Dickeya species relatedness and clade structure determined by comparison of recA sequences

Abstract

Using sequences from the recA locus, we have produced a phylogeny of 188 Dickeya strains from culture collections and identified species relatedness and subspecies clade structure within the genus. Of the six recognized species, Dickeya paradisiaca, D. chrysanthemi and D. zeae were discriminated with long branch lengths. The clade containing the D. paradisiaca type strain included just one additional strain, isolated from banana in Colombia. Strains isolated from Chrysanthemum and Parthenium species made up most of the clade containing the D. chrysanthemi type strain, and the host range of this species was extended to include potato. The D. zeae clade had the largest number of sequevars and branched into two major sister clades that contained all of the Zea mays isolates, and were identified as phylotypes PI and PII. The host range was increased from six to 13 species, including potato. The recA sequence of an Australian sugar-cane strain was sufficiently distinct to rank as a new species-level branch. In contrast to these species, Dickeya dadantii, D. dianthicola and D. dieffenbachiae were distinguished with shorter branch lengths, indicating relatively closer relatedness. The recA sequence for the type strain of D. dadantii clustered separately from other strains of the species. However, sequence comparison of three additional loci revealed that the D. dadantii type strain grouped together with the six other D. dadantii strains that were sequenced. Analysis of all four loci indicated that the D. dadantii strains were most closely related to D. dieffenbachiae. Three further branches (DUC-1, -2 and -3) were associated with these three species, which all diverged from a common origin and can be considered as a species complex. The large clade containing the D. dianthicola type strain comprised 58 strains and had little sequence diversity. One sequevar accounted for the majority of these strains, which were isolated nearly exclusively from eight hosts from Europe. Isolation of this sequevar on multiple occasions from Dianthus and (more recently) potato demonstrates that this lineage has become established in these species. The D. dadantii clade comprised 11 sequevars, and the known host range of the species was extended from eight to 19 species. New hosts included several ornamental species and potato. The clade DUC-1 was made up exclusively of potato strains originating from Europe, which had identical sequences, whilst DUC-2 strains were isolated mostly from a variety of monocotyledonous species. A single strain from Aglaonema sp. made up DUC-3. A single sequevar constituted the D. dieffenbachiae clade. The phylogenetic method described will provide a simple means for identification to the species and intraspecies level, which will support efforts to control these pathogens based on monitoring and surveillance.

Sequence Diversity in the Dickeya fliC Gene: Phylogeny of the Dickeya Genus and TaqMan® PCR for 'D. solani', New Biovar 3 Variant on Potato in Europe

“…Multi Locus Sequence Analysis underpinned that Dickeya constitutes a distinct genetic clade in the soft rot Enterobacteriaceae [2]. Dickeya species are broad host range phytopathogens which principal disease symptom is maceration of plant tissues due to pectinolytic activity [2], [3]. Strains affecting potato are mainly found in three Dickeya species, i.e.…”

“…Erwinia chrysanthemi is known in potato production in some European countries for over 40 years and is associated with slow wilt and internal stem necrosis. These strains are now assigned to D. dianthicola [3], [5]. However, in the past few years a new Dickeya biovar 3 strain, tentatively named ‘ Dickeya solani ’, has emerged as a common major threat, in particular on seed potatoes [5].…”

“…Ralstonia solanacearum [9], Pseudomonas syringae [10] and Xanthomonas [11]. The rec A locus was used for the first phylogenetic analysis of all species within the genus Dickeya , extending previous studies based on 16S rDNA [3]. It displayed new genomic clades and, in particular, a clonal delineation of an emerging biovar 3 variant isolated from potato in the past decade in Europe [12].…”

A Sfp-type phosphopantetheinyl transferase ZmsO is essential for zeamines production and the virulence of Dickeya zeae

“…D. zeae is able to infect both monocotyledons and dicotyledons, while most other Dickeya species could only infect dicotyledons (Goto 1979;Hussain et al 2008;Sinha and Prasad 1977). Phylogenetic analysis of Dickeya species showed that D. zeae is most distinct from other species and contains more sequevars than others (Parkinson et al 2009). This genetic diversity may explain the wide distribution of D. zeae, and the diseases caused by this bacterial pathogen have been documented in many different regions and countries around the world (SabetOur curiosity on the host range determinants and pathogenic mechanisms of D. zeae has led to identification of zeamine and zeamine II, which are structurally similar polyketide molecules with potent antimicrobial activities (Wu et al 2010;Zhou et al 2011;Liao et al 2015).…”

PCR-based methods for detection of Erwinia psidii on guava

“…Several genomic regions, including PCR fragments obtained from rep-PCR profiles (Rico et al 2008), plasmidial sequences (Bereswill et al 1992;Barbé et al 2014) and draft whole genome sequences (Pritchard et al 2013), have been used for the development of specific identification tools for plant pathogenic enterobacteria. The recombinase A (recA) gene is a valuable marker for the major bacterial groups (Eisen, 1995) and for differentiating species in Erwinia and related genera (Waleron et al 2002;Young and Park 2007;Parkinson et al 2009;Wensing et al 2010). Despite the high degree of sequence conservation in the recA gene, the existing sequence polymorphism was useful for differentiating 19 species in Erwinia (Waleron et al 2002).…”