SEARCH · PubMed Health

Results for “Oryza”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

PubMed2025

Beyond parental lines: multi-omics analyses reveal epigenetic and transcriptional mechanisms underlying heterosis in Oryza sativa × Oryza rufipogon hybrids.

Heterosis, or hybrid vigor, refers to the superior phenotypes of a hybrid compared with their parents and is widely exploited in agriculture. Interspecific hybrids within the Oryza genus demonstrate significant potential for the systematic improvement of rice varieties. Nevertheless, the mechanistic basis underlying heterosis in interspecific Oryza hybrids remains poorly understood. Here, we systematically performed phenotypic characterization, whole-genome bisulfite sequencing, RNA sequencing, and small RNA profiling using Oryza sativa L. ssp. japonica cv. Nipponbare (NIP), Oryza rufipogon Griff. acc. CWR, and their resulting F1 hybrid (named as NC). NIP and CWR showed distinct phenotypic and molecular differences. The interspecific hybrid, NC, exhibited significant yield heterosis. In the hybrid, most epigenetic and transcriptional features displayed additive inheritance patterns relative to parental lines. Analysis revealed that domestication-selected genes maintained relatively low DNA methylation coupled with high expression levels in both hybrid and parental lines. Additionally, we identified that non-additive miRNAs were potentially involved in regulating fertility, cell growth, and cell division processes in the hybrid. A significant negative correlation was observed between DNA methylation level and gene expression. Functional enrichment analysis revealed that hybrid-MPV DEGs were significantly associated with flowering time regulation, carbohydrate metabolism, photosynthesis, protein phosphorylation, seed development, and defense responses. Through weighted gene co-expression network analysis, we identified 102 functional gene modules, six of which were significantly associated with yield-related heterosis. Collectively, our results provide a multi-omics framework for understanding interspecific hybridization between elite cultivars and wild rice relatives, highlighting CWR as an untapped genetic reservoir for rice improvement.

Oryza↗

PubMed2026

Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa.

African rice (Oryza glaberrima) was independently domesticated in West Africa around 3000 years ago, and has long been intertwined in the history of the region. Asian rice (Oryza sativa), which was introduced in Africa when European settlers arrived, gradually replaced African rice and has since dominated rice cultivation in the continent. Domesticated rice species are affected by bacterial leaf blight (BLB), which is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Here we show that the bacterial leaf blight pathogen in Africa (AfXoo) belongs to a distinct phylogroup from the one circulating in Asia (AsXoo), and has a different evolutionary history. Analysis of 87 AfXoo genomes identified five main populations, including highly clonal ones, and a more diverse and recombinant population. Tip-dating analysis revealed that the AfXoo population went through a period of expansion, then decline and more recent recovery. We hypothesize this followed the rise and fall of African rice, and that the introduction of O. sativa served as a bottleneck leading to the emergence of current AfXoo populations. We show that AfXoo has a highly conserved repertoire of type III effectors (T3E), but that nonetheless there is variation especially between populations. In the case of transcription activator-like effectors (TALEs), variation can arise quickly through rearrangements, and we hypothesize that the TALE repertoire of AfXoo has been selected to allow the bacteria to colonize both species of cultivated rice found in the continent. Our research provides an attempt to decipher the genetic history of bacterial blight in West Africa, and its past and present impact on rice cultivation in the region.

Journal Article↗

PubMed2026

Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.

