Molecular Plant-microbe Interactions最新文献

Reliable, high-throughput quantification of early fungal infection events is crucial for gene function studies, but it remains labor-intensive. We report an openly available pipeline that automates the detection of β-glucuronidase (GUS)-stained epidermal cells and the intracellular haustoria formed by powdery mildew on barley and wheat leaves. Whole-slide images are captured with a commercial scanner, focus-projected, tiled, and analyzed by deep-learning models trained on expertly annotated datasets. A You Only Look Once (YOLO) network identifies GUS-positive cells, and a companion segmentation model pinpoints haustoria within each cell; automatic focus-layer selection preserves fine structural detail. The workflow runs in minutes per slide on a single workstation and maintains near-perfect agreement with manual counts in both barley and wheat, demonstrating robust cross-species transferability. By delivering single-cell readouts with minimal user input, the pipeline enables rapid functional validation screens and supports large-scale phenotyping of cereal-powdery mildew interactions. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Breeding for sweetpotato (Ipomea batatas) resistance requires accelerating our understanding of genomic sources of resistance. Nucleotide-binding domain leucine-rich repeat receptor (NLR) proteins represent a key component of the plant immune system that mediate plant immune responses. We cataloged the NLR diversity in 32 hexaploid sweetpotato genotypes and three diploid wild relatives using resistance gene enrichment sequencing (RenSeq) to capture and sequence full NLRs. A custom-designed NLR bait library enriched NLR genes with an average 97% target capture rate. We employed a curated database of cloned and functionally characterized NLRs to assign sequenced sweetpotato NLRs to canonical phylogenetic clades. We identified between 800 and 1,200 complete NLRs, highlighting the expanded diversity of coiled-coil NLRs (CNLs) across all genotypes. NLRs among sweetpotato genotypes exhibited large conservation across genotypes. The phylogenetic distance between 6× (hexaploid) and 2× (diploid) genotypes revealed that a small repertoire of I. batatas CNLs diverged from the sweetpotato wild relatives. Finally, we obtained chromosome coordinates in hexaploid (Beauregard) and diploid (Ipomoea trifida) genomes and recorded clustering of NLRs on chromosomes arms. Our study provides a catalog of NLR genes that can be used to accelerate breeding and increase our understanding of the evolutionary dynamics of sweetpotato NLRs. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Plant pathogens deploy nuclear effectors to manipulate the host immune response and reprogram cellular processes. Alternative splicing, a key RNA processing mechanism, plays a pivotal role in determining the fate of immune response-associated genes. Some nuclear effectors have been studied for their roles in the transcription or posttranscriptional regulation of host genes. However, the understanding of how a single nuclear effector engages in multiple regulatory processes within the host nucleus remains limited. Previously, we demonstrated that MoHTR1, a nuclear effector of the rice blast fungus, binds to effector-binding elements in the promoters of target genes and modulates host immunity. To further explore the multifunctionality of MoHTR1, we identified host proteins interacting with MoHTR1. MoHTR1 interacts with the splicing factor OsSR45 in rice nuclear speckles and promotes degradation of OsSR45. MoHTR1 is involved in alternative splicing of mRNAs associated with immune and stress responses. The changes in alternative splicing patterns of these mRNAs are identical in both Magnaporthe oryzae-infected rice and MoHTR1-overexpressing transgenic lines, underscoring the consistent regulatory effect of MoHTR1. Our findings highlight dual roles of MoHTR1 in regulating both transcription and posttranscriptional processes and provide novel insights into how nuclear effectors modulate host immunity through intricate molecular mechanisms. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Zymoseptoria tritici causes Septoria tritici blotch, which significantly reduces yields of wheat. To investigate infection phase-specific gene expression in the pathogen, we analyzed gene expression during infection of susceptible and resistant wheat cultivars, as well as the nonhost species barley, at 1, 3, 6, 10, 17, and 23 days postinoculation (DPI). There were dramatic differences in pathogen gene expression at 10 DPI in the susceptible compared with both resistant interactions. The most pronounced differences in pathogen gene expression were observed at 3 DPI in both the susceptible and resistant host interactions compared with the nonhost. Thirty-one putative effectors showed early expression during the susceptible compared with the nonhost interaction; six were selected for subcellular localization studies. Using Agrobacterium-mediated transient expression in Nicotiana benthamiana, subcellular localization assays revealed that two candidate effectors localized to putative mobile cytosolic bodies when expressed without their signal peptides, suggesting potential roles in intracellular signaling or host gene regulation. When expressed with their signal peptides, four candidate effectors localized to the cytosol, whereas one did not accumulate to detectable levels. Comparison of pathogen gene expression in the susceptible host with expression in the resistant hosts identified genes expressed during the transition from biotrophic to necrotrophic growth at 10 DPI. Comparison of pathogen gene expression in resistant and susceptible hosts, versus in the nonhost barley, identified genes involved in initial colonization and host recognition. These results contribute to understanding candidate effectors that are activated early during infection and may play a role in the suppression of plant immunity. