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Rice sheath blight (RSB), caused by the pathogenic fungus Rhizoctonia solani, poses a significant threat to global food security. The defense mechanisms employed by rice against RSB are not well understood. In our study, we analyzed the interactions between rice and R. solani by comparing the phenotypic changes, ROS content, and metabolite variations in both tolerant and susceptible rice varieties during the early stages of fungal infection. Notably, there were distinct phenotypic differences in the response to R. solani between the tolerant cultivar Zhengdao22 (ZD) and the susceptible cultivar Xinzhi No.1 (XZ). We observed that the activities of five defense-related enzymes in both tolerant and susceptible cultivars changed dynamically from 0 to 72 h post-infection with R. solani. In particular, the activities of superoxide dismutase and peroxidase were closely associated with resistance to RSB. Metabolomic analysis revealed 825 differentially accumulated metabolites (DAMs) between the tolerant and susceptible varieties, with 493 DAMs responding to R. solani infection. Among these, lipids and lipid-like molecules, organic oxygen compounds, phenylpropanoids and polyketides, organoheterocyclic compounds, and organic acids and their derivatives were the most significantly enriched. One DAM, P-coumaraldehyde, which responded to R. solani infection, was found to effectively inhibit the growth of R. solani, Magnaporthe grisea, and Ustilaginoidea virens. Additionally, multiple metabolic pathways, including amino acid metabolism, carbohydrate metabolism, metabolism of cofactors and vitamins, and metabolism of terpenoids and polyketides, are likely involved in RSB resistance. Our research provides valuable insights into the molecular mechanisms underlying the interaction between rice and R. solani.

Chloroplast and mitochondrial DNA (cpDNA and mtDNA) are apart from nuclear DNA (nuDNA) in a eukaryotic cell. The transcription system of chloroplasts differs from those of mitochondria and eukaryotes. In contrast to nuDNA and animal mtDNA, the transcription of cpDNA is still not well understood, primarily due to the unresolved identification of transcription initiation sites (TISs) and transcription termination sites (TTSs) on the genome scale. In the present study, we characterized the transcription of chloroplast (cp) genes with greater accuracy and comprehensive information using PacBio full-length transcriptome data from Arabidopsis thaliana. The major findings included the discovery of four types of artifacts, the validation and correction of cp gene annotations, the exact identification of TISs that start with G, and the discovery of polyA-like sites as TTSs. Notably, we proposed a new model to explain cp transcription initiation and termination at the whole-genome level. Four types of artifacts, degraded RNAs and splicing intermediates deserve the attention from researchers working with PacBio full-length transcriptome data, as these contaminant sequences can lead to incorrect downstream analysis. Cp transcription initiates at multiple promoters and terminates at polyA-like sites. Our study provides new insights into cp transcription and new clues to study the evolution of promoters, TISs, TTSs and polyA tails of eukaryotic genes.

Rice blast, caused by rice blast fungus (Magnaporthe oryzae), is a global threat to food security, with up to 50% yield losses. Panicle blast is a severe form of rice blast, and disease responses vary between cultivars with different genotypes. Reactive oxygen species (ROS)-mediated signaling reactions and the phenylpropanoid pathway are important defense mechanisms involved in recognizing and resisting against fungal infection. To understand rice-M. oryzae interactions in resistant and susceptible cultivars, we determined dynamic changes in the activities of five defense-related enzymes in resistant cultivar jingsui 18 and susceptible cultivar jinyuan 899 infected with M. oryzae from 4 to 25 days after infection. We then performed untargeted metabolomics analyses to profile the metabolomes of the cultivars under infected and non-infected conditions. Dynamic changes in the activities of five defense-related enzymes were closely related to panicle blast resistance in rice. Metabolome data analysis identified 634 differentially accumulated metabolites (DAMs) between resistant and susceptible cultivars following infection, potentially explaining differences in disease response between varieties. The most enriched DAMs were associated with lipids and lipid-like molecules, phenylpropanoids and polyketides, organoheterocyclic compounds, organic acids and derivatives, and lignans, neolignans, and related compounds. Multiple metabolic pathways are involved in resistance to panicle blast in rice, including biosynthesis of other secondary metabolites, amino acid metabolism, lipid metabolism, phenylpropanoid biosynthesis, arachidonic acid metabolism, arginine biosynthesis, tyrosine metabolism, tryptophan metabolism, tyrosine and tryptophan biosynthesis, lysine biosynthesis, and oxidative phosphorylation.

The raw eating quality of sweet potato is complex. As consumers start paying more attention to the raw eating quality of tuberous roots in sweet potato, the evaluation of the raw eating quality of sweet potato is becoming an important issue. Therefore, we measured 16 quality indicators in 81 varieties of sweet potato. It was found that these 16 quality traits had different coefficients of variation (C.V.). Among them, the C.V. of fructose, glucose, and adhesiveness were the largest: 87.95%, 87.43% and 55.09%, respectively. The cluster analysis method was used to define six categories of the different tuberous roots of sweet potato. Group I, III, and IV had a stronger hardness and higher starch and cellulose content. Groups II, V, and VI were softer, with a high moisture and soluble sugar content. The principal component analysis method was used to comprehensively evaluate 16 quality indicators of 81 sweet potato varieties. It was found that Futian1, Taishu14, and Nanshu022 are good varieties in terms of raw eating quality. These varieties have low hardness, high adhesiveness in texture, high soluble sugar content, and low starch and cellulose. Future research should focus on improving the raw eating quality of sweet potato by reducing hardness, starch, and cellulose, while increasing adhesiveness, soluble sugar, and moisture content.