scholarly journals Detection and identification of a novel 16SrXIII subgroup phytoplasma associated with strawberry red leaf disease in Argentina

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2741-2747 ◽  
Author(s):  
Franco D. Fernández ◽  
Natalia G. Meneguzzi ◽  
Fabiana A. Guzmán ◽  
Daniel S. Kirschbaum ◽  
Vilma C. Conci ◽  
...  
Keyword(s):  
Rflp Analysis ◽  
Rrna Gene ◽  
The Novel ◽  
Universal Primer ◽  
Mature Leaves ◽  
Leaf Disease ◽  
Detection And Identification ◽  
Rflp Profile ◽  
Young Leaves ◽  
Leaf Symptoms

Strawberry red leaf phytoplasma was found in strawberry plants from production fields in Lules (Tucumán province) and Bella Vista (Corrientes province), Argentina. Characteristic strawberry red leaf symptoms were stunting, young leaves with yellowing at the edges, mature leaves which curled and were reddish at the abaxial face, flower and fruit deformation and death. The pathogen was detected with phytoplasma-universal primer pairs P1/P7 followed by R16F2n/R16R2 as nested primers in 13 diseased plants. Based on RFLP and sequence analysis of the amplified 16S rRNA gene, the phytoplasma was related to the 16SrXIII group (Mexican periwinkle virescence). In silico the RFLP profile of all the samples analysed revealed the presence of a unique pattern, showing that the novel phytoplasma is different from all the phytoplasmas currently composing the 16SrXIII group. The phylogenetic analysis was consistent with RFLP analysis as the strawberry red leaf phytoplasma was grouped within the 16SrXIII group, but formed a particular cluster. On this basis, the Strawberry red leaf phytoplasma associated with strawberry red leaf disease was assigned to a new subgroup, 16SrXIII-F.

scholarly journals Terminal Restriction Fragment Length Polymorphism for Identification of Cryptosporidium Species in Human Feces

2008 ◽  
Vol 75 (1) ◽  
pp. 108-112 ◽  
Author(s):  
L. S. Waldron ◽  
B. C. Ferrari ◽  
M. R. Gillings ◽  
M. L. Power
Keyword(s):  
Species Identification ◽  
Restriction Fragment ◽  
Rflp Analysis ◽  
Cost Effective ◽  
18S Rrna Gene ◽  
Individual Species ◽  
Rrna Gene ◽  
Species Identity ◽  
Cryptosporidium Hominis ◽  
Detection And Identification

ABSTRACT Effective management of human cryptosporidiosis requires efficient methods for detection and identification of the species of Cryptosporidium isolates. Identification of isolates to the species level is not routine for diagnostic assessment of cryptosporidiosis, which leads to uncertainty about the epidemiology of the Cryptosporidium species that cause human disease. We developed a rapid and reliable method for species identification of Cryptosporidium oocysts from human fecal samples using terminal restriction fragment polymorphism (T-RFLP) analysis of the 18S rRNA gene. This method generated diagnostic fragments unique to the species of interest. A panel of previously identified isolates of species was blind tested to validate the method, which determined the correct species identity in every case. The T-RFLP profiles obtained for samples spiked with known amounts of Cryptosporidium hominis and Cryptosporidium parvum oocysts generated the two expected diagnostic peaks. The detection limit for an individual species was 1% of the total DNA. This is the first application of T-RFLP to protozoa, and the method which we developed is a rapid, repeatable, and cost-effective method for species identification.

scholarly journals Characterization of Phytoplasmas Related to Aster Yellows Group Infecting Annual Plants in Iran, Based on the Studies of 16S rRNA and RP Genes

2014 ◽  
Vol 54 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Fereshteh Vali Sichani ◽  
Masoud Bahar ◽  
Leila Zirak
Keyword(s):  
16S Rrna ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Rrna Gene ◽  
Annual Plants ◽  
Universal Primer ◽  
Aster Yellows ◽  
Central Regions ◽  
Group Specific Primer