Phylogenetic incongruence is increasingly recognized as pervasive, yet the extent to which reticulate evolution occurs between groups separated by substantial geographical distances and deep phylogenetic divergence remains poorly characterized. In the Oryza AA-genome group-a model for plant speciation and domestication-the traditional bifurcation model posits that Australian Oryza meridionalis and African Oryza longistaminata occupy basal branches, distinct from the more recently diversified monophyletic clade comprising Asian and other African lineages, including major cultivars. However, recent evidence from endogenous viral sequences has hinted at unexpected genetic relatedness between African O. longistaminata and Asian Oryza sativa, which are geographically and phylogenetically distant. Here, we conducted a genome-wide survey across 11 Oryza species to systematically identify genomic regions exhibiting phylogenetic incongruence. Widespread phylogenetic discordance was observed, notably involving genomic segments in which O. longistaminata showed phylogenetic proximity to Asian species, contradicting their established deep divergence. To distinguish between introgression and incomplete lineage sorting, we performed four-taxon ABBA-BABA tests, which provided statistical support for introgression. Furthermore, divergence time estimates for these incongruent regions were younger than the species divergence times, suggesting historical introgression between the ancestors of lineages that are currently separated by vast geographical distances. Systematic assessments indicated that potential analytical artifacts, such as compositional bias and substitution saturation, were unlikely to explain the observations. These convergent lines of evidence suggest that ancient introgression had occurred between currently geographically separated and evolutionarily divergent Oryza lineages, leaving detectable footprints across their modern genomes.

Oryza↗

PubMed2026

Morphological characterization, genetic diversity and population structure of the rice blast pathogen Magnaporthe oryzae in Northeast India.

The blast pathogen, Magnaporthe oryzae, is one of the most destructive fungal pathogens of rice worldwide, yet its morphological features, genetic diversity and population structure in Northeast India remain poorly understood. In this study, twenty‒two M. oryzae isolates collected from eight states of Northeast India were characterized using morphological, molecular, and population genetic analyses. Morphological characterization revealed whitish to greyish‒white mycelia with sparse sporulation and colony diameters ranged from 36 to 90 mm, classifying the isolates into 14 fast and 8 slow‒growing groups. Whole genome sequencing was performed to enable both ITS‒based identification and SSR locus mining from the assembled genomes. Molecular identification using ITS rDNA sequences confirmed all isolates as M. oryzae, with 95.5-100% similarity. Phylogenetic analysis grouped the isolates into two major clades and identified seven ITS sequence types (GenBank Accessions: PX273287-PX273293). Genetic diversity assessed using 30 SSR markers revealed substantial polymorphism, with 1-7 alleles per locus and polymorphism information content (PIC) values ranging from 0.00 to 0.81. Heatmap clustering, dendrogram analysis, and distance metrics consistently identified two major genetic groups, with some isolates forming nearly identical clusters and others showing moderate divergence. Principal Component Analysis (PCA) and Principal Coordinates Analysis (PCoA) accounted for 87.8% of the total variance (PC1 and PC2 accounted for 54.4% and 33.4% respectively of the total variance) and revealed distinct outliers. Analysis of Molecular Variance (AMOVA) attributed 80% of the total genetic variation to differences among populations while only 20% was attributed to within population differences highlighting significant inter‒population divergence and clonal population structure. The study revealed substantial morphological and genetic diversity among M. oryzae populations in Northeast India, underscoring the need for region‒specific disease management strategies.

India↗

PubMed2026

Bioengineering and physicochemical optimization of ergothioneine production by Aspergillus oryzae.

Ergothioneine (EGT) is a bioactive, rare variant of histidine with many applications in the medical, pharmaceutical, and food fields. Therefore, we aimed to investigate in this study the impact of genomic and physicochemical factors on EGT production by the industrial filamentous fungus Aspergillus oryzae. Firstly, to facilitate efficient EGT production, we analyzed the subcellular localization of the three EGT biosynthetic enzymes present in A. oryzae. During screening for the most potent producer of EGT among bioengineered transformants, the strain EgtACO overexpressing both AoegtA and AoegtC showed promising EGT production in DPY medium. Five days of incubation was the optimum period, and CZYP medium was the optimum medium for EGT production. Co-cultivation with the nisin Z-producing Lactococcus lactis JCM 7638 yielded EGT production equivalent to that of the EgtACO strain alone. Having broad-spectrum antimicrobial activity without suppressing growth of the EgtACO strain suggested that bacteriocin may help reduce the risk of contamination during long-term cultivation. Moreover, supplementing the production medium with L-methionine or zinc sulfate improved EGT production (1468.5 or 1565 mg/L, respectively). Furthermore, repeated inoculation of the producer strain EgtACO and incubation in blue light were the optimum conditions for EGT production (1895 mg/L). Finally, we achieved cost-effective EGT production using A. oryzae strain EgtACO under the optimal culture conditions using agricultural wastes: potato peel and sweet potato peel (293 and 308 mg/L, respectively).

