scholarly journals Detection and Characterization of a Lethal Yellowing (16SrIV) Group Phytoplasma in Canary Island Date Palms Affected by Lethal Decline in Texas

Plant Disease ◽  
2002 ◽  
Vol 86 (6) ◽  
pp. 676-681 ◽  
Author(s):  
N. A. Harrison ◽  
M. Womack ◽  
M. L. Carpio
Keyword(s):  
Canary Island ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Corpus Christi ◽  
Rdna Sequences ◽  
Leaf Yellowing ◽  
Pcr Products ◽  
Lethal Yellowing ◽  
Polymerase Chain

Polymerase chain reaction (PCR) assays were used to detect phytoplasmas in Canary Island date (Phoenix canariensis) palms displaying symptoms similar to lethal yellowing (LY) disease in Corpus Christi, TX. An rDNA product (1.8 kb) was amplified consistently from 10 of 11 palms by PCR employing phytoplasma universal rRNA primer pair P1/P7. Also, AluI endonu-clease digests and sequencing of P1/P7 products revealed that nontarget Bacillus megaterium-related rDNA sequences of similar size were co-amplified along with phytoplasma rDNA from 10 palms. A 1,402-bp product was obtained from all 11 symptomatic palms when initial P1/P7 products were reamplified by PCR employing nested LY phytoplasma group-specific 16S rRNA primer pair LY16Sf/LY16Sr. Restriction fragment length polymorphism (RFLP) analysis of nested PCR products revealed that palm-infecting phytoplasmas were uniform and most similar to strains composing the coconut lethal yellowing phytoplasma (16SrIV) group. Sequence analysis of 16S rDNA determined the Texas Phoenix palm decline (TPD) phytoplasma to be phylogenetically closest to the Carludovica palmata leaf yellowing (CPY) phytoplasma. rDNA profiles of strains TPD and CPY obtained with AluI were co-identical and distinct from other known 16SrIV group phytoplasmas. On this basis, both strains were classified as members of a new subgroup, 16SrIV-D.

scholarly journals Molecular characterisation of phytoplasmas infecting roses in Poland

2013 ◽  
Vol 55 (1) ◽  
pp. 325-334
Author(s):  
Hanna Śliwa ◽  
Tadeusz Malinowski ◽  
Maria Kamińska
Keyword(s):  
Reference Strain ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Nested Polymerase Chain Reaction ◽  
Aster Yellows ◽  
Leaf Chlorosis ◽  
Leaf Yellowing ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Aster Yellows Phytoplasma

Symptoms of shoot dieback and leaf yellowing followed by leaf chlorosis were observed in naturally infected roses 'Frisco' and 'Suela', cultivated in a commercial greenhouse in Poland. The presence of phytoplasma was demonstrated in affected plants by nested polymerase chain reaction (PCR) with R16Fl/RO and Pl/P7 primer pairs in the first round followed by a second one with R16F2n/R2, fA/rA, Pc399/P1694, R16(I)Fl/Rl and Pl/fArev primer pairs. Restriction fragment length polymorphism (RFLP) analysis of PCR products (primed with primers R16F2n/R2) was done using enzymes AluI, MseI, RsaI and HpaII. Restriction profiles obtained with these enzymes were identical to those of reference strain AY1 belonging to aster yellows phytoplasma group, subgroup I-B (16SrI-B). Nested PCR products from roses 'Frisco' and 'Suela' were sequenced. Analysis of sequences confirmed that the phytoplasma infecting those roses could be classified to aster yellows phytoplasma group, subgroup B.

scholarly journals Characterization of a Phytoplasma Associated with Cabbage Yellows in Iran