Abstract Several annual field crops, vegetables, ornamentals, oilseed crops, and weeds showing phytoplasma diseases symptoms were collected to detect phytoplasmas related to ‘Candidatus Phytoplasma asteris’. The collecting was done in the central regions of Iran. For general detection of phytoplasmas, 16S rRNA gene fragments were amplified using phytoplasma universal primer pair P1/P7 in polymerase chain reaction (PCR) followed by primer pair R16F2n/R16R2 in nested PCR. Then, for finer detection of phytoplasmas related to ‘Ca. P. asteris’, DNA samples were used to extend the rp and tuf gene fragments by PCR using aster yellows group specific primer pairs rp(I)F1A/rp(I)R1A and fTufAy/rTufAy, respectively. Restriction fragment lenght polymorphism (RFLP) analysis of rp gene fragments using digestion with AluI, MseI, and Tsp509I restriction enzymes indicated that aster yellows group related phytoplasmas in these Iranian regions, belong to rpI-B subgroups. Sequence analysis of partial 16S rRNA and rp genes from representative phytoplasma isolates confirmed the RFLP results. This research is the first report of annual plants infected with phytoplasmas related to subgroup rpI-B in Iran.

scholarly journals Detection and identification of phytoplasmas in peach based on woody indexing and molecular methods

2001 ◽  
Vol 7 (1) ◽  
Author(s):  
M. Németh ◽  
I. Ember ◽  
L. Krizbai ◽  
M. Kölber ◽  
R. Hangyál ◽  
...  
Keyword(s):  
Nested Pcr ◽  
Rflp Analysis ◽  
Specific Primers ◽  
Universal Primer ◽  
Detection And Identification ◽  
Molecular Studies ◽  
Pcr Products ◽  
Phytoplasma Infection ◽  
Peach Trees ◽  
Different Parts

Symptoms resembling phytoplasma disease have been observed on peach trees in a seed-source plantation of stone fruits in south Hungary quite recently. In this publication we report on the results of woody indexing of symptomatic peach trees on GF 305 indicator in the field and under greenhouse conditions as well as on molecular studies. Phytoplasma infection detected on GF 305 indicators in greenhouse and field indexing was confirmed by PCR. Nested PCR was conducted using universal primer pairs followed by group and subgroup specific primers for the second amplification. RFLP analysis of nested PCR products was performed using Rsal restriction enzyme. Based on the results of molecular studies it can be concluded that phytoplasmas, belonging to the European stone fruit yellows subgroup (16SrX-B) were identified in peach trees. Further studies on symptomatic peach trees originating from different parts of Hungary are in progress.

scholarly journals First Report of Phytoplasma Infection in Freesia Plant

Plant Disease ◽  
2001 ◽  
Vol 85 (3) ◽  
pp. 336-336 ◽  
Author(s):  
M. Kamińska ◽  
H. Sliwa ◽  
L. Startek
Keyword(s):  
Rflp Analysis ◽  
Dna Amplification ◽  
Unknown Etiology ◽  
Aster Yellows ◽  
Freesia Hybrida ◽  
Group I ◽  
Young Leaves ◽  
Phytoplasma Infection ◽  
Aster Yellows Phytoplasma ◽  
Leaf Symptoms

