Detection of phytoplasmas in dieback, yellow crinkle, and mosaic diseases of papaya using polymerase chain reaction techniques

1996 ◽  
Vol 47 (3) ◽  
pp. 387 ◽  
Author(s):  
B Liu ◽  
DT White ◽  
KB Walsh ◽  
PT Scott
Keyword(s):  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Tissue Samples ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Pcr Product ◽  
Polymerase Chain ◽  
23S Rrna Genes ◽  
The 16S Rrna Gene

Oligonucleotide primers complementary to regions specific to plant-pathogenic mycoplasma-like organisms (phytoplasmas) were used in polymerase chain reactions on tissue samples from dieback, yellow crinkle, and mosaic affected papaya plants. The primer pair P068/P069, which hybridise to internal regions of the 16s rRNA gene, amplified an approximately 560 bp product in dieback, yellow crinkle and mosaic affected papaya. The primer pair P3/P7, which hybridise to the spacer region between the 16s and 23s rRNA genes, amplified an approximately 300 bp fragment in yellow crinkle and mosaic affected papaya, with no product from dieback affected plants. No PCR product was obtained with either set of primers from healthy plants. An identical Alu I restriction enzyme profile was obtained with all three 560 bp products. This study provides the first evidence for the association of phytoplasmas with papaya mosaic and Australian papaya dieback.

scholarly journals Characterization of X-Disease Phytoplasmas in Chokecherry from North Dakota by PCR-RFLP and Sequence Analysis of the rRNA Gene Region

Plant Disease ◽  
2000 ◽  
Vol 84 (11) ◽  
pp. 1235-1240 ◽  
Author(s):  
Y. H. Guo ◽  
Z.-M. Cheng ◽  
J. A. Walla
Keyword(s):  
16S Rrna ◽  
North Dakota ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Pcr Rflp

Genetic variation of X-disease phytoplasma strains from chokecherry (ChX) in North Dakota and nearby sites, and their relatedness with three standard strains of the X-disease phytoplasma group, eastern X-disease (CX), western X-disease (WX), and goldenrod yellows (GR1) phyto-plasmas, were studied. Primer pairs were developed to amplify the 23S ribosomal RNA (rRNA) gene and the 16S/23S spacer region. The rRNA genes (16S rRNA, 23S rRNA, and two ribosomal protein [rp] genes) and the 16S/23S spacer region were amplified by polymerase chain reactions. The restriction fragment length polymorphism (RFLP) patterns of 16S rRNA, 23S rRNA, and rp genes, generated by digestion with four restriction enzymes (AluI, HpaII, MseI, and RsaI), showed no difference among 43 ChX phytoplasma isolates. Sequencing of the 441-bp 16S/23S spacer region revealed variation at four positions among 12 ChX phytoplasma strains. A tRNAIle and other conserved sequences were identified in the spacer region. Among X-disease subgroups, RFLP analysis indicated that ChX is similar to WX, closely related to CX, and easily distinguished from GR1. Sequencing indicated that ChX is closer to CX than to WX. Together, the analyses indicated that ChX phytoplasmas are genetically different from the standard strains of other X-disease phytoplasma subgroups.

Genomic fingerprinting ofFrankiamicrosymbionts fromCeanothuscopopulations using repetitive sequences and polymerase chain reactions

1999 ◽  
Vol 77 (9) ◽  
pp. 1220-1230 ◽  
Author(s):  
Soon-Chun Jeong ◽  
David D Myrold
Keyword(s):  
Dna Sequencing ◽  
Dna Analysis ◽  
Repetitive Sequences ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
23S Rrna ◽  
Genomic Fingerprinting ◽  
Chain Reactions ◽  
Intergenic Spacer Region ◽  
Polymerase Chain

Specificity between Ceanothus species and their microsymbionts, Frankia, were investigated with nodules collected from three geographically separated copopulations of Ceanothus species. Nodules were analyzed using DNA sequencing and repetitive sequence polymerase chain reaction (rep-PCR) techniques. DNA sequencing of the intergenic spacer region between 16S and 23S rRNA genes suggested that Ceanothus-microsymbiotic Frankia are closely related at the intraspecific level. Diversity of the microsymbionts was further analyzed by genomic fingerprinting using repetitive sequences and PCR. A newly designed direct repeat (DR) sequence and a BOX sequence were used as PCR primers after justification that these primers can generate Frankia-specific fingerprints from nodule DNA. Analysis of the nodules using BOX- and DR-PCR showed that Ceanothus-microsymbiotic Frankia exhibited less diversity within each copopulation than among copopulations. These data suggested that geographic separation plays a more important role for divergence of Ceanothus-microsymbiotic Frankia than host plant.Key words: Frankia, Ceanothus, rep-PCR, diversity.

scholarly journals Spontaneous Erythromycin Resistance Mutation in a 23S rRNA Gene, rrlA, of the Extreme Thermophile Thermus thermophilus IB-21

