scholarly journals Genetic relatedness among Campylobacter jejuni serotyped isolates of diverse origin as determined by numerical analysis of amplified fragment length polymorphism (AFLP) profiles

2004 ◽  
Vol 96 (4) ◽  
pp. 795-802 ◽  
Author(s):  
B.L. Siemer ◽  
C.S. Harrington ◽  
E.M. Nielsen ◽  
B. Borck ◽  
N.L. Nielsen ◽  
...  
Keyword(s):  
Numerical Analysis ◽  
Campylobacter Jejuni ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Relatedness ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Diverse Origin

scholarly journals Genomic Relatedness within Five Common Finnish Campylobacter jejuni Pulsed-Field Gel Electrophoresis Genotypes Studied by Amplified Fragment Length Polymorphism Analysis, Ribotyping, and Serotyping

2001 ◽  
Vol 67 (4) ◽  
pp. 1581-1586 ◽  
Author(s):  
Marja-Liisa Hänninen ◽  
Päivikki Perko-Mäkelä ◽  
Hilpi Rautelin ◽  
Birgitta Duim ◽  
Jaap A. Wagenaar
Keyword(s):  
Campylobacter Jejuni ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Gel Electrophoresis ◽  
Genetic Relatedness ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Pulsed Field Gel Electrophoresis ◽  
Polymorphism Analysis ◽  
Pulsed Field

ABSTRACT Thirty-five Finnish Campylobacter jejuni strains with five SmaI/SacII pulsed-field gel electrophoresis (PFGE) genotypes selected among human and chicken isolates from 1997 and 1998 were used for comparison of their PFGE patterns, amplified fragment length polymorphism (AFLP) patterns,HaeIII ribotypes, and heat-stable (HS) serotypes. The discriminatory power of PFGE, AFLP, and ribotyping withHaeIII were shown to be at the same level for this selected set of strains, and these methods assigned the strains into the same groups. The PFGE and AFLP patterns within a genotype were highly similar, indicating genetic relatedness. The same HS serotypes were distributed among different genotypes, and different serotypes were identified within one genotype. HS serotype 12 was only associated with the combined genotype G1 (PFGE-AFLP-ribotype). These studies using polyphasic genotyping methods suggested that common Finnish C. jejuni genotypes form genetic lineages which colonize both humans and chickens.

scholarly journals Genetic Relatedness of Ornamental Ficus Species and Cultivars Analyzed by Amplified Fragment Length Polymorphism Markers

2007 ◽  
Vol 132 (6) ◽  
pp. 807-815 ◽  
Author(s):  
Jinggui Fang ◽  
Jianjun Chen ◽  
Richard J. Henny ◽  
Chih-Cheng T. Chao
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Relatedness ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Ornamental Plant ◽  
Rapid Expansion ◽  
Plant Industry ◽  
Similarity Coefficients ◽  
Woody Root

Ornamental Ficus L. is a group of lactiferous trees, shrubs, and woody root-climbing vines that are cultivated either as landscape plants in the tropics and subtropics or as foliage plants used worldwide for interiorscaping. With the recent rapid expansion of the ornamental plant industry, more new Ficus species and cultivars have been introduced. However, no study has thus far addressed the genetic relationships of cultivated ornamental Ficus. Using amplified fragment length polymorphism (AFLP) markers with near-infrared fluorescence-labeled primers, this study analyzed the genetic relatedness of 56 commercial cultivars across 12 species. Forty-eight EcoRI + 2/MseI + 3 primer set combinations were initially screened, from which six primer sets were selected and used in this investigation. Most cultivars were differentiated by their AFLP fingerprints, and their relationships were determined using the unweighted pair-group method of arithmetic average cluster analysis. The 56 cultivars were divided into 12 clusters that correspond to 12 species, indicating that no interspecific hybrids of ornamental Ficus are in commercial production. The 12 species are genetically diverse, with Jaccard's similarity coefficients ranging from 0.21 to 0.43. However, cultivars within three species—Ficus benjamina L., Ficus elastica Roxb. Ex Hornem., and Ficus pumila L.—are genetically close. Twenty-seven of the 29 cultivars of F. benjamina and five cultivars of F. pumila had Jaccard's similarity coefficients of 0.98 or higher respectively. Nine cultivars of F. elastica shared Jaccard's coefficients higher than 0.96. These results indicate potential genetic vulnerability of these cultivars within the three species. Because there are increasing reports of invasive pests in the ornamental plant industry, strategies for conserving genetic resources and broadening genetic diversity of cultivated Ficus are discussed.

scholarly journals Amplified Fragment Length Polymorphism Fingerprinting to Identify Genetic Relatedness among Lychee Cultivars and Markers Associated with Small-seeded Cultivars

2014 ◽  
Vol 139 (6) ◽  
pp. 657-668 ◽  
Author(s):  
Ashish K. Pathak ◽  
Sudhir P. Singh ◽  
Rakesh Tuli
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Relatedness ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Fingerprinting ◽  
Discriminatory Ability ◽  
Commercial Cultivars ◽  
Small Seed ◽  
Synonymies And Homonymies