Disease symptoms including leaf chlorotic and necrotic spots and stripes resembling freesia leaf necrosis (disease of unknown etiology [2]) were observed in freesia (Freesia × hybrida Klatt.) plants (cvs. Aladyn, Blue Lady, Cortine, Gompy, and White Rapid) naturally infected with Freesia mosaic virus (FMV) and grown in the greenhouse in Poland. The aim of this work was to study the association of the leaf symptoms occurring in freesia cultivars with phytoplasma infection and to identify it. To detect the possible presence of phytoplasmas in freesias, plants showing leaf symptoms (five cultivars) and symptomless plants (‘Blue Lady’, ‘Cortine’, and ‘Gompy’) were assayed for the presence of phytoplasma 16S rDNA fragment by polymerase chain reaction (PCR). For phytoplasma detection samples of young leaves and corms of 15 symptomatic and five symptomless freesias were taken. The samples were collected from the selected plants infected with FMV. In addition, leaf samples from healthy Catharanthus roseus plants and those infected with AKV reference strain of aster yellows (AY) phytoplasma group, subgroup I-B (supplied by W. Jarausch, INRA Bordeaux, France), were included for comparison. The amplification was performed using the universal—rA/fA or R16F1/R0 and group specific—R16(I)F1/R1 phytoplasma primer pairs (1). Phytoplasma identification was accompanied by digestion with AluI and MseI restriction endonucleases and restriction length polymorphism (RFLP) analysis of the R(I)F1/R1 or rA/fA products. DNA amplification product was observed in all nested PCRs containing template DNA derived from the leaves and corms of all symptomatic as well as symptomless and FMV-affected freesias except symptomless freesia ‘Cortine’. Based on RFLP analysis of PCR products and the comparison of the RFLP patterns with those of the strain AKV of aster yellows phytoplasma group (AY I-B), the associated phytoplasmas were identified as phytoplasma 16S rRNA group I, subgroup B. This work provides the first evidence that freesias examined were naturally infected with aster yellows phytoplasma. Detection of phytoplasma in diseased and symptomless but FMV-affected freesias underlines the need to know the role of this pathogen in the etiology of freesia diseases. References: (1) I.-M. Lee et al. Phytopathology 84:559, 1994. (2) H. J. M van Dorst. Neth. J. Plant Pathol. 79:130, 1973.

scholarly journals First Report of a 16SrIX Group (‘Candidatus Phytoplasma phoenicium’-Related) Phytoplasma Associated with a Chrysanthemum Disease

Plant Disease ◽  
2013 ◽  
Vol 97 (8) ◽  
pp. 1110-1110 ◽  
Author(s):  
H. Bayat ◽  
J. Th. J. Verhoeven ◽  
M. Botermans ◽  
D. Peters ◽  
A. Hassani-Mehraban
Keyword(s):  
Nested Pcr ◽  
Ornamental Plants ◽  
Rflp Analysis ◽  
Chrysanthemum Morifolium ◽  
Rrna Gene ◽  
Universal Primer ◽  
First Report ◽  
Production Region ◽  
Lactuca Serriola ◽  
Plant Pathol

In November 2010, approximately 2% of the chrysanthemum (Chrysanthemum morifolium) cv. Paniz plants showed numerous small leaves in the top and stunting in a field collection of the National Research Center of Ornamental Plants in Mahallat, Iran. Next to these plants, some plants of the same collection showed leaves with a reddish and/or chlorotic discoloration around the veins. The observed symptoms were believed to represent infection by a phytoplasma and/or a viroid. Two plants with each type of the symptoms were individually analyzed. Using a total RNA extract from diseased leaves, RT-PCR with primer pairs targeting all known pospiviroids, including Chrysanthemum stunt viroid (CSVd) (3), were negative. Purified DNA was examined for the highly conserved phytoplasma 16S rRNA gene by nested-PCR using the universal primer sets P1/P7 and R16F2n/R16R2 (2). Fragments of 1.2 kb, obtained only from the plants with the small leaves and stunting, were sequenced and one of these sequences, which were identical, was deposited in GenBank (Accession No. KC176800). BLAST analysis of the chrysanthemum phytoplasma sequence exhibited 99% identity to Candidatus Phytoplasma phoenicium (Ca. P. phoenicium) species of the 16SrIX group. Subsequently, in silico RFLP analysis of the nested PCR product with the pDRAW32 program using AluI and TaqI restriction sites used for 16SrIX subgroups A, B, C, D, and E indicated that the 16SrIX chrysanthemum isolate belonged to subgroup D (1). Recently, based on GenBank sequences, several strains of Ca. P. phoenicium have been isolated and identified from diverse host species like Lactuca serriola, L. sativa, Solanum lycopersicon, Sonchus sp. [16SrIX-E], Carthamus tinctorius, and Prunus amygdalus [16SrIX-B] (4) in Iran. The vector species transmitting Ca. P. phoenicium to C. morifolium still needs to be identified. The leafhopper Neoaliturus fenestratus may be a potential vector as it is an often encountered efficient transmitter vector of 16SrIX group phytoplasmas in Iran (2). Next to the susceptibility of chrysanthemum to members of aster yellows, stolbur, and Ca. P. aurantifolia phytoplasma groups, this is, to our knowledge, the first report of a 16SrIX group member infecting chrysanthemum. The detection of this phytoplasma in chrysanthemum can form a new threat to this crop and other ornamentals in the Mahallat flower production region. References: (1) R. E. Davis et al. New Dis. Rep. 20:35, 2010. (2) M. Salehi et al. Plant Pathol. 56:669, 2007. (3) J. Th. J. Verhoeven et al. Eur. J. Plant Pathol. 110:823, 2004. (4) M. G. Zamharir. Afr. J. Microbiol. Res. 5:6013, 2011.

