Author: slquinlan

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

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

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 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

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

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

mBio. 2025 May 20:e0365224. doi: 10.1128/mbio.03652-24. Online ahead of print.

ABSTRACT

Invasive aspergillosis, caused by Aspergillus fumigatus, represents a critical public health concern, particularly due to increasing resistance to triazole antifungals linked to TR₃₄/TR₄₆ cyp51A haplotypes. In our genomic epidemiology study of 157 A. fumigatus isolates from Dutch environmental hotspots and two clinical centers, we identified near-identical genomes in several environmental and patient isolates, indicating a probable link. However, the geographic and temporal data alone are not sufficient to explain direct transmission pathways. Furthermore, a comparison with more than 1,200 globally sourced genomes revealed the extensive dissemination of certain clonal groups across multiple distant regions, raising significant challenges for the utility of genomic epidemiology. The discovery of high genetic diversity and the widespread distribution of some clonal groups challenges current understanding, suggesting that in most cases, tracing the precise source of individual infections will remain extremely difficult, even with increased sampling. In addition, we uncovered that the multi-triazole-resistant TR₃₄/TR₄₆ cyp51A haplotypes are associated with resistance to non-triazole fungicides such as benzimidazole, succinate dehydrogenase inhibitor, and quinone outside inhibitor classes, strongly suggesting an exposure history to multiple agricultural fungicides in these environmental hotspots. This resistance beyond the azole class suggests that strategies targeting only triazoles may be insufficient. Our findings challenge current paradigms and carry significant implications for One Health research and global public health strategies, underscoring the urgency of multidisciplinary approaches to tracking and monitoring fungal resistance.IMPORTANCEOur study links triazole-resistant A. fumigatus isolates cultured from three environmental hotspots to cases of aspergillus disease in two hospitals in the Netherlands. Genome comparisons of isolates from environmental hotspots and patients showed multiple near-identical linked genotypes, consistent with a route of transmission from the environment to patients. Linked cases without clear transmission routes emphasize the need to better understand the ecology of this fungus. Since patients often do not visit rural hotspots, research should explore complex, long-distance transmission mechanisms, including airborne dispersal of conidia or non-agricultural habitats. The multi-fungicide resistance phenotype suggests reducing one class of fungicides alone may not lower resistance selection. Instead, interventions should target modifying environments that promote the growth of fungicide-resistant A. fumigatus and prevent the escape of resistant spores from these hotspots to mitigate the burden of environmental resistance effectively.

PMID:40391955 | DOI:10.1128/mbio.03652-24

Mol Plant Pathol. 2025 May;26(5):e70096. doi: 10.1111/mpp.70096.

ABSTRACT

Harpins are proteins secreted by many gram-negative, plant-pathogenic bacteria that stimulate the hypersensitive reaction (HR), a host cell death defence response, when infiltrated into plant leaves as purified proteins. This activity of harpins was first discovered in Nicotiana tabacum (tobacco), which manifests an especially strong and rapid harpin-activated HR that becomes evident within 12-24 h after infiltration. HrpN is the major harpin of the fire blight pathogen Erwinia amylovora. We discovered natural variation in the HrpN-induced HR among tobacco accessions and identified candidate genes using genetic mapping and bulked-segregant analysis with whole genome sequencing. Virus-induced gene silencing of candidate gene Wall-Associated Kinase 2 (WAK2) abrogated the HR in response to HrpN and HpaG, a harpin from the soybean bacterial pustule pathogen Xanthomonas citri pv. glycines. WAK2 silencing also compromised the avirulence activity of harpin HrpZ in the tobacco wildfire pathogen Pseudomonas syringae pv. tabaci. A natural, disruptive mutation in WAK2 correlated with the inability of tobacco accessions to mount the harpin-mediated HR. We conclude that the predicted receptor-like kinase WAK2 is required for the strong HR induced in tobacco leaves by harpin protein infiltration and can potentially mediate resistance to bacterial pathogens based on harpin recognition.

PMID:40391583 | DOI:10.1111/mpp.70096

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

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