Статті в журналах з теми "Restriction Endonuclease KpnI"
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1
Vasu, Kommireddy, Easa Nagamalleswari, Mai Zahran, Petra Imhof, Shuang-yong Xu, Zhenyu Zhu, Siu-Hong Chan, and Valakunja Nagaraja. "Increasing cleavage specificity and activity of restriction endonuclease KpnI." Nucleic Acids Research 41, no. 21 (August 19, 2013): 9812–24. http://dx.doi.org/10.1093/nar/gkt734.
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2
Bigby, Dianne, and Andrew M. B. Kropinski. "Isolation and characterization of a Pseudomonas aeruginosa bacteriophage with a very limited host range." Canadian Journal of Microbiology 35, no. 6 (June 1, 1989): 630–35. http://dx.doi.org/10.1139/m89-101.
Повний текст джерелаАнотація:
A Pseudomonas aeruginosa bacteriophage, [Formula: see text], with extremely limited host range has been isolated. It belongs to the virus family Podoviridae, morphological type C1, and possesses a head diameter of 45 nm. The phage has a buoyant density in CsCl of 1.516 g/cm3, and its mass is 45 × 106 daltons. The phage particles are composed of double-stranded DNA (49.9 mol% G + C; 42.4 kilobase pairs) and 11 structural proteins (66% by weight). The major head protein, P5, has a Mr of 34 500. The DNA is not cut by SalI or XhoI restriction endonucleases, but is cut by PvuII (1 site), KpnI and BglII (2 sites), PvuI (4 sites), BamHI (7 sites), EcoRI (9 sites), and HindIII (12 sites). A restriction endonuclease map is presented.Key words: Pseudomonas, bacteriophage, DNA, restriction map, structural proteins, electron microscopy.
3
Prère, M. F., and O. Fayet. "Susceptibility of Neisseria gonorrhoeae DNA to cleavage by restriction endonuclease KpnI." Annales de l'Institut Pasteur / Microbiologie 136, no. 3 (May 1985): 329–38. http://dx.doi.org/10.1016/s0769-2609(85)80095-8.
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Chandrashekaran, S. "KpnI restriction endonuclease and methyltransferase exhibit contrasting mode of sequence recognition." Nucleic Acids Research 32, no. 10 (June 2, 2004): 3148–55. http://dx.doi.org/10.1093/nar/gkh638.
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5
Chandrashekaran, Siddamadappa, Matheshwaran Saravanan, Deshpande R. Radha, and Valakunja Nagaraja. "Ca2+-mediated Site-specific DNA Cleavage and Suppression of Promiscuous Activity of KpnI Restriction Endonuclease." Journal of Biological Chemistry 279, no. 48 (September 16, 2004): 49736–40. http://dx.doi.org/10.1074/jbc.m409483200.
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6
Nagy, Éva, Neeraja Idamakanti, and Susy Carman. "Restriction Endonuclease Analysis of Equine Herpesvirus-1 Isolates Recovered in Ontario, 1986–1992, from Aborted, Stillborn, and Neonatal Foals." Journal of Veterinary Diagnostic Investigation 9, no. 2 (April 1997): 143–48. http://dx.doi.org/10.1177/104063879700900206.
Повний текст джерелаАнотація:
Ninety-two equine herpesvirus type 1 isolates were recovered from aborted, stillborn, or neonatal foals from Ontario, Canada, from 1986 to 1992. From this total, 32 strains were randomly chosen for further study. Four or 5 isolates from each winter were selected, each from a different premises, and characterized by restriction enzyme analysis using BamHI, KpnI, BglII, HindIII, and EcoRI. Additional isolates from 2 premises and from a zebra foal were also assessed. For the strains isolated in 1986 and 1989–1992, the DNA pattern of 18 strains was similar to that of type 1P (Kentucky D) for BamHI and KpnI. None of the 32 strains studied could be differentiated by HindIII or EcoRI. Using BglII, an inconsistent fragment pattern and distribution were observed. Of the 8 strains isolated in 1987 and 1988, 7 were assigned into the 1B prototype group. The geographic distribution of 17 type 1P and 12 1B isolates was random across southern Ontario. These findings suggest that both electropherotypes can be recovered from horses in Ontario. The patterns of the additional equine isolates from the same premises were identical. The zebra isolate was different from the prototype equine herpesvirus type 1 and type 4 patterns and from all other equine isolates.
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SON, INSOOK, MARK D. ENGLEN, MARK E. BERRANG, PAULA J. FEDORKA-CRAY, and MARK A. HARRISON. "Genetic Diversity of Arcobacter and Campylobacter on Broiler Carcasses during Processing†." Journal of Food Protection 69, no. 5 (May 1, 2006): 1028–33. http://dx.doi.org/10.4315/0362-028x-69.5.1028.
Повний текст джерелаАнотація:
Broiler carcasses (n = 325) were sampled at three sites along the processing line (prescalding, prechilling, and post-chilling) in a commercial poultry processing plant during five plant visits from August to October 2004. Pulsed-field gel electrophoresis (PFGE) was used to determine the genomic fingerprints of Campylobacter coli (n = 27), Campylobacter jejuni (n = 188), Arcobacter butzleri (n = 138), Arcobacter cryaerophilus 1A (n = 4), and A. cryaerophilus 1B (n = 31) with the restriction enzymes SmaI and KpnI for Campylobacter and Arcobacter, respectively. Campylobacter species were subtyped by the Centers for Disease Control and Prevention PulseNet 24-h standardized protocol for C. jejuni. A modification of this protocol with a different restriction endonuclease (KpnI) and different electrophoresis running conditions produced the best separation of restriction fragment patterns for Arcobacter species. Both unique and common PFGE types of Arcobacter and Campylobacter strains were identified. A total of 32.8% (57 of 174) of the Arcobacter isolates had unique PFGE profiles, whereas only 2.3% (5 of 215) of the Campylobacter isolates belonged to this category. The remaining Arcobacter strains were distributed among 25 common PFGE types; only eight common Campylobacter PFGE types were observed. Cluster analysis showed no associations among the common PFGE types for either genus. Each of the eight common Campylobacter types consisted entirely of isolates from one sampling day, whereas more than half of the common Arcobacter types contained isolates from different sampling days. Our results demonstrate far greater genetic diversity for Arcobacter than for Campylobacter and suggest that the Campylobacter types are specific to individual flocks of birds processed on each sampling day.
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Jomantiene, R., J. L. Maas, R. E. Davis, and E. L. Dally. "Molecular Identification and Classification of a Phytoplasma Associated with Phyllody of Strawberry Fruit in Maryland." Plant Disease 85, no. 3 (March 2001): 335. http://dx.doi.org/10.1094/pdis.2001.85.3.335b.
Повний текст джерелаАнотація:
Several phytoplasmas have been reported to be associated with phyllody of strawberry fruit, including clover yellow edge, clover proliferation, clover phyllody, eastern and western aster yellows, STRAWB2, strawberry multicipita, and Mexican periwinkle virescence phytoplasmas. Plant symptoms in addition to phyllody may include chlorosis, virescence, stunting, or crown proliferation. In this report we describe a new phytoplasma in association with strawberry leafy fruit (SLF) disease in Maryland. Diseased plants exhibited fruit phyllody, floral virescence, leaf chlorosis, and plant stunting. Phytoplasmal 16S rDNA was amplified from SLF diseased plants by using the polymerase chain reaction (PCR) primed by primer pair P1/P7 and was reamplified in nested PCR primed by primer pair R16F2n/R2 (F2n/R2) as previously described (1). These results indicated the presence of a phytoplasma, designated SLF phytoplasma. Identification of SLF phytoplasma was accomplished by restriction fragment length polymorphism (RFLP) analysis of DNA amplified in PCR primed by F2n/R2, using endonuclease enzyme digestion with AluI, HhaI, KpnI, HaeIII, MseI, HpaII, RsaI, and Sau3AI. Phytoplasma classification was done according to the system of Lee et al. (2). RFLP analyses of rDNA amplified in three separate PCRs gave identical patterns. On the basis of collective RFLP patterns of the amplified 16S rDNA, the SLF phytoplasma was classified as a member of group 16SrIII (group III, X-disease phytoplasma group). The HhaI RFLP pattern of SLF 16S rDNA differed from that of the apparently close relative, clover yellow edge (CYE) phytoplasma, and all other phytoplasmas previously described in group III. Based on these results, SLF phytoplasma was classified in a new subgroup, designated subgroup K (III-K), within group III. The 1.2 kbp DNA product of PCR primed by primer pair F2n/R2 was sequenced, and the sequence deposited in GenBank under Accession No. AF 274876. Results from putative restriction site analysis of the sequence were in agreement with the results from actual enzymatic RFLP analysis of rDNA amplified from phylloid strawberry fruit. Although the sequence similarity between the 1.2-kbp fragment from the 16S rDNA of SLF phytoplasma and that of CYE phytoplasma was 99.9%, the Hha1 RFLP pattern of SLF rDNA supports the conclusion that the SLF phytoplasma may be closely related to, but is distinct from, CYE and other strains that are classified in group III. These findings contribute knowledge about the diversity of phytoplasmas affiliated with group III and the diversity of phytoplasmas associated with diseases in strawberry. References: (1) R. Jomantiene et al. Int. J. Syst. Bacteriol. 48:269, 1998. (2) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998.
