scholarly journals Population Structure of Cercospora kikuchii, the Causal Agent of Cercospora Leaf Blight and Purple Seed Stain in Soybean

2008 ◽  
Vol 98 (7) ◽  
pp. 823-829 ◽  
Author(s):  
G. Cai ◽  
R. W. Schneider
Keyword(s):  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Intergenic Spacer ◽  
Chain Reaction ◽  
Cercospora Kikuchii ◽  
Vegetative Compatibility Groups ◽  
Intergenic Spacer Region ◽  
Group I ◽  
Polymerase Chain ◽  
Purple Seed Stain

Random amplified polymorphic DNA (RAPD) and microsatellite-primed polymerase chain reaction (MP-PCR) were used to characterize 164 isolates of Cercospora kikuchii, most of which were collected from Louisiana. Plant tissue (seeds versus leaves), but not host cultivar, had a significant impact on pathogen population differentiation. Cluster analysis showed that the Louisiana population was dominated by a primary lineage (group I) with only a few Louisiana isolates belonging to the minor lineage that also included the non-Louisiana isolates (group II). A previous study showed that isolates could be differentiated according to vegetative compatibility groups (VCGs). However, RAPD and MP-PCR data demonstrated that isolates of C. kikuchii were not generally clustered according to these VCGs. Furthermore, genetic relationships within and between VCGs were examined using sequences of the intergenic spacer region of rDNA. These analyses showed that VCG is not an indicator of evolutionary lineage in this fungus. Our results suggest the likely existence of a cryptically functioning sexual stage in some portion of the C. kikuchii population.

scholarly journals Differentiation of Moraxella Bovoculi sp. nov. from other Coccoid Moraxellae by the Use of Polymerase Chain Reaction and Restriction Endonuclease Analysis of Amplified DNA

2007 ◽  
Vol 19 (5) ◽  
pp. 532-534 ◽  
Author(s):  
John A. Angelos ◽  
Louise M. Ball
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequence ◽  
Restriction Analysis ◽  
Intergenic Spacer ◽  
Restriction Enzyme Digestion ◽  
Chain Reaction ◽  
Gram Negative ◽  
Intergenic Spacer Region ◽  
Polymerase Chain ◽  
Moraxella Bovoculi

Moraxella oris was historically the only coccoid Moraxella identified in cultures of ocular fluid from cattle with infectious bovine keratoconjunctivitis (IBK) and could be morphologically and biochemically differentiated from Moraxella bovis. Moraxella bovoculi sp. nov. is a recently characterized Moraxella isolated from ulcerated eyes of calves with IBK in northern California in 2002. Like Moraxella ovis, M. bovoculi sp. nov. is a gram-negative coccus/diplococcus. All 18 original isolates of M. bovoculi sp. nov. possessed phenylalanine deaminase (PADase) activity and could therefore be differentiated from M. ovis and M. bovis. During the characterization of 44 additional isolates of hemolytic gram-negative cocci that were cultured from ulcerated eyes of IBK-affected calves, 2 PADase-negative isolates were identified that could not be differentiated biochemically from M. ovis; however, the DNA sequence of the 16S-23S intergenic spacer region (ISR) of the isolates matched the 16S-23S ISR DNA sequence of M. bovoculi sp. nov. To facilitate the identification of PADase-negative moraxellae, a polymerase chain reaction (PCR) coupled with restriction enzyme digestion analysis of amplified DNA was developed. Amplification of the 16S-23S ISR followed by AfaI digestion of amplified DNA could differentiate M. bovoculi sp. nov. from M. ovis and other moraxellae. The DNA sequence analysis of the amplified 16S-23S ISR from the 42 PADase-positive isolates of hemolytic gram-negative cocci indicated that all were M. bovoculi sp. nov. and all possessed an AfaI site. A PCR coupled with restriction analysis of amplified DNA can aid in identifying M. bovoculi sp. nov.

