Oryza genus

The genus Pyricularia includes species that are phytopathogenic fungi, which infect different species of Poaceae, such as rice and sorghum. However, few isolates have been genetically characterized in North America. The current study addresses this lack of information by characterizing an additional 57 strains of three grasses ( Stenotaphrum secundatum , Cenchrus ciliaris and Digitaria ciliaris ) from two distant regions of Mexico. A Pyricularia dataset with ITS sequences retrieved from GenBank and the studied sequences were used to build a haplotype network that allowed us to identify a few redundant haplotypes highly related to P...

The taxonomic position of two novel Actinoallomurus strains isolated from rhizosphere soil of wild rice ( Oryza rufipogon Griff.) was established using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WRP6H-15T and WRP9H-5T were closely related to Actinoallomurus spadix JCM 3146T and Actinoallomurus purpureus TTN02-30T . Chemotaxonomic and morphological characteristics of both strains were consistent with members of the genus Actinoallomurus , while phenotypic properties, genome-based comparisons and phylogenomic analyses distinguished strains WRP6H-15T and WRP9H-5T from their closest phylogenetic relatives...

The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory roles in plant development and physiological processes, such as transcription regulation and signal transduction; it is also involved in anthocyanin biosynthesis. In rice, only OsTTG1 was found to be associated with anthocyanin biosynthesis, and evolutionary analysis of the WD40 gene family in multiple species is less studied. Here, a genome-wide analysis of the subfamily belonging to WD40-TTG1 was performed in nine AA genome species: Oryza sativa ssp...

Cytoplasmic male sterility (CMS) lines are important for breeding hybrid crops, and utilization of CMS lines requires strong fertility restorer (Rf) genes. Rf4, a major Rf for Wild-Abortive CMS (CMS-WA), has been cloned in rice. However, the Rf4 evolution and formation of CMS-WA/Rf system remain elusive. Here, we show that the Rf4 locus emerges earlier than the CMS-WA gene WA352 in wild rice, and 69 haplotypes of the Rf4 locus are generated in the Oryza genus through the copy number and sequence variations...

Interest in fermented foods, especially plant-based ones, has increased considerably in the last decade. Miso-a Japanese paste traditionally fermented with soybeans, salt, and kōji (Aspergillus oryzae grown on grains or beans)-has gained attention among chefs for its rich flavour and versatility. Some chefs have even been experimenting with making novel misos with untraditional substrates to create new flavours. Such novel fermented foods also offer new scientific opportunities. To explore the microbial diversity of these new traditional foods, we sampled six misos made by the team at a leading restaurant called Noma in Copenhagen (Denmark), using yellow peas (including a nixtamalised treatment), lupin seeds, Swedish Vreta peas, grey peas, and Gotland lentils as substrates...

Oryza coarctata (2n = 4X = 48, KKLL) is an allotetraploid, undomesticated relative of rice and the only species in the genus Oryza with tolerance to high salinity and submergence. Therefore, it contains important stress and tolerance genes/factors for rice. The initial draft genome published was limited by data and technical restrictions, leading to an incomplete and highly fragmented assembly. This study reports a new, highly contiguous chromosome-level genome assembly and annotation of O...

To investigate the mechanisms by which g-C3 N4 alleviates metal(loid)-induced phytotoxicity, rice seedlings were exposed to 100 and 250 mg/kg graphitic carbon nitride (g-C3 N4 ) with or without coexposure to 10 mg/kg Cd and 50 mg/kg As for 30 days. Treatment with 250 mg/kg g-C3 N4 significantly increased shoot and root fresh weight by 22.4-29.9%, reduced Cd and As accumulations in rice tissues by 20.6-26.6%, and elevated the content of essential nutrients (e.g., K, S, Mg, Cu, and Zn) compared to untreated controls...

BACKGROUND: Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O...

Lipases have valuable potential for industrial use, particularly those mostly active against water-insoluble substrates, such as triglycerides composed of long-carbon chain fatty acids. However, in most cases, engineered variants often need to be constructed to achieve optimal performance for such substrates. Protein engineering techniques have been reported as strategies for improving lipase characteristics by introducing specific mutations in the cap domain of esterases or in the lid domain of lipases or through lid domain swapping...

The botulinum neurotoxin-like toxin from Weissella oryzae (BoNT/Wo) is one of the BoNT-like toxins recently identified outside of the Clostridium genus. We show that, like the canonical BoNTs, BoNT/Wo forms a complex with its non-toxic non-hemagglutinin (NTNH) partner, which in traditional BoNT serotypes protects the toxin from proteases and the acidic environment of the hosts' guts. We here report the cryo-EM structure of the 300 kDa BoNT/Wo-NTNH/Wo complex together with pH stability studies of the complex...

A novel Gram-stain-negative, aerobic, motile and pleomorphic rod-shaped bacterial strain, designated COJ-58T , was isolated from rice paddy soil. Strain COJ-58T grew optimally at 20-30 °C, at pH 5.0-8.0 and with 0-1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain COJ-58T forms a distinct lineage within the family Pleomorphomonadaceae , with highest similarity to Pleomorphomonas carboxyditropha SVCO-16T (95.9 %), Pleomorphomonas koreensis Y9T (95...