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Valiunas, D., A. Alminaite, J. Staniulis, R. Jomantiene, and R. E. Davis. "First Report of Aster Yellows-Related Subgroup I-A Phytoplasma Strains in Carrot, Phlox, Sea-Lavender, Aconitum, and Hyacinth in Lithuania." Plant Disease 85, no. 7 (July 2001): 804. http://dx.doi.org/10.1094/pdis.2001.85.7.804c.
Повний текст джерелаАнотація:
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.
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Dion, Michel, and Claude Hamelin. "Cartographie physique de l'ADN du cytomégalovirus humain souche AD169." Canadian Journal of Microbiology 36, no. 5 (May 1, 1990): 341–47. http://dx.doi.org/10.1139/m90-059.
Повний текст джерелаАнотація:
The whole human cytomegalovirus strain AD169 genome was cloned into plasmid pAT153 in the form of 25 HindIII fragments. Double and triple digestions of the recombinant plasmids with restriction endonucleases BamHI, BglII, ClaI, DraI, EcoRI, EcoRV, HindIII, HpaI, KpnI, PaeR7, PstI, SphI and XbaI yielded a detailed restriction map of human cytomegalovirus DNA. Knowing the exact position of numerous restriction sites in the viral DNA molecule, we have been able to examine very closely the heterologous region between the long and the short segments of the human cytomegalovirus genome. Key words: DNA, physical map, cytomegalovirus, restriction endonucleases, HCMV.
11
Manakova, Elena, Migle Mikutenaite, Dmitrij Golovenko, Saulius Gražulis, and Giedre Tamulaitiene. "Crystal structure of restriction endonuclease Kpn2I of CCGG-family." Biochimica et Biophysica Acta (BBA) - General Subjects 1865, no. 8 (August 2021): 129926. http://dx.doi.org/10.1016/j.bbagen.2021.129926.
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Karpinska, B., and S. Karpinski. "The chloroplast genome of Pinussylvestris; physical map and localization of chloroplast genes." Canadian Journal of Forest Research 23, no. 2 (February 1, 1993): 234–38. http://dx.doi.org/10.1139/x93-031.
Повний текст джерелаАнотація:
A physical map of Pinussylvestris L. chloroplast DNA for three restriction endonucleases (PstI, SacI, and KpnI) has been prepared by hybridization of isolated or cloned restriction fragments. Pinussylvestris chloroplast DNA is about 120 kilobases. Ten chloroplast genes have been localized by hybridization with heterologous chloroplast DNA probes. The genome contains single copies of the 23S and 16S rRNA genes and lacks any large repeated sequences. The restriction site arrangement and gene order have been compared with other known chloroplast DNA genetic maps of pine species.
13
Valiunas, D., A. Alminaite, J. Staniulis, R. Jomantiene, and R. E. Davis. "First Report of Alder Yellows Phytoplasma in the Eastern Baltic Region." Plant Disease 85, no. 10 (October 2001): 1120. http://dx.doi.org/10.1094/pdis.2001.85.10.1120b.
Повний текст джерелаАнотація:
Alnus glutinosa (alder) is widespread in Europe and is an important component of biological diversity in natural forest ecosystems in the Baltic Region. In 2000, diseased trees of A. glutinosa exhibiting characteristically phytoplasmal disease symptoms of shoot proliferation and leaf yellowing were observed in Aukstaitija National Park, Lithuania. In other parts of Europe, alder is affected by a phytoplasmal disease known as alder yellows, which is characterized by symptoms that include yellowing and reduced leaf size, die-back of branches, and decline of trees (2,3). Proliferation of shoots has not been previously reported with this disease. An association between alder yellows and infection by a phytoplasma has been reported in A. glutinosa in Germany and Italy, and a phytoplasma has been found in A. glutinosa in France and Hungary (2,4). We examined symptomatic alder from Lithuania using nested polymerase chain reaction (PCR) (1), primed by P1/P7 and followed by R16F2n/R16R2 (F2n/R2), for amplification of phytoplasmal ribosomal (r) DNA. The results indicated the presence of a phytoplasma, designated ALY-L, in the diseased alder. We classified the ALY-L phytoplasma through restriction fragment length polymorphism (RFLP) analysis of 16S rDNA. A 1.2-kbp fragment (F2n-R2 segment) of rDNA, amplified in PCR primed by F2n/R2, was analyzed using single endonuclease enzyme digestion with AluI, MseI, KpnI, HhaI, HaeIII, HpaI, HpaII, RsaI, HinfI, TaqI, Sau3AI, BfaI, and ThaI. On the basis of collective RFLP patterns, phytoplasma ALY-L was classified as a member of group 16SrV (group V, elm yellows group), subgroup C. The amplified 16S rDNA was cloned in Escherichia coli and sequenced, and the sequence was deposited in the GenBank data library (Accession No. AY028789). Nucleotide sequence alignment revealed that 16S rDNA from phytoplasma ALY-L shared 100% sequence similarity with 16S rDNA (GenBank Accession No. Y16387) from a phytoplasma associated with alder yellows (ALY) disease in Italy. The results support the conclusion that a strain of ALY phytoplasma is present in Lithuania. Phytoplasmas belonging to groups 16SrI (aster yellows phytoplasma group) and III (X-disease phytoplasma group) have been found in herbaceous plant species in Lithuania. This report records the first finding of a group V phytoplasma, and the first finding of a phytoplasma in a tree species in the eastern Baltic Region. These findings contribute knowledge about the diversity of phytoplasmas in the Baltic Region and the distribution of ALY phytoplasma in Europe. Apparently, A. glutinosa may be infected by the phytoplasma but not develop obvious disease symptoms, as has been reported elsewhere (3). Thus, it is possible that ALY-L phytoplasma is widespread, but as yet undetected, throughout the geographic range of alder in the Baltic Region. This possibility is supported by the finding of the monophagous leafhopper vector (Oncopsis alni) of ALY phytoplasma throughout Europe (cited in Maixner and Reinert [3]). Further research is needed to assess the impact of phytoplasmal infections such as those by ALY-related phytoplasma strains on trends in biological diversity in the natural forest ecosystems of the Baltic Region and elsewhere in Europe. References: (1) R. Jomantiene et al. Int. J. Syst. Bacteriol. 48:269, 1998. (2) W. Lederer and E. Seemüller. Eur. J. For. Pathol. 21:90, 1991. (3) M. Maixner and W. Reinert. Eur. J. Plant Pathol. 105:87, 1999. (4) R. Mäurer et al. Phytopathology 83:971, 1993.
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Stevens, Tracy A., Deborah A. Duffield, Edward D. Asper, K. Gilbey Hewlett, Al Bolz, Laurie J. Gage, and Gregory D. Bossart. "Preliminary findings of restriction fragment differences in mitochondrial DNA among killer whales (Orcinus orca)." Canadian Journal of Zoology 67, no. 10 (October 1, 1989): 2592–95. http://dx.doi.org/10.1139/z89-365.
