Editorial: Genome-Wide Analyses of Pectobacterium and Dickeya Species

Arif, Mohammad; Czajkowski, Robert; Chapman, Toni A.

doi:10.3389/fpls.2022.855262

Cited by 13 publications

(17 citation statements)

References 33 publications

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“…New Dickeya species are continually being described due to the broad natural diversity within the genus. To date, descriptions of 12 Dickeya species have been published and their genomes are available 15 , including the most recent additions of D. poaceiphila 31 , D. parazeae 32 , D. oryzae 33 and D. colocasiae 16 . A previously published LAMP assay, designed to detect Dickeya at the genus level, successfully detected eight known Dickeya spp.…”

Section: Discussionmentioning

confidence: 99%

“…Dickeya fangzhongdai is classified within Pectobacteriaceae, a genetically diverse, Gram-negative, facultatively anaerobic bacterial species capable of causing soft rot disease in a range of monocot hosts and also reported to cause bleeding canker disease of pear (Pyrus pyrifolia), a dicot host [8][9][10][11][12] . Dickeya species may persist in soil, surface water, and groundwater, or as epiphytes and saprophytes [13][14][15][16] . Infection by Dickeya species begins with attraction, adhesion, and invasion of the host through wounds and natural openings such as stomata.…”

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confidence: 99%

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Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region

DeLude

Wells

Boomla

et al. 2022

Sci Rep

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Dickeya fangzhongdai, a bacterial pathogen of taro (Colocasia esculenta), onion (Allium sp.), and several species in the orchid family (Orchidaceae) causes soft rot and bleeding canker diseases. No field-deployable diagnostic tool is available for specific detection of this pathogen in different plant tissues. Therefore, we developed a field-deployable loop-mediated isothermal amplification (LAMP) assay using a unique genomic region, present exclusively in D. fangzhongdai. Multiple genomes of D. fangzhongdai, and other species of Dickeya, Pectobacterium and unrelated genera were used for comparative genomic analyses to identify an exclusive and conserved target sequence from the major facilitator superfamily (MFS) transporter gene region. This gene region had broad detection capability for D. fangzhongdai and thus was used to design primers for endpoint PCR and LAMP assays. In-silico validation showed high specificity with D. fangzhongdai genome sequences available in the NCBI GenBank genome database as well as the in-house sequenced genome. The specificity of the LAMP assay was determined with 96 strains that included all Dickeya species and Pectobacterium species as well as other closely related genera and 5 hosts; no false positives or false negatives were detected. The detection limit of the assay was determined by performing four sensitivity assays with tenfold serially diluted purified genomic DNA of D. fangzhongdai with and without the presence of crude host extract (taro, orchid, and onion). The detection limit for all sensitivity assays was 100 fg (18–20 genome copies) with no negative interference by host crude extracts. The assays were performed by five independent operators (blind test) and on three instruments (Rotor-Gene, thermocycler and dry bath); the assay results were concordant. The assay consistently detected the target pathogen from artificially inoculated and naturally infected host samples. The developed assay is highly specific for D. fangzhongdai and has applications in routine diagnostics, phytosanitary and seed certification programs, and epidemiological studies.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region

DeLude

Wells

Boomla

et al. 2022

Sci Rep

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“…et al, 2021). In turn, Pectobacterium is currently divided into 20 recognized species with several new ones reported in 2019-2021, such as P. aquaticum, P. parvum, P. polonicum, P. quasiaquaticum, P. versatile and P. zantedeschiae (Arif et al, 2022).…”

Section: Influen Ce Of O -P Olysaccharide D Iver S It Y On the Ta Xon...mentioning

confidence: 99%

“…The taxonomic reclassifications based on genetic and serological differences within this genus led to the recognition of the genus Pectobacterium , which was later separated into Pectobacterium and Dickeya (Zaczek‐Moczydłowska et al, 2019). The Pectobacterium genus currently includes 20 formally described species, and Dickeya encompasses 12 species with two subspecies (Arif et al, 2022; Boluk et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Pectobacterium and Dickeya genus—A review on structural variations of O‐polysaccharides and their role in the pathogenic process of plants

Szulta

Kornicka

2023

Plant Pathology

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Pectobacterium and Dickeya are gram‐negative phytopathogens representing the Pectobacteriaceae family. Representatives of this genus cause damage to crops worldwide, posing a global threat to agricultural food production. The studies of chemical structures of the bacterial O‐polysaccharide repeating units and the role of these elements in the pathogenesis process are bringing about in‐depth understanding of the complex interactions of pathogenic microbes with plants, leading to potential reduction or elimination of phytopathogens. This review is devoted to structural variation characteristics of the O‐polysaccharides of strains of the Pectobacterium and Dickeya genera, which help with improving classification schemes of these strains. Attention is also paid to the antigenic correlations of these strains within the genus and their O‐polysaccharide‐related bioactivities as well as the possible role of this component in plant–microbe interactions.

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“…The taxonomy of the genus Pectobacterium has been subjected to constant remodeling, re-evaluation, and reorganization, with the simultaneous development of new bacterial classification techniques (Figure 1). For instance, next generation sequencing (NGS), which provides the whole genome sequence, enables analysis of taxonomically complex genera and comparisons of phylogenetic/evolutionary relationships of different species and subspecies of plant pathogenic genera [6, 7]. Currently, Pectobacterium genus includes 20 recognized or proposed species till date.…”

Section: Introductionmentioning

confidence: 99%

Pectobacterium colocasium sp. nov. isolated from taro (Colocasia esculenta)

Klair

Arizala

Dobhal

et al. 2022

Preprint

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Pectobacterium, agenus comprising gram-negative, pectinolytic phytopathogens, is responsible for economic losses in a wide host range of plants. In this study, the bacterial strains PL152T and PL155 were isolated from taro corms in Hawaii in 2018, and characterized using genomic and biochemical assays. The Next Generation Sequencing technologies, Oxford Nanopore MinION and Illumina NovaSeq, were used for whole genome sequencing of the PL152T strain. Short and long reads were assembled using the Unicycler tool accessible at the bioinformatic resource center, and PATRIC (PathoSystems Resource Integration Center) was used to generate a more accurate and reliable hybrid assembly. The 16S rRNA analysis of PL152T with type strains of other known Pectobacterium species showed a close relationship with P. fontis. Multi-locus sequence analysis using nine housekeeping genes (dnaA, gapA, gyrB, recA, dnaN, rpoS, mdh, rpoA and dnaK) differentiated strain PL152T from other species of Pectobacterium and formed a unique and well-defined clade. The concurrent results of average nucleotide identity (ANI) and digital DNA-DNA hybridization, with calculated values lower than 95 and 70%, respectively, supported the delineation of a novel bacterial species. Here, we proposed Pectobacterium colocasium, strain PL152T (=ICMP 24362T; LMG 32536 T) and PL155 as a novel species in the genus Pectobacterium.

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Editorial: Genome-Wide Analyses of Pectobacterium and Dickeya Species

Cited by 13 publications

References 33 publications

Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region

Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region

Pectobacterium and Dickeya genus—A review on structural variations of O‐polysaccharides and their role in the pathogenic process of plants

Pectobacterium colocasium sp. nov. isolated from taro (Colocasia esculenta)

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