scholarly journals Genetic Heterogeneities and Phenotypic Characteristics of Strains of the Genus Abiotrophia and Proposal ofAbiotrophia para-adiacens sp. nov.

2000 ◽  
Vol 38 (2) ◽  
pp. 492-498 ◽  
Author(s):  
Taisei Kanamoto ◽  
Setsuko Sato ◽  
Masakazu Inoue
Keyword(s):  
Dna Sequences ◽  
Rrna Gene ◽  
The Novel ◽  
Genotype 3 ◽  
Pcr Assay ◽  
Genotype 4 ◽  
Arginine Dihydrolase ◽  
Detection And Identification ◽  
Genotype 2 ◽  
Pyridoxal Hydrochloride

The genus Abiotrophia represents a heterogeneous group of fastidious cocci that show a dependence on pyridoxal hydrochloride analogs for growth. The genetic heterogeneity in the genus Abiotrophia was examined by DNA-DNA hybridization, PCR assay of genomic DNA sequences, and restriction fragment length polymorphism and sequence homology analyses of the PCR-amplified 16S rRNA gene. Nine type or reference strains of Abiotrophia defectiva, Abiotrophia adiacens, andAbiotrophia elegans and 36 oral Abiotrophiaisolates including the ones presumptively identified as Gemella morbillorum by the rapid ID32 STREP system were divided into four groups: A. defectiva (genotype 1), A. adiacens(genotype 2), A. elegans (genotype 4), and a fourth species (genotype 3) which we propose be named Abiotrophia para-adiacens sp. nov. A PCR assay specific for detection and identification of the novel Abiotrophia species was developed. A. para-adiacens generally produced β-glucosidase but did not produce α- or β-galactosidase or arginine dihydrolase, did not ferment, trehalose, pullulan, or tagatose, and was serotype IV, V, or VI. Thus, it was distinguished phenotypically from A. adiacens, A. elegans, and A. defectiva as well as, apparently, from the recently described species Abiotrophia balaenopterae sp. nov., which produces arginine dihydrolase and which ferments pullulan but not sucrose (P. A. Lawson et al., Int. J. Syst. Bacteriol. 49:503–506, 1999). Strain ATCC 27527, currently listed as G. morbillorum, was a member of the species A. para-adiacens.

scholarly journals First Report of Aster Yellows-Related Subgroup I-A Phytoplasma Strains in Carrot, Phlox, Sea-Lavender, Aconitum, and Hyacinth in Lithuania

Plant Disease ◽  
2001 ◽  
Vol 85 (7) ◽  
pp. 804-804 ◽  
Author(s):  
D. Valiunas ◽  
A. Alminaite ◽  
J. Staniulis ◽  
R. Jomantiene ◽  
R. E. Davis
Keyword(s):  
16S Rdna ◽  
Nested Pcr ◽  
Sequence Similarity ◽  
Rflp Analysis ◽  
Plant Host ◽  
Aster Yellows ◽  
Mature Leaves ◽  
Young Leaves ◽  
Sea Lavender ◽  
The Baltic

