare imidazolium heterocyclic motif, marking a new structural class in Piper. These findings substantiate the ¹H NMR-based WGCNA as a reliable tool for identifying structural types associated with biological activity, streamlining the process of discovering bioactive natural products in complex extracts.

PMID:40363825 | PMC:PMC12073215 | DOI:10.3390/molecules30092020

Phytopathology. 2025 Jun 22. doi: 10.1094/PHYTO-03-25-0093-R. Online ahead of print.

ABSTRACT

Phony peach disease (PPD), caused by Xylella fastidiosa subsp. multiplex (Xfm), poses a significant threat to commercial peach orchards in Georgia. Early and accurate detection is essential for effective disease management, yet visual assessment remains the primary approach for diagnosing PPD symptoms due to the high cost and logistical challenges of qPCR-based detection of Xfm. We evaluated the accuracy of visual PPD assessment and examined the factors influencing rater performance, symptom reliability, and optimal survey deployment strategies with CART/Random Forest analyses and simulations. Internode length was the most reliable symptom for PPD identification in two peach cultivars, consistently outperforming other physical traits such as canopy flatness and shape. Primer pair C06Xf-bamA had the greatest relative sensitivity, making it the preferred choice for qPCR confirmation. Principal component analysis suggested that rater experience significantly improved agreement with qPCR results and repeated assessments of the same orchards further enhanced consistency for raters. Simulations results suggested that deploying two experienced raters may provide the highest detection diagnostic accuracy for survey purposes, particularly when qPCR-based pathogen detection is unavailable. Last, PPD-affected trees, through PCR verification and visual identification, exhibited higher mortality rates than Xfm-negative trees, reinforcing the need for early detection and removal to limit disease spread. These findings underscore the importance of strategic rater deployment, targeted symptom selection, and integrating molecular diagnostics when feasible.

PMID:40544457 | DOI:10.1094/PHYTO-03-25-0093-R

Plant Physiol. 2025 Jul 3;198(3):kiaf294. doi: 10.1093/plphys/kiaf294.

ABSTRACT

Minimal native and synthetic Polymerase III promoters enable efficient and customizable CRISPR multiplexing in plants, expanding genome engineering capabilities

PMID:40673482 | PMC:PMC12268498 | DOI:10.1093/plphys/kiaf294

Sci Data. 2025 Aug 5;12(1):1362. doi: 10.1038/s41597-025-05131-4.

ABSTRACT

Biological nitrogen fixation (BNF) is the main natural source of new nitrogen inputs in terrestrial ecosystems, supporting terrestrial productivity, carbon uptake, and other Earth system processes. We assembled a comprehensive global dataset of field measurements of BNF in all major N-fixing niches across natural terrestrial biomes derived from the analysis of 376 BNF studies. The dataset comprises 32 variables, including site location, biome type, N-fixing niche, sampling year, quantification method, BNF rate (kg N ha^-1 y^-1), the percentage of nitrogen derived from the atmosphere (%N_dfa), N fixer or N-fixing substrate abundance, BNF rate per unit of N fixer abundance, and species identity. Overall, the dataset combines 1,207 BNF rates for trees, shrubs, herbs, soil, leaf litter, woody litter, dead wood, mosses, lichens, and biocrusts, 152 herb %N_dfa values, 1,005 measurements of N fixer or N-fixing substrate abundance, and 762 BNF rates per unit of N fixer abundance for a total of 424 species across 66 countries. This dataset facilitates synthesis, meta-analysis, upscaling, and model benchmarking of BNF fluxes at multiple spatial scales.

PMID:40764484 | DOI:10.1038/s41597-025-05131-4

Plant Commun. 2025 Jun 3:101393. doi: 10.1016/j.xplc.2025.101393. Online ahead of print.

ABSTRACT

Teucrium chamaedrys, also called wall germander, is a small woody shrub native to the Mediterranean region. Its name is derived from the Greek words meaning ‘ground oak’, since its tiny leaves resemble those of an oak tree. Teucrium species are proliferative producers of diterpenes, which afford them valuable properties widely co-opted in traditional and western medicines. Sequence and assembly of the 3 Gbp tetraploid T. chamaedrys revealed 74 diterpene synthase genes, with the vast representation of these diterpene synthases clustered along four genomic loci. Comparative genomics revealed that this cluster is mirrored in the closely related species, Teucrium marum. Along with the presence of several cytochrome p450 sequences, this region is the one of largest biosynthetic gene clusters identified. Teucrium is well known for accumulating clerodane-type diterpenoids which are produced from a kolavanyl diphosphate precursor. To elucidate the complex biosynthetic pathways of these medicinal compounds, we identified and functionally characterized several kolavanyl diphosphate synthases from T. chamaedrys. Its remarkable chemistry and tetraploidy make T. chamaedrys an interesting and unique model for studying genomic evolution and adaptation in plants.

PMID:40468595 | DOI:10.1016/j.xplc.2025.101393

Front Plant Sci. 2025 Jul 11;16:1607733. doi: 10.3389/fpls.2025.1607733. eCollection 2025.

ABSTRACT

Maize (Zea mays L.) is the most widely produced crop in the world, and conventional production requires significant amounts of synthetic nitrogen fertilizer, which has negative economic and environmental consequences. Maize landraces from Oaxaca, Mexico, can acquire nitrogen from nitrogen-fixing bacteria that live in a mucilage secreted by aerial nodal roots. The development of these nodal roots is a characteristic traditionally associated with the juvenile vegetative stage of maize plants. However, mature Oaxacan landraces develop many more nodes with aerial roots than commercial maize varieties. Our study shows that Oaxacan landraces develop aerial roots during the juvenile and adult vegetative phases and even during early flowering under greenhouse and field conditions. Surprisingly, the development of these roots was only minimally affected by soil nitrogen and ambient humidity. These findings are an essential first step in developing maize varieties to reduce fertilizer needs in maize production across different environmental conditions.

PMID:40718026 | PMC:PMC12289584 | DOI:10.3389/fpls.2025.1607733

Tree Physiol. 2025 Jul 11:tpaf080. doi: 10.1093/treephys/tpaf080. Online ahead of print.

ABSTRACT

Sulfate-proton co-transporters (SULTRs) mediate sulfate uptake, transport, storage, and assimilation in plants. The SULTR family has historically been classified into four groups (SULTR1-SULTR4), with well-characterized roles for SULTR groups 1, 2, and 4. However, the functions of the large and diverse SULTR3 group remain poorly understood. Here, we present an updated phylogenetic analysis of SULTRs across angiosperms, including multiple early-divergent lineages. Our results suggest that the enigmatic SULTR3 group comprises four distinct subfamilies that predate the emergence of angiosperms, providing a basis for reclassifying the SULTR family into seven subfamilies. This expanded classification is supported by subfamily-specific gene structures and amino acid substitutions in the substrate-binding pocket. Structural modeling identified three serine residues uniquely lining the substrate-binding pocket of SULTR3.4, enabling three hydrogen bonds with the phosphate ion. The data support the proposed neofunctionalization of this subfamily for phosphate allocation within vascular tissues. Transcriptome analysis of Populus tremula × alba revealed divergent tissue expression preferences among SULTR subfamilies and between genome duplicates. We observed partitioned expression in vascular tissues among the four SULTR3 subfamilies, with PtaSULTR3.4a and PtaSULTR3.2a preferentially expressed in primary and secondary xylem, respectively. Gene coexpression analysis revealed coordinated expression of PtaSULTR3.4a with genes involved in phosphate starvation responses and nutrient transport, consistent with a potential role in phosphate homeostasis. In contrast, PtaSULTR3.2a was strongly coexpressed with lignification and one-carbon metabolism genes and their upstream transcription regulators. PtaSULTR3.2a belongs to a eudicot-specific branch of the SULTR3.1 subfamily found only in perennial species, suggesting a specialized role in lignifying tissues. Together, our findings provide a refined phylogenetic framework for the SULTR family and suggest that the expanded SULTR3 subfamilies have undergone neofunctionalization during the evolution of vascular and perennial plants.

PMID:40643194 | DOI:10.1093/treephys/tpaf080

Insects. 2025 Jun 24;16(7):653. doi: 10.3390/insects16070653.

ABSTRACT

Blueberry is a high-value fruit crop in the United States, with Georgia and Florida serving as important early-season production regions. In these areas, several thrips species (Thysanoptera: Thripidae), including Frankliniella tritici (Fitch), Frankliniella bispinosa (Morgan), and Scirtothrips dorsalis (Hood), have emerged as economically significant pests. While F. tritici and F. bispinosa primarily damage floral tissues, S. dorsalis targets young foliage. Their rapid reproduction, high mobility, and broad host range contribute to rapid population buildup and complicate the management programs. Species identification is often difficult due to overlapping morphological features and requires the use of molecular diagnostic tools for accurate identification. Although action thresholds, such as 2-6 F. tritici per flower cluster, are used to guide management decisions, robust economic thresholds based on yield loss remain undeveloped. Integrated pest management (IPM) practices include regular monitoring, cultural control (e.g., pruning, reflective mulch), biological control using Orius insidiosus (Say) and predatory mites, and chemical control. Reduced-risk insecticides like spinetoram and spinosad offer effective suppression while minimizing harm to pollinators and beneficial insects. However, the brief flowering period limits the establishment of biological control agents. Developing species-specific economic thresholds and phenology-based IPM strategies is critical for effective and sustainable thrips management in blueberry cropping systems.

PMID:40725285 | DOI:10.3390/insects16070653

Fungal Biol. 2025 Aug;129(5):101590. doi: 10.1016/j.funbio.2025.101590. Epub 2025 May 6.

ABSTRACT

The Fifth International Symposium on Fungal Stress (ISFUS) brought together in Brazil many of the leaders in the field of fungal stress responses, from fourteen countries, for four days of outstanding science ranging from basic research to studies with agricultural, medical, industrial, and environmental significance. In addition to the excellent oral and poster presentations, the Symposium organisers ensured that all participants had ample opportunity to engage, socialise, and network to exchange ideas and share research. The conference was enhanced by the world-class venue near Iguazu Falls, probably the greatest natural phenomenon in South America.

PMID:40707112 | DOI:10.1016/j.funbio.2025.101590

Mol Ecol Resour. 2025 Jul 22:e70012. doi: 10.1111/1755-0998.70012. Online ahead of print.

ABSTRACT

Yellow monkeyflowers (Mimulus guttatus complex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan-genomics in this group, we present four chromosome-scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a single M. guttatus population, one from the closely related selfing species M. nasutus, and one from a more divergent species M. tilingii. All assemblies are highly complete and resolve centromeric and repetitive regions. Comparative analyses reveal such extensive structural variation in repeat-rich, gene-poor regions that large portions of the genome are unalignable across accessions. As a result, this Mimulus pan-genome is primarily informative in genic regions, underscoring limitations of resequencing approaches in such polymorphic taxa. We document gene presence-absence, investigate the recombination landscape using high-resolution linkage data, and quantify nucleotide diversity. Surprisingly, pairwise differences at fourfold synonymous sites are exceptionally high-even in regions of very low recombination-reaching ~3.2% within a single M. guttatus population, ~7% within the interfertile M. guttatus species complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolated M. tilingii. Genome-wide patterns of nucleotide variation show little evidence of linked selection, and instead suggest that the concentration of genes (and likely selected sites) in high-recombination regions may buffer diversity loss. These assemblies, annotations, and comparative analyses provide a robust genomic foundation for Mimulus research and offer new insights into the interplay of recombination, structural variation, and molecular evolution in highly diverse plant genomes.

PMID:40693537 | DOI:10.1111/1755-0998.70012

Phytopathology. 2025 Jun 11. doi: 10.1094/PHYTO-04-25-0143-SC. Online ahead of print.

