Identification and Characterization of Circular RNAs in Brassica rapa in Response to Plasmodiophora brassicae

Abstract BackgroundPlasmodiophora brassicae is a soil-borne pathogen that attacks the roots of cruciferous plants, causing clubroot disease. CircRNAs are non-coding RNAs widely exist in plant and animal species which can acting as “microRNA (miRNA) sponges” and “competing endogenous RNAs (ceRNAs)”. Knowledge of circRNAs has been updated continuously and rapidly. However, the information about circRNAs in the regulation of clubroot-disease resistance is limited in Brassica rapa. ResultsHere, the Chinese cabbage (BJN 222) containing clubroot resistance gene (CRa) resistant to the Pb4 was susceptible to the PbE of P. brassicae. To investigate the mechanism of cicRNAs responsible for clubroot-disease resistance in Brassica rapa, the circRNA-seq was performed roots of BJN 222 at 0 d, 8 d, and 23 d after inoculated with Pb4 and PbE. A total of 1636 circRNAs were detected distributed on 10 chromosomes. Furthermore, total 231 differentially expressed circRNAs between groups were screened. Parental genes of circRNAs functions analysis results indicated that the expression of circRNAs was affected not only by inoculation time but also by the pathogenicity of P. brassicae. However, the “Phenylalanine, tyrosine, and tryptophan biosynthesis” pathway was significant enriched between the two pathotypes at different inoculation times. All the expression of target genes annotated with “receptor-like protein kinase,” “zinc finger protein,” “LRR-repeat protein,” and “hormone-related” identified from the circRNA-miRNA-mRNA network were analyzed. 5 target genes were consistent with the expression pattern of novel_circ_000495 at 8 dpi, but only Bra026508 was significantly up-regulated. ConclusionThe up-regulated novel_circ_000495 might suppressed the expression of miR5656-y, leading to the up-regulation of Bra026508. Our results provided new insights to clubroot resistance mechanisms of B.rapa and laid a foundation for further research on the function of circRNAs responsible for the pathogen infection.