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

Jingxin Zhang,Qiyun Yang,Yucheng Zhang,John Hu,Xiaoming Pu,Qiurong Fan,Dayuan Sun,Birun Lin,Huifang Shen

doi:10.1186/s12864-018-5154-3

Abstract

BackgroundDickeya 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.MethodsWe constructed the complete PA1 genome sequence and used comparative genomics to explore the differences in genomic features between D. fangzhongdai and other Dickeya species.ResultsPA1 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).ConclusionsOrchid-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.

Highlights

Dickeya sp. strain PA1 is the causal agent of bacterial soft rot in Phalaenopsis, an important indoor orchid in China
Our results showed that hemolysin-coregulated protein (Hcp) and valine-glycine repeat protein G (VgrG) were conserved in most Dickeya strains, excluding strains of D. paradisiaca
The G + C content of the homologous zms gene clusters in D. fangzhongdai and D. solani strains was approximately 61%. This was significantly higher than the G + C contents of the whole genomes of the D. fangzhongdai strains (56.60–56.88%) and the D. solani strains (56.10–56.40%). These findings indicated that the gene clusters in the D. fangzhongdai and D. solani strains might have been acquired recently via horizontal gene transfer (HGT) during bacterial differentiation

Summary

Introduction

Dickeya sp. strain PA1 is the causal agent of bacterial soft rot in Phalaenopsis, an important indoor orchid in China. 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. Pathogens in the genus Dickeya, family Pectobacteriaceae [1], cause bacterial soft rot disease, with an increased risk of infection observed in diverse host plants worldwide [2]. D. solani, which is closely related to D. dadantii, has emerged in recent years and mostly infects potato [5]. Strains that cause bleeding cankers on pear trees in China have been proposed as a novel species, namely, D. fangzhongdai, named in honor of Professor Zhongda Fang [7]. Among the previously identified species, D. dieffenbachiae and D. dadantii are closely related and D. dieffenbachiae has been suggested to represent D. dadantii subsp. dieffenbachiae [8]

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