ABSTRACT

Root-knot nematodes (Meloidogyne spp.) are a continuing threat to soybean production, with M. incognita being the predominant species. The deployment of Mi-resistant soybean cultivars is a primary management strategy, but the underlying molecular mechanisms contributing to resistance remain unknown. A single, additive gene for resistance to M. incognita, Rmi1, was previously identified in soybean cv. Forrest and associated with the emigration of second-stage juveniles from the roots. To better understand the Rmi1-mediated resistance response, we used Forrest-derived F₅ RILs differing for Rmi1 to analyze global changes in gene expression in response to M. incognita infection at 2- and 4-days post inoculation. We identified 1,471 differentially expressed (DE) genes in the compatible interaction and 1,037 DE genes in the incompatible interaction. Forty-five percent of DE genes were DE in both interactions, 42% (856) were unique to the compatible interaction, and 13% (261) were unique to the incompatible interaction. Genes uniquely DE in the incompatible interaction included genes involved in cell wall modification, hormone signaling, endomembrane trafficking, and redox reactions providing new insights into the resistance mechanism mediated by Rmi1 in soybean to root-knot nematodes.

PMID:40498525 | DOI:10.1094/PHYTO-04-25-0143-SC

Genetics. 2025 May 14:iyaf091. doi: 10.1093/genetics/iyaf091. Online ahead of print.

ABSTRACT

In maize, there are two meiotic drive systems that target large heterochromatic knobs composed of tandem repeats known as knob180 and TR-1. The first meiotic drive haplotype, Abnormal chromosome 10 (Ab10) confers strong meiotic drive (∼75% transmission as a heterozygote) and encodes two kinesins: KINDR, which associates with knob180 repeats and TRKIN, which associates with TR-1 repeats. Prior data show that meiotic drive is conferred primarily by the KINDR/knob180 system while the TRKIN/TR-1 system seems to have little or no role, making it unclear why Trkin has been maintained in Ab10 haplotypes. The second meiotic drive haplotype, K10L2, confers a low level of meiotic drive (∼51-52%) and only encodes the TRKIN/TR-1 system. Here we used long-read sequencing to assemble the K10L2 haplotype and showed that it has strong homology to an internal portion of the Ab10 haplotype. We also carried out CRISPR mutagenesis to test the role of Trkin on Ab10 and K10L2. The data indicate that the Trkin gene on Ab10 does not improve drive or fitness but instead has a weak deleterious effect when paired with a normal chromosome 10. The deleterious effect is more severe when Ab10 is paired with K10L2: in this context functional Trkin on either chromosome nearly abolishes Ab10 drive. Mathematical modeling based on the empirical data suggest that Trkin is unlikely to persist on Ab10. We conclude that Trkin either confers an advantage to Ab10 in untested circumstances or that it is in the process of being purged from the Ab10 population.

PMID:40365704 | DOI:10.1093/genetics/iyaf091

BMC Microbiol. 2025 Jul 28;25(1):456. doi: 10.1186/s12866-025-04175-1.

ABSTRACT

BACKGROUND: The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates.

RESULTS: Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110 bp and at 370 bp, while strains only displaying the 110 bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification.

CONCLUSIONS: The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.

PMID:40722002 | DOI:10.1186/s12866-025-04175-1

Plant Dis. 2025 Aug 6. doi: 10.1094/PDIS-12-24-2589-SR. Online ahead of print.

ABSTRACT

Gummy stem blight (GSB), caused by three Stagonosporopsis species, S. citrulli, S. cucurbitacearum and S. caricae, is one of the most economically important diseases hindering watermelon production worldwide. Since there is no commercial resistance to GSB in watermelon cultivars, its management depends on cultural practices and preventative fungicides. Therefore, efficient methods for the detection of Stagonosporopsis species that could aid management decisions are required. To help achieve this, a loop-mediated isothermal amplification (LAMP) assay specific to S. citrulli (SCIT850) was developed under two detection formats: fluorescence quantification and endpoint colorimetric detection. The SCIT850 assay was determined to be specific to its target species and exhibited a consistent sensitivity of 1 pg of genomic DNA under both formats. The assay can be combined with a previously reported LAMP assay for the collective detection of the three Stagonosporopsis spp. (STAGY), which have comparable sensitivity to SCIT850 and can aid in species discrimination. A field diagnostic system for GSB-causing Stagonosporopsis was developed by coupling the SCIT850 and STAGY assays to quick DNA extraction protocols. Two DNA extraction methods were tested: one from leaves using cellulose dipsticks, and one from steel rods (typical of spore traps) using Chelex100. With the dipstick method, we detected pathogen DNA in inoculated asymptomatic, mildly infected, and severely infected plants, while with the Chelex100 we detected pathogen DNA from rods infested with as few as 500 spores. The SCIT850 and STAGY assays coupled with these quick sample processing methods could be adapted for field deployment, which would allow growers to make efficient and timely management decisions based on detection of the actual Stagonosporopsis species present in the field.

PMID:40767855 | DOI:10.1094/PDIS-12-24-2589-SR

Plant Dis. 2025 May 22. doi: 10.1094/PDIS-01-25-0117-SR. Online ahead of print.

ABSTRACT

Alternaria brassicicola is the causal agent typically associated with Alternaria leaf blight and head rot (ABHR) disease in broccoli and related crops in the Eastern United States. Recently a new species, A. japonica, has been reported as causing disease in broccoli and other vegetables in this region. We conducted a multi-state pathogen survey during the growing seasons of 2022 and 2023 to assess the distribution and occurrence of A. japonica in relation to A. brassicicola in five broccoli-producing states. Our approach specifically targeted collection of broccoli leaves with lesions typical of ABHR within commercially grown fields managed using either organic or conventional approaches in Connecticut, Massachusetts, New York, Virginia, and Georgia. Only typical ABHR leaf lesions were selected for pathogen isolation and, subsequently, sequencing of the Alternaria major allergen a1 gene was used to identify Alternaria species. The predominant species isolated was A. brassicicola (88% in 2022 and 94% in 2023) and the second most common was A. alternata (12% in 2022 and 6% in 2023), which was obtained from fields in Connecticut and Massachusetts in 2022, and in Virginia in both years. Alternaria japonica was not found in either year. Symptoms of A. alternata were indistinguishable from A. brassicicola, as were colony morphologies. While A. alternata is considered a generalist and of little consequence for broccoli, it is considered a pathogen of significance on multiple crops (blueberry, citrus, pistachios), but there remains scant information on the disease etiology on broccoli. Therefore, we inoculated broccoli with A. alternata in controlled conditions in order to shed light on possible differences in infectivity of these species on broccoli. Results of our study showed that A. alternata is pathogenic on broccoli, capable of initiating infection and causing lesions typical of ABHR. This indicates that future disease surveys of ABHR should conclusively identify species of Alternaria that are causing disease. Additional research is needed to determine the significance of this finding in relation to yield impacts, epidemiology, fungicide resistance, and management recommendations.

PMID:40403277 | DOI:10.1094/PDIS-01-25-0117-SR

Plant Genome. 2025 Jun;18(2):e70055. doi: 10.1002/tpg2.70055.

ABSTRACT

Leaf rust (LR) and stripe rust (YR), which are caused by Puccinia triticina and Puccinia striiformis, respectively, are among the most devastating wheat rusts worldwide. These diseases can be managed by using genetically resistant cultivars, an economical and environmentally safer alternative to fungicides. Over 100 and 80 Lr and Yr resistance genes have been discovered, respectively; however, rust pathogens are overcoming introduced resistance genes in the southeastern United States. Genome-wide association study has emerged as a valuable tool to identify new LR and YR resistance loci. In this study, a panel of 263 soft red winter wheat genotypes was evaluated for LR and YR severity in Plains, GA, and Williamson, GA, in a randomized complete block design of two replicates during 2019 and 2021-2023. Also, LR and YR infection types were assessed on seedlings at the three leaf stage in three greenhouse trials. A total of 26 significant quantitative trait loci (QTL) explaining 0.6%-30.8% phenotypic variance (PV) was detected by at least two of the five GAPIT models (BLINK, CMLM, FarmCPU, GLM, and MLM) tested. Nine major QTL included QLrYr-2A.1 linked to single-nucleotide polymorphism S2A_20855466, which had the highest overall PV (30.8%) for response to both rust pathogens in the field. Using the Chinese Spring Reference Genome Version 1.0, we detected 16 candidate genes, and four known R genes and QTL overlapped two major QTL. Of these QTL, 16 are likely novel genetic loci with potential for marker-assisted selection.

PMID:40495572 | DOI:10.1002/tpg2.70055

Nat Chem Biol. 2025 Jul 16. doi: 10.1038/s41589-025-01970-9. Online ahead of print.

ABSTRACT

Monoterpene indole alkaloids (MIAs) are a large, structurally diverse class of bioactive natural products. These compounds are biosynthetically derived from a stereoselective Pictet-Spengler condensation that generates a tetrahydro-β-carboline scaffold characterized by a 3S stereocenter. However, a subset of MIAs contains a noncanonical 3R stereocenter. Here we report the basis for 3R-MIA biosynthesis in Mitragyna speciosa (kratom). We discover the presence of the iminium species (20S)-3-dehydrocorynantheidine, which supports isomerization of 3S to 3R via oxidation and stereoselective reduction downstream of the initial Pictet-Spengler condensation. Isotopologue feeding experiments identify the sites for downstream MIA pathway biosynthesis as well as the oxidase/reductase pair that catalyzes this epimerization. This oxidase/reductase pair has broad substrate specificity, suggesting that this pathway may be responsible for the formation of many 3R-MIAs and downstream spirooxindole alkaloids in kratom. The elucidation of this epimerization mechanism allows biocatalytic access to a range of pharmacologically active spirooxindole alkaloid compounds.

PMID:40670688 | DOI:10.1038/s41589-025-01970-9

BMC Plant Biol. 2025 Jun 5;25(1):766. doi: 10.1186/s12870-025-06799-x.

ABSTRACT

BACKGROUND: Fruit ripening is a coordinated process that leads to an increase in sugars, decrease in acids and accumulation of pigments. Blueberry fruit exhibit an atypical climacteric ripening behavior. These fruit display an increase in respiration and ethylene production during ripening, however ethylene synthesis is developmentally regulated. In this study, the effect of ethylene on blueberry fruit ripening was investigated via preharvest applications of ethylene-releasing plant growth regulators (PGRs), ethephon and 1-aminocyclopropane 1-carboxylic acid (ACC), in one southern highbush cultivar, Miss Lilly in 2019, and two rabbiteye cultivars, Premier and Powderblue in 2019 and 2020. Further, the effects of these two PGRs on fruit metabolism during ripening in the two rabbiteye cultivars, and postharvest fruit quality in all three cultivars were evaluated.

RESULTS: Both PGRs increased ethylene evolution within 1-3 days after treatment (DAT). Ethephon and ACC applications increased the rate of ripening within 5 DAT in all cultivars, and increased ripe (blue) fruit by up to 35% and 29%, respectively between 7 to 10 DAT compared to the control. Metabolite analysis revealed that PGR treatments resulted in an immediate, but transient increase in sucrose, glucose and fructose, in ‘Premier’ at 3 DAT. Malate decreased at 3 DAT in response to both PGR treatments in ‘Premier’, and at 5 DAT in ethephon treatment in both cultivars. A rapid increase in the concentration of multiple anthocyanins was noted at 3 DAT in response to both PGRs in ‘Premier’ and ‘Powderblue’. Gene expression analysis revealed an increase in transcript abundance of VACUOLAR INVERTASE (vINV) and multiple anthocyanin biosynthesis genes between 1 and 3 DAT after PGR treatments in both cultivars, supporting the metabolite changes. However, the alteration in fruit metabolite concentrations were not sustained, and similar in PGR-treated fruit compared to the control in ripe fruit harvested at 10 DAT. Postharvest fruit quality attributes, such as firmness, total soluble solids, titratable acidity, and visual quality, were not consistently affected by the PGR applications compared to control treatments across all cultivars. A decrease in fruit weight was noted, although not consistently, in response to PGR treatments.

CONCLUSIONS: Overall, this study demonstrates that ethylene plays a crucial role in promoting ripening via rapid and transient stimulation of sugar, acid and anthocyanin metabolism. The promotion of fruit ripening by ethylene-releasing PGRs can lead to minimal but inconsistent changes in fruit quality attributes during postharvest storage.