Повний текст джерелаАнотація:
A preliminary assessment of mitochondrial DNA restriction patterns in the killer whale (Orcinus orca) was conducted using 10 captive North Atlantic killer whales from the southeastern coast of Iceland, a captive-born offspring of one of these whales, and 9 North Pacific killer whales. No restriction pattern variation was seen among these whales, using the enzymes BamH I, Bgl II, Hinf I, Kpn I, or Pvu II. Restriction pattern variation was found using the enzyme Hae III. This restriction endonuclease distinguished the North Atlantic killer whales (type 1) from the North Pacific killer whales. The North Pacific killer whales were further differentiated into two groups: those originating from the "resident" communities of the Vancouver Island region (type 2), and those from the "transient" community of Vancouver Island, as well as those stranded along the Oregon coast (type 3). The observed Hae III restriction pattern differences suggest that mitochondrial DNA analysis will be a valuable technique for investigating regional and local distributions of maternal lineages among killer whale pods, especially in the North Pacific.
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Mansfield, Shawn D., Greg S. Bezanson, and Thomas J. Marrie. "Characterization and cloning of a 37.6-kb plasmid carried byLegionella pneumophilarecovered from patients and hospital water over a 12-year period." Canadian Journal of Microbiology 43, no. 2 (February 1, 1997): 193–97. http://dx.doi.org/10.1139/m97-025.
Повний текст джерелаАнотація:
For 12 years, strains of Legionella pneumophila serogroup 1 harbouring a 37.6-kb (23 MDa) plasmid have predominated among patient and potable water isolates at the Victoria General Hospital, Halifax, N.S. Plasmid DNA recovered from 24 strains isolated between 1983 and 1995 was digested with the restriction endonucleases EcoRI, HindIII, KpnI, PvuII, XbaI, and BamHI. The distribution of cutting sites indicated that the 23-MDa size group had remained essentially unchanged during this period, suggesting the persistence of a single plasmid type. Further fragmentation pattern analysis permitted the construction of a physical map of the prototype 23-MDA plasmid, pLp4269. Double digestion with BamHI–HindIII enabled the cloning of 94.4% of pLp4269 into pBluescript vector. A 2.1-kb fragment was not clonable. Plasmid pLp4269 is the first of the smaller Legionella extrachromosomal DNAs to be characterized in this way.Key words: Legionella, plasmid, stability, map, cloning.
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Barrett, John W., Om P. Rajora, F. C. H. Yeh, Bruce P. Dancik, and Curtis Strobeck. "Mitochondrial DNA variation and genetic relationships of Populus species." Genome 36, no. 1 (February 1, 1993): 87–93. http://dx.doi.org/10.1139/g93-012.
Повний текст джерелаАнотація:
We examined variation in and around the region coding for the cytochrome c oxidase I (coxI) and ATPase 6 (atp6) genes in the mitochondrial genomes of four Populus species (P. nigra, P. deltoides, P. maximowiczii, and P. tremuloides) and the natural hybrid P. × canadensis (P. deltoides × P. nigra). Total cellular DNAs of these poplars were digested with 16 restriction endonucleases and probed with maize mtDNA-specific probes (CoxI and Atp6). The only variant observed for Atp6 was interspecific, with P. maximowiczii separated from the other species as revealed by EcoRI digestions. No intraspecific mtDNA variation was observed among individuals of P. nigra, P. maximowiczii, P. × canadensis, or P. tremuloides for the CoxI probe. However, two varieties of P. deltoides were distinct because of a single site change in the KpnI digestions, demonstrating that P. deltoides var. deltoides (eastern cottonwood) and var. occidentalis (plains cottonwood) have distinct mitochondrial genomes in the region of the coxI gene. Populus × canadensis shared the same restriction fragment patterns as its suspected maternal parent P. deltoides. Nucleotide substitutions per base in and around the coxI and atp6 genes among the Populus species and the hybrid ranged from 0.0017 to 0.0077. The interspecific estimates of nucleotide substitution per base suggested that P. tremuloides was furthest removed from P. deltoides and P. × canadensis and least diverged from P. nigra. Populus maximowiczii was placed between these two clusters.Key words: mitochondrial DNA, poplars, phylogenetics, variation, restriction fragment length polymorphisms.
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Accioly, I. V., I. M. C. Cunha, J. C. M. Tavares, and W. F. Molina. "Chromosome Banding in Crustacea. I. Karyotype, Ag-NORs, C Banding and Treatment with EcoRI, PstI and KpnI Restriction Endonucleases in Artemia franciscana." Biota Amazônia 4, no. 2 (June 30, 2014): 15–19. http://dx.doi.org/10.18561/2179-5746/biotaamazonia.v4n2p15-19.
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Lee, I. M., K. D. Bottner, and M. C. Black. "First Report of Yucca Phyllody Associated with 16SrI-A Phytoplasmas in Texas." Plant Disease 91, no. 4 (April 2007): 467. http://dx.doi.org/10.1094/pdis-91-4-0467c.
Повний текст джерелаАнотація:
Buckley's yucca (Yucca constricta Buckl.) is a native flowering perennial plant widely distributed in Texas and northeast Mexico. It is also grown as an ornamental plant in its native range as well as in other dry regions in the United States and Mexico. In 2006, during an extended drought, Buckley's yucca plants sporadically exhibited phyllody and abnormal bud proliferation on the inflorescence in Uvalde County in southwestern Texas. Symptoms resembled those caused by phytoplasmal infection. Samples from four symptomatic and two asymptomatic yucca plants were collected. Total nucleic acid was extracted from abnormal bud tissue. To assess the etiological aspect of the disease nested PCR using phytoplasma specific primer pair P1/16S-SR or P1/P7 followed by R16F2n/R16R2n was employed for the detection of putative phytoplasmas (2). An amplicon of approximately 1.2 kb was amplified from all four symptomatic yucca plants but not from asymptomatic plants. Restriction fragment length polymorphism (RFLP) patterns of 16S rDNA digested singly with AluI, KpnI, HpaII, MseI, HhaI, and RsaI endonucleases indicated that affected yucca plants were infected by a phytoplasma belonging to aster yellows group 16SrI (‘Candidatus Phytoplasma asteris’), subgroup 16SrI-A (1). Nucleotide sequence analysis of cloned 16S rDNA (GenBank Accession No. EF190067) confirmed the results on the basis of RFLP analyses. Yucca phyllody has not been reported elsewhere. This disease appears to be newly emerging in Texas with only a few affected plants. To our knowledge, this is the first report of 16SrI-A phytoplasma infecting a Yucca sp. References: (1) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (2) I.-M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004.
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Min, H., S. B. Hu, Z. N. Li, Y. F. Wu, C. P. Zhang, and T. Wei. "A Phytoplasma Associated with an Outbreak of an Unusual Disease of Chrysanthemum in China in 2008." Plant Disease 93, no. 8 (August 2009): 840. http://dx.doi.org/10.1094/pdis-93-8-0840a.
Повний текст джерелаАнотація:
In August of 2008, a disease of chrysanthemum (Dendranthema morifolium (Ramat.) Tzvel) caused losses of 70 to 80% in one of the largest chrysanthemum gardens in Yangling, Shanxi Province, China. Chrysanthemum plants in nearby areas also were affected to various degrees. Symptoms included flattened stems, shortening of internodes, yellowing of leaf margins, root death, and dwarfing of plants. Affected plants eventually collapsed. On the basis of these symptoms, a phytoplasma was suspected. Total nucleic acids were extracted from 0.5 g of phloem tissue from stems of eight symptomatic and eight asymptomatic plants by the cetyltrimethylammoniumbromide (CTAB) method (1). To amplify phytoplasma DNA, primer pairs R16mF2/R16mR1, followed by R16F2n/R16R1 (2), were used in a nested PCR. A final amplicon product (1.2 kb) was obtained from all symptomatic plants but not from asymptomatic ones. Restriction fragment length polymorphism (RFLP) analyses of R16F2n/R16R1 amplicons with MseI, AluI, HhaI, HaeIII, KpnI, RsaI, and HpaII endonucleases indicated that all symptomatic plants, but none of the asymptomatic plants, contained a phytoplasma strain of group 16SrI, subgroup B (3). A search of rDNA sequences in GenBank revealed a similarity (>99%) to aster yellow phytoplasma, 16SrI group, thereby confirming strain identity based on RFLP analysis. These results indicate the disease of chrysanthemum is associated with a phytoplasma related to the aster yellow phytoplasma group. Sequences were deposited in GenBank (Accession No. FJ543467). A vector of this phytoplasma in chrysanthemum has not been identified. References: (1) E. Angelini et al. Vitis 40:79, 2001. (2) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (3) I. M. Lee et al. Int. J. Syst. Evol. Microbiol. 48:1153, 1998.