Amplified fragment length polymorphism (AFLP) was used to assess genetic relatedness among 23 popular commercial cultivars of lychee (Litchi chinensis) and identify the markers associated with small-seeded cultivars. A combination of three primer pairs with high discriminatory ability was selected for resolving the identity of lychee cultivars. The marker system resolved the instances of synonymies and homonymies. The two cultivars, Dehrarose and Dehradun, whose names are often used interchangeably, could be discriminated by AFLP. A cultivar, Calcuttia (H), grown in the Punjab region was found genetically very similar to China (M) of Bihar region in India, suggesting that both could be the same clone. A number of cultivars with contrasting seed size were included in the study. The cultivars Bedana, Seedless Late, and China were positioned in one group, unlike the grouping previously reported based on morphological traits. The AFLP fingerprinting revealed five marker fragments exclusive to the genotypes, which bear fruit with small seed and large pulp.

scholarly journals Campylobacter jejuni isolated from poultry and humans in Styria, Austria: epidemiology and ciprofloxacin resistance

2003 ◽  
Vol 130 (3) ◽  
pp. 377-386 ◽  
Author(s):  
I. HEIN ◽  
C. SCHNECK ◽  
M. KNÖGLER ◽  
G. FEIERL ◽  
P. PLESS ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Gel Electrophoresis ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Pulsed Field Gel Electrophoresis ◽  
Pulsed Field ◽  
Time Period ◽  
Ciprofloxacin Resistance

Sixty-six broiler flocks were sampled to determine the presence of Campylobacter spp. at slaughter in 1998. Thirty flocks (45%) tested positive and C. jejuni was identified in all isolates. Combined pulsed-field gel electrophoresis/amplified fragment length polymorphism (PFGE/AFLP) subtyping of 177 isolates from 24 positive flocks revealed 62 subtypes; 16 flocks harboured more than one subtype. When subtyping 101 clinical C. jejuni isolates collected in the same time period and area, 60 PFGE/AFLP types were identified. Comparison of subtypes from poultry and human isolates revealed three shared PFGE/AFLP types, which were present in 11 human isolates. Fifty per cent of all poultry isolates and 39% of all human isolates were resistant to ciprofloxacin. The present study confirms the increase in ciprofloxacin resistance in both human and poultry C. jejuni isolates in Austria, as observed in several countries worldwide. A small number of human isolates shared PFGE/AFLP types with poultry isolates, however, further studies should also focus on the identification of other sources of C. jejuni infection in humans.

scholarly journals Application of Amplified Fragment Length Polymorphism Fingerprinting for Taxonomy and Identification of the Soft Rot Bacteria Erwinia carotovora and Erwinia chrysanthemi

2002 ◽  
Vol 68 (4) ◽  
pp. 1499-1508 ◽  
Author(s):  
Anna O. Avrova ◽  
Lizbeth J. Hyman ◽  
Rachel L. Toth ◽  
Ian K. Toth
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Relatedness ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Erwinia Carotovora ◽  
Soft Rot ◽  
Erwinia Chrysanthemi ◽  
Aflp Fingerprinting ◽  
Mean Similarity

ABSTRACT The soft rot bacteria Erwinia carotovora and Erwinia chrysanthemi are important pathogens of potato and other crops. However, the taxonomy of these pathogens, particularly at subspecies level, is unclear. An investigation using amplified fragment length polymorphism (AFLP) fingerprinting was undertaken to determine the taxonomic relationships within this group based on their genetic relatedness. Following cluster analysis on the similarity matrices derived from the AFLP gels, four clusters (clusters 1 to 4) resulted. Cluster 1 contained Erwinia carotovora subsp. carotovora (subclusters 1a and 1b) and Erwinia carotovora subsp. odorifera (subcluster 1c) strains, while cluster 2 contained Erwinia carotovora subsp. atroseptica (subcluster 2a) and Erwinia carotovora subsp. betavasculorum (subcluster 2b) strains. Clusters 3 and 4 contained Erwinia carotovora subsp. wasabiae and E. chrysanthemi strains, respectively. While E. carotovora subsp. carotovora and E. chrysanthemi showed a high level of molecular diversity (23 to 38% mean similarity), E. carotovora subsp. odorifera, E. carotovora subsp. betavasculorum, E. carotovora subsp. atroseptica, and E. carotovora subsp. wasabiae showed considerably less (56 to 76% mean similarity), which may reflect their limited geographical distributions and/or host ranges. The species- and subspecies-specific banding profiles generated from the AFLPs allowed rapid identification of unknown isolates and the potential for future development of diagnostics. AFLP fingerprinting was also found to be more differentiating than other techniques for typing the soft rot erwinias and was applicable to all strain types, including different serogroups.

scholarly journals Use of Amplified-Fragment Length Polymorphism To Study the Ecology of Campylobacter jejuni in Environmental Water and To Predict Multilocus Sequence Typing Clonal Complexes

2012 ◽  
Vol 78 (7) ◽  
pp. 2470-2473 ◽  
Author(s):  
Simon Lévesque ◽  
Karen St-Pierre ◽  
Eric Frost ◽  
Robert D. Arbeit ◽  
Sophie Michaud
Keyword(s):  
Campylobacter Jejuni ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Multilocus Sequence Typing ◽  
Population Genetic ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Environmental Water ◽  
Content Type

ABSTRACTWe determined the genetic variability among water isolates ofCampylobacter jejuniby using amplified-fragment length polymorphism (AFLP) and multilocus sequence typing (MLST). Across a highly diverse collection of isolates, AFLP clusters did not correlate with MLST clonal complexes, suggesting that AFLP is not reliable for deciphering population genetic relationships and may be problematic for larger epidemiologic analyses.

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