scholarly journals Clover Proliferation Group (16SrVI) Subgroup A (16SrVI-A) Phytoplasma is a Probable Causal Agent of Potato Purple Top Disease in Washington and Oregon

Plant Disease ◽  
2004 ◽  
Vol 88 (4) ◽  
pp. 429-429 ◽  
Author(s):  
I.-M. Lee ◽  
K. D. Bottner ◽  
J. E. Munyaneza ◽  
G. A. Secor ◽  
N. C. Gudmestad
Keyword(s):  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Nested Polymerase Chain Reaction ◽  
Axillary Shoots ◽  
Rdna Sequences ◽  
Etiological Role ◽  
16S Rdna Sequences ◽  
Purple Top Disease ◽  
Potato Purple Top ◽  
Potato Seedlings

An epidemic of purple top disease of potato (Solanum tuberosum) occurred in the Columbia Basin Region of Washington and Oregon in 2002 and 2003, causing great economic loss in the potato industry (1). Symptoms of potato purple top (PPT) were characterized by upright terminal shoots, upward leaf rolling, chlorosis, red or purplish discoloration of new leaves, proliferation of axillary shoots with basal swelling, and the formation of aerial tubers. Preliminary studies on PPT disease suggested phytoplasma as a possible cause (1). In this study, 78 potato samples (including five asymptomatic) were collected from five fields throughout the region. A nested polymerase chain reaction (PCR) with primer pair P1/P7 in the first amplification followed with primer pair R16F2n/R16R2 was performed to detect the presence of phytoplasmas in infected plants (2). Restriction fragment length polymorphism (RFLP) and phylogenetic analyses of amplified 16S rDNA sequences were used for phytoplasma identification. Eighty-four percent (63% in the first amplification) of the symptomatic samples and 60% (0% in the first amplification) of the asymptomatic samples tested positive. Low phytoplasma titers and the presence of PCR inhibitors accounts for the low detection rate in the first PCR amplifications. RFLP analyses of 16S rDNA with enzymes MseI, AluI, HhaI, RsaI, and HpaII indicated that the phytoplasma associated with PPT belonged to the clover proliferation (CP) group (16SrVI) subgroup A (16SrVI-A) (2). 16SrVI-A currently consists of three members, CP (GenBank Accession No. AY500130), potato witches'-broom (GenBank Accession No. AY500818), and vinca virescence (VR) (GenBank Accession No. AY500817), a strain of beet leafhopper-transmitted virescence agent (BLTVA) phytoplasma (2). The taxonomic affiliation of PPT phytoplasma was confirmed by phylogenetic analysis of cloned 16S rDNA (GenBank Accession Nos. PPT4, AY496004; PPT8, AY496005). The 16S rDNA sequences of the PPT strains were closely related to VR with 99.7% sequence homology compared with 99.2% with CP. A high correlation between the symptoms and the presence of 16SrVI-A phytoplasmas in the potato plants suggests that these phytoplasmas play an etiological role in PPT disease. To gain further evidence, a modified test of Koch's postulates was conducted. Infected tissues from four phytoplasma-positive potato samples (including PPT4 and PPT8) were grafted onto healthy potato seedlings. Within 60 days after grafting, the potato seedlings developed symptoms similar to those in the original diseased samples. The newly infected plants were maintained through cuttings. RFLP analysis of 16S rDNA indicated that the phytoplasmas detected in each of the seedlings and cuttings were identical to those in the scions. These results confirmed the probable etiological role of CP group, subgroup 16SrVI-A phytoplasma strains in PPT disease in Washington and Oregon. There are two other confirmed cases of phytoplasmas (BLTVA and aster yellows phytoplasma) associated with PPT disease in Utah (4) and Mexico (3). References: (1) P. B. Hamm et al. Potato Prog. Vol. 3, No. 1, 2003. (2) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) N. E. Leyva-Lopez et al. Can. J. Microbiol. 48:1062, 2002. (4) C. D. Smart et al. Phytopathology 83:1399, 1993.

scholarly journals 16S rDNA sequences and phylogenetic analyses ofMicrocystisstrains with and without phycoerythrin

1998 ◽  
Vol 164 (1) ◽  
pp. 119-124 ◽  
Author(s):  
Shigeto Otsuka ◽  
Shoichiro Suda ◽  
Renhui Li ◽  
Masayuki Watanabe ◽  
Hiroshi Oyaizu ◽  
...  
Keyword(s):  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Rdna Sequences ◽  
16S Rdna Sequences

scholarly journals Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea

2004 ◽  
Vol 54 (2) ◽  
pp. 487-491 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Phenotypic Properties ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Isoprenoid Quinones ◽  
Type Strains