Three strains of novel oleaginous yeast species were isolated from soil samples collected in Shiga Prefecture, Japan. The sequences of the internal transcribed spacer (ITS) region and the D1/D2 region of the large subunit (LSU) of the rRNA genes indicated that these novel yeast species are members of the genus Hannaella . The results of molecular phylogenetic analysis indicated that strains 38-3 and 8s1 were closely related to Hannaella oryzae . They differed by 10 nucleotide substitutions and one gap (1.77 %) in the D1/D2 region of the LSU of the rRNA genes and by 17-18 nucleotide substitutions and 10-11 gaps (5...

Forty-eight Acidobacteriota strains were isolated from soils and sediments in Japan. Among them, six representative strains, designated W79T , W786T , Red222T , Red802T , Red803T , and Red804T , were subjected to the taxonomic classification. These six strains are Gram-stain-negative, non-spore-forming, rod-shaped, and facultative anaerobic bacterium that can reduce ferric iron. Phylogenetic and phylogenomic trees based on 16S rRNA genes and multiple single-copy gene sequences showed that strains Red222T , Red802T , Red803T , and Red804T formed a cluster with the type strains of Geothrix species, but strains W79T and W786T created an independent cluster from any other type strains...

A novel actinobacterium, designated as strain WRP15-2T , was isolated from rhizosphere soil of rice plant (Oryza rufipogon). The strain was Gram-stain-positive, aerobic, and non-motile. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain WRP15-2T fell into the genus Saccharopolyspora. The strain shared the highest 16S rRNA gene sequence similarity with the type strains Saccharopolyspora kobensis JCM 9109T (99.1%), Saccharopolyspora indica VRC122T (98.9%), and Saccharopolyspora antimicrobica DSM 45119T (98...

Rice (Oryza L.) is an essential food for more than 50 percent of the world's population and is the world's second-largest grain crop. Pigmented rice comes in various colors, such as black, red, brown, and green. Anthocyanins, like cyanidin-3-O-glucoside and peonidin-3-O-glucoside, are the primary color pigments in colored rice, whereas proanthocyanidins and flavan-3-ol oligosaccharides, with catechins as the central synthesis unit, are found in brown rice. This review article's aim is to give information and a summary of rice activities, research methods, also mechanisms of action (Oryza L...

The investigation of natural alternatives to conventional fungicides is of imminent need. Mosiera bullata (Britton & P. Wilson) Bisse is a Cuban endemic plant species belonging to the Myrtaceae family. The objective of the present study was to perform a bioassay-guided fractionation to explore the potential of extracts and fractions from M. bullata leaves against a panel of fungal plant pathogens. The M. bullata total extract was confirmed to have good antifungal activity against R. oryzae (IC50 = 4.86 µg/mL) and moderate activity against F...

Pyricularia oryzae, a blast fungus of gramineous plants, is composed of various host-genus specific pathotypes. The avirulence of an Avena isolate on wheat is conditioned by PWT3 and PWT4. We isolated the third avirulence gene from the Avena isolate and designated it as PWT7. PWT7 was effective as an avirulence gene only at the seedling stage or on leaves. PWT7 homologs were widely distributed in a subpopulation of the Eleusine pathotype and the Lolium pathotype but completely absent in the Triticum pathotype (the wheat blast fungus)...

Gram-negative, aerobic, motile by means of two or more polar or subpolar flagella, rod-shaped strain NS12-5T and Gram-negative, facultatively anaerobic, yellow-coloured, rod-shaped strain RP8T were isolated from rice rhizosphere soil and fermented fruits of Liriope platyphylla in the Republic of Korea, respectively. The result of phylogenetic analyses based on 16S rRNA gene sequences showed that strain NS12-5T was most closely related to Ideonella aquatica 4Y11T with 99.79 % sequence similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain NS12-5T and species of the genus Ideonella were 75...

The genus Dickeya includes plant pathogenic bacteria attacking a wide range of crops and ornamentals as well as a few environmental isolates from water. Defined on the basis of six species in 2005, this genus now includes 12 recognized species. Despite the description of several new species in recent years, the diversity of the genus Dickeya is not yet fully explored. Many strains have been analyzed for species causing diseases on economically important crops, such as for the potato pathogens D. dianthicola and D...

Vegetative to reproductive phase transition in phototropic plants is an important developmental process and is sequentially mediated by the expression of micro-RNA MIR172 . To obtain insight into the evolution, adaptation, and function of MIR172 in photophilic rice and its wild relatives, we analyzed the genescape of a 100 kb segment harboring MIR172 homologs from 11 genomes. The expression analysis of MIR172 revealed its incremental accumulation from the 2-leaf to 10-leaf stage, with maximum expression coinciding with the flag-leaf stage in rice...