Comparative genomics analysis of Dickeya zeae CE1 causing bacterial soft rot of Canna edulis

Abstract:

[Background] Dickeya zeae causes bacterial soft rot of several important crops such as banana and rice and may cause heavy losses. Canna edulis is resistant to many biotic and abiotic stressors and only a few pests are reported for this plant. Bacterial soft rot of C. edulis caused by D. zeae CE1 was first reported by our research group. [Objective] This study was conducted to sequence the whole genome of D. zeae CE1 and to compare this strain genomically with the other Guangdong strains of this pathogen from banana (strains MS1 and MS2) and rice (strains EC1, EC2 and ZJU1202), in order to explore any genetic differentiation related to the interaction between pathogenic D. zeae bacteria and their hosts. [Methods] The third-generation sequencing combined with next-generation sequencing method was used to construct the complete genome of strain CE1. Next, comparative genomics was adopted to compare the evolutionary relationships and genomic characteristics of strain CE1 with other strains of the pathogen isolated from banana and rice plants. [Results] The complete genome size of CE1 was 4 714 731 bp, with 4 052 coding genes predicted. Similarly with the taxonomic relation between C. edulis and banana, the strains from C. edulis and banana were closely related showing by the phylogenetic tree, but they were notably different from rice strains. The OrthoMCL analysis revealed that the bacterial gene clusters encoding important pathogenic factors such as: bacterial secretion systems, flagellar proteins, extracellular polysaccharides, and the clustered regularly interspaced short palindromic repeats (CRISPR), did not have obvious differences that corresponded to different types of hosts. Further analysis revealed that 80 genes were specific to the C. edulis and banana strains, while 42 genes were specific to the rice strains. According to the functional prediction, two of the gene clusters found in the specific loci of C. edulis and banana strains were related to fatty acid synthase and quorum sensing, respectively. However, more rice strain-specific genes were involved in carbohydrates transport and metabolism compared to the C. edulis and banana strains; in addition, there was a specific gene cluster from rice strains found in the adjacent genomic locus of the CRISPR array. [Conclusion] comparative genomic analysis have determined the phylogenetic relationship among C. edulis strain, banana strains, and rice strains and found several gene loci that might be involved in the interaction between these D. zeae strains and the hosts of different types. It is recommend providing an early warning to growers that crops closely related to banana and rice may be at risk of infection from these important pathogenic bacteria.