Distinct genomic contexts predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae

Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether presence-absence variation patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying presence-absence variation because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene presence-absence variation in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that presence-absence variation genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of presence-absence variation and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between presence-absence variation genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience presence-absence variation with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that presence-absence variation genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene presence-absence variation can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.

Hydroxamate siderophores secreted by plant endophytic Pseudomonas putida elicit defense against blast disease in rice incited by Magnaporthe oryzae

Our study focuses on hydroxamate-type siderophores from Pseudomonas putida BP25, known for chelating ferric iron and aiding microbial growth in iron-deficient environments. Confirmed through CAS-agar and tetrazolium tests, a purified siderophore extract was obtained via ion-exchange chromatography. Applying varying concentrations of this siderophore to rice seedlings demonstrated concentration-dependent effects on shoot and root phenotypes. Prophylactic application on rice leaves significantly reduced blast severity (68.7%-97.0%), surpassing curative application (47.5%-86.87%). Additionally, the siderophore treatment elevated peroxidase, polyphenol oxidase, and total phenols in rice plants. Defense-related genes linked to salicylic acid (OsPR1.1, OsNPR1, and OsPDF2.2), and other pathways (Oshox24, OsCLE, and OsGLP3-3, OsEIN2.4, and OsCSE) promoting blast suppression showed upregulation. However, the OsACS6 gene associated with ethylene-induced internodal elongation was significantly downregulated. Overall, our findings propose that the siderophore from P. putida BP25 induces defense gene transcription, offering potential for sustainable rice production via bio-formulation.

Intraspecific Variation of Transposable Elements Reveals Differences in the Evolutionary History of Fungal Phytopathogen Pathotypes

Transposable elements (TEs) contribute to intraspecific variation and play important roles in the evolution of fungal genomes. However, our understanding of the processes that shape TE landscapes is limited, as is our understanding of the relationship between TE content, population structure, and evolutionary history of fungal species. Fungal plant pathogens, which often have host-specific populations, are useful systems in which to study intraspecific TE content diversity. Here, we describe TE dynamics in five lineages of Magnaporthe oryzae, the fungus that causes blast disease of rice, wheat, and many other grasses. We identified differences in TE content across these lineages and showed that recent lineage-specific expansions of certain TEs have contributed to overall greater TE content in rice-infecting and Setaria-infecting lineages. We reconstructed the evolutionary histories of long terminal repeat-retrotransposon expansions and found that in some cases they were caused by complex proliferation dynamics of one element and in others by multiple elements from an older population of TEs multiplying in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice- and wheat-infecting M. oryzae lineages and a region showing evidence of homologous recombination between those lineages, which could have facilitated such a transfer. By investigating intraspecific TE content variation, we uncovered key differences in the proliferation dynamics of TEs in various pathotypes of a fungal plant pathogen, giving us a better understanding of the evolutionary history of the pathogen itself.

Cell wall polysaccharides of endophytic Pseudomonas putida elicit defense against rice blast disease

AIMS

To characterize the functional role of extracellular polysaccharides and lipopolysaccharide (LPS) extracted from endophytic Pseudomonas putida BP25 (PpBP25) against rice blast.