PMID:40474063 | DOI:10.1186/s12870-025-06799-x

bioRxiv [Preprint]. 2025 May 28:2025.05.23.655667. doi: 10.1101/2025.05.23.655667.

ABSTRACT

Repairing a damaged body part is critical for the survival of any organism. In plants, tissue damage induces rapid responses that activate defense, regeneration and wound healing. While early wound signaling mediated by phytohormones, electrical signals and reactive oxygen species is well-characterized, the mechanisms governing the final stages of wound healing remain poorly understood. Here, we show that wounding in Arabidopsis leaves induces localized cooling, likely due to evaporative water loss, accompanied by the activation of cold-responsive genes. The subsequent disappearance of localized cooling and deactivation of cold-responsive genes serve as a quantitative marker of wound healing. Based on these observations, we developed a workflow by leveraging computer vision and deep learning to monitor the dynamics of wound healing. We found that CBFs transcription factors relay injury-induced cooling signal to wound healing. Thus, our work advances our understanding of tissue repair and provides a tool to quantify wound healing in plants.

PMID:40502075 | PMC:PMC12154623 | DOI:10.1101/2025.05.23.655667

PLoS Genet. 2025 Jul 16;21(7):e1011742. doi: 10.1371/journal.pgen.1011742. Online ahead of print.

ABSTRACT

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used genotype-by-sequencing data to score more than 10,000 maize and teosinte lines for the presence or absence of each driver. Fewer than ~0.5% of modern inbred lines carry chromosomal drivers. In contrast, among individuals from 5331 open-pollinated landraces, 6.32% carried Ab10, 5.16% carried K10L2, and 12.28% carried at least one B chromosome. These frequencies are consistent with those reported in previous studies. Using a GWAS approach we identified unlinked loci that associate with the presence or absence of the selfish genetic elements. Many significant SNPs are positively associated with the drivers, suggesting that there may have been selection for alleles that ameliorate their negative fitness consequences. We then assessed the contributions of population structure, associated loci, and the environment on the distribution of each chromosomal driver. There was no significant relationship between any chromosomal driver and altitude, contrary to conclusions based on smaller studies. Our data suggest that the distribution of the major chromosomal drivers is primarily influenced by neutral processes and the deleterious fitness consequences of the drivers themselves. While each driver has a unique relationship to genetic background and the environment, they are largely unconstrained by either.

PMID:40668866 | DOI:10.1371/journal.pgen.1011742

bioRxiv [Preprint]. 2025 May 27:2025.05.22.655462. doi: 10.1101/2025.05.22.655462.

ABSTRACT

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used genotype-by-sequencing data to score more than 10,000 maize and teosinte lines for the presence or absence of each driver. Less than ~0.5% of modern inbred lines carry chromosomal drivers. Among individuals from 5331 open-pollinated landraces, 6.32% carried Ab10, 5.16% carried K10L2, and 12.28% carried at least one B chromosome. Using a GWAS approach we identified unlinked loci that associate with the presence or absence of the selfish genetic elements. Many genetic modifiers are positively associated with the drivers, suggesting that there may have been selection for alleles that ameliorate their negative fitness consequences. We then assessed the contributions of population structure, associated loci, and the environment on the distribution of each chromosomal driver. There was no significant relationship between any chromosomal driver and altitude, contrary to conclusions based on smaller studies. Our data suggest that the distribution of the major chromosomal drivers is primarily influenced by neutral processes and the deleterious fitness consequences of the drivers themselves. While each driver has a unique relationship to genetic background and the environment, they are largely unconstrained by either.

PMID:40501570 | PMC:PMC12154789 | DOI:10.1101/2025.05.22.655462

Nature. 2025 Jul;643(8072):705-711. doi: 10.1038/s41586-025-09201-w. Epub 2025 Jul 16.

ABSTRACT

Biological nitrogen fixation (BNF) is the largest natural source of new nitrogen (N) that supports terrestrial productivity^1,2, yet estimates of global terrestrial BNF remain highly uncertain^3,4. Here we show that this uncertainty is partly because of sampling bias, as field BNF measurements in natural terrestrial ecosystems occur where N fixers are 17 times more prevalent than their mean abundances worldwide. To correct this bias, we develop new estimates of global terrestrial BNF by upscaling field BNF measurements using spatially explicit abundances of all major biogeochemical N-fixing niches. We find that natural biomes sustain lower BNF, 65 (52-77) Tg N yr^-1, than previous empirical bottom-up estimates^3,4, with most BNF occurring in tropical forests and drylands. We also find high agricultural BNF in croplands and cultivated pastures, 56 (54-58) Tg N yr^-1. Agricultural BNF has increased terrestrial BNF by 64% and total terrestrial N inputs from all sources by 60% over pre-industrial levels. Our results indicate that BNF may impose stronger constraints on the carbon sink in natural terrestrial biomes and represent a larger source of agricultural N than is generally considered in analyses of the global N cycle^5,6, with implications for proposed safe operating limits for N use^7,8.

PMID:40670639 | DOI:10.1038/s41586-025-09201-w

Sci Adv. 2025 May 23;11(21):eadw3433. doi: 10.1126/sciadv.adw3433. Epub 2025 May 21.

ABSTRACT

Activation of synthetic centromeres on chromosome 4 in maize leads to its breakage and formation of trisomic fragments called neochromosomes. A limitation of neochromosomes is their low and unpredictable transmission rates due to trisomy. Here, we report that selecting for dicentric recombinants through male crosses uncovers stabilized chromosome 4 fission events, which split it into 4a-4b complementary chromosome pairs, where 4a carries a native centromere and 4b carries a synthetic one. The cells rapidly stabilized chromosome ends by de novo telomere formation, and the new centromeres spread among genes without altering their expression. When both 4a and 4b chromosomes were made homozygous, they segregated through meiosis indistinguishably from wild type and gave rise to healthy plants with normal seed set, indicating that the synthetic centromere was fully functional. This work leverages synthetic centromeres to engineer chromosome fission, raising the diploid chromosome number of maize from 20 to 22.

PMID:40397737 | PMC:PMC12094224 | DOI:10.1126/sciadv.adw3433

Integr Comp Biol. 2025 May 8:icaf028. doi: 10.1093/icb/icaf028. Online ahead of print.

ABSTRACT

Climate change is simultaneously increasing atmospheric carbon dioxide concentrations ([CO2]) and temperatures. We conducted a multi-factorial growth chamber experiment to examine how these climate change factors interact to influence the expression of ecologically-relevant traits, clines in these traits, and natural selection on morphology and phenology of diverse accessions of Boechera stricta (Brassicaceae) sourced from a broad elevational gradient in Colorado, USA. Plastic shifts in a key allocation trait (root mass fraction) in response to temperature accord with the direction of selection for probability of flowering, indicating that plasticity in this trait could be adaptive. However, plasticity in a foliar functional trait (leaf dry matter content) in response to temperature and [CO2] did not align with the direction of selection, indicating that plasticity could reduce fitness based on plant carbon allocation strategies. For another ecologically-important phenotype, selection favors resource acquisitive trait values (higher specific leaf area) under elevated [CO2] and resource conservative trait values (lower specific leaf area) at lower [CO2], despite the lack of plasticity in this trait. This pattern of selection counters published reports that elevated [CO2] induces low specific leaf area but could enable plants to reproduce across a greater period of the growing season under increasingly warm climates. Indeed, warmer temperatures prolonged the duration of flowering. This plasticity is likely adaptive, as selection favored increased flowering duration in the higher temperature treatment level. Thus, the two major results that emerged from our study are that climate change could impose novel and unanticipated patterns of natural selection on plant traits and that plasticity in these traits can be a maladaptive response to stress.

PMID:40338630 | DOI:10.1093/icb/icaf028

Trends Ecol Evol. 2025 Jun 13:S0169-5347(25)00132-6. doi: 10.1016/j.tree.2025.05.001. Online ahead of print.

ABSTRACT

The resilience of ecosystems to climate disruption requires internal feedbacks that support the stability of ecosystem structure and function. Such feedbacks may include sustained interactions between plants and soil [plant-soil feedback (PSF)]. Theoretically, PSF could either boost or degrade ecosystem resilience. Three criteria must be met to attribute resilience to PSF: (i) The presence or amount of PSF must be manipulated; (ii) the ecosystem must face climate disruption after PSF is manipulated; and (iii) PSF must alter the resistance or recovery of ecosystem structure or function to disruption. Several case studies suggest that PSF may support (or degrade) resilience, but no study has yet met all criteria. Doing so could yield novel insights into how aboveground-belowground interactions shape ecosystem resilience to climate change.

PMID:40517042 | DOI:10.1016/j.tree.2025.05.001

Mol Ecol. 2025 Jul 17:e70033. doi: 10.1111/mec.70033. Online ahead of print.

ABSTRACT

Endemic pathogens continue to pose threats of recurring outbreaks, especially in agricultural settings. How these outbreaks unfold and what drives the variability in disease epidemics is less understood. We addressed this question in the Xanthomonas-tomato pathosystem by developing an integrated approach that linked the within-field quantitative signature of local pathogen diversity to climatic conditions to explain variable bacterial disease epidemics across fields. Using strain-resolved metagenomics, we found that pathogen heterogeneity with multiple co-occurring lineages is common. Higher disease severity was associated with higher pathogen diversity. Considering these observations, we used response-specific regression models to investigate the role of environmental variables in driving differences in disease and strain dynamics. Abrupt and frequent changes in environmental factors explained the variability of disease severity. We observed variable lineage dynamics across fields, but at least two lineages with divergent, climate-dependent fitness strategies coexisted throughout the growing season without either of them taking the lead. We further profiled the dynamics of single-nucleotide polymorphism variants in the pathogen population and observed that some alleles are temporarily favoured by specific climatic conditions encountered throughout the growing season, leading to oscillating seasonal patterns of allelic frequencies. These alleles can be referred to as seasonal alleles. Overall, our study revealed that the seasonal fluctuations in pathogen strain composition, diversity and climate-influenced pathogen fitness play a significant role in shaping the severity and variability of bacterial spot disease outbreaks.

PMID:40673408 | DOI:10.1111/mec.70033

BioTech (Basel). 2025 Jun 12;14(2):48. doi: 10.3390/biotech14020048.

ABSTRACT

Interspecific and intersectional crosses have introduced valuable genetic traits for blueberry (Vaccinium sect. Cyanococcus) cultivar improvement. Introgression from Vaccinium species at the diploid, tetraploid, and hexaploid levels has been found in cultivated blueberries. Continued efforts to integrate wild blueberry genetic resources into blueberry breeding are essential to broaden the genetic diversity of cultivated blueberries. However, performing heteroploid crosses among Vaccinium species is challenging. Polyploid induction through tissue culture has been useful in bridging ploidy barriers. Mixoploid or chimeric shoots often are produced, along with solid polyploid mutants. These chimeras are mostly discarded because of their genome instability and the difficulty in identifying periclinal mutants carrying germline mutations. Since induced polyploidy in blueberries often results in a low frequency of solid mutant lines, it is important to recover solid polyploids through chimera dissociation. In this study, two vegetative propagation methods, i.e., axillary and adventitious shoot induction, were evaluated for their efficiency in chimera dissociation. Significantly higher rates of chimera dissociation were found in adventitious shoot induction compared to axillary shoot induction. Approximately 89% and 82% of the adventitious shoots induced from mixoploid lines 145.11 and 169.40 were solid polyploids, respectively, whereas only 25% and 53% of solid polyploids were recovered through axillary shoot induction in these lines. Effective chimera dissociation provides useful and stable genetic materials to enhance blueberry breeding.

PMID:40558397 | DOI:10.3390/biotech14020048

PLoS Genet. 2025 Jun 2;21(6):e1011735. doi: 10.1371/journal.pgen.1011735. Online ahead of print.