Plant Disease ◽  
2007 ◽  
Vol 91 (5) ◽  
pp. 625-630 ◽  
Author(s):  
M. Salehi ◽  
K. Izadpanah ◽  
M. Siampour
Keyword(s):  
Nested Pcr ◽  
Fragment Length Polymorphism ◽  
Phylogenetic Analyses ◽  
Fars Province ◽  
Beet Leafhopper ◽  
Circulifer Haematoceps ◽  
Pcr Products ◽  
Disease Agent ◽  
Polymerase Chain

In 2001, a disease tentatively named Iranian cabbage yellows (ICY) was observed in cabbage fields of Zarghan (Fars Province, Iran). The major symptoms of the disease were yellowing, little leaves, plant stunting, opening of the head, and proliferation of the buds at the base of the stem into a witches'-broom. Among leafhoppers collected in cabbage fields, only Circulifer haematoceps transmitted the ICY agent. The disease agent was transmitted by the leafhopper from cabbage to cabbage, cauliflower, rape, and periwinkle, causing phytoplasma-type symptoms in these plants. Polymerase chain reaction (PCR) using phytoplasma-specific primer pair P1/P7 and nested PCR using P1/P7 and R16F2n/R16R2 primer pairs amplified products of expected size (1.8 and 1.2 kb, respectively) from symptomatic cabbage plants. Both restriction fragment length polymorphism (RFLP) of nested PCR products (1.2 kb) and phylogenetic analyses of 16S–23S rDNA spacer region sequence indicated that the ICY phytoplasma had the closest relationship to subgroup A members of the clover proliferation group, including beet leafhopper-transmitted virescence agent, ‘Candidatus Phytoplasma trifolii’, Columbia Basin potato purple top phytoplasma, and vinca virescence phytoplasma. Cabbage is reported as a new natural host to the 16SrVI group of phytoplasmas.

scholarly journals Morphological and Molecular Characterization of Globodera Populations from Oregon and Idaho

2011 ◽  
Vol 101 (4) ◽  
pp. 480-491 ◽  
Author(s):  
A. M. Skantar ◽  
Z. A. Handoo ◽  
I. A. Zasada ◽  
R. E. Ingham ◽  
L. K. Carta ◽  
...  
Keyword(s):  
Fragment Length Polymorphism ◽  
Globodera Pallida ◽  
Second Stage ◽  
Rdna Sequences ◽  
Individual Bands ◽  
Stage Juvenile ◽  
Polymerase Chain ◽  
Stylet Length ◽  
Morphological And Molecular Characterization

An unusual population of cyst nematode was found in soils collected from a Powell Butte, OR field with a cropping history including potato, wheat, other crops, and significant weed presence. These nematodes could not be placed with certainty into any known species and exhibited some unique morphological features in some specimens. Compared with Globodera pallida, the cyst body length was slightly longer and the second-stage juvenile stylet length was slightly shorter. In some individuals, the J2 stylet knob height was greater and the tail annules were more prominent than in G. pallida, and the tail abruptly narrowed, with a slight constriction near the posterior third of the hyaline terminus. Compared with G. rostochiensis, the hyaline tail terminus had a larger number of refractive bodies, and cysts of this population had a smaller Granek's ratio and fewer cuticular ridges between the anus and vulva. In some individuals, the tail termini of second-stage juveniles were more bluntly pointed, and the stylet knobs were more anteriorly directed with greater height. Unlike G. tabacum, the cyst wall often lacked a network-like pattern and, in some individuals, the juvenile tail terminus distinctly narrowed after a constriction. Molecularly, the population was distinct from G. pallida, G. rostochiensis, and G. tabacum. Multiplex polymerase chain reaction of the internal transcribed spacer (ITS) rDNA region gave results similar to G. tabacum; however, ITS restriction fragment length polymorphism patterns were observed to have individual bands in common with G. rostochiensis and G. pallida. Phylogenetic analysis based on ITS1 and -2 rDNA sequences showed greatest similarity to populations from Argentina and Chile; together, they form a moderately supported clade, distinct from G. rostochiensis, G. tabacum, G. “mexicana,” European type G. pallida, and several G. pallida populations from South America.