A Gram-negative, motile, non-spore-forming, rod-shaped strain, TF-27T (=KCCM 41648T=JCM 11814T), was isolated from a tidal flat in Korea. This organism grew well at 25–35 °C, with optimum growth at 30 °C. Strain TF-27T grew optimally in the presence of 2 % NaCl; it did not grow without NaCl or in the presence of >8 % NaCl. Strain TF-27T simultaneously contained both menaquinones and ubiquinones as isoprenoid quinones. The predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acids in strain TF-27T were iso-C15 : 0 (20·6 %) and iso-C15 : 0 2-OH and/or C16 : 1 ω7c (21·1 %). The DNA G+C content of strain TF-27T was 42 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-27T falls within the radiation of the cluster that is encompassed by the genus Shewanella. Levels of 16S rDNA sequence similarity between strain TF-27T and the type strains of Shewanella species were 93·2–96·8 %. On the basis of phenotypic properties and phylogenetic data, strain TF-27T should be placed in the genus Shewanella as a novel species, for which the name Shewanella gaetbuli sp. nov. is proposed.

Monophyly and phylogenetic relationships of Thereva and therevine genus-groups (Insecta:Diptera:Therevidae) based on EF-1α, 28S rDNA and mitochondrial 16S rDNA sequences

2007 ◽  
Vol 21 (3) ◽  
pp. 279 ◽  
Author(s):  
Kevin C. Holston ◽  
Michael E. Irwin ◽  
Brian M. Wiegmann
Keyword(s):  
16S Rdna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
28S Rdna ◽  
Partial Recovery ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Holarctic Region ◽  
Species Groups

Phylogenetic analyses using 28S rDNA, elongation factor (EF)-1α, and mt 16S rDNA sequences were performed to test the monophyly of Thereva Latreille. Two of the three Afrotropical Thereva species groups lack the genitalia characters that unambiguously diagnose Thereva in the Holarctic Region, but phylogenetic relationships among Thereva species groups and therevine genera are poorly understood. Using an extensive taxonomic sample (39 of the 62 therevine genera) and Thereva, sensu lato (15 spp.), simultaneous analyses of all three gene partitions recovered Nearctic and Palaearctic Thereva species in a well supported clade that includes the Afrotropical seminitida-group but excludes the Afrotropical analis- and turneri-groups. Stronger phylogenetic signal from the EF-1α partition, measured by the skewness statistic and proportion of total parsimony informative characters, dominated conflicting signal from the 16S partition and weaker, but more congruent, signal from 28S. Reducing the taxonomic sample in analyses of Therevinae reduced homoplasy, increased phylogenetic structure and partitioned Bremer support values and reduced incongruence with 28S for the 16S partition. Although molecular analyses yielded partial recovery of informal therevine genus-groups, morphological diagnoses of higher-level groups are poorly supported with the exception of Cyclotelini. The ‘Holarctic radiation’ refers to a diverse clade of genera closely related to Pandivirilia Irwin & Lyneborg and Acrosathe Irwin & Lyneborg widely distributed throughout the Holarctic Region that is the sister-group to Thereva, sensu stricto. Results from these analyses underscore the importance of male and female genitalia characters in recognising monophyletic groups and regional endemism in therevine diversification.

scholarly journals Phylogenetic Analysis of Nonthermophilic Members of the Kingdom Crenarchaeota and Their Diversity and Abundance in Soils

1998 ◽  
Vol 64 (11) ◽  
pp. 4333-4339 ◽  
Author(s):  
Daniel H. Buckley ◽  
Joseph R. Graber ◽  
Thomas M. Schmidt
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Pcr Primers ◽  
Soil Samples ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Long Term Ecological Research

