Introduction: Rice, a cornerstone of global food security, faces escalating demands for enhanced yield and disease resistance. We collected 300 high-quality genomes, representing both cultivated (Oryza sativa indica, O. sativa japonica, and O. sativa aus) and wild species (O. rufipogon, O. glaberrima, and O. barthii). Methods: Leveraging HMMER, NLR-Annotator, and OrthoFinder, we systematically identified 148,077 leucine-rich repeat (LRR) and 143,459 nucleotide-binding leucine-rich repeat (NLR) genes, with LRR receptor-like kinases (LRR-RLKs) dominating immune receptor proportions, followed by coiled-coil domain containing (CNL)-type NLRs and LRR receptor-like proteins (LRR-RLPs). Results: Benchmarking Universal Single-Copy Orthologs (BUSCO) assessments confirmed robust genome quality (average score: 94.78). Strikingly, 454 TIR-NB-LRR (TNL) genes—typically rare in monocots—were detected, challenging prior assumptions. Phylogenetic analysis with Arabidopsis TNLs highlighted five O. glaberrima genes clustering with dicot TNLs; these genes featured truncated PLN03210 motifs fused to nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) and LRR domains. Conclusions: By bridging structural genomics, evolutionary dynamics, and domestication-driven adaptation, this work provides a foundation for targeted breeding strategies and advances functional studies of plant immunity in rice.

Root-associated microbiomes vary across environmental settings and root compartments, but these patterns remain poorly understood in wild woody plants. Here, we compared bacterial and fungal communities in the rhizosphere and root endosphere of Rhododendron yunnanense across four montane sampling sites in Yunnan, China, using 16S rRNA gene and internal transcribed spacer (ITS) amplicon sequencing. α-diversity differences were mainly reflected in amplicon sequence variant (ASV) richness, whereas Shannon and Simpson diversity varied less among site–compartment combinations. Bray–Curtis community composition was significantly associated with sampling site, root compartment, and their interaction for both bacteria and fungi. Stable and core ASV analyses further showed limited overlap between the rhizosphere and endosphere. Under the predefined core criteria, only three bacterial ASVs were shared between compartments, while no fungal ASV qualified as a shared core member. The extent of stable-ASV overlap varied among sampling sites and differed between bacterial and fungal communities. Indicator-value analysis, paired abundance testing, and Random Forest classification converged on a smaller set of compartment-associated genera. Thirteen taxonomically interpretable genera were retained for main-text interpretation, including five bacterial genera associated with the endosphere and eight fungal genera, of which Phialocephala was associated with the rhizosphere. Together, these results show that sampling site and root compartment are both associated with marked differentiation of the R. yunnanense root microbiome. The low overlap of stable and core taxa further indicates substantial microbial turnover between the rhizosphere and endosphere, providing a basis for future functional validation of compartment-associated taxa.

Background: Camellia species are highly ornamental but sensitive to habitat temperature, making cross-border domestication challenging. Methods: In this study, physiological indicators and transcriptome data of Camellia reticulata ‘shizhitou’ were analyzed to identify key factors involved in the response to cold. Results: The findings provide a scientific basis for the conservation of Camellia germplasm resources and breeding of cold-tolerant varieties. Under prolonged low-temperature stress, significant changes were observed in the physiological indices of C. reticulata ‘shizhitou’. Among soluble substances, soluble protein content continuously increased, while soluble sugar content exhibited a fluctuation pattern of increase–decrease–increase. Under prolonged low-temperature stress, significant changes were observed in the physiological indexes of C. reticulata ‘shizhitou’, while soluble sugar content exhibited a fluctuation pattern of increase–decrease–increase. Overall, soluble sugar and soluble protein contents were significantly positively correlated. Chlorophyll content initially decreased and then increased, whereas peroxidase (POD) and catalase (CAT) activities fluctuated and were negatively correlated with chlorophyll content. Malondialdehyde (MDA) content showed an irregular fluctuation trend. A total of 56,424 unigenes were obtained by transcriptome sequencing, of which 39,278 were annotated, while 10,816 differentially expressed genes (DEGs) were identified, including 5748 up-regulated and 5068 down-regulated genes, with 143 DEGs commonly shared across conditions. Congclusions: Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that low-temperature stress significantly influenced glucose metabolism, lipid metabolism, and amino acid metabolism, and the core pathways of cold stress included zeatin synthesis, hormone signaling, and galactose metabolism. Both physiological responses and transcriptome-based enrichment of DEGs indicate that the redox system and metabolic pathways play crucial regulatory roles in C. reticulata under cold stress.