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Jomantiene, R. R., J. L. Maas, F. Takeda, and R. E. Davis. "Molecular Identification and Classification of Strawberry Phylloid Fruit Phytoplasma in Group 16SrI, New Subgroup." Plant Disease 86, no. 8 (August 2002): 920. http://dx.doi.org/10.1094/pdis.2002.86.8.920c.
Повний текст джерелаАнотація:
Plants of commercial strawberry (Fragaria × ananassa Duch., cv. Camarosa) exhibiting extensive fruit phyllody (development of leafy structures from achenes) were observed in a winter greenhouse production facility in West Virginia. In July 2001, 95 dormant, cold-stored plants were purchased from a California strawberry nursery, potted and grown in this West Virginia facility. Five of the plants developed fruits with phylloid growths. These fruits were assessed for phytoplasma infection using nested polymerase chain reactions (PCRs) in which initial ribosomal (r) DNA amplification was primed by phytoplasma-universal primer pair P1/P7 (2), and rDNA reamplification was primed by primer pair R16F2n/R16R2 (1). Amplification of phytoplasma-characteristic 1.2-kbp 16S rDNA in the nested reactions primed by R16F2n/R16R2 confirmed that the symptomatic plants were infected by a phytoplasma, termed strawberry phylloid fruit (StrawbPhF) phytoplasma. No phytoplasma DNAs were amplified from healthy plants. Restriction fragment length polymorphism (RFLP) patterns of 16S rDNA digested with AluI, KpnI, HhaI, HaeIII, HpaII, MseI, RsaI, and Sau3A1 restriction endonucleases indicated that StrawbPhF phytoplasma belonged to group 16SrI (group I, aster yellows phytoplasma group) according to the phytoplasma classification system of Lee et al. (4). However, the collective patterns distinguished StrawbPhF from its closest known relative, clover phyllody (CPh) phytoplasma, and from all other phytoplasmas classified in group 16SrI. On the basis of the RFLP patterns of 16S rDNA, the StrawbPhF was classified in group 16SrI, new subgroup R. The StrawbPhF phytoplasma 1.2-kbp 16S rDNA PCR product was cloned in Escherichia coli using TOPO TA Cloning Kit (Invitrogen, Carlsbad, CA), sequenced, and the sequence deposited in GenBank under Accession No. AY102275. The StrawbPhF 16S rDNA sequence shared 99.9 and 99.8% similarity with the two sequence heterogeneous operons, rrnA and rrnB, respectively, of CPh phytoplasma, and shared 99.9% similarity with 16S rDNA of the unclassified cirsium yellows (CirY) phytoplasma (GenBank Accession No. AF200431) reported in Cirsium arvense L. in Lithuania (3). The restriction sites in 16S rDNA of StrawbPhF were identical to those in 16S rDNA of CPh rrnA and CirY. Three restriction sites (AluI, HaeIII, and MseI) and three base substitutions distinguished StrawbPhF 16S rDNA from rrnB of CPh phytoplasma. No evidence was obtained for the presence of a second (sequence heterogeneous) rRNA operon in StrawbPhF phytoplasma, as reported in CPh phytoplasma (4), which clearly distinguishes this phytoplasma from CPh phytoplasma. Future studies on StrawbPhF phytoplasma may provide important information on the evolution of phytoplasmas. References: (1) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (2) R. Jomantiene et al. Int. J. Syst. Bacteriol. 48:269, 1998. (3) R. Jomantiene et al. Phytopathology 90:S39, 2000. (4) I.-M. Lee et al. Int J. Syst. Bacteriol. 48:1153, 1998.
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Jomantiene, R., J. L. Maas, E. L. Dally, and R. E. Davis. "First Report of Clover Yellow Edge and STRAWB2 Phytoplasmas in Strawberry in Maryland." Plant Disease 83, no. 11 (November 1999): 1072. http://dx.doi.org/10.1094/pdis.1999.83.11.1072c.
Повний текст джерелаАнотація:
Commercial strawberry (Fragaria × ananassa Duchesne) plants that were either chlorotic and severely stunted or exhibiting fruit phyllody were collected in Maryland. The plants were assessed for phytoplasma infection by nested polymerase chain reactions primed by phytoplasma universal primer pairs R16mF2/R1 and F2n/R2 (2) or P1/P7 (3) and F2n/R2 for amplification of phytoplasma 16S ribosomal (r) DNA (16S rRNA gene) sequences. Phytoplasma-characteristic 1.2-kbp DNA sequences were amplified from all diseased plants. No phytoplasma-characteristic DNAs were amplified from healthy plants. Restriction fragment length polymorphism patterns of rDNA digested with AluI, KpnI, HhaI, HaeIII, HpaII, MseI, RsaI, and Sau3A1 endonucleases indicated that chlorotic and stunted plants were infected by a phytoplasma that belonged to subgroup 16SrIII-B (clover yellow edge [CYE] subgroup) and that the plant exhibiting fruit phyllody was infected by a phytoplasma that belonged to subgroup 16SrI-K (STRAWB2 subgroup). The STRAWB2 phytoplasma was first reported from strawberry plants grown in Florida and characterized as representative of a new subgroup of the aster yellows group, 16SrI (3); this is the first report of this phytoplasma occurring in strawberry outside of Florida. A STRAWB2-infected plant produced phylloid fruits in two consecutive years of observation in the greenhouse; the plant previously had been field-grown in a breeder's evaluation plots in Beltsville, MD. The CYE phytoplasma was first experimentally transmitted by leafhopper to commercial strawberry and F. virginiana Duchesne in Ontario Canada (1); this is the first report of natural CYE phytoplasma infection of strawberry in Maryland. CYE phytoplasma-infected plants, representing ≈5% of the total number of plants of one advanced sselection, were located in a breeder's evaluation plots in Beltsville. References: (1) L. N. Chiykowski. Can. J. Bot. 54:1171, 1976. (2) D. E. Gunderson and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (3) R. Jomantiene et al. Int. J. Syst. Bacteriol. 48:269, 1998.
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Zhang, JW, G. Stamatoyannopoulos, and NP Anagnou. "Laotian (delta beta) degree-thalassemia: molecular characterization of a novel deletion associated with increased production of fetal hemoglobin." Blood 72, no. 3 (September 1, 1988): 983–88. http://dx.doi.org/10.1182/blood.v72.3.983.983.
Повний текст джерелаАнотація:
Abstract We have identified and molecularly characterized a novel deletion in the beta-globin gene cluster that increases fetal hemoglobin (HbF) synthesis in a 24-year-old Laotian man who is heterozygous for this mutation. The patient is asymptomatic with a mild anemia, hypochromia, and microcytosis (Ht = 39%, MCH = 22.8 pg, MCV = 71 fl), normal levels of HbA2 (3.0%) and 11.5% HbF (G gamma A gamma ratio 60 to 40), with heterocellular distribution (52% F cells). Extensive restriction endonuclease mapping defined the 5′ breakpoint within the IVS II of the delta-globin gene, between positions 775 to 781 very similar to the 5′ breakpoint of the Sicilian delta beta-thalassemia. However, the 3′ breakpoint was localized between two Pst I sites 4.7 kb 3′ of the beta- globin gene, thus ending about 0.7 kb upstream from the 3′ breakpoint of the Sicilian delta beta-thalassemia. This results in a 12.5 kb deletion of DNA. It is of interest that the 5′ breakpoint of the deletion residues within an AT-rich region which has been proposed as a specific recognition signal for recombination events, while the 3′ breakpoint lies within a cluster of L1 repetitive sequences (formerly known as Kpn I family repeats). The presence of the 3′ breakpoints of several other deletions within this region of L1 repeats also suggests that such sequences might serve as hot spots for recombination and eventually lead to thalassemia deletions. The similarity of the 5′ and 3′ breakpoints of these delta beta-thalassemias underscores the putative regulatory role of the deleted and juxtaposed sequences on the expression of the gamma-globin genes in adult life.