ABSTRACT

In ciliates, cortical organelles, including ciliary arrays, are positioned at precise locations along two polarity axes: anterior-posterior and circumferential (lateral). We explored the poorly understood mechanism of circumferential patterning, which generates left-right asymmetry. The model ciliate Tetrahymena has a single anteriorly-located oral apparatus. During cell division, a single new oral apparatus forms near the equator of the parental cell and along the longitude of the parental organelle. Cells homozygous for hypoangular 1 (hpo1) alleles, assemble multiple oral apparatuses positioned either to the left or right flanking the normal oral longitude. Using comparative next-generation sequencing, we identified HPO1 as a gene encoding an ARMC9-like protein. Hpo1 colocalizes with the ciliary basal bodies, forming a bilateral concentration gradient, with the high point on the cell’s right side and a sharp drop-off that marks the longitude at which oral development initiates on the ventral side. A second Hpo1 concentration drop-off is present on the dorsal surface, where it marks the position for development of a cryptic oral apparatus that forms in the janus mutants. Hpo1 acts bilaterally to exclude oral development from the cell’s right side. Hpo1 interacts with the Beige-Beach domain protein Bcd1, a cell’s left side-enriched factor, whose loss also confers multiple oral apparatuses on the ventral surface. A loss of both Hpo1 and Bcd1 is lethal and profoundly disrupts the positioning, organization and size of the forming oral apparatus (including its internal left-right polarity). We conclude that in ciliates, the circumferential patterning involves gradient-forming factors that are concentrated on either the cell’s right or left side and that the two sides of the cortex interact to create boundary effects that induce, position and shape developing cortical organelles.

PMID:40455876 | DOI:10.1371/journal.pgen.1011735

Plant Methods. 2025 May 20;21(1):66. doi: 10.1186/s13007-025-01375-8.

ABSTRACT

High resolution three-dimensional (3D) point clouds enable the mapping of cotton boll spatial distribution, aiding breeders in better understanding the correlation between boll positions on branches and overall yield and fiber quality. This study developed a segmentation workflow for point clouds of 18 cotton genotypes to map the spatial distribution of bolls on the plants. The data processing workflow includes two independent approaches to map the vertical and horizontal distribution of cotton bolls. The vertical distribution was mapped by segmenting bolls using PointNet++ and identifying individual instances through Euclidean clustering. For horizontal distribution, TreeQSM segmented the plant into the main stem and individual branches. PointNet++ and Euclidean clustering were then used to achieve cotton boll instance segmentation. The horizontal distribution was determined by calculating the Euclidean distance of each cotton boll relative to the main stem. Additionally, branch types were classified using point cloud meshing completion and the Dijkstra shortest path algorithm. The results highlight that the accuracy and mean intersection over union (mIoU) of the 2-class segmentation based on PointNet++ reached 0.954 and 0.896 on the whole plant dataset, and 0.968 and 0.897 on the branch dataset, respectively. The coefficient of determination (R²) for the boll counting was 0.99 with a root mean squared error (RMSE) of 5.4. For the first time, this study accomplished high-granularity spatial mapping of cotton bolls and branches, but directly predicting fiber quality from 3D point clouds remains a challenge. This method provides a promising tool for 3D cotton plant mapping of different genotypes, which potentially could accelerate plant physiological studies and breeding programs.

PMID:40394606 | DOI:10.1186/s13007-025-01375-8

Front Plant Sci. 2025 Jun 30;16:1588485. doi: 10.3389/fpls.2025.1588485. eCollection 2025.

ABSTRACT

Pearl millet [Cenchrus americanus (L.) Morrone, formerly Pennisetum glaucum (L.) R. Br.] is the sixth most important cereal globally and is used for forage and feed in the U.S. To identify genomic regions governing important physiological, agronomic and yield related traits, a recombinant inbred line population derived from the cross between Tift 99D₂B_{1 ×} Tift 454 was phenotyped in the field in 2006, 2007 and 2013. In addition, the population was phenotyped for root-knot nematode resistance in the greenhouse during 2009. Using a previously generated genetic map containing 505 single nucleotide polymorphism markers and composite interval mapping, we identified 45 QTLs for eight traits (plant height, stem diameter, days to heading, panicle diameter, panicle length, 1000 seed weight, Pyricularia leaf spot disease, and root-knot nematode egg mass) across almost all linkage groups. These QTLs explained 6.31 to 32.51% of phenotypic variance for each trait and were consistently detected over different environments. Plant height and days to heading were colocalized on LG2 and LG5 showing maturity and plant height are linked and influence each other, similarly to other cereal crops. Interestingly, 5 of 19 QTLs linked to plant height, stem diameter, panicle diameter, and panicle length colocalized to the same locations on LG3, indicating breeding for one trait could simultaneously improve the other. The markers and genes identified in the present study can be used in developing high yielding pearl millet varieties using marker-assisted selection.

PMID:40661761 | PMC:PMC12256767 | DOI:10.3389/fpls.2025.1588485

Plant J. 2025 Jul;123(1):e70304. doi: 10.1111/tpj.70304.

ABSTRACT

Targeted demethylation by DNA glycosylases (DNGs) results in differential methylation between parental alleles in the endosperm, which drives imprinted expression. Here, we performed RNA sequencing on endosperm derived from DNG mutant mdr1 and wild-type (WT) endosperm. Consistent with the role of DNA methylation in gene silencing, we find 108 genes and 96 TEs differentially expressed (DE) transcripts that lost expression in the hypermethylated mdr1 mutant. Compared with other endosperm transcripts, the mdr1 targets are enriched for TEs (particularly Helitrons), and DE genes are depleted for both core genes and GO term assignments, suggesting that the majority of DE transcripts are TEs and pseudo-genes. By comparing DE genes to imprinting calls from prior studies, we find that the majority of DE genes have maternally biased expression, and approximately half of all maternally expressed genes (MEGs) are DE in this study. In contrast, no paternally expressed genes (PEGs) are DE. DNG-dependent imprinted genes are distinguished by maternal demethylation and expression primarily in the endosperm, so we also performed Enzymatic Methyl-seq on hybrids to identify maternal demethylation and utilized a W22 gene expression atlas to identify genes expressed primarily in the endosperm. Overall, approximately ⅔ of all MEGs show evidence of regulation by DNGs. Taken together, this study solidifies the role of MDR1 in the regulation of maternally expressed, imprinted genes and TEs and identifies subsets of genes with DNG-independent imprinting regulation.

PMID:40587880 | DOI:10.1111/tpj.70304

Annu Rev Phytopathol. 2025 Jun 4. doi: 10.1146/annurev-phyto-121823-080201. Online ahead of print.

ABSTRACT

Necrotrophic bacteria within the order Enterobacterales cause significant agricultural losses, with few effective management options available for producers. These pathogens have evolved at least two distinct strategies for infecting plants. Soft rot pathogens in the family Pectobacteriaceae, such as Dickeya and Pectobacterium, rely on secreting plant cell wall-degrading enzymes. In contrast, Pantoea necrotrophs depend on the production of phosphonate phytotoxins, a type of secondary metabolite, for their pathogenicity. This review summarizes recent discoveries on the virulence mechanisms of bacterial necrotrophs and current knowledge of factors that influence their host range and interactions with plant immune defenses. A deeper understanding of bacterial necrotroph host range determinants could inform the development and deployment of enhanced genetic resistance strategies.

PMID:40465659 | DOI:10.1146/annurev-phyto-121823-080201

J Gen Virol. 2025 Jul;106(7). doi: 10.1099/jgv.0.002119.

ABSTRACT

Orthotospovirus tomatomaculae [tomato spotted wilt virus (TSWV)] is a major pathogen in horticultural and row crops worldwide including the USA. In this study, tomato spotted wilt disease incidence was monitored in Arachis hypogaea (peanut; year 1990 to 2024) and Nicotiana tabacum (tobacco; year 2000 to 2024) in commercial farmers’ fields in the Southeastern USA. Furthermore, nucleocapsid (N), nonstructural movement (NSm) and nonstructural silencing suppressor (NSs) protein gene sequences of TSWV global populations from North America, South America, Europe, Asia-Pacific, Africa and Australia were compared with local US population and analysed to understand the genetic variability in the virus genome. In our study, full-length sequences of 94 N, 111 NSm and 78 NSs genes were amplified from TSWV-infected A. hypogaea (peanut), Capsicum annuum (pepper), N. tabacum (tobacco) and Solanum lycopersicum (tomato). nt-based phylogenetic analysis of N, NSm and NSs genes correlated with the geographical location of the TSWV isolates, with notably higher substitution rates in the population of recent years. In addition, the least genetic variability was observed in the N gene of the local population upon comparison with other global TSWV population. The neutrality test of TSWV suggested a non-neutral evolution of the virus genome. Low variation among the selected genes might be attributed to strong purifying selection pressure in the populations. Furthermore, estimation of selection pressure (dN/dS) on small (S) segment-encoded N protein and nonstructural protein showed higher purifying selection than the movement protein encoded by the medium (M) segment of the TSWV isolates. Single-likelihood ancestor counting suggested an overall negative selection pressure on several codons of the selected genes, which indicated that natural selection and population bottleneck events might have influenced the evolution of TSWV. Our study also deciphered high gene flow and low genetic differentiation amid the different TSWV population sets. Additionally, BEAST analysis of TSWV N gene sequences from GA predicted the most common recent ancestor existed ~25 years ago. This data was further correlated with disease incidence data from peanut and tobacco crops obtained in the last three decades. These findings suggest the intermixing of TSWV isolates between peanut, pepper, tobacco and tomato crops, while the virus genome has undergone strong purifying selection.

PMID:40622855 | DOI:10.1099/jgv.0.002119

mSphere. 2025 Jun 17:e0002325. doi: 10.1128/msphere.00023-25. Online ahead of print.

ABSTRACT

Allicin tolerance (alt) clusters in phytopathogenic bacteria, which provide resistance to thiosulfinates like allicin, are challenging to find using conventional approaches due to their varied architecture and the paradox of being vertically maintained within genera despite likely being horizontally transferred. This results in significant sequential diversity that further complicates their identification. Natural language processing (NLP), like techniques such as those used in DeepBGC, offers a promising solution by treating gene clusters like a language, allowing for identifying and collecting gene clusters based on patterns and relationships within the sequences. We curated and validated alt-like clusters in Pantoea ananatis 97-1R, Burkholderia gladioli pv. gladioli FDAARGOS 389, and Pseudomonas syringae pv. tomato DC3000. Leveraging sequences from the RefSeq bacterial database, we conducted comparative analyses of gene synteny, gene/protein sequences, protein structures, and predicted protein interactions. This approach enabled the discovery of several novel alt-like clusters previously undetectable by other methods, which were further validated experimentally. Our work highlights the effectiveness of NLP-like techniques for identifying underrepresented gene clusters and expands our understanding of the diversity and utility of alt-like clusters in diverse bacterial genera. This work demonstrates the potential of these techniques to simplify the identification process and enhance the applicability of biological data in real-world scenarios.IMPORTANCEThiosulfinates, like allicin, are potent antifeedants and antimicrobials produced by Allium species and pose a challenge for phytopathogenic bacteria. Phytopathogenic bacteria have been shown to utilize an allicin tolerance (alt) gene cluster to circumvent this host response, leading to economically significant yield losses. Due to the complexity of mining these clusters, we applied techniques akin to natural language processing to analyze Pfam domains and gene proximity. This approach led to the identification of novel alt-like gene clusters, showcasing the potential of artificial intelligence to reveal elusive and underrepresented genetic clusters and enhance our understanding of their diversity and role across various bacterial genera.

PMID:40525872 | DOI:10.1128/msphere.00023-25

Molecules. 2025 Apr 30;30(9):2020. doi: 10.3390/molecules30092020.

