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Abstract
Rice foot rot caused by Dickeya zeae is an important bacterial disease of rice worldwide. In this study, we identified a new strain EC2 from rice in Guangdong province, China. This strain differed from the previously identified strain from rice in its biochemical characteristics, pathogenicity, and genomic constituents. To explore genomic discrepancies between EC2 and previously identified strains from rice, a complete genome sequence of EC2 was obtained and used for comparative genomic analyses. The complete genome sequence of EC2 is 4,575,125 bp in length. EC2 was phylogenetically closest to previously identified Dickeya strains from rice, but not within their subgroup. In terms of secretion systems, genomic comparisons revealed that EC2 harbored only type I (T1SS), typeⅡ (T2SS), and type VI (T6SS) secretion systems. The flagella cluster of this strain possessed specific genomic characteristics like other D. zeae strains from Guangdong and from rice; within this locus, the genetic diversity among strains from rice was much lower than that of within strains from non-rice hosts. Unlike other strains from rice, EC2 lost the zeamine cluster, but retained the clustered regularly interspaced short palindromic repeats-1 (CRISPR-1) array. Compared to the other D. zeae strains containing both exopolysaccharide (EPS) and capsular polysaccharide (CPS) clusters, EC2 harbored only the CPS cluster, while the other strains from rice carried only the EPS cluster. Furthermore, we found strain MS1 from banana, carrying both EPS and CPS clusters, produced significantly more EPS than the strains from rice, and exhibited different biofilm-associated phenotypes. Comparative genomics analyses suggest EC2 likely evolved through a pathway different from the other D. zeae strains from rice, producing a new type of rice foot rot pathogen. These findings emphasize the emergence of a new type of D. zeae strain causing rice foot rot, an essential step in the early prevention of this rice bacterial disease.
Highlights
Rice foot rot is an important bacterial disease affecting rice (Oryza sativa L.), and first reported in Japan [1], and spread to the other important rice-growing countries, including China, South Korea, the Philippines, India, Indonesia, and Bangladesh [2,3,4]
The D. zeae pathogen was found to cause rice foot rot in Qingyuan city, China In October 2016, rice plants from the fields of Qingyuan city showed symptoms of leaf yellowing and necrosis (Fig 1A), and rice spikes failed to pollinate and form grains (Fig 1B)
Biolog analysis confirmed EC2 as the strain from genus Dickeya, as well as other D. zeae strains from Guangdong Province (EC1 isolated from rice, MS1 isolated from banana, and CE1 isolated from C. edulis ker.)
Summary
Rice foot rot is an important bacterial disease affecting rice (Oryza sativa L.), and first reported in Japan [1], and spread to the other important rice-growing countries, including China, South Korea, the Philippines, India, Indonesia, and Bangladesh [2,3,4]. D. zeae contains a group of pathogens infecting important plants in the Poaceae like rice and maize, which indicate distinct genetic variants in D. zeae [15, 16] This was consistent with the genetic evolution analysis of Dickeya species based on recA gene sequences; indicated that there were different sequence variants (sequevars) isolated from different host plants existed among D. zeae strains [17]. These findings indicate the differentiation and genetic evolution of D. zeae strains might be an outcome of long-term interactions between pathogens and hosts
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