A re-evaluation of the taxonomy of phytopathogenic genera Dickeya and Pectobacterium using whole-genome sequencing data

Zhang, Yucheng; Fan, Qiurong; Loria, Rosemary

doi:10.1016/j.syapm.2016.04.001

Cited by 100 publications

(67 citation statements)

References 44 publications

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“…In this study, we analysed all valid Brenneria species using concatenated partial sequences of gyrB , infB , and atpD genes and the 16S rRNA gene. Our results are in agreement with those from previous studies (Naushad, Brian, & Gupta, ; Zhang, Fan, & Loria, ) where phylogenetic trees based on 16S rRNA showed differentiation of Brenneria species. However, we found some heterogeneities in this clade, agreeing with previous reports that encountered difficulties in forming a monophyletic clade for Brenneria species (Brady et al, ).…”

Section: Discussionsupporting

confidence: 93%

Identification and characterization of bacterial strains associated with diseased oak trees in Northern Iran

et al. 2019

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Oak decline syndrome is characterized by periodic occurrences of decline and death of oaks over widespread areas. An outbreak of a new emerging disease on oak trees was reported in the Hyrcanian forest of Iran (Mazandaran and Golestan provinces) that showed stem bleeding and canker symptoms. Bacterial isolates were characterized through biochemical and physiological tests, protein electrophoresis, DNA fingerprinting (rep‐PCR, ERIC and BOX primers) and sequencing of 16S rRNA and MLSA (multilocus sequencing analysis) for housekeeping genes (gyrB, infB and atpD). A complex community of the genus Brenneria spp. (Brenneria goodwinii, Brenneria roseae subsp. roseae, Brenneria sp. and Brenneria nigrifluens) and a few isolates in the genus Gibbsiella were identified as major groups involved. Isolate differentiation was more accurate using concatenated partial gene sequences within the main groups. All bacterial isolates showed hypersensitivity reactions (HR) on Pelargonium leaves (Pelargonium × hortorum). Pathogenicity studies of different Brenneria and Gibbsiella strains revealed that they have potential to cause the disease in oak seedlings and devastating oak canker and stem bleeding symptoms in northern Iran. Due to the presence of several potentially pathogenic agent(s) associated with the oak decline, identification of the principal agent(s) is of major interest. To our knowledge, this is the first report of potentially pathogenic bacteria associated with oak bleeding and canker in Iran.

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Section: Discussionsupporting

confidence: 93%

Identification and characterization of bacterial strains associated with diseased oak trees in Northern Iran

et al. 2019

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“…This is consistent with some previous studies. For instance, D. dadantii NCPPB 2976 is part of the dieffenbachiae subspecies and has been shown to be clearly different from the other D. dadantii subsp dadantii strains based on ANI values (Zhang et al ., ). Among, D. solani , strain RNS 0512A was proposed to define a novel D. solani sub‐group based on the high number and wide distribution of nucleotide variations compared to other D. solani strains (Khayi et al ., ).…”

Section: Resultsmentioning

confidence: 97%

“…According to a large phylogenomic analysis of 895 single copy gene families, D. paradisiaca was pinpointed as the first diverging species within Dickeya , while other species formed two groups, referred hereafter as to clusters I and II (Zhang et al ., ). Cluster I encompassed D. zeae and D. chrysanthemi , while in cluster II, D. solani and D. dadantii formed the sister‐lineage of D. dianthicola (Zhang et al ., ). Species corresponding to these two clusters display different behaviours.…”

Section: Introductionmentioning

confidence: 97%

“…). It is noteworthy, that in this study, strains M074 and M005, annotated as D. chrysanthemi and D. solani , respectively, branch in‐between D. dianthicola and the D. solani / D. dadantii group within Cluster II, thus far away from the type strains of their species (Zhang et al ., ). Dickeya fangzhongdai branched at the base of the Cluster II in a tree based on seven housekeeping genes (Tian et al ., ).…”

Section: Introductionmentioning

confidence: 97%

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The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Duprey

Taïb

Léonard

et al. 2019

Environmental Microbiology

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Summary Dickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep‐branching species among Dickeya genus, its precise phylogenetic position remained elusive. Here, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquatica strain 174/2 for acidic fruits such as tomato and cucumber and show that exposure of this bacterium to acidic pH induces twitching motility. An in‐depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes, we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothesize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflect adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.

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“…) are overall consistent with the species phylogeny: D. dadantii, Dickeya solani , and D . dianthicola sequences generally group together, while Dickeya zeae and D. chrysanthemi sequences form a separate cluster . This suggests that the pel genes were transmitted vertically during the diversification of Dickeya .…”

Section: Resultsmentioning

confidence: 97%

Transcriptional start site turnover in the evolution of bacterial paralogous genes – the pelE‐pelD virulence genes in Dickeya

et al. 2016

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After a gene duplication event, the resulting paralogous genes frequently acquire distinct expression profiles, roles, and/or functions but the underlying mechanisms are poorly understood. While transcription start site (TSS) turnover, i.e., the repositioning of the TSS during evolution, is widespread in eukaryotes, it is less documented in bacteria. Using pelD and pelE, two closely related paralogous genes encoding key virulence factors in Dickeya, a gamma proteobacterial genus of phytopathogens, we show that pelE has been selected as an initiator of bacterial aggression, while pelD acts at a later stage, thanks to modifications in the transcriptional regulation of these two genes. This expression change is linked to a few mutations that caused a shift in the position of the pelETSS and the rapid divergence in the regulation of these genes after their duplication. Genomic surveys detected additional examples of putative turnovers in other bacteria. This first report of TSS shifting in bacteria suggests that this mechanism could play a major role in paralogous genes fixation in prokaryotes.

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A re-evaluation of the taxonomy of phytopathogenic genera Dickeya and Pectobacterium using whole-genome sequencing data

Cited by 100 publications

References 44 publications

Identification and characterization of bacterial strains associated with diseased oak trees in Northern Iran

Identification and characterization of bacterial strains associated with diseased oak trees in Northern Iran

The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Transcriptional start site turnover in the evolution of bacterial paralogous genes – the pelE‐pelD virulence genes in Dickeya

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