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Zhang, JW, G. Stamatoyannopoulos, and NP Anagnou. "Laotian (delta beta) degree-thalassemia: molecular characterization of a novel deletion associated with increased production of fetal hemoglobin." Blood 72, no. 3 (September 1, 1988): 983–88. http://dx.doi.org/10.1182/blood.v72.3.983.bloodjournal723983.
Повний текст джерелаАнотація:
We have identified and molecularly characterized a novel deletion in the beta-globin gene cluster that increases fetal hemoglobin (HbF) synthesis in a 24-year-old Laotian man who is heterozygous for this mutation. The patient is asymptomatic with a mild anemia, hypochromia, and microcytosis (Ht = 39%, MCH = 22.8 pg, MCV = 71 fl), normal levels of HbA2 (3.0%) and 11.5% HbF (G gamma A gamma ratio 60 to 40), with heterocellular distribution (52% F cells). Extensive restriction endonuclease mapping defined the 5′ breakpoint within the IVS II of the delta-globin gene, between positions 775 to 781 very similar to the 5′ breakpoint of the Sicilian delta beta-thalassemia. However, the 3′ breakpoint was localized between two Pst I sites 4.7 kb 3′ of the beta- globin gene, thus ending about 0.7 kb upstream from the 3′ breakpoint of the Sicilian delta beta-thalassemia. This results in a 12.5 kb deletion of DNA. It is of interest that the 5′ breakpoint of the deletion residues within an AT-rich region which has been proposed as a specific recognition signal for recombination events, while the 3′ breakpoint lies within a cluster of L1 repetitive sequences (formerly known as Kpn I family repeats). The presence of the 3′ breakpoints of several other deletions within this region of L1 repeats also suggests that such sequences might serve as hot spots for recombination and eventually lead to thalassemia deletions. The similarity of the 5′ and 3′ breakpoints of these delta beta-thalassemias underscores the putative regulatory role of the deleted and juxtaposed sequences on the expression of the gamma-globin genes in adult life.
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Jomantiene, R., J. L. Maas, E. L. Dally, R. E. Davis, and J. D. Postman. "First Report of Clover Proliferation Phytoplasma in Strawberry." Plant Disease 83, no. 10 (October 1999): 967. http://dx.doi.org/10.1094/pdis.1999.83.10.967c.
Повний текст джерелаАнотація:
In 1996, diseased plants of Fragaria virginiana Duchesne were collected from a native population in Quebec, Canada, and sent to the National Clonal Germplasm Repository in Corvallis, OR, where grafting onto disease-free plants of F. chiloensis (L.) Duchesne (4) was performed. Plants of both species were sent to Beltsville, MD, for identification of a phytoplasma possibly associated with the disease symptoms of dwarfing and multibranching crowns. A phytoplasma was found in both species and characterized as the strawberry “multicipita” (SM) phytoplasma, which is representative of subgroup 16SrVI-B, a new subgroup of the clover proliferation (CP) group (2). In 1999, we observed commercial strawberry (Fragaria × ananassa Duchesne) plants collected in California and Maryland that were stunted and chlorotic or exhibited these symptoms in addition to small, distorted leaves. Infected F. × ananassa plants, as well as diseased F. virginiana and grafted F. chiloensis plants previously infected by the SM phytoplasma, were assessed for phytoplasma infection by nested polymerase chain reactions primed by phytoplasma universal primer pairs R16mF2/R1 and F2n/R2 (1) or P1/P7 (3) and F2n/R2 for amplification of phytoplasma 16S rDNA (16S rRNA gene) sequences. Phytoplasma-characteristic 1.2-kbp DNA sequences were amplified from all diseased plants. No DNA sequences were amplified from healthy plants. Restriction fragment length polymorphism patterns of rDNA digested with AluI, KpnI, HhaI, HaeIII, HinfI, HpaII, MseI, RsaI, and Sau3A1 endonucleases indicated that all plants were infected by a phytoplasma that belonged to subgroup 16SrVI-A (CP phytoplasma subgroup) and that diseased F. virginiana and grafted F. chiloensis plants were infected by both SM and CP. This is the first report of the CP phytoplasma, subgroup 16SrVI-A, infecting strawberry. This report also indicates that the occurrence of the CP phytoplasma in strawberry may be widespread in North America and that F. chiloensis, F. virginiana, and F. × ananassa plants are susceptible to infection by the CP phytoplasma. References: (1) D. E. Gunderson and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (2) R. Jomantiene et al. HortScience 33:1069, 1998. (3) R. Jomantiene et al. Int. J. Syst. Bacteriol. 48:269, 1998. (4) J. D. Postman et al. Acta Hortic. 471:25, 1998.
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Samad, A., P. V. Ajayakumar, A. K. Shasany, Mahesh K. Gupta, M. Alam, and S. Rastogi. "Occurrence of a Clover Proliferation (16SrVI) Group Phytoplasma Associated with Little Leaf Disease of Portulaca grandiflora in India." Plant Disease 92, no. 5 (May 2008): 832. http://dx.doi.org/10.1094/pdis-92-5-0832a.
Повний текст джерелаАнотація:
Portulaca grandiflora (family Portulacaceae), commonly known as moss rose purslane, is a popular ornamental plant widely grown in temperate climates because it blooms all summer. Portulaca is also used for medicinal purposes since it is rich in vitamins A, B1, and C and has antimicrobial and cytotoxic activity. Since March 2005, 30 to 50% of P. grandiflora plants in the ornamental gardens as well as in pots at the Central Institute of Medicinal and Aromatic Plants, Lucknow, India have displayed symptoms resembling phytoplasma infection. Disease symptoms start as a typical bud proliferation, downward curling, and diminishing size of leaves, followed by overall stunted growth and yellowing of the whole plant from April to June. Some plants also formed rosettes and a proliferation of axillary shoots resulting in a witches'-broom appearance. Typical pleomorphic bodies, mostly spherical to oval, ranging from 340 to 1,100 nm were observed only in sieve elements of infected plants by transmission electron microscopy (TEM). On the basis of symptoms, TEM observations, PCR, and response to antibiotic treatment, the causal organism was identified as phytoplasma (1). Total genomic DNA from healthy and infected plants was extracted with the CTAB buffer method (2). Of 27 suspected samples screened by PCR, 23 were phytoplasma positive. Presence of phytoplasmas in plants was demonstrated by a nested PCR assay employing primer pair P1/P6 followed by R16F2n/R16R2 that generated rDNA products of 1.5 and 1.2 kb, respectively, only from symptomatic plants. No differences among phytoplasmas in Portulaca plants were detected by restriction fragment length polymorphism (RFLP) analysis of nested rDNA (1.2 kb) products using endonucleases BamHI, RsaI, AluI, HpaII, and EcoRI. Comparative analysis of RFLP patterns with those derived from reference phytoplasmas tentatively identified the Portulaca little leaf (PLL) phytoplasma as a member of 16S rDNA RFLP group 16SrVI (3). A nested PCR product (1.25 kb) was cloned with a TOPO TA cloning kit (Invitrogen, Carlsbad, CA) and sequenced. The sequence was deposited in the GenBank database (Accession No. EF651786). Sequence analysis revealed the PLL phytoplasma to be most similar (98%) to Indian brinjal little leaf (Accession No. EF186820) and ‘Candidatus Phytoplasma trifolii’ (Accession No. AY390261), two 16SrVI group phytoplasmas previously reported from India and Canada, respectively. The status of PLL (EF651786) was also verified by in silico RFLP analysis (4) of the F2n/R2 sequence of six closely related strains (Accession Nos. AF228052, AY390261, AY270156, AY409070, AY409069, and EF186820) of the 16SrVI group using 17 restriction enzymes (AluI, BamHI, BfaI, BsfUI, DraI, EcoRI, HaeIII, HhaI, HinfI, HpaI, HpaII, KpnI, MseI, Sau3AI, RsaI, SspI, and TaqI). In silico restriction digestion and virtual gel plotting showed similar patterns for all enzymes. To our knowledge, this is the first report of a 16SrVI group phytoplasma infecting Portulaca plants in India. References: (1) P. V. Ajayakumar et al. Aust. Plant Dis. Notes 2:67, 2007. (2) S. P. S. Khanuja et al. Plant Mol. Biol. Rep. 17:74, 1999. (3) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (4) W. Wei et al. Int. J. Syst. Evol. Mic. 57:1855, 2007.
