Turnip mosaic virus (TuMV) constitutes one of the primary diseases affecting Brassica rapa, severely impacting its production and resulting in crop failures in various regions worldwide. Recent research has demonstrated the significance of plant translation initiation factors, specifically the eIF4E and eIF4G family genes, as essential recessive disease resistance genes. In our study, we conducted evolutionary and gene expression studies, leading us to identify eIF(iso)4E.c as a potential TuMV-resistant gene. Leveraging CRISPR/Cas9 technology, we obtained mutant B. rapa plants with edited eIF(iso)4E.c gene. We confirmed eIF(iso)4E.c confers resistance against TuMV through phenotypic observations and virus content evaluations. Furthermore, we employed ribosome profiling assays on eif(iso)4e.c mutant seedlings to unravel the translation landscape in response to TuMV. Interestingly, we observed a moderate correlation between the fold changes in gene expression at the transcriptional and translational levels (R² = 0.729). Comparative analysis of ribosome profiling and RNA-seq data revealed that plant–pathogen interaction, and MAPK signaling pathway–plant pathways were involved in eIF(iso)4E.c-mediated TuMV resistance. Further analysis revealed that sequence features, coding sequence length, and normalized minimal free energy, influenced the translation efficiency of genes. Our study highlights that the loss of eIF(iso)4E.c can result in a highly intricate translation mechanism, acting synergistically with transcription to confer resistance against TuMV.

The soil-resident pathogen, Plasmodiophora brassicae, infects cruciferous crops, causing obligate parasitic clubroot disease and posing a significant threat to the Brassica vegetable industry in China. To learn more about its pathogenesis, we reported a Nanopore sequencing-derived 25.3 Mb high-quality genome sequence of P. brassicae pathotype 4 strain (P.b 4). Comparing the P.b 4 genome with that of the published P. brassicae e3 genome (P.b e3) identified single nucleotide polymorphisms, structural variations, and small insertions and deletions. We then carried out RNA-sequencing of root samples from a clubroot-susceptible line at 5, 14, and 28 days after inoculation (DAI), and classified genes into five categories based on their expression patterns. Interestingly, 158 genes were highly expressed at 14 DAI, which were enriched in budding cell isotropic bud growth, ascospore wall assembly, spore wall assembly, spore wall biogenesis, and ascospore wall biogenesis. Subsequently, we bioinformatically predicted 555 secreted effector candidates, among which only 125 were expressed during infection and had amino acid lengths less than 400. The putative effector Pb010018, which was highly expressed at 14 DAI, was validated to have a signal peptide using a yeast secretion system. Luciferase activity and co-immunoprecipitation assays demonstrated that Pb010018 interacts with serine hydroxymethyltransferase BrSHMT1, and expression analysis showed that SHMT1 was upregulated in both Arabidopsis and B. rapa during infection. Furthermore, after infection, the Arabidopsis shmt1 mutant (atshmt1) showed reduced severity of clubroot disease, together with downregulated expression of Pb010018. Our results offer new insights into plant–pathogen interaction mechanisms, and provide the possibility for improving Brassica resistance to clubroot disease.