ABSTRACT Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom Crenarchaeotathat is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (−1.5 to 32°C), in contrast to the high-temperature environments (temperature, >80°C) required for growth of the currently recognized crenarchaeotal species. We determined the diversity and abundance of the nonthermophilic members of the Crenarchaeota in soil samples taken from cultivated and uncultivated fields located at the Kellogg Biological Station’s Long-Term Ecological Research site (Hickory Corners, Mich.). Clones were generated from 16S rDNA that was amplified by using broad-specificity archaeal PCR primers. Twelve crenarchaeotal sequences were identified, and the phylogenetic relationships between these sequences and previously described crenarchaeotal 16S rDNA sequences were determined. Phylogenetic analyses included nonthermophilic crenarchaeotal sequences found in public databases and revealed that the nonthermophilic Crenarchaeota group is composed of at least four distinct phylogenetic clusters. A 16S rRNA-targeted oligonucleotide probe specific for all known nonthermophilic crenarchaeotal sequences was designed and used to determine their abundance in soil samples. The nonthermophilicCrenarchaeota accounted for as much as 1.42% ± 0.42% of the 16S rRNA in the soils analyzed.

scholarly journals Characterization of a ‘Bacteroidetes’ symbiont in Encarsia wasps (Hymenoptera: Aphelinidae): proposal of ‘Candidatus Cardinium hertigii’

2004 ◽  
Vol 54 (3) ◽  
pp. 961-968 ◽  
Author(s):  
Einat Zchori-Fein ◽  
Steve J. Perlman ◽  
Suzanne E. Kelly ◽  
Nurit Katzir ◽  
Martha S. Hunter
Keyword(s):  
Electron Microscopy ◽  
16S Rdna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences

Previously, analysis of 16S rDNA sequences placed a newly discovered lineage of bacterial symbionts of arthropods in the ‘Bacteroidetes’. This symbiont lineage is associated with a number of diverse host reproductive manipulations, including induction of parthenogenesis in several Encarsia parasitoid wasps (Hymenoptera: Aphelinidae). In this study, electron microscopy and phylogenetic analysis of the 16S rRNA and gyrB genes of symbionts from Encarsia hispida and Encarsia pergandiella are used to describe and further characterize these bacteria. Phylogenetic analyses based on these two genes showed that the Encarsia symbionts are allied with the Cytophaga aurantiaca lineage within the ‘Bacteroidetes’, with their closest described relative being the acanthamoeba symbiont ‘Candidatus Amoebophilus asiaticus’. The Encarsia symbionts share 97 % 16S rDNA sequence similarity with Brevipalpus mite and Ixodes tick symbionts and 88 % sequence similarity with ‘Candidatus A. asiaticus’. Electron microscopy revealed that many of the bacteria found in the ovaries of the two Encarsia species contained a regular, brush-like array of microfilament-like structures that appear to be characteristic of the symbiont. Finally, the role of this bacterium in parthenogenesis induction in E. hispida was confirmed. Based on phylogenetic analyses and electron microscopy, classification of the symbionts from Encarsia as ‘Candidatus Cardinium hertigii’ is proposed.

Two Intracellular Symbiotic Bacteria from the Mulberry Psyllid Anomoneura mori (Insecta, Homoptera)

1998 ◽  
Vol 64 (10) ◽  
pp. 3599-3606 ◽  
Author(s):  
Takema Fukatsu ◽  
Naruo Nikoh
Keyword(s):  
In Situ Hybridization ◽  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Symbiotic Bacteria ◽  
Polymorphism Analysis ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Molecular Phylogenetic

ABSTRACT We characterized the intracellular symbiotic bacteria of the mulberry psyllid Anomoneura mori by performing a molecular phylogenetic analysis combined with in situ hybridization. In its abdomen, the psyllid has a large, yellow, bilobed mycetome (or bacteriome) which consists of many round uninucleated mycetocytes (or bacteriocytes) enclosing syncytial tissue. The mycetocytes and syncytium harbor specific intracellular bacteria, the X-symbionts and Y-symbionts, respectively. Almost the entire length of the bacterial 16S ribosomal DNA (rDNA) was amplified and cloned from the whole DNA ofA. mori, and two clones, the A-type and B-type clones, were identified by restriction fragment length polymorphism analysis. In situ hybridization with specific oligonucleotide probes demonstrated that the A-type and B-type 16S rDNAs were derived from the X-symbionts and Y-symbionts, respectively. Molecular phylogenetic analyses of the 16S rDNA sequences showed that these symbionts belong to distinct lineages in the γ subdivision of the Proteobacteria. No 16S rDNA sequences in the databases were closely related to the 16S rDNA sequences of the X- and Y-symbionts. However, the sequences that were relatively closely related to them were the sequences of endosymbionts of other insects. The nucleotide compositions of the 16S rDNAs of the X- and Y-symbionts were highly AT biased, and the sequence of the X-symbiont was the most AT-rich bacterial 16S rDNA sequence reported so far.