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Bel Hadj Ali, Insaf, Hamed Chouaieb, Yusr Saadi Ben Aoun, Emna Harigua-Souiai, Hejer Souguir, Alia Yaacoub, Oussaïma El Dbouni, et al. "Dipeptidyl peptidase III as a DNA marker to investigate epidemiology and taxonomy of Old World Leishmania species." PLOS Neglected Tropical Diseases 15, no. 7 (July 26, 2021): e0009530. http://dx.doi.org/10.1371/journal.pntd.0009530.
Повний текст джерелаАнотація:
Background Dipeptidyl peptidase III (DPPIII) member of M49 peptidase family is a zinc-dependent metallopeptidase that cleaves dipeptides sequentially from the N-terminus of its substrates. In Leishmania, DPPIII, was reported with other peptidases to play a significant role in parasites’ growth and survival. In a previous study, we used a coding sequence annotated as DPPIII to develop and evaluate a PCR assay that is specific to dermotropic Old World (OW) Leishmania species. Thus, our objective was to further assess use of this gene for Leishmania species identification and for phylogeny, and thus for diagnostic and molecular epidemiology studies of Old World Leishmania species. Methodology Orthologous DDPIII genes were searched in all Leishmania genomes and aligned to design PCR primers and identify relevant restriction enzymes. A PCR assays was developed and seventy-two Leishmania fragment sequences were analyzed using MEGA X genetics software to infer evolution and phylogenetic relationships of studied species and strains. A PCR-RFLP scheme was also designed and tested on 58 OW Leishmania strains belonging to 8 Leishmania species and evaluated on 75 human clinical skin samples. Findings Sequence analysis showed 478 variable sites (302 being parsimony informative). Test of natural selection (dN-dS) (-0.164, SE = 0.013) inferred a negative selection, characteristic of essential genes, corroborating the DPPIII importance for parasite survival. Inter- and intra-specific genetic diversity was used to develop universal amplification of a 662bp fragment. Sequence analyses and phylogenies confirmed occurrence of 6 clusters congruent to L. major, L. tropica, L. aethiopica, L. arabica, L. turanica, L. tarentolae species, and one to the L. infantum and L. donovani species complex. A PCR-RFLP algorithm for Leishmania species identification was designed using double digestions with HaeIII and KpnI and with SacI and PvuII endonucleases. Overall, this PCR-RFLP yielded distinct profiles for each of the species L. major, L. tropica, L. aethiopica, L. arabica and L. turanica and the L. (Sauroleishmania) L. tarentolae. The species L. donovani, and L. infantum shared the same profile except for strains of Indian origin. When tested on clinical samples, the DPPIII PCR showed sensitivities of 82.22% when compared to direct examination and was able to identify 84.78% of the positive samples. Conclusion The study demonstrates that DPPIII gene is suitable to detect and identify Leishmania species and to complement other molecular methods for leishmaniases diagnosis and epidemiology. Thus, it can contribute to evidence-based disease control and surveillance.
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Canale, M. C., and I. P. Bedendo. "‘Candidatus Phytoplasma brasiliense’ (16SrXV-A Subgroup) Associated with Cauliflower Displaying Stunt Symptoms in Brazil." Plant Disease 97, no. 3 (March 2013): 419. http://dx.doi.org/10.1094/pdis-09-12-0874-pdn.
Повний текст джерелаАнотація:
Cauliflower stunt, caused by a phytoplasma of the group 16SrIII-J, was reported in the beginning of 2012 and has occurred with high incidences of infected plants (up to 90%) in crops located in the state of São Paulo in the southeast region of Brazil (3). Diseased plants exhibit general stunting, malformation of inflorescence, reddening leaves, and vessel necrosis (3). Further investigations with plants displaying identical symptoms collected in Nova Bassano, state of Rio Grande do Sul, Brazilian south region, have revealed the presence of a phytoplasma distinct from 16SrIII-J subgroup. Four symptomatic plus four asymptomatic samples were assayed from a field, and the presence of phytoplasma was evidenced by nested PCR assays performed with primers P1/Tint followed by R16F2n/16R2 in three affected plants, which amplified genomic fragments of 1.2 kb from the 16S rRNA gene. No amplification occurred in non-affected samples. Nested PCR products analyzed by conventional RFLP (2) using the enzymes AluI, RsaI, KpnI, HpaII, MseI, HhaI, MboI, and BstUI pointed to the presence of a phytoplasma belonging to group 16SrXV-A in all three phytoplasma-positive samples. Virtual RFLP analysis based on restriction patterns, derived from in silico digestion with 17 endonucleases (4), confirmed the previous results obtained from those samples by conventional RFLP. The 16S rDNA sequences of this phytoplasma identified in cauliflower (GenBank Accession No. JN818845) shared 99% sequence similarity with the reference phytoplasma for subgroup 16SrXV-A (Hibiscus witches'-broom phytoplasma, AF147708), designated ‘Candidatus Phytoplasma brasiliense.’ Analysis of putative restriction sites showed excellent identity between the phytoplasma studied here and the reference phytoplasma. In addition, the arrangement of branches of a phylogenetic tree constructed with phytoplasmas representing diverse 16Sr groups and subgroups supported that the phytoplasma found in cauliflower is closed related to the representative of the subgroup 16SrXV-A. Association of distinct phytoplasmas with the same kind of disease is not rare and the present pathosystem constitutes a new example. Members of this subgroup have been described almost exclusively in Brazil and previously reported in Sida sp., periwinkle, and hibiscus (1). In some European countries, as well as in the United States and Canada, phytoplasmas belonging to group 16SrI has been associated with this type of disease, which has been reported for various species of the genus Brassica, as published in previous works (3). However, a representative of the group 16SrVI was described in infected plants in Iran (3). Although the 16SrIII-J phytoplasma is currently the most important agent of cauliflower stunt in Brazil, and members of 16SrI are prevalent in other countries, this study revealed that a 16Sr XV-A phytoplasma may be also associated with this important disease of brassicas. Besides, the findings here reported expand the natural host range, including cauliflower as new host for phytoplasmas affiliated with 16SrXV-A. References: (1) B. Eckstein et al. Plant Dis. 95:363, 2009. (2) I. M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) M. C. C. Rappussi et al. Eur. J. Plant. Pathol. 133:829, 2012. (4) Wei et al. Int. J. Syst. Evol. Microbiol. 57:1855, 2007.
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Harrison, N. A., D. E. Legard, R. DiBonito, and P. A. Richardson. "Detection and Differentiation of Phytoplasmas Associated with Diseases of Strawberry in Florida." Plant Disease 81, no. 2 (February 1997): 230. http://dx.doi.org/10.1094/pdis.1997.81.2.230b.
