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rDNA Region (rdna + region)

Distribution by Scientific Domains

Life Sciences	87%

Selected Abstracts

Evolutionary Relationships of the Dutch Elm Disease Fungus Ophiostoma novo-ulmi to Other Ophiostoma Species Investigated by Restriction Fragment Length Polymorphism Analysis of the rDNA Region

JOURNAL OF PHYTOPATHOLOGY, Issue 9-10 2000
N. D. Pipe
Restriction fragment length polymorphisms (RFLPs) in the ribosomal RNA gene (rDNA) region were used to assess relationships between the Dutch elm disease fungi Ophiostoma novo-ulmi and Ophiostoma ulmi, the recently described Himalayan Dutch elm disease pathogen, Ophiostoma himal-ulmi, the morphologically similar sapstain fungi, Ophiostoma piceae and Ophiostoma quercus, and several Ophiostoma species from hardwood trees, including Ophiostoma stenoceras and Ophiostoma proliferum. A distance matrix and cluster analysis indicated that the rDNA region of O. himal-ulmi is more closely related to those of O. novo-ulmi and O. ulmi than to those of O. piceae and O. quercus and is more distantly related to O. stenoceras and the other Ophiostoma species, which formed a separate clade. The rDNA region of O. quercus was found to be at least as closely related to that of O. novo-ulmi and O. ulmi as it is to that of O. piceae. The implications of these results for the evolution of the Dutch elm disease fungi are discussed. [source]

Botryosphaeriaceae associated with Eucalyptus canker diseases in Colombia

FOREST PATHOLOGY, Issue 2 2009
C. A. Rodas
Summary The identities of Botryosphaeriaceae causing cankers on Eucalyptus in Colombia were investigated using morphological and DNA sequence comparisons. The pathogenicity of the species was also assessed on 42 Eucalyptus grandis clones planted at four different sites. Two species of the Botryosphaeriaceae were found to occur on E. grandis in Colombia. Neofusicoccum ribis was the more common species, and also the most pathogenic. Botryosphaeria dothidea was found only in one zone of Colombia, and was also less pathogenic than N. ribis. These two species could be distinguished easily based on DNA sequences of the ITS1/ITS2 rDNA region and EF1-,, in addition to conidial sizes. Significant differences in resistance of clones to these pathogens were also evident from the various trials. [source]

Studies on anastomosis groups of Rhizoctonia solani isolates causing disease in two forest nurseries in Poland