Phytoplasma strains that belong to group 16SrI (aster yellows phytoplasma group), subgroup A (I-A, North American tomato big bud phytoplasma subgroup) were discovered in diverse plant species in Lithuania. Plants in which the strains were found exhibited symptoms characteristic of infections by phytoplasma. Carrot (Daucus sativus) with carrot proliferation disease exhibited symptoms of proliferation of the crown, chlorosis of young leaves, and reddening of mature leaves. Diseased phlox (Phlox paniculata) exhibited symptoms of virescence and leaf chlorosis. Diseased sea-lavender (Limonium sinuatum) exhibited abnormal proliferation of shoots, chlorosis of young leaves, reddening of mature leaves, and degeneration of flowers. Diseased hyacinth (Hyacinthus orientalis) exhibited chlorosis of leaves and undeveloped flowers. Diseased Aconitum sp. exhibited proliferation of shoots. Phytoplasma-characteristic ribosomal (r) DNA was detected in the plants by use of the polymerase chain reaction (PCR). The rDNA was amplified in PCR primed by primer pair P1/P7 and reamplified in nested PCR primed by primer pair R16F2n/R16R2 (F2n/R2), as previously described (1). The phytoplasmas were classified through restriction fragment length polymorphism (RFLP) analysis of 16S rDNA, amplified in the nested PCR primed by F2n/R2, using single endonuclease enzyme digestion with AluI, MseI, KpnI, HhaI, HaeIII, HpaI, HpaII, RsaI, HinfI, TaqI, and Sau3AI. Collective RFLP patterns indicated that all detected phytoplasma strains were affiliated with subgroup I-A. The 16S rDNA amplified from the phytoplasma (CarrP phytoplasma) in diseased carrot was cloned in Escherichia coli, sequenced, and the sequence deposited in the GenBank data library (GenBank accession no. AF291682). The 16S rDNAs of CarrP and tomato big bud (GenBank acc. no. AF222064) phytoplasmas shared 99.8% nucleotide sequence similarity. Phytoplasmas belonging to group 16SrIII (3), group 16SrV (D. Valiunas, unpublished data), and subgroup I-C in group 16SrI (2,3) occur in Lithuania. This report records the first finding of a subgroup I-A phytoplasma in the Baltic region and expands the known plant host range of this phytoplasma subgroup. References: (1) R. Jomantiene et al. Int. J. Syst. Bacteriol. 48:269, 1998. (2) Jomantiene et al. Phytopathology 90:S39, 2000. (3) Staniulis et al. Plant Dis. 84:1061, 2000.

Karakter Morfologi Daun Ubi Jalar Sebagai Bahan Pangan Suku Dani Distrik Kurulu Jayawijaya

Agrotek ◽  
2018 ◽  
Vol 2 (3) ◽  
Author(s):  
Antonius Suparno ◽  
Opalina Logo ◽  
Dwiana Wasgito Purnomo
Keyword(s):  
Sweet Potato ◽  
Leaf Morphology ◽  
Food Source ◽  
Staple Food ◽  
Sweet Potatoes ◽  
General Outline ◽  
Leaf Vein ◽  
Mature Leaves ◽  
Young Leaves ◽  
Tuber Roots

Sweet potato serves as a staple food for people in Jayawijaya. Many cultivars of sweet potatoes have been cultivated by Dani tribe in Kurulu as foot for their infant, child and adult as well as feeding especially for pigs. Base on the used of sweet potatoes as food source for infant and child, this study explored 10 different cultivars. As for the leaf morphology, it was indentified that the mature leaves have size around 15 � 18 cm. general outline of the leaf is reniform (40%), 60% have green colour leaf, 50% without leaf lobe, 60% of leaf lobes number is one, 70% of shape of central leaf lobe is toothed. Abazial leaf vein pigmentation have purple (40%), and petiole pigmentation is purple with green near leaf (60%), besides its tuber roots, sweet potatoes are also harvested for its shoots and green young leaves for vegetables.