An Assessment of Genetic Relationships between Members of the Phytophthora megasperma Complex and Phytophthora vignae using Molecular Markers

1993 ◽  
Vol 6 (4) ◽  
pp. 295 ◽  
Author(s):  
SC Whisson ◽  
BJ Howlett ◽  
ECY Liew ◽  
DJ Maclean ◽  
JM Manners ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Protein Patterns ◽  
Separate Species ◽  
Phytophthora Megasperma ◽  
Polymerase Chain ◽  
Mitochondrial Rflps

Genetic relationships between Phytophora megasperma f. sp. glycinea (Pmg) and morphologically similar taxa, P. megasperma f. sp. medicaginis (Pmm), P. megasperma f. sp. trifolii (Pmt), P. megasperma from Douglas Fir (PmDF) and asparagus (PmAS) and Phytophthora vignae, were explored by restriction fragment length polymorphism (RFLP) analysis of nuclear DNA using random genomic multi-copy, cDNA, and ribosomal DNA probes as well as random amplified polymorphic DNA (RAPDs) and RFLP analysis of ribosomal intergenic spacer regions amplified by the polymerase chain reaction (PCR). Each method detected large differences between these taxa and P. megasperma f. sp. glycinea. P. vignae was more closely related to P. megasperma f. sp. glycinea than the other taxa on the basis of the cDNA RFLPs and RFLPs of PCR amplified rDNA intergenic spacer regions. We conclude that each of the taxa examined represent separate species. This supports the most recent reclassification based on mitochondrial RFLPs and electrophoretic protein patterns of the host-specific taxa to P. sojae (Pmg), P. trifolii (Pmt) and P. medicaginis (Pmm).

Rapid Polymerase Chain Reaction/DNA Probe Membrane-Based Assay for the Detection of Listeria and Listeria monocytogenes in Food

2000 ◽  
Vol 63 (3) ◽  
pp. 337-342 ◽  
Author(s):  
L. O'CONNOR ◽  
J. JOY ◽  
M. KANE ◽  
T. SMITH ◽  
M. MAHER
Keyword(s):  
Polymerase Chain Reaction ◽  
Microbiological Quality ◽  
Intergenic Spacer ◽  
Pcr Primers ◽  
Dna Probe ◽  
23S Rrna ◽  
Chain Reaction ◽  
Intergenic Spacer Region ◽  
Rapid Polymerase Chain Reaction ◽  
Polymerase Chain

We describe the development of polymerase chain reaction (PCR)/DNA probe membrane-based colorimetric assays for the detection and identification of Listeria and L. monocytogenes. PCR primers designed from the 16S to 23S rRNA intergenic spacer region amplified products that were reverse hybridized to membrane-bound oligonucleotide probes specific for Listeria and L. monocytogenes with a detection limit of 1 to 10 CFU/25 ml in inoculated raw and pasteurized milk samples. These qualitative assays have the potential to be integrated into testing laboratories for monitoring the microbiological quality of foods.

scholarly journals RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD™) MARKERS FOR ESTIMATING GENETIC RELATIONSHIPS IN MANGIFERA INDICA L.

HortScience ◽  
1992 ◽  
Vol 27 (6) ◽  
pp. 574c-574
Author(s):  
Raymond J. Schnell ◽  
Robert J. Knight
Keyword(s):  
Family Relationships ◽  
Linkage Mapping ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Mangifera Indica ◽  
Germplasm Collection ◽  
Chain Reaction ◽  
Mapping Analysis ◽  
Polymerase Chain ◽  
Nei's Genetic Distance

Genetic relationships between commercial mango cultivars are often speculative and only the maternal parent is generally known. RAPD™ primers were used with the polymerase chain reaction (PCR) to provide markers useful in determining individual identity, family relationships, and linkage mapping analysis. In mango, 53 RAPD primers were screened for markers and 27 proved useful. Genomic DNA was isolated from 70 clones of mango maintained in the USDA germplasm collection. DNA from these clones was amplified with each of the 27 primers. Data were scored as the presence or absence of bands. Groupings of the clones using UPGMA based on Nei's genetic distance gave distinct clusters. RAPD clusters vs. clusters based on isozyme analysis are compared.