scholarly journals ‘Candidatus Phytoplasma asteris’ Strains Associated with Oil Palm Lethal Wilt in Colombia

Plant Disease ◽  
2014 ◽  
Vol 98 (3) ◽  
pp. 311-318 ◽  
Author(s):  
Elizabeth Alvarez ◽  
Juan F. Mejía ◽  
Nicoletta Contaldo ◽  
Samanta Paltrinieri ◽  
Bojan Duduk ◽  
...  
Keyword(s):  
Oil Palm ◽  
Sequence Data ◽  
Severe Disease ◽  
Rflp Analysis ◽  
Nested Polymerase Chain Reaction ◽  
Aster Yellows ◽  
Rdna Sequences ◽  
Polymerase Chain ◽  
Reference Strains

The distribution of lethal wilt, a severe disease of oil palm, is spreading throughout South America. An incidence of about 30% was recorded in four commercial fields in Colombia. In this study, phytoplasmas were detected in symptomatic oil palm by using specific primers, based on 16S ribosomal DNA (rDNA) sequences, in nested polymerase chain reaction assays. The phytoplasmas were then identified as ‘Candidatus Phytoplasma asteris’, ribosomal subgroup 16SrI-B, through the use of restriction fragment length polymorphism (RFLP) analysis and sequencing. Cloning and sequencing of 16S rDNA from selected strains, together with phylogenetic analysis, confirmed the classification. Moreover, collective RFLP characterization of the groEL, amp, and rp genes, together with sequence data, distinguished the aster yellows strain detected in Colombian oil-palm samples from other aster yellows phytoplasmas used as reference strains; in particular, from an aster yellows strain infecting corn in the same country.

Molecular Characterization of Aflatoxin Biosynthesis Genes of Aspergillus flavus from Peanuts Production Area

2019 ◽  
Author(s):  
I. Lavkor
Keyword(s):  
Fragment Length Polymorphism ◽  
Intergenic Spacer ◽  
Aflatoxin Contamination ◽  
Aflatoxin Biosynthesis ◽  
Fungal Isolates ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Production Area ◽  
Polymerase Chain

In this study, molecular analysis of (100%) all fungal isolates, which were sampled from soil and air besides from infected peanut plants in the peanut planting area, were identified in â-tubulin gene by Polymerase Chain Reaction (PCR). PCR products of fungal isolates were restricted by BglII enzyme within Restriction Fragment Length Polymorphism (RFLP). The intergenic spacer (IGS) region for aflatoxin biosynthesis genes (aflJ-aflR) were determined in 254 (78.2%) A. flavus isolates using PCR-RFLP. Selected 100 isolates were detected as A. flavus by â-tubulin sequence gene fragments and comparisons of sequence showed 96–100% similarity. 254 out of 325 isolates contained aflatoxin biosynthesis genes (aflJ-aflR), whereas 213 out of 254 isolates produced aflatoxin. The results acquired in study remarked that A. flavus was the species responsible for aflatoxin contamination. Aflatoxin gene cluster in populations can be advantage for comprehension of the toxicological risk as well as the election of biocontrol isolates.

scholarly journals Characterization of Ascaris from Ecuador and Zanzibar

2014 ◽  
Vol 89 (4) ◽  
pp. 512-515 ◽  
Author(s):  
A.M. Sparks ◽  
M. Betson ◽  
G. Oviedo ◽  
C. Sandoval ◽  
P.J. Cooper ◽  
...  
Keyword(s):  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Its Region ◽  
Restriction Enzymes ◽  
Zoonotic Transmission ◽  
Pcr Rflp ◽  
Double Digestion ◽  
Polymerase Chain ◽  
Shed Light