FOREST PATHOLOGY, Issue 2 2006
S. St, pniewska-Jarosz
Summary Thirty-eight isolates of Rhizoctonia spp. were isolated from Scots pine (Pinus sylvestris) seedlings with damping-off symptoms, originating from two forest nurseries in central-west Poland (Wronczyn and Jarocin) and from diseased seedlings grown in soil from Wronczyn nursery. Majority of these isolates (79%) had multinucleate cells and were identified as Rhizoctonia solani. The remaining isolates were recognized as binucleate Rhizoctonia spp. R. solani isolates were characterized using hyphal anastomosis and were divided into five anastomosis groups (AG). The most prevalent was AG5 (37% of isolates), followed by AG2-1 (30%) and 27% of the isolates were identified as AG4. Groups AG1-IB and AG2-2 were only represented by single isolates. The virulence recorded as mortality (in percentage) was comparatively high for binucleate and multinucleate isolates of Rhizoctonia spp. Sequence analysis of the polymerase chain reaction (PCR)-amplified internal transcribed spacer (ITS) rDNA region was used for phylogenetic analysis. The dendrogram showed that isolates were distinctly separated based on their AG types and there was no relationship between pathogenicity on Scots pine seedlings and the AG to which the isolates belong to. The results are discussed with respect to pathogenic potential of the various AG groups. Résumé Trente-huit isolats de Rhizoctonia spp. ont été isolés de semis de Pin sylvestre (Pinus sylvestris) présentant des symptômes de fonte, dans deux pépinières forestières du Centre-Ouest de la Pologne (Wronczyn and Jarocin) et de semis malades élevés dans du sol provenant de la pépinière de Wronczyn. La majorité de ces isolats (79%) ont des cellules multi-nucléées et ont été identifiés comme des Rhizoctonia solani. Le reste des isolats ont été reconnus comme des Rhizoctonia spp. binucléés. Les isolats de R. solani ont été caractérisés en utilisant l'anastomose d'hyphes et répartis dans cinq groupes d'anastomoses (AG). Le plus important est le groupe AG5 (37% des isolats), suivi par AG2-1 (30%) et AG4 (27%). Les groupes AG1-IB et AG2-2 sont représentés chacun par seulement un isolat. La virulence, estimée par le pourcentage de mortalité, est relativement forte pour les isolats binucléés et multinucléés de Rhizoctonia spp. L'analyse des séquences de la région ITS de l'ADNr amplifiées par PCR a été utilisée pour l'analyse phylogénétique. Le dendrogramme montre que les isolats sont séparés selon leur groupe d'anastomose mais il n'y a pas de relation entre le groupe d'anastomose et la virulence sur semis de Pin sylvestre. Les résultats sont discutés dans la perspective du pouvoir pathogène des différents groupes d'anastomoses. Zusammenfassung Von Kiefernsämlingen (Pinus sylvestris) mit Umfallkrankheit, die aus zwei Forstbaumschulen in Zentral-Westpolen stammten (Wronczyn und Jarocin) und aus erkrankten Sämlingen, die in Bodenproben aus der Baumschule Wronczyn kultiviert worden waren, wurden 38 Stämme von Rhizoctonia spp. isoliert. Die meisten dieser Isolate (79%) hatten vielkernige Zellen und wurden als R. solani identifiziert. Die restlichen Isolate waren zweikernige Rhizoctonia spp. Die Isolate von R. solani wurden durch Anastomosierungstests charakterisiert und fünf Anastomosierungsgruppen zugeordnet. Die häufigste Gruppe war AG5 (37% der Isolate), gefolgt von AG2-1 (30%) und AG4 (27%). Die Gruppe AG1-IB und AG2-2 waren nur durch einzelne Isolate vertreten. Die Virulenz (gemessen als % Mortalität) war sowohl für zweikernige als auch für vielkernige Isolate vergleichsweise hoch. Mit den Sequenzen der PCR-amplifizierten ITS-rDNA-Region wurde eine phylogenetische Analyse durchgeführt. Das Dendrogramm zeigte, dass die Isolate aufgrund ihrer Zugehörigkeit zu den Anastomosierungsgruppen deutlich voneinander getrennt waren, und es bestand keine Beziehung zwischen ihrer Virulenz gegenüber Kiefernsämlingen und der Gruppenzugehörigkeit. Die Befunde werden im Hinblick auf das pathogene Potential der verschiedenen Anastomosierungsgruppen diskutiert. [source]

Genetic differentiation of Mediterranean horse mackerel (Trachurus mediterraneus) populations as revealed by mtDNA PCR-RFLP analysis

JOURNAL OF APPLIED ICHTHYOLOGY, Issue 2 2009
By C. Turan
Summary The genetic population structure of Mediterranean horse mackerel, Trachurus mediterraneus, from seven locations throughout the Black, Marmara, Aegean and eastern Mediterranean seas was investigated using restriction fragment length polymorphism (RFLP) analysis of the mtDNA 16S rDNA region. An approximately 2000-bp segment was screened in 280 individuals using six restriction enzymes, resulting in 10 composite haplotypes. The most common haplotype was present in 56.42% individuals; the next most frequent haplotype was present in 22.85% individuals. Average haplotype diversity within samples was moderate (0.38), and nucleotide diversity was low (0.00435). Mean nucleotide divergence for the seven sampling sites was 0.0028. Nucleotide divergence among samples was moderate, with the highest value detected between the Aegean Sea (Izmir) and the eastern Black Sea (Trabzon) populations (0.007055), and the lowest (,0.000043) between the Marmara Sea (Adalar) and the western Black Sea (Sile) populations. In Monte Carlo pairwise comparisons of haplotype frequencies, the Sinop from the middle Black Sea, Trabzon from the eastern Black Sea, and Iskenderun Bay from the north-eastern Mediterranean Sea exhibited highly significant (P < 0.001) geographical differentiation from each other and from all other populations. Mantel's test indicated that the nucleotide divergence among populations of T. mediterraneus was not significantly associated with their geographical isolation (r = ,0.2963; P > 0.05). Consequently, the mtDNA 16S rDNA region provided evidence for the existence of three distinct T. mediterraneus populations (Sinop, Trabzon and Iskenderun Bay) in the Black and north-eastern Mediterranean seas. [source]