Повний текст джерелаАнотація:
Strawberry (Fragaria × ananassa Duchesne) plants with symptoms suggestive of phytoplasmal disease were identified in commercial fields and a breeder's plot in west central Florida during the 1995 to 1996 winter growing season. Affected plants were all conspicuously stunted and unproductive. Primary symptoms on cvs. Rosa Linda and Carlsbad and on a breeder's accession resembled those of strawberry green petal (SGP). Plants displayed sparse clusters of virescent flowers with enlarged sepals and phylloid receptacles that failed to develop fully into fleshy structures or redden on ripening. Symptoms on cv. Oso Grande were more typical of multiplier disease and included a proliferation of branch crowns producing numerous small leaves with spindly petioles. Oso Grande and Carlsbad originated as transplants from a nursery in Montreal, Canada, whereas Rosa Linda transplants were from Nova Scotia. Plants were assessed for phytoplasma infection by polymerase chain reaction with total DNAs from leaves and petioles as template and phytoplasma-specific ribosomal RNA primers P1 and P7 (3), or mollicute-specific ribosomal protein (rp) gene primers rpF1 and rpR4 (2). Amplification of a 1.8-kb rDNA or 1.2-kb rp gene product, respectively, confirmed infection of Rosa Linda (7 of 7 plants), Carlsbad (3 of 7), Oso Grande (4 of 4), and a single breeder's accession. No products were amplified from DNAs of healthy plants. Restriction fragment length polymorphism patterns of rDNA digested with AluI, EcoRI, HaeIII, HhaI, HpaII, KpnI, ScaI, or Tru9I endonucleases, or of rp gene products digested with AluI, DraI, RsaI, TaqI, or Tru9I, revealed no differences among phytoplasma strains affecting both Rosa Linda and Carlsbad. Collectively, patterns were comparable to those of clover phyllody and SGP phytoplasmas, two Canadian strains previously classified as members of phytoplasma 16S rRNA (rr)-ribosomal protein (rp) group 16S rI, subgroup C (16S rI-C (rr-rp)) (1). Similarly, no differences were evident among phytoplasmas associated with all four diseased Oso Grande plants. Both rDNA and rp fragment profiles associated with this cultivar were characteristic of strains such as tomato big bud and eastern aster yellows delineated as 16S rI-A (rr-rp) subgroup members (1). However, AluI rDNA and TaqI rp fragment patterns were unique, identifying Oso Grande-infecting strains as representatives of a new subgroup within the larger 16S rI (rr-rp) group. Cumulative rDNA and rp fragment profiles of the phytoplasma associated with the breeder's accession matched those of the Mexican periwinkle virescence phytoplasma, identifying this strain as a 16S rI-I (rr-rp) subgroup member (1) and a second possible etiological agent of SGP. This is the first report of phytoplasmas infecting strawberry in Florida. References: (1) D. E. Gundersen et al. Int. J. Syst. Bacteriol. 46:64, 1996. (2) P.-O. Lim and B. B. Sears. J. Bacteriol. 174:2602, 1993. (3) C. D. Smart et al. Appl. Environ. Microbiol. 62:2988, 1996.
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Jomantiene, R., J. D. Postman, H. G. Montano, J. L. Maas, R. E. Davis, and K. B. Johnson. "First Report of Clover Yellow Edge Phytoplasma in Corylus (Hazelnut)." Plant Disease 84, no. 1 (January 2000): 102. http://dx.doi.org/10.1094/pdis.2000.84.1.102b.
Повний текст джерелаАнотація:
During investigations into the cause of a stunt syndrome affecting cultivated European hazelnut trees (Corylus avellana L.) in Oregon, the clover yellow edge (CYE) phytoplasma was detected for the first time in this crop. The cause of hazelnut stunt syndrome (HSS) is unknown, but the disease has been transmitted by grafting and apparently has moved within orchards through root grafts (1). Severely affected trees persist for many years, but their nut production is greatly reduced. Previous attempts to detect viruses, bacteria, and other pathogens have been unsuccessful. HSS has been observed only in Oregon and already had been present for more than 10 years when it was first reported in 1970 (1). In June, 1999, leaf samples were collected from two affected and two apparently healthy (symptomless) hazelnut trees in a field plot at Oregon State University, Corvallis, and from a healthy greenhouse-grown tree. Leaf samples were sent to the USDA Beltsville, MD, laboratory, where they were assessed for phytoplasma infection, using nested polymerase chain reactions (PCRs). PCRs were primed by phytoplasma universal primer pairs P1/P7 and F2n/R2 (3) for amplification of phytoplasma 16S ribosomal (r) DNA (16S rRNA gene) sequences according to the procedures of Gunderson and Lee (2). Phytoplasma-characteristic 1.2-kbp DNA sequences were amplified from all field-tree samples. No DNA sequences were amplified from samples of the greenhouse-grown tree. Restriction fragment length polymorphism patterns of rDNA digested with AluI, KpnI, HhaI, HaeIII, HpaII, MseI, RsaI, and Sau3A1 endonucleases indicated that all diseased hazelnut trees as well as symptomless field trees were infected by a phytoplasma classified in group 16SrIII (peach X-disease group), subgroup B (III-B, type strain CYE phytoplasma). No phytoplasmas were detected in samples from the greenhouse-grown tree. Nucleotide sequences were determined for 16Sr DNA fragments amplified from the hazelnut CYE phytoplasma in nested PCRs primed with F2n/R2. The sequences were deposited in GenBank under Accession no. AF189288. Sequence similarity between 16Sr DNAs of the hazelnut CYE strain (CYE-Or) and the Canadian clover yellow edge strain (CYE-C, GenBank Accession no. AF175304) phytoplasma was 99.9%. Decline and yellows disorders of hazelnut in Germany and Italy have been associated with infections by apple proliferation, pear decline, and European stone fruit yellows phytoplasmas (4). These phytoplasmas are classified in 16Sr group X, the apple proliferation group of phytoplasmas. This is the first report of the CYE phytoplasma infecting Corylus. References: (1) H. R. Cameron. Plant Dis. Rep. 54:69, 1970. (2) D. E. Gunderson and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (3) R. Jomantiene et al. HortScience 33:1069, 1998. (4) C. Marcone et al. Plant Pathol. 45:857,1996.
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Akhtar, S., A. J. Khan, and R. W. Briddon. "A Distinct Strain of Chickpea chlorotic dwarf virus Infecting Pepper in Oman." Plant Disease 98, no. 2 (February 2014): 286. http://dx.doi.org/10.1094/pdis-07-13-0690-pdn.
Повний текст джерелаАнотація:
During a field survey in 2011, pepper (Capsicum annum) plants showing symptoms suggestive of geminivirus infection were observed in three fields in the Al-Sharqiya region of Oman. Symptoms observed included upward leaf curling leading to cupping and stunting with 15 to 25% disease incidence in surveyed fields. Total DNA was extracted from the leaves of seven symptomatic plants and subjected to rolling circle amplification (RCA). The RCA product was digested with several restriction endonucleases to obtain unit length of ~2.6 to 2.8, typical of geminivirus. Out of seven samples, only four yielded a product of ~2.6 kb in size by KpnI digestion. The fragments were cloned in pUC19 and sequenced. The partial sequences of four isolates were >95% identical to each other at the nucleotide (nt) level and thus only one isolate (P-25) was fully sequenced, determined to be 2,572 nt in length, and its sequence deposited in GenBank (KF111683). The P-25 sequence showed a genome organization typical of a mastrevirus, with four open reading frames (ORFs), two in virion-sense and two in complementary-sense. The virion and complementary-sense ORFs were separated by a long intergenic region, containing a predicted hairpin structure with the nonanucleotide sequence (TAATATTAC) in the loop, and a short intergenic region. An initial comparison to all sequences in the NCBI database using BlastN showed the isolate to have the highest level of sequence identity with isolates of the dicot-infecting mastrevirus Chickpea chlorotic dwarf virus (CpCDV). Subsequent alignments of all available CpCDV isolates using the species demarcation tool (2) showed the isolate P-25 to share between 83.6 and 90.3% identity to isolates of CpCDV available in databases, with the highest (90.3%) to CpCDV strain A originating from Syria (FR687959) (3). Amino acid sequence comparison showed that the predicted proteins encoded by the four ORFs of P-25 (coat protein [CP], movement protein [MP], replication associated protein A [RepA], and RepB) share 91.5, 88.2, 89.1, and 90.8% amino acid sequence identity, respectively, with the homologous proteins of the CpCDV isolate from Syria. Based on the recently revised mastreviruses species and strain demarcation criteria (78 and 94% whole genome nt identity, respectively) proposed by Muhire et al. (2), the results indicate that isolate P-25 represents a newly identified strain (strain F) of CpCDV. The presence of CpCDV in symptomatic pepper plants was further confirmed by Southern blot hybridization technique using digoxygenin (DIG) labeled probe prepared from CpCDV isolate P-25. The genus Mastrevirus consists of geminiviruses with single component genomes that are transmitted by leafhoppers. Mastreviruses have so far only been identified in the Old World and infect either monocotyledonous or dicotyledonous plants (1). To our knowledge, this is the first report of a mastrevirus on the Arabian Peninsula and the first record of pepper as host of CpCDV. Recently, several begomoviruses of diverse geographic origins have been found infecting vegetable crops in Oman. The propensity of geminiviruses to evolve through recombination may lead to evolution of recombinant CpCDV with new host adaptability. Due to extensive agricultural/travel links of Oman with rest of the world, there exists high probability for the spread of this virus. References: (1) M. I. Boulton. Physiol. Mol. Plant Pathol. 60:243, 2002. (2) B. Muhire et al. Arch. Virol. 158:1411, 2013 (3) H. Mumtaz et al. Virus Genes 42:422, 2011.