AbstractTo shed light on the epidemiology of ascariasis in Ecuador and Zanzibar, 177 adult worms retrieved by chemo-expulsion from either people or pigs were collected, measured and subjected to polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis of the ribosomal internal transcribed spacer (ITS) region. Upon double digestion with RsaI and HaeIII, PCR-RFLP analysis revealed the presence of A. lumbricoides in people and A. suum in pigs in Ecuador. In contrast, while there are no pigs on Zanzibar, of the 56 worms obtained from people, one was genotyped as A. suum. No additional genetic variation was detected upon further PCR-RFLP analysis with several other restriction enzymes. Upon measurement, worm mass and length differed by location and by species, A. suum being lighter and longer. While there is no evidence to suggest zoonotic transmission in Ecuador, an enduring historical signature of previous zoonotic transmission remains on Zanzibar.

scholarly journals Erigeron Witches'-Broom Phytoplasma in Brazil Represents New Subgroup VII-B in 16S rRNA Gene Group VII, the Ash Yellows Phytoplasma Group

Plant Disease ◽  
2002 ◽  
Vol 86 (10) ◽  
pp. 1142-1148 ◽  
Author(s):  
Thereza S. L. Barros ◽  
Robert E. Davis ◽  
Renato O. Resende ◽  
Ellen L. Dally
Keyword(s):  
16S Rdna ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Gene Group ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Polymerase Chain ◽  
Restriction Fragment Length

A previously undescribed phytoplasma, Erigeron witches'-broom phytoplasma, was detected in diseased plants of Erigeron sp. and Catharanthus roseus exhibiting symptoms of witches'-broom and chlorosis in the state of São Paulo, Brazil. On the basis of restriction fragment length polymorphism (RFLP) analysis of 16S rDNA amplified in the polymerase chain reaction (PCR), Erigeron witches'-broom phytoplasma was classified in group 16SrVII (ash yellows phytoplasma group), new subgroup VII-B. Phylogenetic analysis of 16S rDNA sequences indicated that this phytoplasma represents a new lineage that is distinct from that of described strains of ash yellows phytoplasma. Erigeron witches'-broom phytoplasma is the first member of the ash yellows phytoplasma group to be recorded in Brazil.

scholarly journals Molecular characterization of aflatoxigenic and non-aflatoxigenic aspergillus isolates

2007 ◽  
Author(s):  
◽  
Phakamile Truth Mngadi
Keyword(s):  
Biosynthetic Pathway ◽  
Fragment Length Polymorphism ◽  
Rapd Analysis ◽  
Rflp Analysis ◽  
Aflatoxin Production ◽  
Molecular Methods ◽  
Economic Losses ◽  
Genetic Studies ◽  
Polymerase Chain

For decades the genus Aspergillus (of fungi) has been classified based on morphological and growth criteria. Members of the Aspergillus section Flavi are economically valuable and methods of differentiating them are thus very important. Several molecular methods have been developed to distinguish these strains. Also, a number of biochemical and genetic studies have been used in order to provide a better means of classification (Lee et al., 2004). Aflatoxins, the most frequently studied mycotoxins, are produced by certain Aspergillus species/strains/isolates of fungi. The aflatoxin biosynthetic pathway studies have led to a number of discoveries. Several structural and regulatory genes (and their enzymes) involved in the biosynthesis of aflatoxins have been discovered and purified (Trail et al., 1995). Aflatoxin production and contamination of agricultural crops are major causes of economic losses in agriculture. Thus, better methods of characterization/differentiation are required for both aflatoxigenic and non-aflatoxigenic isolates. Molecular biology is one of the current tools used to differentiate between these isolates. Polymerase Chain Reaction (PCR)-based randomly amplified polymorphic DNA (RAPD) analysis has been used successfully in the analysis of DNA relatedness of species of fungi, bacteria, plants and animals. Dendograms which evaluate/assess the likeness between different isolates has also been used (Martinez et al., 2001). Restriction fragment length polymorphism (RFLP) analysis has been applied to a number of studies to detect differences between fungi and to establish relationships between them. Therefore, the scope of this study was to investigate RAPD analysis (with dendograms) and detection of RFLPs by hybridization as molecular methods that can distinctly differentiate or characterize the aflatoxigenic and non-aflatoxigenic Aspergillus isolates.