scholarly journals Molecular Detection of Novel Borrelia Species, Candidatus Borrelia javanense, in Amblyomma javanense Ticks from Pangolins

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 728
Author(s):  
Bao-Gui Jiang ◽  
Ai-Qiong Wu ◽  
Jia-Fu Jiang ◽  
Ting-Ting Yuan ◽  
Qiang Xu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Detection ◽  
Southern China ◽  
Natural Circulation ◽  
Rrna Gene ◽  
The Novel ◽  
Flagellin Gene ◽  
Manis Javanica ◽  
The 16S Rrna Gene ◽  
Novel Agent

A novel Borrelia species, Candidatus Borrelia javanense, was found in ectoparasite ticks, Amblyomma javanense, from Manis javanica pangolins seized in anti-smuggling operations in southern China. Overall, 12 tick samples in 227 (overall prevalence 5.3%) were positive for Candidatus B. javanense, 9 (5.1%) in 176 males, and 3 (5.9%) in 51 females. The phylogenetic analysis, based on the 16S rRNA gene and the flagellin gene sequences of the Borrelia sp., exhibited strong evidence that Candidatus B. javanense did not belong to the Lyme disease Borrelia group and the relapsing fever Borrelia group but another lineage of Borrelia. The discovery of the novel Borrelia species suggests that A. javanense may be the transmit vector, and the M. javanica pangolins should be considered a possible origin reservoir in the natural circulation of these new pathogens. To our knowledge, this is the first identification of a novel Borrelia species agent in A. javanense from pangolins. Whether the novel agent is pathogenic to humans is unknown and needs further research.

scholarly journals The role of JrPPOs in the browning of walnut explants

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shugang Zhao ◽  
Hongxia Wang ◽  
Kai Liu ◽  
Linqing Li ◽  
Jinbing Yang ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Production Efficiency ◽  
Phenolic Content ◽  
Leaf Tissue ◽  
Limiting Factor ◽  
Mature Leaves ◽  
Survival Percentage ◽  
Highly Active ◽  
Young Leaves

Abstract Background Tissue culture is an effective method for the rapid breeding of seedlings and improving production efficiency, but explant browning is a key limiting factor of walnut tissue culture. Specifically, the polymerization of PPO-derived quinones that cause explant browning of walnut is not well understood. This study investigated explants of ‘Zanmei’ walnut shoot apices cultured in agar (A) or vermiculite (V) media, and the survival percentage, changes in phenolic content, POD and PPO activity, and JrPPO expression in explants were studied to determine the role of PPO in the browning of walnut explants. Results The results showed that the V media greatly reduced the death rate of explants, and 89.9 and 38.7% of the explants cultured in V media and A media survived, respectively. Compared with that of explants at 0 h, the PPO of explants cultured in A was highly active throughout the culture, but activity in those cultured in V remained low. The phenolic level of explants cultured in A increased significantly at 72 h but subsequently declined, and the content in the explants cultured in V increased to a high level only at 144 h. The POD in explants cultured in V showed high activity that did not cause browning. Gene expression assays showed that the expression of JrPPO1 was downregulated in explants cultured in both A and V. However, the expression of JrPPO2 was upregulated in explants cultured in A throughout the culture and upregulated in V at 144 h. JrPPO expression analyses in different tissues showed that JrPPO1 was highly expressed in stems, young leaves, mature leaves, catkins, pistils, and hulls, and JrPPO2 was highly expressed in mature leaves and pistils. Moreover, browning assays showed that both explants in A and leaf tissue exhibited high JrPPO2 activity. Conclusion The rapid increase in phenolic content caused the browning and death of explants. V media delayed the rapid accumulation of phenolic compounds in walnut explants in the short term, which significantly decreased explants mortality. The results suggest that JrPPO2 plays a key role in the oxidation of phenols in explants after branch injury.

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