Abstract
BackgroundDickeya zeae is a bacterial species that infects monocotyledons and dicotyledons. Two antibiotic-like phytotoxins named zeamine and zeamine II were reported to play an important role in rice seed germination, and two genes associated with zeamines production, i.e., zmsA and zmsK, have been thoroughly characterized. However, other virulence factors and its molecular mechanisms of host specificity and pathogenesis are hardly known.ResultsThe complete genome of D. zeae strain EC1 isolated from diseased rice plants was sequenced, annotated, and compared with the genomes of other Dickeya spp.. The pathogen contains a chromosome of 4,532,364 bp with 4,154 predicted protein-coding genes. Comparative genomics analysis indicates that D. zeae EC1 is most co-linear with D. chrysanthemi Ech1591, most conserved with D. zeae Ech586 and least similar to D. paradisiaca Ech703. Substantial genomic rearrangement was revealed by comparing EC1 with Ech586 and Ech703. Most virulence genes were well-conserved in Dickeya strains except Ech703. Significantly, the zms gene cluster involved in biosynthesis of zeamines, which were shown previously as key virulence determinants, is present in D. zeae strains isolated from rice, and some D. solani strains, but absent in other Dickeya species and the D. zeae strains isolated from other plants or sources. In addition, a DNA fragment containing 9 genes associated with fatty acid biosynthesis was found inserted in the fli gene cluster encoding flagellar biosynthesis of strain EC1 and other two rice isolates but not in other strains. This gene cluster shares a high protein similarity to the fatty acid genes from Pantoea ananatis.ConlusionOur findings delineate the genetic background of D. zeae EC1, which infects both dicotyledons and monocotyledons, and suggest that D. zeae strains isolated from rice could be grouped into a distinct pathovar, i.e., D. zeae subsp. oryzae. In addition, the results of this study also unveiled that the zms gene cluster presented in the genomes of D. zeae rice isolates and D. solani strains, and the fatty acid genes inserted in the fli gene cluster of strain EC1 were likely derived from horizontal gene transfer during later stage of bacterial evolution.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1545-x) contains supplementary material, which is available to authorized users.
Highlights
Dickeya zeae is a bacterial species that infects monocotyledons and dicotyledons
We found that the gene cluster encoding for phytotoxin zeamine biosynthesis is conserved only in the D. zeae strains isolated from rice plants and the D. solani strains isolated from potato
In this study, we present a complete genome sequence of D. zeae strain EC1 isolated from rice plants, which together with the other four released complete genome sequences of Dickeya species, i.e., D. chrysanthemi Ech1591, D. zeae Ech586, D. dadantii 3937, and D. paradisiaca Ech703, allows detailed genomic comparison to study bacterial evolution and identify clues associated with pathogenesis and host specificity
Summary
Dickeya zeae is a bacterial species that infects monocotyledons and dicotyledons. Two antibiotic-like phytotoxins named zeamine and zeamine II were reported to play an important role in rice seed germination, and two genes associated with zeamines production, i.e., zmsA and zmsK, have been thoroughly characterized. Genetic analysis and biochemical characterization of the pathogenic mechanisms of D. zeae were initiated only in recent years [5,6,7,8], following the outbreak of the rice root rot disease in China [9] These studies led to identification of a new family of phytotoxins, i.e., zeamine and zeamine II [5,6], which appear to act as the key virulence determinants of the pathogen as mutation of the zeamine synthase genes zmsA and zmsK resulted in partial or almost complete loss of virulence on rice seeds germination [6,7]. The regulatory mechanisms that govern virulence gene expression are largely unknown, except that an acyl-homoserine lactone (AHL) quorum sensing (QS) system was shown to be involved in the regulation of certain virulence traits in D. zeae, including bacterial motility and biofilm development [8]
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