Verrucophora farcimen gen. et sp. nov. (Dictyochophyceae, Heterokonta),a bloom-forming ichthyotoxic flagellate from the Skagerrak, Norway,

JOURNAL OF PHYCOLOGY, Issue 5 2007
Bente Edvardsen
Since 1998, a heterokont flagellate initially named Chattonella aff. verruculosa has formed recurrent extensive blooms in the North Sea and the Skagerrak, causing fish mortalities. Cells were isolated from the 2001 bloom off the south coast of Norway, and monoalgal cultures were established and compared with the Chattonella verruculosa Y. Hara et Chihara reference strain NIES 670 from Japan. The cells in Norwegian cultured isolates were very variable in size and form, being large oblong (up to 34 ,m long) to small rounded (5,9 ,m in diameter) with two unequal flagella, numerous chloroplasts, and mucocysts. The SSU and partial LSU rDNA sequences of strains from Norway and Japan were compared and differed by 0.4% (SSU) and 1.3% (LSU), respectively. Five strains from Norway were identical in the LSU rDNA region. Phylogenetic analyses based on heterokont SSU and concatenated SSU + LSU rDNA sequences placed C. aff. verruculosa and the Japanese C. verruculosa within the clade of Dictyochophyceae, with the picoflagellate Florenciella parvula Eikrem as the closest relative. Ultrastructure, morphology, and pigment composition supported this affinity. We propose the name Verrucophora farcimen sp. et gen. nov. for this flagellate and systematically place it within the class Dictyochophyceae. Our studies also show that C. verruculosa from Japan is genetically and morphologically different but closely related to V. farcimen. The species is transferred from the class Raphidophyceae to the class Dictyochophyceae and renamed Verrucophora verruculosa. We propose a new order, Florenciellales, to accommodate V. farcimen, V. verruculosa, and F. parvula. [source]

Identification and Pathogenicity of Rhizoctonia spp.

JOURNAL OF PHYTOPATHOLOGY, Issue 2 2006
Causing Wirestem of Betula nigra in China
Abstract During July 2004, wirestem was frequently observed on the seedlings of Betula nigra at Dehong district in Yunnan Province, China. Isolates of Rhizoctonia spp. consistently obtained from their diseased leaves, roots and stems were identified as belonging to binucleate Rhizoctonia anastomosis groups (AG) AG-P and AG-R, and R. solani AG-I IB and AG-4 HG-I, based on cultural characteristics, nuclear staining, anastomisis reaction and analysis of their ITS rDNA region. The percentage of recovery of AG-P, AG-1, AG-R and AG-4 was 48%, 39%, 8% and 3%, respectively. This is the first report of wirestem of red birch cause by binucleate Rhizoctonia AG-P and AG-R, and R. solani AG-1 IB and AG-4 HG-I in China. [source]

Evolutionary Relationships of the Dutch Elm Disease Fungus Ophiostoma novo-ulmi to Other Ophiostoma Species Investigated by Restriction Fragment Length Polymorphism Analysis of the rDNA Region

Development of species-specific primers for the ectoparasitic nematode species Xiphinema brevicolle, X. diffusum, X. elongatum, X. ifacolum and X. longicaudatum (Nematoda: Longidoridae) based on ribosomal DNA sequences

ANNALS OF APPLIED BIOLOGY, Issue 3 2005
CLAUDIO M G OLIVEIRA
Summary The objective of this study was to develop single-step PCR species-specific primers that reliably discriminate four economically important Xiphinema species (X. brevicolle, X. elongatum, X. ifacolum and X. longicaudatum) and X. diffusum that is taxonomically very similar to X. brevicolle. Each species-specific reverse primer was located in the ITS-1 rDNA region and was used in combination with a universal forward primer located in the 18S rDNA gene. Primer reliability was confirmed by screening seven and 11 populations, respectively of X. diffusum and X. elongatum. Potential species-specific primers were also identified for X. brevicolle, X. longicaudatum and X. ifacolum, however too few populations of these species were available to thoroughly assess their reliability. For all species-specific primers, specificity was demonstrated by the absence of cross-reactions with 14 non-target Xiphinema species. Multiplex PCR was effective and reproducible for two (X. longicaudatum and X. ifacolum) or three (X. brevicolle, X. diffusum and X. elongatum) of the target nematode species, thus improving the applicability of the diagnostic primers. [source]