Transcriptome analysis of the interaction between Acidovorax citrulli and cucumber

Abstract:

[Background] Bacterial fruit blotch of cucurbits is a serious seed-borne bacterial disease, and its pathogen is Acidovorax citrulli. So far, the understanding of the interaction mechanism between pathogen and its hosts is extremely limited. Cucumber, a model plant in the Cucurbitaceae family, is one of the hosts and easy to be infected. The transcriptome analysis of the interaction of Ac-cucumber can lay an important foundation for exploring the interaction mechanism of Ac and its host.[Objective] To analyze the responses of both Ac and cucumber under the interaction. [Methods] 6 d cotyledons of cucumber were inoculated with bacteria cell suspension, and 48 h cotyledons post inoculation were sampled for transcriptome sequencing. The RNASeq technology was used to analyze the gene expression features of Ac FC440 strain interacting with 9930 cwltivar of cucumber. [Results] The sequencing data shows that the correlation between different replicates of each sample was strong, and the comparison rate with the reference genome was over 95%. Cluster analysis indicates that the expression patterns of the control were opposite to that of the treatment, and the sample processing achieved a certain effect, indicating that the overall quality of the data was high. Six differentially expressed genes were selected for RT-qPCR verification, and the results showed that the expression level of the six genes were basically consistent with the transcriptome results, indicating that the transcriptome sequencing results were relatively reliable. Under 48 h interaction between Ac and cucumber, there were 1 618 genes and 8 698 genes expressed differentially, respectively. Gene ontology (GO) analysis shows that differential genes of bacteria are significantly enriched in the cell membrane (37.5%) and membrane part (27.0%) in cellular components, oxidation-reduction process (66.7%) in biological process and hydrolase activity (66.5%) in molecular function. Differential genes of cucumber are significantly enriched in plastid (22.2%) and chloroplast (21.3%) in cellular components, catalytic activity (70.0%) in molecular functions and carbohydrate derivative metabolic process (32.2%) in biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that pathogenic related genes in bacteria were significantly enriched in the quorum sensing and bacterial chemotaxis pathways, and the genes of quorum sensing were down-regulated more than others. Genes regulating expression of calcium-dependent protein kinase (CDPK), calmodulin and calmodulin-like (CaMCML) and respiratory burst oxidase homologne (Rboh) in cucumber were up-regulated, and genes regulating expression of phenylalanine ammonia-lyase (PAL) and glutathione S-transferase (GST) are the most abundant ones and up-regulated in the corresponding metabolic pathways. [Conclusion] The quality of transcriptome sequencing data of Ac and cucumber interaction was high. Quorum sensing correlated to the pathogenicity of FC440 strain in Ac. The main path that cucumber's defense reaction against to Ac infection is activated by Ca²⁺ signal. PAL and GST play an important role in resistance of cucumber to Ac. This study lays the foundation for further exploration on the interaction mechanism between Ac and its host.