scholarly journals Phylogenetic Relationships of Xylella fastidiosa Strains Isolated from Landscape Ornamentals in Southern California

2007 ◽  
Vol 97 (7) ◽  
pp. 857-864 ◽  
Author(s):  
Rufina Hernandez-Martinez ◽  
Karla A. de la Cerda ◽  
Heather S. Costa ◽  
Donald A. Cooksey ◽  
Francis P. Wong
Keyword(s):  
Southern California ◽  
Genetic Characterization ◽  
Xylella Fastidiosa ◽  
Random Amplified Polymorphic Dna ◽  
Intergenic Spacer ◽  
Disease Symptoms ◽  
Intergenic Spacer Region ◽  
Rapd Pcr ◽  
Polymerase Chain ◽  
Maidenhair Tree

Xylella fastidiosa is an insect-borne, xylem-limited pathogenic bacterium that has been associated with a rise in incidence of diseased landscape ornamentals in southern California. The objective of this study was to genetically characterize strains isolated from ornamental hosts to understand their distribution and identity. Strains of X. fastidiosa isolated from ornamentals were characterized using a multiprimer polymerase chain reaction (PCR) system, random amplified polymorphic DNA (RAPD)-PCR, and sequence analysis of the 16S-23S rDNA intergenic spacer region (ISR). Based on RAPD-PCR and 16S-23S rDNA ISR, strains isolated from daylily, jacaranda, and magnolia clustered with members of X. fastidiosa subsp. sandyi and caused oleander leaf scorch but not Pierce's disease symptoms in glasshouse assays on oleander and grape, respectively. This demonstrated both that our groupings based on genetic characterization were valid and that strains of X. fastidiosa subsp. sandyi are present in hosts other than oleander. Strains isolated from Spanish broom, cherry, and one strain isolated from western redbud clustered with X. fastidiosa subsp. fastidiosa members. Strains isolated from purple-leafed plum, olive, peach, plum, sweetgum, maidenhair tree, crape myrtle, and another western redbud strain clustered with members of X. fastidiosa subsp. multiplex. All strains isolated from mulberry and one from heavenly bamboo formed a separate cluster that has not yet been defined as a subspecies.

RFLP analysis of rRNA intergenic spacer regions of 23 isolates of the entomopathogenPaecilomyces farinosus

1997 ◽  
Vol 75 (12) ◽  
pp. 2038-2044 ◽  
Author(s):  
J. S. K. Chew ◽  
D. B. Strongman ◽  
R. M. MacKay
Keyword(s):  
Ribosomal Rna ◽  
Population Biology ◽  
Genetic Relationships ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Restriction Enzyme Digestion ◽  
Paecilomyces Fumosoroseus ◽  
Chain Reaction ◽  
Ecological Requirements ◽  
Polymerase Chain

Genetic relationships between 23 eastern Canadian isolates of the entomopathogen Paecilomyces farinosus (Holm ex S.F. Gray) Brown & Smith were investigated by comparison of DNA fragments produced by restriction enzyme digestion of polymerase chain reaction amplified ribosomal RNA intergenic spacer regions. The variation observed was limited to 40% or less of these regions. All P. farinosus isolates were very dissimilar to isolates of the entomopathogens Beauveria bassiana (Bals.) Vuill. and Paecilomyces fumosoroseus (Wize) Brown & Smith. Seventeen P. farinosus isolates from six different hosts and diverse habitats yielded identical or nearly identical results. Two groups, each with three isolates from two different hosts, were distinct from the main group of isolates. Each of the three P. farinosus groups included some isolates that produced synnemata and some that did not, indicating multiple evolutionary losses of the ability to produce this sporulation structure. We conclude that eastern Canadian P. farinosus, while genetically and phenotypically variable, is not composed largely of strains with strict ecological requirements. Key words: entomopathogenic fungus, population biology, RFLP, ribosomal RNA intergenic spacer.

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