2001 ◽  
Vol 183 (14) ◽  
pp. 4382-4385 ◽  
Author(s):  
Steven T. Gregory ◽  
Jamie H. D. Cate ◽  
Albert E. Dahlberg
Keyword(s):  
Genetic Manipulation ◽  
Thermus Thermophilus ◽  
Resistance Mutation ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Erythromycin Resistance ◽  
23S Rrna Gene ◽  
Resistant Mutants ◽  
23S Rrna Genes

ABSTRACT Spontaneous, erythromycin-resistant mutants of Thermus thermophilus IB-21 were isolated and found to carry the mutation A2058G in one of two 23S rRNA operons. The heterozygosity of these mutants indicates that A2058G confers a dominant or codominant phenotype in this organism. This mutation provides a valuable tool for the genetic manipulation of the 23S rRNA genes ofThermus.

Detection of rye chromosome 2R using the polymerase chain reaction and sequence-specific DNA primers

Genome ◽  
1994 ◽  
Vol 37 (1) ◽  
pp. 19-22 ◽  
Author(s):  
J.-H. Lee ◽  
R. A. Graybosch ◽  
D. J. Lee
Keyword(s):  
Polymerase Chain Reaction ◽  
Wheat Chromosome ◽  
Specific Marker ◽  
Chain Reaction ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Pcr Product ◽  
Polymerase Chain ◽  
Wheat Lines ◽  
Dna Primers

Sequences derived from a rye gamma secalin gene were used as primers in polymerase chain reactions using DNA obtained from a series of wheat and triticale genetic stocks. A 473-bp fragment, the predicted size based on the distance between the selected primers, was found only in rye, triticales, and wheat lines carrying rye chromosome 2RS. Use of triticale lines with various wheat chromosome substitutions confirmed the chromosomal origin of the rye-specific marker. The presence of the 473-bp PCR product was always associated with the production of 75K secalins in grain samples. Thus, the primer sequences, and the clone of origin (pSC503), were both derived from the SEC-2 locus of rye chromosome 2RS.Key words: wheat (Triticum aestivum), rye (Secale cereale), chromosomal translocations, chromosomal substitutions, DNA polymerase chain reaction, sequence-specific primers.

scholarly journals Identification of Mycobacterium kansasiiby Using a DNA Probe (AccuProbe) and Molecular Techniques

1999 ◽  
Vol 37 (4) ◽  
pp. 964-970 ◽  
Author(s):  
Elvira Richter ◽  
Stefan Niemann ◽  
Sabine Rüsch-Gerdes ◽  
Sven Hoffner
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Pattern ◽  
Molecular Techniques ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Genetic Analyses ◽  
New Formulation ◽  
The 16S Rrna Gene

The newly formulated Mycobacterium kansasii AccuProbe was evaluated, and the results obtained with the new version were compared to the results obtained with the old version of this test by using 116 M. kansasii strains, 1 Mycobacterium gastri strain, and 19 strains of several mycobacterial species. The sensitivity of this new formulation was 97.4% and the specificity was 100%. Still, three M. kansasii strains were missed by this probe. To evaluate the variability within the species, genetic analyses of the hsp65 gene, the spacer sequence between the 16S and 23S rRNA genes, and the 16S rRNA gene of several M. kansasii AccuProbe-positive strains as well as all AccuProbe-negative strains were performed. Genetic analyses of the oneM. gastri strain from the comparative assay and of two further M. gastri strains were included because of the identity of the 16S rRNA gene in M. gastri to that inM. kansasii. The data confirmed the genetic heterogeneity of M. kansasii. Furthermore, a subspecies with an unpublished hsp65 restriction pattern and spacer sequence was described. The genetic data indicate that all M. kansasii strains missed by the AccuProbe test belong to one subspecies, the newly described subspecies VI, as determined by thehsp65 restriction pattern and the spacer sequence. Since the M. kansasii strains that are missed are rare and allM. gastri strains are correctly negative, the new formulated AccuProbe provides a useful tool for the identification ofM. kansasii.

scholarly journals Reassessment of the phylogenetic relationships of Thiomonas cuprina

2007 ◽  
Vol 57 (11) ◽  
pp. 2720-2724 ◽  
Author(s):  
Donovan P. Kelly ◽  
Yoshihito Uchino ◽  
Harald Huber ◽  
Ricardo Amils ◽  
Ann P. Wood
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Significant Similarity ◽  
23S Rrna Gene ◽  
The 16S Rrna Gene

