Abstract
Worldwide, Dickeya (formerly Erwinia chrysanthemi) is causing soft rot diseases on a large diversity of crops and ornamental plants. Strains affecting potato are mainly found in D. dadantii, D. dianthicola and D. zeae, which appear to have a marked geographical distribution. Furthermore, a few Dickeya isolates from potato are attributed to D. chrysanthemi and D. dieffenbachiae. In Europe, isolates of Erwinia chrysanthemi biovar 1 and biovar 7 from potato are now classified in D. dianthicola. However, in the past few years, a new Dickeya biovar 3 variant, tentatively named ‘Dickeya solani’, has emerged as a common major threat, in particular in seed potatoes. Sequences of a fliC gene fragment were used to generate a phylogeny of Dickeya reference strains from culture collections and with this reference backbone, to classify pectinolytic isolates, i.e. Dickeya spp. from potato and ornamental plants. The reference strains of the currently recognized Dickeya species and ‘D. solani’ were unambiguously delineated in the fliC phylogram. D. dadantii, D. dianthicola and ‘D. solani’ displayed unbranched clades, while D. chrysanthemi, D. zeae and D. dieffenbachiae branched into subclades and lineages. Moreover, Dickeya isolates from diagnostic samples, in particular biovar 3 isolates from greenhouse ornamentals, formed several new lineages. Most of these isolates were positioned between the clade of ‘D. solani’ and D. dadantii as transition variants. New lineages also appeared in D. dieffenbachiae and in D. zeae. The strains and isolates of D. dianthicola and ‘D. solani’ were differentiated by a fliC sequence useful for barcode identification. A fliC TaqMan®real-time PCR was developed for ‘D. solani’ and the assay was provisionally evaluated in direct analysis of diagnostic potato samples. This molecular tool can support the efforts to control this particular phytopathogen in seed potato certification.
Highlights
The genus Dickeya was established by the reclassification of Pectobacterium (Erwinia) chrysanthemi and Brenneria paradisiaca as D. chrysanthemi and D. paradisiaca, respectively and for the accommodation of four new species, i.e. D. dadantii, D. dianthicola, D. dieffenbachiae and D. zeae; based on analysis of 16S rRNA gene sequences, DNA:DNA reassociation kinetics and phenotypic features including biochemical and serological reactions [1]
This paper reports on the application of fliC sequences to differentiate Dickeya strains at the species and infraspecific level and to diagnose ‘D. solani’ with a fliC barcode or TaqManH real-time PCR
A single amplicon of approximately 650 bp was produced for all strains tested of D. chrysanthemi, D. dadantii, D. dianthicola, ‘D. solani’ and D. zeae
Summary
The genus Dickeya was established by the reclassification of Pectobacterium (Erwinia) chrysanthemi and Brenneria paradisiaca as D. chrysanthemi and D. paradisiaca, respectively and for the accommodation of four new species, i.e. D. dadantii, D. dianthicola, D. dieffenbachiae and D. zeae; based on analysis of 16S rRNA gene sequences, DNA:DNA reassociation kinetics and phenotypic features including biochemical and serological reactions [1]. 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 assigned to D. dianthicola [3,5]. Across wide environmental conditions it causes extensive maceration of the seed tuber, rapid wilting and blackleg-like symptoms in the stem with decomposition of the pith. Both D. dianthicola and ‘D. solani’ are disseminated by infected or contaminated seed tubers. Seed certification generally implements a zero tolerance for blackleg in field inspections of high grade seed
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