METHODS AND RESULTS

We profiled the transcriptome of endobacterized rice seedlings using RNA-seq. Fluorescence imaging of interaction between Magnaporthe:: gfp and P. putida:: mCherry was performed on rice phylloplane using confocal laser scanning microscopy (CLSM). Microbial polysaccharides, exopolysaccharide (EPS), and LPS extracted from PpBP25 were characterized using Fourier-transform infrared-spectroscopic analysis (FTIR). Biochemical assays and gene expression analysis were conducted on EPS- and LPS-treated rice seedlings. A detached-leaf assay was designed to test the blasticidal-effect of bacterial-endophyte, EPS, and LPS on rice phylloplane. PpBP25 elicited defense in rice with a consequently altered seedling phenotype. Rice cultivar, Pusa Basmati-1, colonized by PpBP25 showed an altered transcriptome profile displaying a total of 110-downregulated and 68-upregulated genes (P < 0.005) representing growth/development and defense pathways, respectively. CLSM of PpBP25 bacterized phylloplane showed reduced conidial-germination and mycelial-biomass of Magnaporthe oryzae. To decipher the elicitor role of polysaccharides, we purified and characterized EPS and LPS using FTIR. Rice treated with the EPS and LPS showed root-growth inhibition the phenotype of MAMP-triggered immunity. While the EPS showed blast suppressive activity at 1-20 mg mL-1 (79.80%-86.87% reduction over control), the LPS exhibited 78.0%-79.8% reduction at 20-200 μg mL-1on rice. Polysaccharides treated seedling showed elevated activities of peroxidase and polyphenol-oxidase activities, and total-phenols content. Treated plantlets showed up regulation of OsPR1.1,OsPR3, OsGLP3-3,OsZFP179, and Oshox24 as well as downregulation of OsACS6.

CONCLUSIONS

We showed that P. putida Bp25 and its cell wall-associated polysaccharides could elicit defense against rice blast.

Fungal oxysterol-binding protein-related proteins promote pathogen virulence and activate plant immunity

Oxysterol-binding protein-related proteins (ORPs) are a conserved class of lipid transfer proteins that are closely involved in multiple cellular processes in eukaryotes, but their roles in plant-pathogen interactions are mostly unknown. We show that transient expression of ORPs of Magnaporthe oryzae (MoORPs) in Nicotiana benthamina plants triggered oxidative bursts and cell death; treatment of tobacco Bright Yellow-2 suspension cells with recombinant MoORPs elicited the production of reactive oxygen species. Despite ORPs being normally described as intracellular proteins, we detected MoORPs in fungal culture filtrates and intercellular fluids from barley plants infected with the fungus. More importantly, infiltration of Arabidopsis plants with recombinant Arabidopsis or fungal ORPs activated oxidative bursts, callose deposition, and PR1 gene expression, and enhanced plant disease resistance, implying that ORPs may function as endogenous and exogenous danger signals triggering plant innate immunity. Extracellular application of fungal ORPs exerted an opposite impact on salicylic acid and jasmonic acid/ethylene signaling pathways. Brassinosteroid Insensitive 1-associated Kinase 1 was dispensable for the ORP-activated defense. Besides, simultaneous knockout of MoORP1 and MoORP3 abolished fungal colony radial growth and conidiation, whereas double knockout of MoORP1 and MoORP2 compromised fungal virulence on barley and rice plants. These observations collectively highlight the multifaceted role of MoORPs in the modulation of plant innate immunity and promotion of fungal development and virulence in M. oryzae.

Mutations of two FERONIA-like receptor genes enhance rice blast resistance without growth penalty

Genes that provide resistance to fungi and/or bacteria usually reduce plant growth and ultimately affect grain yield. Thus, crop breeding programs need to find genetic resources that balance disease resistance with growth. The receptor kinase FERONIA regulates cell growth and survival in Arabidopsis. Here, we investigate, in rice, the role of members of the FERONIA-like receptor (FLR) gene family in the balance between growth and the response to the fungal pathogen Magnaporthe oryzae (Pyricularia oryzae), which causes the most devastating disease in rice. We carried out genome-wide gene expression and functional screenings in rice via a gene knockout strategy, and we successfully knocked out 14 FLR genes in rice. Using these genetic resources, we found that mutations in the FLR2 and FLR11 genes provide resistance to rice blast without a profound growth penalty. Detailed analyses revealed that FLR2 mutation increased both defense-related gene expression and M. oryzae-triggered production of reactive oxygen species. Thus, our results highlight novel genetic tools for studying the underlying molecular mechanisms of enhancing disease resistance without growth penalty.