Aspergillus oryzae↗

PubMed1978

Purification and characterization of the two molecular forms of membrane acid protease from Aspergillus oryzae.

Two forms (M1 and M2) of the membrane-bound acid protease of Aspergillus oryzae have been purified by extraction with Triton X-100, washing with cold acetone, and repeated gel filtration on Bio-Gel A-15 m in the presence and absence of Triton X-100. The purified membrane enzymes, M1 and M2, moved as a single band in acrylamide gel electrophoresis and had apparent molecular weights of 150 000 and 60 000, respectively, as estimated by sodium dodecyl sulfate/acrylamide gel electrophoresis. These two membrane enzymes activated bovine pancreatic trypsinogen and had the same pH optima in the acid pH range. They immunologically cross-reacted with each other and with an extracellular acid protease from A. oryzae, and contained carbohydrate, ranging from 52.5 to 80.5% and comprising three hexoses, glucose, galactose, and mannose. While these catalytic, chemical and immunological properties are similar to those of the extracellular acid protease from A. oryzae, both membrane enzyme differed in their hydrophobic properties from external enzymes. Thus they are activated by the detergent Triton X-100 and some polar lipids.

Aspergillus↗

PubMed2025

Transposable elements create distinct genomic niches for effector evolution among Magnaporthe oryzae lineages.

BACKGROUND: Plant-pathogen interactions are characterized by evolutionary arms races. At the molecular level, fungal effectors can target important plant functions, while plants evolve to improve effector recognition. Rapid evolution in genes encoding effectors can be facilitated by transposable elements (TEs). In Magnaporthe oryzae, the causal agent of blast disease in several cereals and grasses, TEs play important roles in chromosomal evolution as well as the gain or loss of effector genes in host specialized lineages. However, a global understanding of TE dynamics driving effector evolution at population scale and across lineages is lacking. RESULTS: Here, we focus on 16 AVR effector loci assessed across a global sampling of 11 reference genomes and 447 newly generated draft genome assemblies from publicly available short-read sequencing data across all major M. oryzae lineages and outgroups. We classified each effector based on evidence for duplication, deletion and translocation processes among lineages. Next, we determined AVR gain and loss dynamics across lineages allowing for a broad categorization of effector dynamics. Each AVR was integrated in a distinct genomic niche determined by the TE activity profile contributing to the diversification at the locus. We quantified TE contributions to effector niches and found that TE identity helped diversify AVR loci. We used the large genomic dataset to recapitulate the evolution of the rice blast AVR1-CO39 locus. CONCLUSIONS: Taken together, our work demonstrates how TE dynamics are an integral component of M. oryzae effector evolution, likely facilitating escape from host recognition. In-depth tracking of effector loci is a valuable tool to predict the durability of host resistance.

Ascomycota↗

PubMed2026

The rice cellulose synthase-like D4 gene (OsCSLD4) is required for resistance to Xanthomonas pv. oryzae.

Plant cell walls serve as a physical support and a barrier to pathogen invasion. Cellulose is the main component of cell walls. The cellulose synthase-like D (CSLD) subfamily genes are required for plant normal development. In rice, Oscsld4 mutant plants are dwarfed and have narrow, rolled leaves. The role of OsCSLD4 in rice immune responses is unclear. We carried out a forward genetic screen using rice mutants expressing the XA21 immune receptor to identify components required for the resistance to Xanthomonas oryzae pv. oryzae (Xoo). One mutant from the screen carries a loss-of-function mutation in OsCSLD4. OsCSLD4 is required for resistance to Xoo mediated by both the XA21 and XA26 immune receptors and also participates in the basal resistance to Xoo. Hallmarks of the XA21-mediated immune response, including induction of the defense marker gene KO5, reactive oxygen species (ROS) burst and the phosphorylation of mitogen-activated protein kinases (MAPKs), are not compromised in the Oscsld4 mutant. These findings suggest that OsCSLD4 does not function as a core signaling component of the immune receptor pathway, but rather maintains the structural integrity of the cell wall as an effective physical barrier. This structural defense is essential for the full manifestation of both innate and receptor-mediated immunity.

