Phylogeny and classification of 
               
                  Dickeya
               
             based on multilocus sequence analysis

Marrero, Glorimar; Schneider, Kevin; Jenkins, Daniel M.; Alvarez, Anne M.

doi:10.1099/ijs.0.046490-0

Cited by 47 publications

(48 citation statements)

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“…, three Pectobacterium species and two Dickeya dadantii isolates. The later two bacterial isolates, D. dadantii Ech586 and D. dadantii Ech703, should be reclassified as two different species, Dickeya zeae Ech586 and Dickeya paradisiaca Ech703, respectively [72]. It may be that the bacterial chitin synthase plays a role in the parasitic interaction between these bacteria and their plant hosts.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi

et al. 2016

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BackgroundChitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the development of many of them. This polysaccharide is produced by type 2 glycosyltransferases, called chitin synthases (CHS). There are several contradictory classifications of CHS isoenzymes and, as regards their evolutionary history, their origin and diversity is still a matter of debate.ResultsA genome-wide analysis resulted in the detection of more than eight hundred putative chitin synthases in proteomes associated with about 130 genomes. Phylogenetic analyses were performed with special care to avoid any pitfalls associated with the peculiarities of these sequences (e.g. highly variable regions, truncated or recombined sequences, long-branch attraction). This allowed us to revise and unify the fungal CHS classification and to study the evolutionary history of the CHS multigenic family. This update has the advantage of being user-friendly due to the development of a dedicated website (http://wwwabi.snv.jussieu.fr/public/CHSdb), and it includes any correspondences with previously published classifications and mutants. Concerning the evolutionary history of CHS, this family has mainly evolved via duplications and losses. However, it is likely that several horizontal gene transfers (HGT) also occurred in eukaryotic microorganisms and, even more surprisingly, in bacteria.ConclusionsThis comprehensive multi-species analysis contributes to the classification of fungal CHS, in particular by optimizing its robustness, consensuality and accessibility. It also highlights the importance of HGT in the evolutionary history of CHS and describes bacterial chs genes for the first time. Many of the bacteria that have acquired a chitin synthase are plant pathogens (e.g. Dickeya spp; Pectobacterium spp; Brenneria spp; Agrobacterium vitis and Pseudomonas cichorii). Whether they are able to produce a chitin exopolysaccharide or secrete chitooligosaccharides requires further investigation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0815-9) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi

et al. 2016

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“…Because of the low discriminatory power of 16S rRNA gene analysis, several housekeeping genes have instead been used for phylogenetic analyses; these housekeeping loci have included rpoB , gyrB , dnaJ and recA . Moreover, MLSA has become a powerful alternative to 16S rRNA gene or single housekeeping gene phylogenetic analysis .…”

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confidence: 99%

Phylogenetics of family Enterobacteriaceae and proposal to reclassify Escherichia hermannii and Salmonella subterranea as Atlantibacter hermannii and Atlantibacter subterranea gen. nov., comb. nov.

Hata

Natori

Mizuno

et al. 2016

Microbiology and Immunology

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Multilocus sequence analysis based on hypervariable housekeeping proteins was utilized to differentiate closely related species in the family Enterobacteriaceae. Of 150 housekeeping proteins, the top 10 hypervariable proteins were selected and concatenated to obtain distance data. Distances between concatenated proteins within the family were 0.9-41.2%, whereas the 16S rRNA and atpD-gyrB-infB-rpoB concatenated sequence (4MLSA) distances were 0.8-6.0% and 0.9-22.1%, respectively. These data indicate that phylogenetic analysis by concatenation of hypervariable proteins is a powerful tool for discriminating species in the family Enterobacteriaceae. To confirm the discriminatory power of the 10 chosen concatenated hypervariable proteins (C10HKP), phylogenetic trees based on C10HKP, 4MLSA, and the 16S rRNA gene were constructed. Comparison of average bootstrap values among C10HKP, 4MLSA and 16S rRNA genes indicated that the C10HKP tree was the most reliable. Location via the C10HKP tree was consistent with existing assignments for almost all species in the family Enterobacteriaceae. However, the C10HKP tree suggested that several species (including Enterobacter massiliensis, Escherichia vulneris, Escherichia hermannii, and Salmonella subterranea) should be reassigned to different clusters than those defined in previous analyses. Furthermore, E. hermannii and S. subterranea appeared to fall onto a branch independent from those occupied by the other Enterobacteriaceae. Therefore, we propose Atlantibacter gen. nov., such that E. hermannii and S. subterranea would be transferred to genus Atlantibacter as Atlantibacter hermannii, comb. nov. and Atlantibacter subterranea. comb. nov., respectively.

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“…However, pineapple industry particularly in Malaysia has been badly affected by disease tribulation. Various diseases caused by bacterial infection have been reported and the most severe is bacterial heart rot (BHR) caused by Erwinia chrysanthemi or newly known as Dickeya zeae (Marrero et al, 2013). BHR was first reported in Malaysia by Johnston in year 1957 (Lim, 1985;Toth et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Dissemination pattern of bacterial heart rot (BHR) disease and screening of the disease resistance among commercial pineapple varieties in Malaysia

Nor¹,

Zainol²,

Abdullah³

et al. 2019

MJM

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Aims: Bacterial heart rot (BHR) disease caused by Erwinia chrysanthemi or the new nomenclature Dickeya zeae was identified as the lethal disease of pineapple and caused massive losses for the farmers due to non-satisfactory solutions. Thus, this study aims to understand the disease dissemination pattern and screen for tolerance pineapple variety prior to establishment of disease management strategies. Methodology and results: Dissemination of BHR disease was observed visually in 2 study plots consisting 200 plants in each plot. Single plant inoculation of the pathogen was done in each plot namely Plot A at the edge and Plot B at the middle. Disease incidence was recorded at weekly interval for 12 weeks. The pattern of disease spreading in both plots was then mapped based on the results. Separately, 8 commercial pineapple varieties (Maspine, N36, MD2, Morris, Sarawak, Kristal, Gandul and Josapine) were screened for their resistance towards BHR. The varieties screening study was carried out using complete randomized block design. Overall, disease incidence (DI) was observed lower in plot A compared to Plot B. Percentage of DI in Plot A increased continuously from week 1 to 12, but in plot B the DI was stagnant starting from week 3 onwards. This study revealed that there is highly significant difference in percentage of infection between varieties tested. Josapine and MD2 were the most infected varieties based on lesion on plant. Both were found susceptible to BHR. Besides that, Chrystal Honey, Maspine and Sarawak varieties were less infected and classified as moderately resistance compared to other varieties. Conclusion, significance and impact of study: Inoculum source was recognized as determinant factor for dissemination of BHR. Aggregation pattern was observed, and disease spreading was severe when disease started from the edge of the plot compared to in the middle. These findings will help farmers to choose the varieties of interest and plan for disease control measure based on first observed disease symptom in their field. This study is also important to researchers and plant breeders for varietal improvement in the future.

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Phylogeny and classification of Dickeya based on multilocus sequence analysis

Cited by 47 publications

References 46 publications

Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi

Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi

Phylogenetics of family Enterobacteriaceae and proposal to reclassify Escherichia hermannii and Salmonella subterranea as Atlantibacter hermannii and Atlantibacter subterranea gen. nov., comb. nov.

Dissemination pattern of bacterial heart rot (BHR) disease and screening of the disease resistance among commercial pineapple varieties in Malaysia

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