ABSTRACT

The discovery of bioactive natural products is often challenged by the complexity of isolating and characterizing active compounds within diverse mixtures. Previously, we introduced a ¹H NMR-based weighted gene correlation network analysis (WGCNA) approach to identify spectral features linked to growth inhibitory activity of Piper (Piperaceae) leaf extracts against model plant, fungal, and bacterial organisms. This method enabled us to prioritize specific spectral features linked to bioactivity, offering a targeted approach to natural product discovery. In this study, we validate the predictive capacity of the WGCNA by isolating the compounds responsible for the bioactivity-associated resonances and confirming their antifungal efficacy. Using growth inhibition assays, we verified that the isolated compounds, including three novel antifungal agents, exhibited significant bioactivity. Notably, one of these compounds contains a rare imidazolium heterocyclic motif, marking a new structural class in Piper. These findings substantiate the ¹H NMR-based WGCNA as a reliable tool for identifying structural types associated with biological activity, streamlining the process of discovering bioactive natural products in complex extracts.

PMID:40363825 | PMC:PMC12073215 | DOI:10.3390/molecules30092020

Phytopathology. 2025 Jun 22. doi: 10.1094/PHYTO-03-25-0093-R. Online ahead of print.

ABSTRACT

Phony peach disease (PPD), caused by Xylella fastidiosa subsp. multiplex (Xfm), poses a significant threat to commercial peach orchards in Georgia. Early and accurate detection is essential for effective disease management, yet visual assessment remains the primary approach for diagnosing PPD symptoms due to the high cost and logistical challenges of qPCR-based detection of Xfm. We evaluated the accuracy of visual PPD assessment and examined the factors influencing rater performance, symptom reliability, and optimal survey deployment strategies with CART/Random Forest analyses and simulations. Internode length was the most reliable symptom for PPD identification in two peach cultivars, consistently outperforming other physical traits such as canopy flatness and shape. Primer pair C06Xf-bamA had the greatest relative sensitivity, making it the preferred choice for qPCR confirmation. Principal component analysis suggested that rater experience significantly improved agreement with qPCR results and repeated assessments of the same orchards further enhanced consistency for raters. Simulations results suggested that deploying two experienced raters may provide the highest detection diagnostic accuracy for survey purposes, particularly when qPCR-based pathogen detection is unavailable. Last, PPD-affected trees, through PCR verification and visual identification, exhibited higher mortality rates than Xfm-negative trees, reinforcing the need for early detection and removal to limit disease spread. These findings underscore the importance of strategic rater deployment, targeted symptom selection, and integrating molecular diagnostics when feasible.

PMID:40544457 | DOI:10.1094/PHYTO-03-25-0093-R

Plant Physiol. 2025 Jul 3;198(3):kiaf294. doi: 10.1093/plphys/kiaf294.

ABSTRACT

Minimal native and synthetic Polymerase III promoters enable efficient and customizable CRISPR multiplexing in plants, expanding genome engineering capabilities

PMID:40673482 | PMC:PMC12268498 | DOI:10.1093/plphys/kiaf294

Sci Data. 2025 Aug 5;12(1):1362. doi: 10.1038/s41597-025-05131-4.

ABSTRACT

Biological nitrogen fixation (BNF) is the main natural source of new nitrogen inputs in terrestrial ecosystems, supporting terrestrial productivity, carbon uptake, and other Earth system processes. We assembled a comprehensive global dataset of field measurements of BNF in all major N-fixing niches across natural terrestrial biomes derived from the analysis of 376 BNF studies. The dataset comprises 32 variables, including site location, biome type, N-fixing niche, sampling year, quantification method, BNF rate (kg N ha^-1 y^-1), the percentage of nitrogen derived from the atmosphere (%N_dfa), N fixer or N-fixing substrate abundance, BNF rate per unit of N fixer abundance, and species identity. Overall, the dataset combines 1,207 BNF rates for trees, shrubs, herbs, soil, leaf litter, woody litter, dead wood, mosses, lichens, and biocrusts, 152 herb %N_dfa values, 1,005 measurements of N fixer or N-fixing substrate abundance, and 762 BNF rates per unit of N fixer abundance for a total of 424 species across 66 countries. This dataset facilitates synthesis, meta-analysis, upscaling, and model benchmarking of BNF fluxes at multiple spatial scales.

PMID:40764484 | DOI:10.1038/s41597-025-05131-4

Plant Commun. 2025 Jun 3:101393. doi: 10.1016/j.xplc.2025.101393. Online ahead of print.

ABSTRACT

Teucrium chamaedrys, also called wall germander, is a small woody shrub native to the Mediterranean region. Its name is derived from the Greek words meaning ‘ground oak’, since its tiny leaves resemble those of an oak tree. Teucrium species are proliferative producers of diterpenes, which afford them valuable properties widely co-opted in traditional and western medicines. Sequence and assembly of the 3 Gbp tetraploid T. chamaedrys revealed 74 diterpene synthase genes, with the vast representation of these diterpene synthases clustered along four genomic loci. Comparative genomics revealed that this cluster is mirrored in the closely related species, Teucrium marum. Along with the presence of several cytochrome p450 sequences, this region is the one of largest biosynthetic gene clusters identified. Teucrium is well known for accumulating clerodane-type diterpenoids which are produced from a kolavanyl diphosphate precursor. To elucidate the complex biosynthetic pathways of these medicinal compounds, we identified and functionally characterized several kolavanyl diphosphate synthases from T. chamaedrys. Its remarkable chemistry and tetraploidy make T. chamaedrys an interesting and unique model for studying genomic evolution and adaptation in plants.

PMID:40468595 | DOI:10.1016/j.xplc.2025.101393

Front Plant Sci. 2025 Jul 11;16:1607733. doi: 10.3389/fpls.2025.1607733. eCollection 2025.

ABSTRACT

Maize (Zea mays L.) is the most widely produced crop in the world, and conventional production requires significant amounts of synthetic nitrogen fertilizer, which has negative economic and environmental consequences. Maize landraces from Oaxaca, Mexico, can acquire nitrogen from nitrogen-fixing bacteria that live in a mucilage secreted by aerial nodal roots. The development of these nodal roots is a characteristic traditionally associated with the juvenile vegetative stage of maize plants. However, mature Oaxacan landraces develop many more nodes with aerial roots than commercial maize varieties. Our study shows that Oaxacan landraces develop aerial roots during the juvenile and adult vegetative phases and even during early flowering under greenhouse and field conditions. Surprisingly, the development of these roots was only minimally affected by soil nitrogen and ambient humidity. These findings are an essential first step in developing maize varieties to reduce fertilizer needs in maize production across different environmental conditions.

PMID:40718026 | PMC:PMC12289584 | DOI:10.3389/fpls.2025.1607733

Tree Physiol. 2025 Jul 11:tpaf080. doi: 10.1093/treephys/tpaf080. Online ahead of print.

ABSTRACT

Sulfate-proton co-transporters (SULTRs) mediate sulfate uptake, transport, storage, and assimilation in plants. The SULTR family has historically been classified into four groups (SULTR1-SULTR4), with well-characterized roles for SULTR groups 1, 2, and 4. However, the functions of the large and diverse SULTR3 group remain poorly understood. Here, we present an updated phylogenetic analysis of SULTRs across angiosperms, including multiple early-divergent lineages. Our results suggest that the enigmatic SULTR3 group comprises four distinct subfamilies that predate the emergence of angiosperms, providing a basis for reclassifying the SULTR family into seven subfamilies. This expanded classification is supported by subfamily-specific gene structures and amino acid substitutions in the substrate-binding pocket. Structural modeling identified three serine residues uniquely lining the substrate-binding pocket of SULTR3.4, enabling three hydrogen bonds with the phosphate ion. The data support the proposed neofunctionalization of this subfamily for phosphate allocation within vascular tissues. Transcriptome analysis of Populus tremula × alba revealed divergent tissue expression preferences among SULTR subfamilies and between genome duplicates. We observed partitioned expression in vascular tissues among the four SULTR3 subfamilies, with PtaSULTR3.4a and PtaSULTR3.2a preferentially expressed in primary and secondary xylem, respectively. Gene coexpression analysis revealed coordinated expression of PtaSULTR3.4a with genes involved in phosphate starvation responses and nutrient transport, consistent with a potential role in phosphate homeostasis. In contrast, PtaSULTR3.2a was strongly coexpressed with lignification and one-carbon metabolism genes and their upstream transcription regulators. PtaSULTR3.2a belongs to a eudicot-specific branch of the SULTR3.1 subfamily found only in perennial species, suggesting a specialized role in lignifying tissues. Together, our findings provide a refined phylogenetic framework for the SULTR family and suggest that the expanded SULTR3 subfamilies have undergone neofunctionalization during the evolution of vascular and perennial plants.

PMID:40643194 | DOI:10.1093/treephys/tpaf080

Insects. 2025 Jun 24;16(7):653. doi: 10.3390/insects16070653.

ABSTRACT

Blueberry is a high-value fruit crop in the United States, with Georgia and Florida serving as important early-season production regions. In these areas, several thrips species (Thysanoptera: Thripidae), including Frankliniella tritici (Fitch), Frankliniella bispinosa (Morgan), and Scirtothrips dorsalis (Hood), have emerged as economically significant pests. While F. tritici and F. bispinosa primarily damage floral tissues, S. dorsalis targets young foliage. Their rapid reproduction, high mobility, and broad host range contribute to rapid population buildup and complicate the management programs. Species identification is often difficult due to overlapping morphological features and requires the use of molecular diagnostic tools for accurate identification. Although action thresholds, such as 2-6 F. tritici per flower cluster, are used to guide management decisions, robust economic thresholds based on yield loss remain undeveloped. Integrated pest management (IPM) practices include regular monitoring, cultural control (e.g., pruning, reflective mulch), biological control using Orius insidiosus (Say) and predatory mites, and chemical control. Reduced-risk insecticides like spinetoram and spinosad offer effective suppression while minimizing harm to pollinators and beneficial insects. However, the brief flowering period limits the establishment of biological control agents. Developing species-specific economic thresholds and phenology-based IPM strategies is critical for effective and sustainable thrips management in blueberry cropping systems.

PMID:40725285 | DOI:10.3390/insects16070653

Fungal Biol. 2025 Aug;129(5):101590. doi: 10.1016/j.funbio.2025.101590. Epub 2025 May 6.

ABSTRACT

The Fifth International Symposium on Fungal Stress (ISFUS) brought together in Brazil many of the leaders in the field of fungal stress responses, from fourteen countries, for four days of outstanding science ranging from basic research to studies with agricultural, medical, industrial, and environmental significance. In addition to the excellent oral and poster presentations, the Symposium organisers ensured that all participants had ample opportunity to engage, socialise, and network to exchange ideas and share research. The conference was enhanced by the world-class venue near Iguazu Falls, probably the greatest natural phenomenon in South America.

PMID:40707112 | DOI:10.1016/j.funbio.2025.101590

Mol Ecol Resour. 2025 Jul 22:e70012. doi: 10.1111/1755-0998.70012. Online ahead of print.

ABSTRACT

Yellow monkeyflowers (Mimulus guttatus complex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan-genomics in this group, we present four chromosome-scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a single M. guttatus population, one from the closely related selfing species M. nasutus, and one from a more divergent species M. tilingii. All assemblies are highly complete and resolve centromeric and repetitive regions. Comparative analyses reveal such extensive structural variation in repeat-rich, gene-poor regions that large portions of the genome are unalignable across accessions. As a result, this Mimulus pan-genome is primarily informative in genic regions, underscoring limitations of resequencing approaches in such polymorphic taxa. We document gene presence-absence, investigate the recombination landscape using high-resolution linkage data, and quantify nucleotide diversity. Surprisingly, pairwise differences at fourfold synonymous sites are exceptionally high-even in regions of very low recombination-reaching ~3.2% within a single M. guttatus population, ~7% within the interfertile M. guttatus species complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolated M. tilingii. Genome-wide patterns of nucleotide variation show little evidence of linked selection, and instead suggest that the concentration of genes (and likely selected sites) in high-recombination regions may buffer diversity loss. These assemblies, annotations, and comparative analyses provide a robust genomic foundation for Mimulus research and offer new insights into the interplay of recombination, structural variation, and molecular evolution in highly diverse plant genomes.