Localization of the Br Polymorphism on a 144 bp Exon of the GPIa Gene and Its Application in Platelet DNA Typing

1994 ◽  
Vol 71 (05) ◽  
pp. 651-654 ◽  
Author(s):  
Rainer Kalb ◽  
Sentot Santoso ◽  
Katja Unkelbach ◽  
Volker Kiefel ◽  
Christian Mueller-Eckhardt
Keyword(s):  
Genomic Organization ◽  
Fragment Length Polymorphism ◽  
Human Platelet ◽  
Dna Typing ◽  
Rflp Analysis ◽  
Serological Typing ◽  
Allele Specific ◽  
Polymerase Chain ◽  
Alloimmune Thrombocytopenia ◽  
Rflp Typing

SummaryAlloimmunization against the human platelet alloantigen system Br (HPA-5) is the second most common cause of neonatal alloimmune thrombocytopenia (NAIT) in Caucasian populations. We have recently shown that a single base polymorphism at position 1648 on platelet mRNA coding for GPIa results in an aminoacid substitution at position 505 on the mature GPIa which is associated with the two serological defined Br phenotypes.Since DNA-typing of platelet alloantigens offers possibilities for useful clinical applications, we designed genomic DNA-based restriction fragment length polymorphism (RFLP) typing for Br alloantigens. To establish this technique we analyzed the genomic organization of GPIa adjacent to the polymorphic base. Using the polymerase chain reaction (PCR) of blood cell DNA we have identified two introns (approximately 1.7 and 1.9 kb) flanking a 144 bp coding sequence of the GPIa gene encompassing the polymorphic base 1648. Based on the in- tron sequence, a PCR primer was constructed to amplify a 274 bp fragment which was used for allele-specific RFLP to determine the Br genotypes. The results of RFLP analysis using Mnll endonuclease obtained from 15 donors (2 Br37*, 2 Br^ and 11 Brb/b) correlate perfectly with serological typing by monoclonal antibody-specific immobilization of platelet antigens (MAIPA) assay.

scholarly journals Molecular Characterization and Classification of Phytoplasmas Associated with Canola Yellows and a New Phytoplasma Strain Associated with Dandelions

Plant Disease ◽  
2001 ◽  
Vol 85 (1) ◽  
pp. 76-79 ◽  
Author(s):  
Keri Wang ◽  
Chuji Hiruki
Keyword(s):  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Universal Primers ◽  
Dna Fragments ◽  
Chain Reaction ◽  
Aster Yellows ◽  
Distinct Subgroup ◽  
16S Ribosomal Dna ◽  
Polymerase Chain

DNA isolated from symptomatic canola (Brassica napus, Brassica rapa) and dandelion (Taraxacum officinale) was used to amplify 16S ribosomal DNA fragments by polymerase chain reaction using two pairs of universal primers P1/P6 and R16F2n/R2. Restriction fragment length polymorphism (RFLP) analysis of the amplified DNA fragments using endonucleases AluI, HhaI, HpaII, MseI, RsaI, and Sau 3AI revealed two distinct types of phytoplasmas in canola with similar symptoms. One had the same RFLP profiles as the phytoplasmas in subgroup 16SrI-A, whereas the other one had RFLP profiles similar to those of phytoplasmas in subgroup 16SrI-B. Phytoplasmas were detected in symptomatic dandelion plants that were collected from canola and alfalfa fields where severe alfalfa witches'-broom occurred. Comparative studies indicated that two different phytoplasmas were associated with the dandelion plants. One was identified as a member of subgroup 16SrI-A, whereas another one was classified as a member of a distinct subgroup in the aster yellows group on the basis of the unique RFLP patterns.

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