Rice false smut, caused by Ustilaginoidea virens, threatens rice production by reducing yields and contaminating grains with harmful ustiloxins. However, studies on resistance genes are scarce. In this study, the resistance level of IR28 (resistant cultivar) to U. virens was validated through artificial inoculation. Notably, a reactivation of resistance genes after transient down-regulation during the first 3 to 5 dpi was observed in IR28 compared to WX98 (susceptible cultivar). Cluster results of a principal component analysis and hierarchical cluster analysis of differentially expressed genes (DEGs) in the transcriptome exhibited longer expression patterns in the early infection phase of IR28, consistent with its sustained resistance response. Results of GO and KEGG enrichment analyses highlighted the suppression of immune pathways when the hyphae first invade stamen filaments at 5 dpi, but sustained up-regulated DEGs were linked to the ‘Plant–pathogen interaction’ (osa04626) pathway, notably disease-resistant protein RPM1 (K13457, CNLs, coil-coiled NLR). An analysis of CNLs identified 245 proteins containing Rx-CC and NB-ARC domains in the Oryza sativa Indica genome. Partial candidate CNLs were shown to exhibit up-regulation at both 1 and 5 dpi in IR28. This study provides insights into CNLs’ responses to U. virens in IR28, potentially informing resistance mechanisms and genetic breeding targets.

Peach gummosis, primarily caused by Botryosphaeria dothidea, leads to progressive tree decline, yet how the host-associated microbiome differs between symptomatic and asymptomatic trees remains poorly understood. Sampling was conducted in a commercial orchard in Zaoyang, Hubei Province, China. Symptomatic trees were peach cultivar ‘Zhongtao 3’ and asymptomatic trees were nectarine cultivar ‘Qiuhongzhu’, grown in the same orchard. We profiled bacterial (16S rRNA) and fungal (ITS) communities from bulk soil, rhizosphere soil, root rhizoplane, root endosphere, basal and mid-trunk bark, and basal and mid-trunk xylem, and examined compositional shifts, predicted functional potential, and co-occurrence networks. Disease status significantly altered community composition in both kingdoms. Beta dispersion increased only in symptomatic trunk tissues, indicating that community destabilization is localized at the infection site. LEfSe and functional analyses showed that diseased tissues were depleted of biocontrol-relevant genera (Bacillus spp., Streptomyces spp.) and negatively correlated with function-predicted cellulolysis and iron respiration, while pathogen-associated fungi (Neocucurbitaria spp., Xenoacremonium spp., Neocosmospora spp.) were enriched. Co-occurrence networks revealed that bacterial networks were simpler in symptomatic trees: bacterial edge number declined by 39.0% versus 19.6% for fungi, accompanied by reduced cross-kingdom connectivity. Alpha diversity remained largely unchanged. These findings demonstrate that difference were spatially structured and taxonomically asymmetric erosion of interaction complexity rather than a uniform collapse of diversity. Bacterial connectivity in symptomatic tissues is a candidate target for microbiome-informed management of peach gummosis.