PMID:40693537 | DOI:10.1111/1755-0998.70012

Phytopathology. 2025 Jun 11. doi: 10.1094/PHYTO-04-25-0143-SC. Online ahead of print.

ABSTRACT

Root-knot nematodes (Meloidogyne spp.) are a continuing threat to soybean production, with M. incognita being the predominant species. The deployment of Mi-resistant soybean cultivars is a primary management strategy, but the underlying molecular mechanisms contributing to resistance remain unknown. A single, additive gene for resistance to M. incognita, Rmi1, was previously identified in soybean cv. Forrest and associated with the emigration of second-stage juveniles from the roots. To better understand the Rmi1-mediated resistance response, we used Forrest-derived F₅ RILs differing for Rmi1 to analyze global changes in gene expression in response to M. incognita infection at 2- and 4-days post inoculation. We identified 1,471 differentially expressed (DE) genes in the compatible interaction and 1,037 DE genes in the incompatible interaction. Forty-five percent of DE genes were DE in both interactions, 42% (856) were unique to the compatible interaction, and 13% (261) were unique to the incompatible interaction. Genes uniquely DE in the incompatible interaction included genes involved in cell wall modification, hormone signaling, endomembrane trafficking, and redox reactions providing new insights into the resistance mechanism mediated by Rmi1 in soybean to root-knot nematodes.

PMID:40498525 | DOI:10.1094/PHYTO-04-25-0143-SC

Genetics. 2025 May 14:iyaf091. doi: 10.1093/genetics/iyaf091. Online ahead of print.

ABSTRACT

In maize, there are two meiotic drive systems that target large heterochromatic knobs composed of tandem repeats known as knob180 and TR-1. The first meiotic drive haplotype, Abnormal chromosome 10 (Ab10) confers strong meiotic drive (∼75% transmission as a heterozygote) and encodes two kinesins: KINDR, which associates with knob180 repeats and TRKIN, which associates with TR-1 repeats. Prior data show that meiotic drive is conferred primarily by the KINDR/knob180 system while the TRKIN/TR-1 system seems to have little or no role, making it unclear why Trkin has been maintained in Ab10 haplotypes. The second meiotic drive haplotype, K10L2, confers a low level of meiotic drive (∼51-52%) and only encodes the TRKIN/TR-1 system. Here we used long-read sequencing to assemble the K10L2 haplotype and showed that it has strong homology to an internal portion of the Ab10 haplotype. We also carried out CRISPR mutagenesis to test the role of Trkin on Ab10 and K10L2. The data indicate that the Trkin gene on Ab10 does not improve drive or fitness but instead has a weak deleterious effect when paired with a normal chromosome 10. The deleterious effect is more severe when Ab10 is paired with K10L2: in this context functional Trkin on either chromosome nearly abolishes Ab10 drive. Mathematical modeling based on the empirical data suggest that Trkin is unlikely to persist on Ab10. We conclude that Trkin either confers an advantage to Ab10 in untested circumstances or that it is in the process of being purged from the Ab10 population.

PMID:40365704 | DOI:10.1093/genetics/iyaf091

BMC Microbiol. 2025 Jul 28;25(1):456. doi: 10.1186/s12866-025-04175-1.

ABSTRACT

BACKGROUND: The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates.

RESULTS: Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110 bp and at 370 bp, while strains only displaying the 110 bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification.

CONCLUSIONS: The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.

PMID:40722002 | DOI:10.1186/s12866-025-04175-1

Plant Dis. 2025 Aug 6. doi: 10.1094/PDIS-12-24-2589-SR. Online ahead of print.

ABSTRACT

Gummy stem blight (GSB), caused by three Stagonosporopsis species, S. citrulli, S. cucurbitacearum and S. caricae, is one of the most economically important diseases hindering watermelon production worldwide. Since there is no commercial resistance to GSB in watermelon cultivars, its management depends on cultural practices and preventative fungicides. Therefore, efficient methods for the detection of Stagonosporopsis species that could aid management decisions are required. To help achieve this, a loop-mediated isothermal amplification (LAMP) assay specific to S. citrulli (SCIT850) was developed under two detection formats: fluorescence quantification and endpoint colorimetric detection. The SCIT850 assay was determined to be specific to its target species and exhibited a consistent sensitivity of 1 pg of genomic DNA under both formats. The assay can be combined with a previously reported LAMP assay for the collective detection of the three Stagonosporopsis spp. (STAGY), which have comparable sensitivity to SCIT850 and can aid in species discrimination. A field diagnostic system for GSB-causing Stagonosporopsis was developed by coupling the SCIT850 and STAGY assays to quick DNA extraction protocols. Two DNA extraction methods were tested: one from leaves using cellulose dipsticks, and one from steel rods (typical of spore traps) using Chelex100. With the dipstick method, we detected pathogen DNA in inoculated asymptomatic, mildly infected, and severely infected plants, while with the Chelex100 we detected pathogen DNA from rods infested with as few as 500 spores. The SCIT850 and STAGY assays coupled with these quick sample processing methods could be adapted for field deployment, which would allow growers to make efficient and timely management decisions based on detection of the actual Stagonosporopsis species present in the field.

PMID:40767855 | DOI:10.1094/PDIS-12-24-2589-SR

Plant Dis. 2025 May 22. doi: 10.1094/PDIS-01-25-0117-SR. Online ahead of print.

ABSTRACT

Alternaria brassicicola is the causal agent typically associated with Alternaria leaf blight and head rot (ABHR) disease in broccoli and related crops in the Eastern United States. Recently a new species, A. japonica, has been reported as causing disease in broccoli and other vegetables in this region. We conducted a multi-state pathogen survey during the growing seasons of 2022 and 2023 to assess the distribution and occurrence of A. japonica in relation to A. brassicicola in five broccoli-producing states. Our approach specifically targeted collection of broccoli leaves with lesions typical of ABHR within commercially grown fields managed using either organic or conventional approaches in Connecticut, Massachusetts, New York, Virginia, and Georgia. Only typical ABHR leaf lesions were selected for pathogen isolation and, subsequently, sequencing of the Alternaria major allergen a1 gene was used to identify Alternaria species. The predominant species isolated was A. brassicicola (88% in 2022 and 94% in 2023) and the second most common was A. alternata (12% in 2022 and 6% in 2023), which was obtained from fields in Connecticut and Massachusetts in 2022, and in Virginia in both years. Alternaria japonica was not found in either year. Symptoms of A. alternata were indistinguishable from A. brassicicola, as were colony morphologies. While A. alternata is considered a generalist and of little consequence for broccoli, it is considered a pathogen of significance on multiple crops (blueberry, citrus, pistachios), but there remains scant information on the disease etiology on broccoli. Therefore, we inoculated broccoli with A. alternata in controlled conditions in order to shed light on possible differences in infectivity of these species on broccoli. Results of our study showed that A. alternata is pathogenic on broccoli, capable of initiating infection and causing lesions typical of ABHR. This indicates that future disease surveys of ABHR should conclusively identify species of Alternaria that are causing disease. Additional research is needed to determine the significance of this finding in relation to yield impacts, epidemiology, fungicide resistance, and management recommendations.

PMID:40403277 | DOI:10.1094/PDIS-01-25-0117-SR

Plant Genome. 2025 Jun;18(2):e70055. doi: 10.1002/tpg2.70055.

ABSTRACT

Leaf rust (LR) and stripe rust (YR), which are caused by Puccinia triticina and Puccinia striiformis, respectively, are among the most devastating wheat rusts worldwide. These diseases can be managed by using genetically resistant cultivars, an economical and environmentally safer alternative to fungicides. Over 100 and 80 Lr and Yr resistance genes have been discovered, respectively; however, rust pathogens are overcoming introduced resistance genes in the southeastern United States. Genome-wide association study has emerged as a valuable tool to identify new LR and YR resistance loci. In this study, a panel of 263 soft red winter wheat genotypes was evaluated for LR and YR severity in Plains, GA, and Williamson, GA, in a randomized complete block design of two replicates during 2019 and 2021-2023. Also, LR and YR infection types were assessed on seedlings at the three leaf stage in three greenhouse trials. A total of 26 significant quantitative trait loci (QTL) explaining 0.6%-30.8% phenotypic variance (PV) was detected by at least two of the five GAPIT models (BLINK, CMLM, FarmCPU, GLM, and MLM) tested. Nine major QTL included QLrYr-2A.1 linked to single-nucleotide polymorphism S2A_20855466, which had the highest overall PV (30.8%) for response to both rust pathogens in the field. Using the Chinese Spring Reference Genome Version 1.0, we detected 16 candidate genes, and four known R genes and QTL overlapped two major QTL. Of these QTL, 16 are likely novel genetic loci with potential for marker-assisted selection.

PMID:40495572 | DOI:10.1002/tpg2.70055

Nat Chem Biol. 2025 Jul 16. doi: 10.1038/s41589-025-01970-9. Online ahead of print.

ABSTRACT

Monoterpene indole alkaloids (MIAs) are a large, structurally diverse class of bioactive natural products. These compounds are biosynthetically derived from a stereoselective Pictet-Spengler condensation that generates a tetrahydro-β-carboline scaffold characterized by a 3S stereocenter. However, a subset of MIAs contains a noncanonical 3R stereocenter. Here we report the basis for 3R-MIA biosynthesis in Mitragyna speciosa (kratom). We discover the presence of the iminium species (20S)-3-dehydrocorynantheidine, which supports isomerization of 3S to 3R via oxidation and stereoselective reduction downstream of the initial Pictet-Spengler condensation. Isotopologue feeding experiments identify the sites for downstream MIA pathway biosynthesis as well as the oxidase/reductase pair that catalyzes this epimerization. This oxidase/reductase pair has broad substrate specificity, suggesting that this pathway may be responsible for the formation of many 3R-MIAs and downstream spirooxindole alkaloids in kratom. The elucidation of this epimerization mechanism allows biocatalytic access to a range of pharmacologically active spirooxindole alkaloid compounds.

PMID:40670688 | DOI:10.1038/s41589-025-01970-9

BMC Plant Biol. 2025 Jun 5;25(1):766. doi: 10.1186/s12870-025-06799-x.

ABSTRACT

BACKGROUND: Fruit ripening is a coordinated process that leads to an increase in sugars, decrease in acids and accumulation of pigments. Blueberry fruit exhibit an atypical climacteric ripening behavior. These fruit display an increase in respiration and ethylene production during ripening, however ethylene synthesis is developmentally regulated. In this study, the effect of ethylene on blueberry fruit ripening was investigated via preharvest applications of ethylene-releasing plant growth regulators (PGRs), ethephon and 1-aminocyclopropane 1-carboxylic acid (ACC), in one southern highbush cultivar, Miss Lilly in 2019, and two rabbiteye cultivars, Premier and Powderblue in 2019 and 2020. Further, the effects of these two PGRs on fruit metabolism during ripening in the two rabbiteye cultivars, and postharvest fruit quality in all three cultivars were evaluated.

RESULTS: Both PGRs increased ethylene evolution within 1-3 days after treatment (DAT). Ethephon and ACC applications increased the rate of ripening within 5 DAT in all cultivars, and increased ripe (blue) fruit by up to 35% and 29%, respectively between 7 to 10 DAT compared to the control. Metabolite analysis revealed that PGR treatments resulted in an immediate, but transient increase in sucrose, glucose and fructose, in ‘Premier’ at 3 DAT. Malate decreased at 3 DAT in response to both PGR treatments in ‘Premier’, and at 5 DAT in ethephon treatment in both cultivars. A rapid increase in the concentration of multiple anthocyanins was noted at 3 DAT in response to both PGRs in ‘Premier’ and ‘Powderblue’. Gene expression analysis revealed an increase in transcript abundance of VACUOLAR INVERTASE (vINV) and multiple anthocyanin biosynthesis genes between 1 and 3 DAT after PGR treatments in both cultivars, supporting the metabolite changes. However, the alteration in fruit metabolite concentrations were not sustained, and similar in PGR-treated fruit compared to the control in ripe fruit harvested at 10 DAT. Postharvest fruit quality attributes, such as firmness, total soluble solids, titratable acidity, and visual quality, were not consistently affected by the PGR applications compared to control treatments across all cultivars. A decrease in fruit weight was noted, although not consistently, in response to PGR treatments.