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Fusarium wilt of strawberry, caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. fragariae (Fof), is one of the greatest threats to cultivated strawberry. The pathogen penetrates strawberry plants through roots, severely affecting roots and crowns and resulting in rapid wilting and death. Research into the genetic basis of resistance to Fof has identified five loci, FW1 to FW5, that confer resistance to Fusarium wilt of strawberry and one Fof effector, SIX6. Although it is hypothesized that FW1 recognizes the SIX6 effector, the underlying resistance gene is unknown. A new isolate of Fof that breaks FW1-mediated resistance recently emerged and poses a significant threat to the California strawberry industry, the source of 88 to 91% of the strawberries produced in the United States. There are still significant gaps surrounding the molecular and physiological interaction between Fof and strawberry and the evolution of pathogenicity of Fof isolates unaffected by FW1. This review summarizes our current knowledge, identifies knowledge gaps, and provides a summary of genomic and molecular tools currently available to study the Fof-strawberry interaction. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Despite large omics datasets, the prediction of eukaryotic genes is still challenging. We have developed a new method to improve the prediction of eukaryotic genes and demonstrate its utility using the genome of the fungal wheat pathogen Zymoseptoria tritici. From 10,933 to 13,260 genes were predicted by four previous annotations, but only one third were identical. A novel bioinformatics suite, InGenAnnot, was developed to improve Z. tritici gene annotation using Iso-Seq full-length transcript sequences. The best gene models were selected among different ab initio gene predictions, according to transcript and protein evidence. Overall, 13,414 reannotated gene models (RGMs) were predicted, improving previous annotations. Iso-Seq transcripts outlined 5' and 3' untranslated regions for 73% of the RGMs and alternative transcripts mainly due to intron retention. Our results showed that the combination of different ab initio gene predictions and evidence-driven curation improved gene annotation of a eukaryotic genome. It also provided new insights into the transcriptional landscape of this fungus. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Cercospora janseana is the causal agent of narrow brown leaf spot (NBLS) on rice, an increasingly problematic disease in the southern United States. Historically, this disease was considered sporadic and a minor nuisance; however, recent NBLS epidemics and the resulting detrimental impacts on yield underscore the need for a deeper understanding of the pathogen's population biology. In this study, we used whole-genome sequencing of 136 C. janseana isolates collected from Louisiana and Texas to investigate genetic diversity, population structure, and possible reproductive strategies. Our results revealed a high level of genetic diversity across sampling years and locations. Population structure and phylogenetic analyses identified two distinct lineages, with most isolates belonging to a dominant lineage found in both states. Despite the disparity in observed lineage frequencies, overall population differentiation was minimal, indicating ongoing gene flow across regional boundaries. Linkage disequilibrium decay and index of association analyses revealed evidence for a population that predominantly reproduces clonally with infrequent sexual reproduction. However, nearly equal frequencies of mating type idiomorphs in most sampled populations indicate ongoing or past sexual reproduction to some extent. Taken together, these results suggest that C. janseana populations are diverse, migrate between production regions, and exhibit a mixed mode of reproduction. These findings have important implications for the development of integrated disease management and pathogen monitoring practices to ultimately mitigate the impacts of this resurgent disease. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Plants recognize pathogen-associated molecular patterns via pattern recognition receptors, leading to the activation of pattern-triggered immunity in response to pathogen attack. Phytophthora infestans ceramide D (Pi-Cer D) is a sphingolipid from the oomycete pathogen P. infestans. Pi-Cer D is cleaved by the plant extracellular ceramidase NEUTRAL CERAMIDASE 2 (NCER2), and the resulting 9-methyl-branched sphingoid base is recognized by the plant receptor RESISTANT TO DFPM-INHIBITION OF ABSCISIC ACID SIGNALING 2 (RDA2) at the plasma membrane to transduce a defense signal. However, additional components are likely involved in sphingolipid recognition, which remain to be identified. Here, we employed a screen based on Lumi-Map technology to look for Arabidopsis (Arabidopsis thaliana) mutants with altered defense responses to Pi-Cer D. We identified three mutants showing diminished responses to Pi-Cer D and elf18, each carrying mutations in STAUROSPORIN AND TEMPERATURE SENSITIVE 3-LIKE A (STT3A), which encodes an oligosaccharyltransferase. The stt3a mutants exhibited higher susceptibility to the pathogen Colletotrichum higginsianum than the wild type. In stt3a mutants, the molecular mass of NCER2 and RDA2 proteins appeared smaller, indicating that STT3A is involved in posttranslational modification of the proteins. An enzymatic deglycosylation assay revealed that NCER2 and RDA2 are N-glycosylated. These findings suggest that STT3A contributes to plant immunity via posttranslational modification of proteins including NCER2 and RDA2. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.