Oryza↗

PubMed1977

A cell wall proteo-heteroglycan from Piricularia oryzae: further studies of the structure.

The carbohydrate part of a proteo-heteroglycan from Piricularia oryzae was further studied by chemical and immunological methods. Acetolysis studies of the proteo-heteroglycan and exo-alpha-D-mannanase resistant core showed a (1 leads to 6) mannan back-bone structure with side chains composed of one to four mannose units, and some of which are terminated by D-glucose or D-galactofuranose. The mode of attachment of the terminal glucose was characterized to be alphaGlc(1 leads to 6)Man by inhibition reaction with oligosaccharides. Rabbit anti-serum formed against P. oryzae cells had three specificities, the first one for alphaGlc(1 leads to 6)alphamannosyl, the second one for alphaMan(1 leads to 3)alphamannosyl, and the last one for alphaGal-f(1 leads to 2)alphamannosyl residues. The most immunodominant side chain structure of the P. oryzae heteroglycan was shown to be alphaGlc(1 leads to 6)alphaMan(1 leads to 2)alphaMan(1 leads to 2)Man.

Carbohydrates↗

PubMed2026

Evolutionary constraints and regulatory plasticity shape host specialization in the Magnaporthe oryzae species complex.

Rice blast caused by Magnaporthe oryzae threatens global rice production, and wheat blast emergence highlights the pathogen's capacity for host shifts. Although numerous studies have described M. oryzae genome organization and infection mechanisms, critical questions remain regarding the evolutionary drivers of stable host specialization. Importantly, the blast pathogen comprises a species complex of genetically differentiated, host-adapted lineages rather than single homogeneous species. To address this knowledge gap, we integrate evidence from evolutionary genomics, transcriptomics, and metabolomics to develop the "Constrained Plasticity" framework. We argue that host adaptation arises from three interacting layers: genomic scaffolding (including epigenetic and noncoding RNA regulation), regulatory networks (enabling transcriptional plasticity), and metabolic compatibility (determining physiological success). This systems-level perspective explains the long-term stability of host-adapted lineages and the rare breakdowns resulting in host shifts, such as wheat blast. This framework generates testable predictions for pathogen emergence and provides a roadmap for developing lineage-aware resistance strategies.

Oryza↗

PubMed1975

Aspergillus oryzae acid proteinase. Purification and properties, and formation of pi-chymotrypsin.

An acid proteinase from Aspergillus oryzae was isolated from a commercial powder by successive (NH4)2SO4 fractionation, acetone precipitation, and ion-exchange chromatography on phosphate- and DEAE-cellulose columns. The purified enzyme was found to be homogeneous by ultracentrifuge-sedimentation analysis (S20, W equal 3.63S), but electrofocusing in polyacrylamide gels and electrophoresis at pH 3.2 revealed that it consists of two very closely migrating bands. No difference in the amino acid composition and enzymic activities of the two partially separated bands could be detected, and it was concluded that the acid proteinase exists in two molecular forms. The enzyme activates bovine trypsinogen and chymotrypsinogen at pH 3.5 (the kappacat. and Km values at 35degrees C are 11.3S- minus 1, 0.10mM and 1.14S- minus 1, 0.18mM respectively). It hydrolyses the Phe-Phe bond of the synthetic pepsin substrates Z-His-Phe-Phe-OEt (kappacat. equal 1.65S- minus 1, Km equal 0.640mM at pH 3.5, 30degrees C) and Z-Ala-Ala-Phe-Phe-OPy4Pr (kappacat. equal 0.37S- minus 1, Km equal 0.037 mM at pH2.9, 39degrees C), where Z represents benzyloxycarbonyl and OPy4Pr represents 3-(4-pyridyl)-propyl 1-ester. Activation of bovine chymotrypsinogen results from the cleavage of the Arg(15)-Ile(16) bond in the zymogen. No other cleavages were observed. The use of A. oryzae proteinase provides a simple tool for the production of pi-chymotrypsin in good yield and purity.

