Genomic analysis of the Phalaenopsis pathogen Dickeya sp. PA1, representing the emerging species Dickeya fangzhongdai

Background Dickeya sp. strain PA1 is the causal agent of bacterial soft rot in Phalaenopsis , an important indoor orchid in China. PA1 and a few other strains were grouped into a novel species, Dickeya fangzhongdai , and only the orchid-associated strains have been shown to cause soft rot symptoms. Methods We constructed the complete PA1 genome sequence and used comparative genomics to explore the differences in genomic features between D . fangzhongdai and other Dickeya species. Results PA1 has a 4,979,223-bp circular genome with 4269 predicted protein-coding genes. D . fangzhongdai was phylogenetically similar to Dickeya solani and Dickeya dadantii . The type I to type VI secretion systems (T1SS–T6SS), except for the stt -type T2SS, were identified in D . fangzhongdai . The three phylogenetically similar species varied significantly in terms of their T5SSs and T6SSs, as did the different D . fangzhongdai strains. Genomic island (GI) prediction and synteny analysis (compared to D . fangzhongdai strains) of PA1 also indicated the presence of T5SSs and T6SSs in strain-specific regions. Two typical CRISPR arrays were identified in D . fangzhongdai and in most other Dickeya species, except for D . solani . CRISPR-1 was present in all of these Dickeya species, while the presence of CRISPR-2 varied due to species differentiation. A large polyketide/nonribosomal peptide (PK/NRP) cluster, similar to the zeamine biosynthetic gene cluster in Dickeya zeae rice strains, was discovered in D . fangzhongdai and D . solani . The D . fangzhongdai and D . solani strains might recently have acquired this gene cluster by horizontal gene transfer (HGT). Conclusions Orchid-associated strains are the typical members of D . fangzhongdai . Genomic analysis of PA1 suggested that this strain presents the genomic characteristics of this novel species. Considering the absence of the stt -type T2SS, the presence of CRISPR loci and the zeamine biosynthetic gene cluster, D . fangzhongdai is likely a transitional form between D. dadantii and D . solani . This is supported by the later acquisition of the zeamine cluster and the loss of CRISPR arrays by D . solani . Comparisons of phylogenetic positions and virulence determinants could be helpful for the effective quarantine and control of this emerging species.