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Adamovic, D., I. Djalovic, P. Mitrovic, S. Kojic, M. Starovic, B. Purar, and D. Josic. "First Report of 16SrXII-A Subgroup Phytoplasma (Stolbur) Associated with Reddening of Oenothera biennis in Serbia." Plant Disease 98, no. 6 (June 2014): 841. http://dx.doi.org/10.1094/pdis-12-13-1225-pdn.
Повний текст джерелаАнотація:
Evening primrose (Oenothera biennis L.) is a biennial medicinal, edible, and ornamental plant species. It has attracted great interest for its seed oil that contains gamma linolenic acid, thus distinguishing this plant as a main commercial source of this essential fatty acid (4). This species has been grown as a permanent member of a medicinal plant collection established near Backi Petrovac (northern Serbia) for 22 years. The first disease symptoms were recognized as red spots on leaf rosette in July 2011, spreading gradually during vegetative growth and covering 1/3 to 1/2 of the leaf surface. Symptoms, observed on 16% of the plants (32 of 200) in the second half of May 2012 and on 23% (69 of 300) at the beginning of May 2013, appeared as reddening of lower leaves of flower-bearing stems. Affected plants exhibited stunted growth, while reddening spread over other leaves of flower-bearing stems. In severely affected plants, the flower-bearing stems were poorly developed, frequently forming witches' brooms. For that reason, 30 reddened and 20 symptomless leaves (2 leaves per plant) were sampled in both July 2012 and 2013 and total nucleic acids were extracted. Direct PCR assays were performed using phytoplasma universal primer pair P1/P7 (2) to amplify 1,800-bp fragments (the 16S rRNA gene, the 16S-23S intergenic spacer region, and a part of the 5′ region of the 23S rRNA gene). PCR products were used in nested PCR with primers R16F2n/R2 (2) to amplify 1,200-bp fragments. The identification of phytoplasmas was done using RFLP (restriction fragments length polymorphisms) analyses of R16F2n/R2 amplicons digested with AluI, Kpn I, HpaII, TruI1, or HhaI endonucleases (Thermo Scientific, Lithuania) (2). RFLP patterns were identical to that of STOL reference strain of the 16SrXII-A subgroup, indicating that symptomatic plants were infected with phytoplasma (2). The 16S rDNA nucleotide sequence of representative strain E7 was deposited in GenBank under accession number KF850526. The BLASTn search showed 100% homology to an Iranian strain (KF263684.1) from peach and Serbian strains JQ730742.1 and JQ730750 from valerian and corn, respectively, all belonging to ‘Candidatus Phytoplasma solani’ (Stolbur). Sequencing data confirmed the association of Stolbur phytoplasma with affected O. biennis plants. It has already been reported that phytoplasma infection caused yellows disease of O. biennis (1). Also, the virescence of O. hookeri was associated with phytoplasma strain OAY from aster yellows (AY) group (subgroups 16SrI-B), and selected as the reference strain for the novel taxon ‘Ca. P. asteris’ (3). Here we provide the first report of naturally occurring Stolbur phytoplasma disease of O. biennis in Serbia. References: (1) S. F. Hwang et al. Z. Pflanzenkr. Pflanzenschutz 105:64, 1998. (2) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) I.-M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:1037, 2004. (4) E. Small and P. M. Catling. Canadian Medicinal Crops. NRC Research Press, Ottawa, Ontario, Canada, 1999.
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Lin, ZhaoWei, Weiwei Song, Qinghua Tang, and Xiuli Meng. "First Report of 16SrII Group Related Phytoplasma Associated with Areca Palm Yellow Leaf Disease on Areca catechu in China." Plant Disease, July 19, 2023. http://dx.doi.org/10.1094/pdis-03-23-0587-pdn.
Повний текст джерелаАнотація:
The areca palm, Areca catechu L., family Arecaceae is an important herbal medicine which has potential for the treatment of parasitic diseases, digestive function disorders and depression (Peng et al. 2015). Yellow leaf disease (YLD), caused by phytoplasma, is a destructive disease of Areca catechu. In 1981, the YLD was first discovered in Tunchang, Hainan, China. According to the investigation in 2020, the occurrence area of YLD was 32 102.38 hm2 in Hainan, China, resulting in 50%-60% yield loss. Previous researchers based on 16S rDNA gene PCR amplification analysis showed that YLD in Hainan was caused by 16SrI group phytoplasma (Che et al. 2010). In August, 2022, yellow leaf symptoms were observed on middle and lower leaves of Areca catechu. Forty symptomatic plants and three asymptomatic samples were collected in Wenchang, Hainan, China (19°33′9″N, 110°48′5″E). Forty-three samples (0.1g each) were used to extract total DNA (TIANGEN plant genomic DNA extraction kit). Phytoplasma universal primers named P1/P7 (Schneider et al. 1995) and R16F2n/R16R2 (Gundersen and Lee 1996) for 16Sr DNA and primers named fTuf1/rTuf1 and fTufu/rTufu (Schneider et al. 1997) for tuf genes were used for amplifying phytoplasma sequences from isolated DNA samples by nested PCR. No fragment was amplified in asymptomatic plants and four out of forty symptomatic samples could amplify target fragment. R16F2n/R16R2 amplicons (1 248 bp) and fTufu/rTufu amplicons (845 bp) from four symptomatic Areca catechu samples were sequenced in BGI (https://genomics.cn/). The 16Sr DNA GenBank accession numbers of four positive strains (named HNWC5, HNDZ1, HNDZ3 and HNDZ6) were OQ586072, OQ586085, OQ586086, OQ586087, respectively and the tuf GenBank accession numbers were OQ595209, OQ595210, OQ595211, OQ595212, respectively. Sequence alignment showed that the 16S rDNA and tuf sequence of HNDZ1, HNDZ3 and HNDZ6 were 100% consistent. 16S rDNA of HNWC5 was 99.96% consistent with HNDZ1 and tuf of HNWC5 was 98.31% consistent with HNDZ1. Interestingly, blast search based on 16S rDNA gene of HNWC5 showed 100% sequence identity with that of 16SrII group phytoplasma such as 'Eclipta prostrata' phytoplasma strain Ep1(MH144204.1), 'Aeschynomene americana' phytoplasma isolate AA1(MH231157.1) and 'Acacia confusa' witches'-broom phytoplasma isolate HK6(ON408364.1). Blast search based on tuf gene of HNWC5 showed 98.7% sequence identity with that of bamboo witches'-broom phytoplasma (FJ853160.1) and 91.02% sequence identity with that of 'podocarpus nagi' fasciation phytoplasma (KR633146) and 90.78% sequence identity with that of 'Musa acuminata' elephantiasis disease phytoplasma (MF983708). The phylogenetic tree was constructed based on 16Sr DNA gene by MEGA 7.0 employing neighbor-joining (NJ) method with 1000 bootstrap value (Kumar et al. 2016). The result indicated that the HNWC5, HNDZ1, HNDZ3 and HNDZ6 phytoplasma strains clustered a subclade in 16SrII group. The virtual RFLP analysis based on the 16Sr DNA gene sequence was performed by the online phytoplasma classification tool iPhyClassifier (Zhao et al. 2009) using restriction endonucleases of AluI, BamHI, BfaI, BstUI, DraI, EcoRI, HaeIII, HhaI, HinfI, HpaI, HpaII, KpnI, Sau3AI, MseI, RsaI, SspI and TaqI. The result indicated that HNWC5 was most similar to the reference pattern of peanut witches'-broom phytoplasma (16SrII-A subgroup, GenBank accession: L33765) and the pattern similarity coefficient of HNWC5 is 1.00. However, the HpaII restriction endonuclease pattern of HNDZ1, HNDZ3 and HNDZ6 was different from L33765 and the similarity coefficient was 0.97, which indicated this strain may represent a new subgroup within the 16SrII group. To our knowledge, this is the first report of 16SrII group related phytoplasma associated with YLD on Areca catechu in China. Our study contributes to understanding the polymorphism of phytoplasma causing YLD and provides an important reference for pathogen specific detection.