Amino Acids↗

PubMed1977

Extracellular acid protease of Aspergillus oryzae grown on liquid media: multiple forms due to association with heterogeneous polysaccharides.

The acid protease (EC 2.4.23.6) that is produced extracellularly when Aspergillus oryzae is grown on liquid media has been isolated and characterized. The enzyme was purified by precipitation with tannic acid, chromatography on Duolite A-2, and gel filtration on Sephadex G-100. The last step yielded four active components, with varying molecular weights ranging from 42,000 to 60,000. Two of them, designated E1 and E1a, with molecular weights of 60,000 and 55,000, respectively, were heterogeneous on isoelectric focusing, both giving at least three enzyme species with different isoelectric points, whereas the other two, E1b and E2, with molecular weights of 49,000 and 42,000, respectively, were essentially homogeneous. These four enzymes activated bovine pancreatic trypsinogen and had the same pH optima in the acid pH range. They had essentially the same amino acid composition and immunologically cross-reacted with each other. These catalytic, chemical, and immunological properties are similar to those of acid protease A1 and A2 from A. oryzae grown on solid bran media. Unlike acid protease from solid bran culture, which contains both carbohydrate-containing and the carbohydrate-free species, all of the four enzymes, E1, E1a, E1b, and E2, contained carbohydrate, ranging from 18.9 to 43% and comprising three hexoses, glucose, galactose, and mannose. The carbohydrate portions were polysaccharide in nature and heterogeneous with respect to both molecular weight and sugar composition, and at least a part of the carbohydrate was present in the form of homopolysaccharides such as galactan and mannan. These findings indicate that polysaccharide chains with different molecular weights and with different chemical compositions are apparently responsible for the microheterogeneity of acid protease.

Amino Acids↗

PubMed1976

Heterokaryosis and parasexuality in Pyricularia oryzae Cavara.

Auxotrophs in three different races of Pyricularia oryzae were obtained following ultraviolet mutagenesis, and tested for complementarity on minimal medium. Prototrophic growth resulted between combinations of different auxotrophs of single strains, but not between strains. The growth did not result form crossfeeding, but required at least transitory heterokaryosis. Putative diploids, i.e., large prototrophic conidia, were readily isolated from the heterokaryons. In addition, conidia with nearly every possible combination of parental markers were found, showing that P. oryzae does indeed complete the parasexual cycle. The degree of genetic recombination found here may help to explain the extreme variability of this organism.

Cell Nucleus↗

PubMed2025

Exploring effector protein dynamics and natural fungicidal potential in rice blast pathogen Magnaporthe oryzae.

Rice blast, caused by Magnaporthe oryzae, is one of the most destructive fungal diseases in rice, resulting in major economic losses worldwide. Genetic and genomic studies have identified key genes and proteins, such as AvrPik variants and MAX proteins, that are crucial for the pathogen's virulence. These effector proteins interact with specific alleles of the Pik gene family on rice chromosome 11, modulating the host's immune response. In this study, we investigated 35 plant-derived metabolites known for their antifungal properties as potential fungicides against M. oryzae. Using molecular docking, we identified Hecogenin and Cucurbitacin E as strong binders to MAX40 and APIKL2A proteins, which are essential for the fungus's immune evasion and pathogenicity. Molecular dynamics simulations further confirmed that these compounds form stable, strong interactions with the target proteins, validating their potential as therapeutic agents. Additionally, the compounds were evaluated based on Lipinski's rule of five and toxicity predictions, indicating their suitability for agricultural use. These results suggest that Hecogenin and Cucurbitacin E could serve as promising lead candidates in the development of novel fungicides for rice blast, offering new strategies for crop protection and sustainable agricultural practices.