CONCLUSIONS: Overall, this study demonstrates that ethylene plays a crucial role in promoting ripening via rapid and transient stimulation of sugar, acid and anthocyanin metabolism. The promotion of fruit ripening by ethylene-releasing PGRs can lead to minimal but inconsistent changes in fruit quality attributes during postharvest storage.

PMID:40474063 | DOI:10.1186/s12870-025-06799-x

bioRxiv [Preprint]. 2025 May 28:2025.05.23.655667. doi: 10.1101/2025.05.23.655667.

ABSTRACT

Repairing a damaged body part is critical for the survival of any organism. In plants, tissue damage induces rapid responses that activate defense, regeneration and wound healing. While early wound signaling mediated by phytohormones, electrical signals and reactive oxygen species is well-characterized, the mechanisms governing the final stages of wound healing remain poorly understood. Here, we show that wounding in Arabidopsis leaves induces localized cooling, likely due to evaporative water loss, accompanied by the activation of cold-responsive genes. The subsequent disappearance of localized cooling and deactivation of cold-responsive genes serve as a quantitative marker of wound healing. Based on these observations, we developed a workflow by leveraging computer vision and deep learning to monitor the dynamics of wound healing. We found that CBFs transcription factors relay injury-induced cooling signal to wound healing. Thus, our work advances our understanding of tissue repair and provides a tool to quantify wound healing in plants.

PMID:40502075 | PMC:PMC12154623 | DOI:10.1101/2025.05.23.655667

PLoS Genet. 2025 Jul 16;21(7):e1011742. doi: 10.1371/journal.pgen.1011742. Online ahead of print.

ABSTRACT

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used genotype-by-sequencing data to score more than 10,000 maize and teosinte lines for the presence or absence of each driver. Fewer than ~0.5% of modern inbred lines carry chromosomal drivers. In contrast, among individuals from 5331 open-pollinated landraces, 6.32% carried Ab10, 5.16% carried K10L2, and 12.28% carried at least one B chromosome. These frequencies are consistent with those reported in previous studies. Using a GWAS approach we identified unlinked loci that associate with the presence or absence of the selfish genetic elements. Many significant SNPs are positively associated with the drivers, suggesting that there may have been selection for alleles that ameliorate their negative fitness consequences. We then assessed the contributions of population structure, associated loci, and the environment on the distribution of each chromosomal driver. There was no significant relationship between any chromosomal driver and altitude, contrary to conclusions based on smaller studies. Our data suggest that the distribution of the major chromosomal drivers is primarily influenced by neutral processes and the deleterious fitness consequences of the drivers themselves. While each driver has a unique relationship to genetic background and the environment, they are largely unconstrained by either.

PMID:40668866 | DOI:10.1371/journal.pgen.1011742

bioRxiv [Preprint]. 2025 May 27:2025.05.22.655462. doi: 10.1101/2025.05.22.655462.

ABSTRACT

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used genotype-by-sequencing data to score more than 10,000 maize and teosinte lines for the presence or absence of each driver. Less than ~0.5% of modern inbred lines carry chromosomal drivers. Among individuals from 5331 open-pollinated landraces, 6.32% carried Ab10, 5.16% carried K10L2, and 12.28% carried at least one B chromosome. Using a GWAS approach we identified unlinked loci that associate with the presence or absence of the selfish genetic elements. Many genetic modifiers are positively associated with the drivers, suggesting that there may have been selection for alleles that ameliorate their negative fitness consequences. We then assessed the contributions of population structure, associated loci, and the environment on the distribution of each chromosomal driver. There was no significant relationship between any chromosomal driver and altitude, contrary to conclusions based on smaller studies. Our data suggest that the distribution of the major chromosomal drivers is primarily influenced by neutral processes and the deleterious fitness consequences of the drivers themselves. While each driver has a unique relationship to genetic background and the environment, they are largely unconstrained by either.

PMID:40501570 | PMC:PMC12154789 | DOI:10.1101/2025.05.22.655462

Nature. 2025 Jul;643(8072):705-711. doi: 10.1038/s41586-025-09201-w. Epub 2025 Jul 16.

ABSTRACT

Biological nitrogen fixation (BNF) is the largest natural source of new nitrogen (N) that supports terrestrial productivity^1,2, yet estimates of global terrestrial BNF remain highly uncertain^3,4. Here we show that this uncertainty is partly because of sampling bias, as field BNF measurements in natural terrestrial ecosystems occur where N fixers are 17 times more prevalent than their mean abundances worldwide. To correct this bias, we develop new estimates of global terrestrial BNF by upscaling field BNF measurements using spatially explicit abundances of all major biogeochemical N-fixing niches. We find that natural biomes sustain lower BNF, 65 (52-77) Tg N yr^-1, than previous empirical bottom-up estimates^3,4, with most BNF occurring in tropical forests and drylands. We also find high agricultural BNF in croplands and cultivated pastures, 56 (54-58) Tg N yr^-1. Agricultural BNF has increased terrestrial BNF by 64% and total terrestrial N inputs from all sources by 60% over pre-industrial levels. Our results indicate that BNF may impose stronger constraints on the carbon sink in natural terrestrial biomes and represent a larger source of agricultural N than is generally considered in analyses of the global N cycle^5,6, with implications for proposed safe operating limits for N use^7,8.

PMID:40670639 | DOI:10.1038/s41586-025-09201-w

Sci Adv. 2025 May 23;11(21):eadw3433. doi: 10.1126/sciadv.adw3433. Epub 2025 May 21.

ABSTRACT

Activation of synthetic centromeres on chromosome 4 in maize leads to its breakage and formation of trisomic fragments called neochromosomes. A limitation of neochromosomes is their low and unpredictable transmission rates due to trisomy. Here, we report that selecting for dicentric recombinants through male crosses uncovers stabilized chromosome 4 fission events, which split it into 4a-4b complementary chromosome pairs, where 4a carries a native centromere and 4b carries a synthetic one. The cells rapidly stabilized chromosome ends by de novo telomere formation, and the new centromeres spread among genes without altering their expression. When both 4a and 4b chromosomes were made homozygous, they segregated through meiosis indistinguishably from wild type and gave rise to healthy plants with normal seed set, indicating that the synthetic centromere was fully functional. This work leverages synthetic centromeres to engineer chromosome fission, raising the diploid chromosome number of maize from 20 to 22.

PMID:40397737 | PMC:PMC12094224 | DOI:10.1126/sciadv.adw3433

Integr Comp Biol. 2025 May 8:icaf028. doi: 10.1093/icb/icaf028. Online ahead of print.

ABSTRACT

Climate change is simultaneously increasing atmospheric carbon dioxide concentrations ([CO2]) and temperatures. We conducted a multi-factorial growth chamber experiment to examine how these climate change factors interact to influence the expression of ecologically-relevant traits, clines in these traits, and natural selection on morphology and phenology of diverse accessions of Boechera stricta (Brassicaceae) sourced from a broad elevational gradient in Colorado, USA. Plastic shifts in a key allocation trait (root mass fraction) in response to temperature accord with the direction of selection for probability of flowering, indicating that plasticity in this trait could be adaptive. However, plasticity in a foliar functional trait (leaf dry matter content) in response to temperature and [CO2] did not align with the direction of selection, indicating that plasticity could reduce fitness based on plant carbon allocation strategies. For another ecologically-important phenotype, selection favors resource acquisitive trait values (higher specific leaf area) under elevated [CO2] and resource conservative trait values (lower specific leaf area) at lower [CO2], despite the lack of plasticity in this trait. This pattern of selection counters published reports that elevated [CO2] induces low specific leaf area but could enable plants to reproduce across a greater period of the growing season under increasingly warm climates. Indeed, warmer temperatures prolonged the duration of flowering. This plasticity is likely adaptive, as selection favored increased flowering duration in the higher temperature treatment level. Thus, the two major results that emerged from our study are that climate change could impose novel and unanticipated patterns of natural selection on plant traits and that plasticity in these traits can be a maladaptive response to stress.

PMID:40338630 | DOI:10.1093/icb/icaf028

Trends Ecol Evol. 2025 Jun 13:S0169-5347(25)00132-6. doi: 10.1016/j.tree.2025.05.001. Online ahead of print.

ABSTRACT

The resilience of ecosystems to climate disruption requires internal feedbacks that support the stability of ecosystem structure and function. Such feedbacks may include sustained interactions between plants and soil [plant-soil feedback (PSF)]. Theoretically, PSF could either boost or degrade ecosystem resilience. Three criteria must be met to attribute resilience to PSF: (i) The presence or amount of PSF must be manipulated; (ii) the ecosystem must face climate disruption after PSF is manipulated; and (iii) PSF must alter the resistance or recovery of ecosystem structure or function to disruption. Several case studies suggest that PSF may support (or degrade) resilience, but no study has yet met all criteria. Doing so could yield novel insights into how aboveground-belowground interactions shape ecosystem resilience to climate change.

PMID:40517042 | DOI:10.1016/j.tree.2025.05.001

Mol Ecol. 2025 Jul 17:e70033. doi: 10.1111/mec.70033. Online ahead of print.

ABSTRACT

Endemic pathogens continue to pose threats of recurring outbreaks, especially in agricultural settings. How these outbreaks unfold and what drives the variability in disease epidemics is less understood. We addressed this question in the Xanthomonas-tomato pathosystem by developing an integrated approach that linked the within-field quantitative signature of local pathogen diversity to climatic conditions to explain variable bacterial disease epidemics across fields. Using strain-resolved metagenomics, we found that pathogen heterogeneity with multiple co-occurring lineages is common. Higher disease severity was associated with higher pathogen diversity. Considering these observations, we used response-specific regression models to investigate the role of environmental variables in driving differences in disease and strain dynamics. Abrupt and frequent changes in environmental factors explained the variability of disease severity. We observed variable lineage dynamics across fields, but at least two lineages with divergent, climate-dependent fitness strategies coexisted throughout the growing season without either of them taking the lead. We further profiled the dynamics of single-nucleotide polymorphism variants in the pathogen population and observed that some alleles are temporarily favoured by specific climatic conditions encountered throughout the growing season, leading to oscillating seasonal patterns of allelic frequencies. These alleles can be referred to as seasonal alleles. Overall, our study revealed that the seasonal fluctuations in pathogen strain composition, diversity and climate-influenced pathogen fitness play a significant role in shaping the severity and variability of bacterial spot disease outbreaks.

PMID:40673408 | DOI:10.1111/mec.70033

BioTech (Basel). 2025 Jun 12;14(2):48. doi: 10.3390/biotech14020048.

ABSTRACT

Interspecific and intersectional crosses have introduced valuable genetic traits for blueberry (Vaccinium sect. Cyanococcus) cultivar improvement. Introgression from Vaccinium species at the diploid, tetraploid, and hexaploid levels has been found in cultivated blueberries. Continued efforts to integrate wild blueberry genetic resources into blueberry breeding are essential to broaden the genetic diversity of cultivated blueberries. However, performing heteroploid crosses among Vaccinium species is challenging. Polyploid induction through tissue culture has been useful in bridging ploidy barriers. Mixoploid or chimeric shoots often are produced, along with solid polyploid mutants. These chimeras are mostly discarded because of their genome instability and the difficulty in identifying periclinal mutants carrying germline mutations. Since induced polyploidy in blueberries often results in a low frequency of solid mutant lines, it is important to recover solid polyploids through chimera dissociation. In this study, two vegetative propagation methods, i.e., axillary and adventitious shoot induction, were evaluated for their efficiency in chimera dissociation. Significantly higher rates of chimera dissociation were found in adventitious shoot induction compared to axillary shoot induction. Approximately 89% and 82% of the adventitious shoots induced from mixoploid lines 145.11 and 169.40 were solid polyploids, respectively, whereas only 25% and 53% of solid polyploids were recovered through axillary shoot induction in these lines. Effective chimera dissociation provides useful and stable genetic materials to enhance blueberry breeding.

