Home About us Contact
|
Home About us Contact | ||
|
|
||
Genomic Fingerprinting (genomic + fingerprinting)
Selected AbstractsThe structure of a local population of phytopathogenic Pseudomonas brassicacearum from agricultural soil indicates development under purifying selection pressureENVIRONMENTAL MICROBIOLOGY, Issue 3 2001Johannes Sikorski Among the isolates of a bacterial community from a soil sample taken from an agricultural plot in northern Germany, a population consisting of 119 strains was obtained that was identified by 16S rDNA sequencing and genomic fingerprinting as belonging to the recently described species Pseudomonas brassicacearum. Analysis of the population structure by allozyme electrophoresis (11 loci) and random amplified polymorphic DNA,polymerase chain reaction (RAPD,PCR; four primers) showed higher resolution with the latter method. Both methods indicated the presence of three lineages, one of which dominated strongly. Stochastic tests derived from the neutral theory of evolution (including Slatkin's exact test, Watterson's homozygosity test and the Tajima test) indicated that the population had developed under strong purifying selection pressure. The presence of strains clearly divergent from the majority of the population can be explained by in situ evolution or by influx of strains as a result of migration or both. Phytopathogenicity of a P. brassicacearum strain determined with tomato plants reached the level obtained with the type strain of the known pathogen Pseudomonas corrugata. The results show that a selective sweep was identified in a local population. Previously, a local selective sweep had not been seen in several populations of different bacterial species from a variety of environmental habitats. [source] Genetic variations among Mycoplasma bovis strains isolated from Danish cattleFEMS MICROBIOLOGY LETTERS, Issue 1 2000Lughano J.M. Kusiluka Abstract The genetic heterogeneity of Mycoplasma bovis strains isolated in Denmark over a 17-year period was investigated. Forty-two field strains isolated from different geographic locations and specimens, including strains from 21 herds involved in two outbreaks of M. bovis -induced mastitis, and the type strain of M. bovis (PG45T) were assayed for variations in the BglII and MfeI restriction sites in the chromosomal DNA by using the amplified fragment length polymorphism (AFLP) fingerprinting technique. The obtained genomic fingerprints consisted of 62,68 AFLP fragments in the size range of 50,500 bp. Among the analyzed strains, 18 different AFLP profiles were detected. The similarity between individual fingerprints, calculated by Dice similarity coefficient, ranged from 0.9 to 1.0. Twenty-five strains, including 23 which were isolated during two outbreaks of M. bovis -induced mastitis which occurred 2 years apart, showed indistinguishable AFLP patterns. More genetic diversity was observed among the recent strains. The similarity of the genotypes of the field strains to that of the M. bovis type strain (PG45T) was 97.7%. The results of this study have demonstrated a remarkable genomic homogeneity of Danish strains of M. bovis that were probably epidemiologically related and which have remained stable for a considerable length of time. Furthermore, this study has demonstrated that AFLP can be used for genomic fingerprinting and discrimination of M. bovis strains. [source] Two Genetically Distinct Populations of Colletotrichum gloeosporioides Penz.JOURNAL OF PHYTOPATHOLOGY, Issue 3 2005Causing Anthracnose Disease of Yam (Dioscorea spp.) Abstract Variation within Colletotrichum gloeosporioides, the causal agent of yam anthracnose disease, is still poorly defined and this hinders breeding for resistance. Two morphotypes of C. gloeosporioides, designated slow-growing grey (SGG) and fast-growing salmon (FGS), are associated with anthracnose disease of yam in Nigeria. The morphotypes are distinguishable based on colony and conidial morphology, growth rate, virulence, as well as vegetative compatibility, but molecular differentiation of SGG and FGS strains is needed to facilitate epidemiological studies. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified small subunit (18S) rDNA fragments, and microsatellite-primed PCR (MP-PCR) genomic fingerprinting were employed to provide a basis for molecular differentiation of the morphotypes. DGGE analysis revealed patterns that clearly differentiated isolates of the aggressive defoliating SGG from the moderately virulent non-defoliating FGS strains. Genetic analysis based on 52 MP-PCR markers revealed highly significant differentiation between the SGG and FGS populations on yam (GST = 0.22; Nei's genetic identity = 0.85; , = 0.28, P < 0.001), indicating that the SGG and FGS morphotypes represent genetically differentiated populations. The results of the molecular typing using DGGE and MP-PCR analyses were consistent with the disease phenotype caused by the two morphotypes. Consequently, these molecular techniques might be used, at least partly, to replace time-consuming virulence studies on yam. [source] Occurrence of Pseudomonas avellanae (Psallidas) Janse et al. and related pseudomonads on wild Corylus avellana trees and genetic relationships with strains isolated from cultivated hazelnutsJOURNAL OF PHYTOPATHOLOGY, Issue 9-10 2000M. Scortichini Surveys in submediterranean forests of central Italy were carried out during 1996,98 to verify the possible presence of bacterial canker caused by Pseudomonas avellanae in wild hazelnut trees (Corylus avellana L.). Wilted twigs were noticed several times especially in summer. In other cases, wild C. avellana trees growing near to hazelnut orchards appeared completely wilted. Isolates that were pathogenic to C. avellana, showing a different degree of virulence, were obtained in both situations. Biochemical, physiological and nutritional tests as well as the comparison of whole-cell protein profiles, revealed the presence of 16 isolates identical to P. avellanae reference strains that had previously been isolated in the same area and five deviating isolates. Repetitive-PCR genomic fingerprinting performed by using BOX (Box elements), ERIC (Enterobacterial Repetitive Interkingdom Consensus) and REP (Repetitive Extragenic Palindromic) primer sets and analysed by means of upgma, revealed the existence of two main groups of pseudomonads pathogenic to C. avellana. Group A includes P. avellanae strains isolated in northern Greece and central Italy as well as the isolates obtained from the wild C. avellana trees grown near the cultivated hazelnut orchards. Group B includes strains previously isolated in northern, southern and other areas of central Italy as well as the isolates obtained from C. avellana wild trees showing twig dieback. Control measures should be taken to avoid the spread of bacterial canker of hazelnut in the forests of central Italy. [source] Rapid identification of pseudomonas avellanae field isolates, causing hazelnut decline in central italy, by repetitive PCR genomic fingerprintingJOURNAL OF PHYTOPATHOLOGY, Issue 3 2000M. Scortichini Pseudomonas avellanae is the main cause of hazelnut (Corylus avellana L.) decline, the so called ,moria', in central Italy where it has already killed more than 30 000 trees. Its current identification is very long requiring biochemical, physiological and nutritional tests as well as pathogenicity tests and takes not less than 6 months for its completion. In the present study the reliability of the repetitive polymerase chain reaction (rep-PCR) technique for a rapid and accurate identification of such a pathogen was compared with the traditional identification method. In order to assess the variability of the pathogen, REP, BOX and ERIC primer sets were used in preliminary work to generate genomic fingerprints of 60 P. avellanae reference strains previously isolated from different areas of hazelnut cultivation. ERIC primers yielded the most discriminative clustering of strains that were grouped according to their geographic origin. Sixty field isolates collected from hazelnut orchards of central Italy, planted with different cultivars, during the years 1996,98 were submitted to either the traditional identification methods or to rep-PCR by using ERIC primers. The latter technique accurately identified all the isolates that were also identified by the traditional methods. Whole-cell protein analysis by means of sodium dodecyl sulphate-polyacrylamide gel electrophoresis confirmed this achievement. Rep-PCR can be successfully adopted for the rapid and accurate identification of P. avellanae in central Italy and it constitutes a very useful tool for the sanitation of the area. Zusammenfassung Eine schnelle Bestimmung von Pseudomonas avellanae -Feldisolaten, dem Erreger einer HaselnuIapoplexie in Zentralitalien, durch rep-PCR genomisches Fingerprinting [source] | ||||||||||