The published sequence of the 16S rRNA gene of Thiomonas cuprina strain Hö5 (=DSM 5495T) (GenBank accession no. U67162) was found to be erroneous. The 16S rRNA genes from the type strain held by the DSMZ since 1990 (DSM 5495T =NBRC 102145T) and strain Hö5 maintained frozen in the Universität Regensburg for 23 years (=NBRC 102094) were sequenced and found to be identical, but to show no significant similarity to the U67162 sequence. This also casts some doubt on the previously published 5S and 23S rRNA gene sequences (GenBank accession nos U67171 and X75567). The correct 16S rRNA gene sequence showed 99.8 % identity to those from Thiomonas delicata NBRC 14566T and ‘Thiomonas arsenivorans’ DSM 16361. The properties of these three species are re-evaluated, and emended descriptions are provided for the genus Thiomonas and the species Thiomonas cuprina.

scholarly journals Rapid Detection and Estimation by Pyrosequencing of 23S rRNA Genes with a Single Nucleotide Polymorphism Conferring Linezolid Resistance in Enterococci

2003 ◽  
Vol 47 (11) ◽  
pp. 3620-3622 ◽  
Author(s):  
Alistair Sinclair ◽  
Catherine Arnold ◽  
Neil Woodford
Keyword(s):  
Fragment Length Polymorphism ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Linezolid Resistance ◽  
Gene Copies ◽  
23S Rrna Gene ◽  
23S Rrna Genes

ABSTRACT Pyrosequencing was used to detect rapidly and estimate the number of 23S rRNA genes with a G2576T mutation in 43 linezolid-resistant and -susceptible clinical isolates of enterococci. The method showed 100% concordance with PCR-restriction fragment length polymorphism for detecting isolates homozygous for either G2576 or T2576 or heterozygous for this mutation. A good correlation was found between linezolid MICs and the number of 23S rRNA gene copies carrying the mutation.

scholarly journals Towards a Genome-Based Taxonomy for Prokaryotes

2005 ◽  
Vol 187 (18) ◽  
pp. 6258-6264 ◽  
Author(s):  
Konstantinos T. Konstantinidis ◽  
James M. Tiedje
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Content ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
A Genome ◽  
The 16S Rrna Gene

ABSTRACT The ranks higher than the species in the prokaryotic taxonomy are primarily designated based on phylogenetic analysis of the 16S rRNA gene sequences, but no definite standards exist for the absolute relatedness (measured by 16S rRNA or other means) between the ranks. Accordingly, it remains unknown how comparable the ranks are between different organisms. To gain insights into this question, we studied the relationship between shared gene content and genetic relatedness for 175 fully sequenced strains, using as a robust measure of relatedness the average amino acid identity (AAI) of the shared genes. Our results reveal that adjacent ranks (e.g., phylum versus class) frequently show extensive overlap in terms of genetic and gene content relatedness of the grouped organisms, and hence, the current system is of limited predictive power in this respect. The overlap between nonadjacent ranks (e.g., phylum versus family) is generally limited and attributable to clear inconsistencies of the taxonomy. In addition to providing means for standardizing taxonomy, our AAI-based approach provides a means to evaluate the robustness of alternative genetic markers for phylogenetic purposes. For instance, the 23S rRNA gene was found to be as good a marker as the 16S rRNA gene, while several of the widely distributed protein-coding genes, such as the RNA polymerase and gyrase subunits, show a strong phylogenetic signal, albeit less strong than the rRNA genes (0.78 > R 2 > 0.69 for the protein-coding genes versus R 2 = 0.84 for the rRNA genes). The AAI approach outlined here could contribute significantly to a genome-based taxonomy for all microbial organisms.

scholarly journals Genetic Diversity and Phylogeny of Rhizobia That Nodulate Acacia spp. in Morocco Assessed by Analysis of rRNA Genes

1998 ◽  
Vol 64 (12) ◽  
pp. 4912-4917 ◽  
Author(s):  
Bouchaib Khbaya ◽  
Marc Neyra ◽  
Philippe Normand ◽  
Karim Zerhari ◽  
Abdelkarim Filali-Maltouf
Keyword(s):  
Genetic Diversity ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
The Third ◽  
The 16S Rrna Gene ◽  
Rdna Analysis ◽  
Restriction Fragment Length

ABSTRACT Forty rhizobia nodulating four Acacia species (A. gummifera, A. raddiana, A. cyanophylla, and A. horrida) were isolated from different sites in Morocco. These rhizobia were compared by analyzing both the 16S rRNA gene (rDNA) and the 16S-23S rRNA spacer by PCR with restriction fragment length polymorphism (RFLP) analysis. Analysis of the length of 16S-23S spacer showed a considerable diversity within these microsymbionts, but RFLP analysis of the amplified spacer revealed no additional heterogeneity. Three clusters were identified when 16S rDNA analysis was carried out. Two of these clusters include some isolates which nodulate, nonspecifically, the four Acacia species. These clusters, A and B, fit within the Sinorhizobiumlineage and are closely related to S. meliloti and S. fredii, respectively. The third cluster appeared to belong to theAgrobacterium-Rhizobium galegae phylum and is more closely related to the Agrobacterium tumefaciens species. These relations were confirmed by sequencing a representative strain from each cluster.

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