PMID:40558397 | DOI:10.3390/biotech14020048

PLoS Genet. 2025 Jun 2;21(6):e1011735. doi: 10.1371/journal.pgen.1011735. Online ahead of print.

ABSTRACT

In ciliates, cortical organelles, including ciliary arrays, are positioned at precise locations along two polarity axes: anterior-posterior and circumferential (lateral). We explored the poorly understood mechanism of circumferential patterning, which generates left-right asymmetry. The model ciliate Tetrahymena has a single anteriorly-located oral apparatus. During cell division, a single new oral apparatus forms near the equator of the parental cell and along the longitude of the parental organelle. Cells homozygous for hypoangular 1 (hpo1) alleles, assemble multiple oral apparatuses positioned either to the left or right flanking the normal oral longitude. Using comparative next-generation sequencing, we identified HPO1 as a gene encoding an ARMC9-like protein. Hpo1 colocalizes with the ciliary basal bodies, forming a bilateral concentration gradient, with the high point on the cell’s right side and a sharp drop-off that marks the longitude at which oral development initiates on the ventral side. A second Hpo1 concentration drop-off is present on the dorsal surface, where it marks the position for development of a cryptic oral apparatus that forms in the janus mutants. Hpo1 acts bilaterally to exclude oral development from the cell’s right side. Hpo1 interacts with the Beige-Beach domain protein Bcd1, a cell’s left side-enriched factor, whose loss also confers multiple oral apparatuses on the ventral surface. A loss of both Hpo1 and Bcd1 is lethal and profoundly disrupts the positioning, organization and size of the forming oral apparatus (including its internal left-right polarity). We conclude that in ciliates, the circumferential patterning involves gradient-forming factors that are concentrated on either the cell’s right or left side and that the two sides of the cortex interact to create boundary effects that induce, position and shape developing cortical organelles.

PMID:40455876 | DOI:10.1371/journal.pgen.1011735

Plant Methods. 2025 May 20;21(1):66. doi: 10.1186/s13007-025-01375-8.

ABSTRACT

High resolution three-dimensional (3D) point clouds enable the mapping of cotton boll spatial distribution, aiding breeders in better understanding the correlation between boll positions on branches and overall yield and fiber quality. This study developed a segmentation workflow for point clouds of 18 cotton genotypes to map the spatial distribution of bolls on the plants. The data processing workflow includes two independent approaches to map the vertical and horizontal distribution of cotton bolls. The vertical distribution was mapped by segmenting bolls using PointNet++ and identifying individual instances through Euclidean clustering. For horizontal distribution, TreeQSM segmented the plant into the main stem and individual branches. PointNet++ and Euclidean clustering were then used to achieve cotton boll instance segmentation. The horizontal distribution was determined by calculating the Euclidean distance of each cotton boll relative to the main stem. Additionally, branch types were classified using point cloud meshing completion and the Dijkstra shortest path algorithm. The results highlight that the accuracy and mean intersection over union (mIoU) of the 2-class segmentation based on PointNet++ reached 0.954 and 0.896 on the whole plant dataset, and 0.968 and 0.897 on the branch dataset, respectively. The coefficient of determination (R²) for the boll counting was 0.99 with a root mean squared error (RMSE) of 5.4. For the first time, this study accomplished high-granularity spatial mapping of cotton bolls and branches, but directly predicting fiber quality from 3D point clouds remains a challenge. This method provides a promising tool for 3D cotton plant mapping of different genotypes, which potentially could accelerate plant physiological studies and breeding programs.

PMID:40394606 | DOI:10.1186/s13007-025-01375-8

Front Plant Sci. 2025 Jun 30;16:1588485. doi: 10.3389/fpls.2025.1588485. eCollection 2025.

ABSTRACT

Pearl millet [Cenchrus americanus (L.) Morrone, formerly Pennisetum glaucum (L.) R. Br.] is the sixth most important cereal globally and is used for forage and feed in the U.S. To identify genomic regions governing important physiological, agronomic and yield related traits, a recombinant inbred line population derived from the cross between Tift 99D₂B_{1 ×} Tift 454 was phenotyped in the field in 2006, 2007 and 2013. In addition, the population was phenotyped for root-knot nematode resistance in the greenhouse during 2009. Using a previously generated genetic map containing 505 single nucleotide polymorphism markers and composite interval mapping, we identified 45 QTLs for eight traits (plant height, stem diameter, days to heading, panicle diameter, panicle length, 1000 seed weight, Pyricularia leaf spot disease, and root-knot nematode egg mass) across almost all linkage groups. These QTLs explained 6.31 to 32.51% of phenotypic variance for each trait and were consistently detected over different environments. Plant height and days to heading were colocalized on LG2 and LG5 showing maturity and plant height are linked and influence each other, similarly to other cereal crops. Interestingly, 5 of 19 QTLs linked to plant height, stem diameter, panicle diameter, and panicle length colocalized to the same locations on LG3, indicating breeding for one trait could simultaneously improve the other. The markers and genes identified in the present study can be used in developing high yielding pearl millet varieties using marker-assisted selection.

PMID:40661761 | PMC:PMC12256767 | DOI:10.3389/fpls.2025.1588485

Plant J. 2025 Jul;123(1):e70304. doi: 10.1111/tpj.70304.

ABSTRACT

Targeted demethylation by DNA glycosylases (DNGs) results in differential methylation between parental alleles in the endosperm, which drives imprinted expression. Here, we performed RNA sequencing on endosperm derived from DNG mutant mdr1 and wild-type (WT) endosperm. Consistent with the role of DNA methylation in gene silencing, we find 108 genes and 96 TEs differentially expressed (DE) transcripts that lost expression in the hypermethylated mdr1 mutant. Compared with other endosperm transcripts, the mdr1 targets are enriched for TEs (particularly Helitrons), and DE genes are depleted for both core genes and GO term assignments, suggesting that the majority of DE transcripts are TEs and pseudo-genes. By comparing DE genes to imprinting calls from prior studies, we find that the majority of DE genes have maternally biased expression, and approximately half of all maternally expressed genes (MEGs) are DE in this study. In contrast, no paternally expressed genes (PEGs) are DE. DNG-dependent imprinted genes are distinguished by maternal demethylation and expression primarily in the endosperm, so we also performed Enzymatic Methyl-seq on hybrids to identify maternal demethylation and utilized a W22 gene expression atlas to identify genes expressed primarily in the endosperm. Overall, approximately ⅔ of all MEGs show evidence of regulation by DNGs. Taken together, this study solidifies the role of MDR1 in the regulation of maternally expressed, imprinted genes and TEs and identifies subsets of genes with DNG-independent imprinting regulation.

PMID:40587880 | DOI:10.1111/tpj.70304

Annu Rev Phytopathol. 2025 Jun 4. doi: 10.1146/annurev-phyto-121823-080201. Online ahead of print.

ABSTRACT

Necrotrophic bacteria within the order Enterobacterales cause significant agricultural losses, with few effective management options available for producers. These pathogens have evolved at least two distinct strategies for infecting plants. Soft rot pathogens in the family Pectobacteriaceae, such as Dickeya and Pectobacterium, rely on secreting plant cell wall-degrading enzymes. In contrast, Pantoea necrotrophs depend on the production of phosphonate phytotoxins, a type of secondary metabolite, for their pathogenicity. This review summarizes recent discoveries on the virulence mechanisms of bacterial necrotrophs and current knowledge of factors that influence their host range and interactions with plant immune defenses. A deeper understanding of bacterial necrotroph host range determinants could inform the development and deployment of enhanced genetic resistance strategies.

PMID:40465659 | DOI:10.1146/annurev-phyto-121823-080201

J Gen Virol. 2025 Jul;106(7). doi: 10.1099/jgv.0.002119.

ABSTRACT

Orthotospovirus tomatomaculae [tomato spotted wilt virus (TSWV)] is a major pathogen in horticultural and row crops worldwide including the USA. In this study, tomato spotted wilt disease incidence was monitored in Arachis hypogaea (peanut; year 1990 to 2024) and Nicotiana tabacum (tobacco; year 2000 to 2024) in commercial farmers’ fields in the Southeastern USA. Furthermore, nucleocapsid (N), nonstructural movement (NSm) and nonstructural silencing suppressor (NSs) protein gene sequences of TSWV global populations from North America, South America, Europe, Asia-Pacific, Africa and Australia were compared with local US population and analysed to understand the genetic variability in the virus genome. In our study, full-length sequences of 94 N, 111 NSm and 78 NSs genes were amplified from TSWV-infected A. hypogaea (peanut), Capsicum annuum (pepper), N. tabacum (tobacco) and Solanum lycopersicum (tomato). nt-based phylogenetic analysis of N, NSm and NSs genes correlated with the geographical location of the TSWV isolates, with notably higher substitution rates in the population of recent years. In addition, the least genetic variability was observed in the N gene of the local population upon comparison with other global TSWV population. The neutrality test of TSWV suggested a non-neutral evolution of the virus genome. Low variation among the selected genes might be attributed to strong purifying selection pressure in the populations. Furthermore, estimation of selection pressure (dN/dS) on small (S) segment-encoded N protein and nonstructural protein showed higher purifying selection than the movement protein encoded by the medium (M) segment of the TSWV isolates. Single-likelihood ancestor counting suggested an overall negative selection pressure on several codons of the selected genes, which indicated that natural selection and population bottleneck events might have influenced the evolution of TSWV. Our study also deciphered high gene flow and low genetic differentiation amid the different TSWV population sets. Additionally, BEAST analysis of TSWV N gene sequences from GA predicted the most common recent ancestor existed ~25 years ago. This data was further correlated with disease incidence data from peanut and tobacco crops obtained in the last three decades. These findings suggest the intermixing of TSWV isolates between peanut, pepper, tobacco and tomato crops, while the virus genome has undergone strong purifying selection.

PMID:40622855 | DOI:10.1099/jgv.0.002119

mSphere. 2025 Jun 17:e0002325. doi: 10.1128/msphere.00023-25. Online ahead of print.

ABSTRACT

Allicin tolerance (alt) clusters in phytopathogenic bacteria, which provide resistance to thiosulfinates like allicin, are challenging to find using conventional approaches due to their varied architecture and the paradox of being vertically maintained within genera despite likely being horizontally transferred. This results in significant sequential diversity that further complicates their identification. Natural language processing (NLP), like techniques such as those used in DeepBGC, offers a promising solution by treating gene clusters like a language, allowing for identifying and collecting gene clusters based on patterns and relationships within the sequences. We curated and validated alt-like clusters in Pantoea ananatis 97-1R, Burkholderia gladioli pv. gladioli FDAARGOS 389, and Pseudomonas syringae pv. tomato DC3000. Leveraging sequences from the RefSeq bacterial database, we conducted comparative analyses of gene synteny, gene/protein sequences, protein structures, and predicted protein interactions. This approach enabled the discovery of several novel alt-like clusters previously undetectable by other methods, which were further validated experimentally. Our work highlights the effectiveness of NLP-like techniques for identifying underrepresented gene clusters and expands our understanding of the diversity and utility of alt-like clusters in diverse bacterial genera. This work demonstrates the potential of these techniques to simplify the identification process and enhance the applicability of biological data in real-world scenarios.IMPORTANCEThiosulfinates, like allicin, are potent antifeedants and antimicrobials produced by Allium species and pose a challenge for phytopathogenic bacteria. Phytopathogenic bacteria have been shown to utilize an allicin tolerance (alt) gene cluster to circumvent this host response, leading to economically significant yield losses. Due to the complexity of mining these clusters, we applied techniques akin to natural language processing to analyze Pfam domains and gene proximity. This approach led to the identification of novel alt-like gene clusters, showcasing the potential of artificial intelligence to reveal elusive and underrepresented genetic clusters and enhance our understanding of their diversity and role across various bacterial genera.

PMID:40525872 | DOI:10.1128/msphere.00023-25