Oryza↗

PubMed1977

[Isolation and properties of leucine aminopeptidase from Aspergillus oryzae].

Homogenious leucine aminopeptidase is purified from "oryzine"--mixture of enzymes produced by surface culture of Asperigillus oryzae using treatment with activated characoal, followed by DEAE-cellulose and hydroxylapatite chromatographies, Biogel P-100 gel-filtration and polyacrylamide-gel electrophoresis. The enzyme has pH optimum 9.0 and the molecular weight 37500 as estimated by gil-filtration through Sephadex G-100 (superfine) and SDS-polyacrylamide gel electrophoresis. Leucine aminopeptidase from Asp. oryzae has a broad substrate specificity, therefore, cleaving with the highest rate the peptides carrying N-terminal leucine. The enzyme is completely inhibited with EDTA and beta-mercaptoethanol, and it is a metalloenzyme.

Aspergillus↗

PubMed1976

[Isolation and properties of the acid carboxypeptidase of Aspergillus oryzae].

Caboxypeptidase with pH optimum 4--5 for peptide substrates is isolated from "oryzine", the enzyme mixture produced by Aspergillus oryzae, by means of successive salt fractionation, Sephadex G-75 gel filtration, chromatography on amberlite IRC-50, hydroxylapatite, DEAE-cellulose and polyacrylamide gel electrophoresis. Its molecular weight, as determined by means of polyacrylamide gel electrophoresis in the presence of sodium dolecylsulphate, was found to be 37 000. The enzyme has a broad substrate specificity and does not possess dipeptidase and esterase activities. Acid carboxypeptidase from Asp. oryzae is not a metalloenzyme, it is inactivated by specific inhibitors of serine proteases and by compounds blocking SH-groups. The enzyme is suggested to contain functionally important serine and cysteine residues and to be acid carboxipeptidase.

Aspergillus↗

PubMed2025

Growth-limiting drought increases sensitivity of Asian rice (Oryza sativa) leaves to heat shock through physiological and spatially distinct transcriptomic responses.

Growth-limiting droughts (GLD) impair tissue expansion and delay developmental transitions but are often not considered as stressors, as many physiological traits are only slightly altered relative to well-watered counterparts. Concurrently, cell size, biochemical makeup, and transcriptome profiles vary along the leaf blade in accordance with the partitioning of distinct functions to spatially defined regions of the leaf. This suggests that because different parts of the leaf have underlying differences in their transcriptome profiles, they might respond to GLD in distinctive ways. Moreover, how antagonistic stressors influence physiology and gene expression in different zones of leaves is an open question. In this study, we profiled growth, anatomy, and gas exchange in Asian rice (Oryza sativa) leaves developed in well-watered and GLD conditions, with or without a secondary heat shock. We dissected leaves into seven equal-length segments for transcriptome analysis in these conditions. We hypothesized that GLD would make the leaves more sensitive to heat shock and would disrupt the underlying heterogeneity of the leaf transcriptome. GLD plants were more strongly affected by heat shock with respect to gas exchange and the number and types of genes that were differentially expressed and that these differences varied along the leaf blade. We developed an eFP browser tool with these data to facilitate exploration and hypothesis testing. These findings show that even mild drought treatments are sufficient to impact responses to antagonistic stressors and that substantial within-organ variance exists with respect to stress responses.

Oryza↗

PubMed1978

[alpha-Amylase activity in lysosomes of Aspergillus oryzae (author's transl)].

The alpha-amylase of mycelial cells of Aspergillus oryzae exists in a particular form in 8000 g pellet. The lysosomal localization of acid phosphatase is confirmed by electron microscopy. The purification of lysosomes by discontinuous gradient of sucrose in D2O shows that alpha-amylase activity is bound to these particles.

Acid Phosphatase↗