Genome comparison of the epiphytic bacteria Erwinia billingiae and E. tasmaniensis with the pear pathogen E. pyrifoliae

AbstractTilletia controversa causing dwarf bunt of wheat is a quarantine pathogen in several countries. Therefore, its specific detection is of great phytosanitary importance. Genomic regions routinely used for phylogenetic inferences lack suitable polymorphisms for the development of species-specific markers. We therefore compared 21 genomes of six Tilletia species to identify DNA regions that were unique and conserved in all T. controversa isolates and had no or limited homology to other Tilletia species. A loop-mediated isothermal amplification (LAMP) assay for T. controversa was developed based on one of these DNA regions. The specificity of the assay was verified using 223 fungal samples comprising 43 fungal species including 11 Tilletia species, in particular 39 specimens of T. controversa, 92 of T. caries and 40 of T. laevis, respectively. The assay specifically amplified genomic DNA of T. controversa from pure cultures and teliospores. Only Tilletia trabutii generated false positive signals. The detection limit of the LAMP assay was 5 pg of genomic DNA per reaction. A test performance study that included five laboratories in Germany resulted in 100% sensitivity and 97.7% specificity of the assay. Genomic regions, specific to common bunt (Tilletia caries and Tilletia laevis together) are also provided.

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Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽

10.3390/v13010027 ◽

2020 ◽

Vol 13 (1) ◽

pp. 27

Author(s):

Jun Kwon ◽

Sang Guen Kim ◽

Hyoun Joong Kim ◽

Sib Sankar Giri ◽

Sang Wha Kim ◽

...

Keyword(s):

Morphological Traits ◽

Open Reading Frames ◽

Genome Comparison ◽

The Novel ◽

Promising Alternative ◽

Isolation And Characterization ◽

Global Issue ◽

Reading Frames ◽

Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

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Production Assessment and Genome Comparison Revealed High Yield Potential and Novel Specific Alleles Associated with Fertility and Yield in Neo-Tetraploid Rice

Rice ◽

10.1186/s12284-020-00387-3 ◽

2020 ◽

Vol 13 (1) ◽

Cited By ~ 2

Author(s):

Hang Yu ◽

Muhammad Qasim Shahid ◽

Qihang Li ◽

Yudi Li ◽

Cong Li ◽

...

Keyword(s):

Yield Potential ◽

High Yield ◽

Genome Comparison ◽

High Yield Potential

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Temporal Changes of the Epiphytic Bacteria Community From the Marine Macroalga Ulva lactuca (Santa Marta, Colombian-Caribbean)

Current Microbiology ◽

10.1007/s00284-020-02302-x ◽

2021 ◽

Author(s):

Natalia Beatriz Comba González ◽

Albert Nicolás Niño Corredor ◽

Liliana López Kleine ◽

Dolly Montoya Castaño

Keyword(s):

Temporal Changes ◽

Ulva Lactuca ◽

Epiphytic Bacteria ◽

Marine Macroalga

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Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

Journal of Clinical Microbiology ◽

10.1128/jcm.02589-14 ◽

2014 ◽

Vol 53 (1) ◽

pp. 191-200 ◽

Cited By ~ 78

Author(s):

Walter Demczuk ◽

Tarah Lynch ◽

Irene Martin ◽

Gary Van Domselaar ◽

Morag Graham ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Large Scale ◽

Epidemiological Studies ◽

23S Rrna ◽

Genome Comparison ◽

Whole Genome ◽

Content Type ◽

Genomic Epidemiology ◽

High Level ◽

Sequence Types

A large-scale, whole-genome comparison of CanadianNeisseria gonorrhoeaeisolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While someN. gonorrhoeaemultiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaicpenAalleles, followed in 2000/2001 with thepenAmosaic X allele and then in 2007 with ST1407 strains with thepenAmosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated withpenAmosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

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Development of a Bio-PCR Protocol for the Detection of Xanthomonas arboricola pv. pruni

Plant Disease ◽

10.1094/pdis-09-10-0650 ◽

2011 ◽

Vol 95 (9) ◽

pp. 1109-1115 ◽

Cited By ~ 9

Author(s):

E. L. Ballard ◽

R. G. Dietzgen ◽

L. I. Sly ◽

C. Gouk ◽

C. Horlock ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Real Time ◽

Field Evaluation ◽

Subtractive Hybridization ◽

Epiphytic Bacteria ◽

Supportive Evidence ◽

Chain Reaction ◽

Dna Library ◽

Xanthomonas Arboricola ◽

Polymerase Chain

A real-time SYBR Green I assay was developed and evaluated as a biological and enzymatic polymerase chain reaction (Bio-PCR) protocol for the detection of Xanthomonas arboricola pv. pruni. Suppression subtractive hybridization was used to generate a X. arboricola pv. pruni-specific subtracted DNA library, using X. arboricola pv. corylina as the driver strain. Primer pair 29F/R, designed from cloned sequence, showed no homology to GenBank sequences and amplified a 344-bp product in all X. arboricola pv. pruni isolates. Compared with other published X. arboricola pv. pruni primers, this primer pair was shown to be the only one capable of differentiating X. arboricola pv. pruni from all other X. arboricola pathovars. A real-time assay was developed and shown to be capable of detecting less than 10 CFU and 0.1 pg of DNA. Epiphytic bacteria isolated from plum tissue was used to further evaluate the specificity of the assay. A Bio-PCR protocol, developed for field evaluation, confirmed X. arboricola pv. pruni isolation from asymptomatic and symptomatic plum tissue over a 9-week period between host flowering and the first appearance of leaf and fruit symptoms in an orchard. Dilution plating enabled X. arboricola pv. pruni numbers to be quantified, providing supportive evidence for the usefulness of the Bio-PCR protocol in plant pathology and quarantine surveillance.

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Genome comparison from the charge distribution of proteins

Seibutsu Butsuri ◽

10.2142/biophys.41.s75_3 ◽

2001 ◽

Vol 41 (supplement) ◽

pp. S75

Author(s):

R. Ke ◽

S. Mitaku

Keyword(s):

Charge Distribution ◽

Genome Comparison

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