scholarly journals Alteromonas litorea sp. nov., a slightly halophilic bacterium isolated from an intertidal sediment of the Yellow Sea in Korea

2004 ◽  
Vol 54 (4) ◽  
pp. 1197-1201 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Soo-Hwan Yeo ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Halophilic Bacterium ◽  
The Yellow Sea ◽  
Intertidal Sediment ◽  
Phenotypic Properties ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Slightly Halophilic Bacterium ◽  
Type Strains

A Gram-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain TF-22T, was isolated from an intertidal sediment in Korea. This organism grew optimally at 30–37 °C and in the presence of 2–5 % (w/v) NaCl. It did not grow without NaCl or in the presence of more than 14 % (w/v) NaCl. Strain TF-22T was characterized chemotaxonomically as having ubiquinone-8 as the predominant respiratory lipoquinone and C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c as the major fatty acids. The DNA G+C content of strain TF-22T was 46·0 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-22T falls within the γ-subclass of the Proteobacteria and forms a coherent cluster with Alteromonas macleodii and Alteromonas marina. Levels of 16S rDNA similarity between strain TF-22T and the type strains of two Alteromonas species were in the range 98·1–98·6 %. The level of DNA–DNA relatedness between strain TF-22T and the type strains of two Alteromonas species was 15·7–18·5 %. Therefore, on the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain TF-22T should be placed in the genus Alteromonas as a novel species, for which the name Alteromonas litorea sp. nov. is proposed. The type strain is TF-22T (=KCCM 41775T=JCM 12188T).

scholarly journals An Emerging Potato Purple Top Disease Associated with a New 16SrIII Group Phytoplasma in Montana

Plant Disease ◽  
2009 ◽  
Vol 93 (9) ◽  
pp. 970-970 ◽  
Author(s):  
I.-M. Lee ◽  
K. D. Bottner ◽  
M. Sun
Keyword(s):  
16S Rdna ◽  
Nested Pcr ◽  
Restriction Enzymes ◽  
The United States ◽  
Disease Spread ◽  
Potential Threat ◽  
Universal Primer ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Potato Purple Top

Potato purple top (PPT) is a devastating disease that occurs in the United States, Canada, Mexico, Russia, and elsewhere causing great economic loss to the potato industry through substantially reduced tuber yield and quality. Chips and fries processed from infected tubers often develop brown discoloration, greatly reducing their marketability. At least seven distinct phytoplasma strains belonging to five different phytoplasma groups (16SrI, 16SrII, 16SrVI, 16SrXII, and 16SrXVIII) have been reported to cause purple top and related symptoms in potato (3). During an unusual drought in 2007, a newly emerging potato disease with extensive yellowish or reddish purple discoloration of terminal shoots and leaves, similar to PPT symptoms, was observed in isolated potato fields in Montana where over 50% of plants exhibited symptoms. Shoot tissues were collected from three symptomatic plants and 17 tubers randomly collected from 17 other symptomatic plants. The tubers were cold treated to induce sprouting and then planted in the greenhouse. All tubers produced plants of which seven exhibited PPT symptoms including severe stunting. Total nucleic acid was extracted from leaf veinal tissue, stolons, or tubers of 10 symptomatic and 10 asymptomatic plants (both field-collected and greenhouse samples) as previously described (3). A nested-PCR assay, using universal primer pair P1/16S-SR followed by R16F2n/R16R2n, was performed as previously described (2,3) to detect phytoplasmas in these samples. Phytoplasma strains were detected in all symptomatic plants. Restriction fragment length polymorphism (RFLP) analyses of nested-PCR products (approximately 1.2 kb) with seven key restriction enzymes (AluI, MseI, HhaI, Tsp509I, HpaII, RsaI, and BfaI) indicated that all samples contained a very similar or identical phytoplasma most closely related to reference strain MW1 (belonging to subgroup 16SrIII-F) (1). Analysis of cloned 16S rDNA sequences confirmed the identity of this new phytoplasma and sequences of three representative PPT-MT strains were deposited in GenBank with Accession Nos. FJ226074–FJ226076. Computer-simulated RFLP analyses of 1.2-kb 16S rDNA sequences of this new phytoplasma and representative members in the peach X-disease phytoplasma group (16SrIII) available in GenBank indicated the strain is distinct and represents a new subgroup, 16SrIII-M (4). This study also indicated that the phytoplasma is tuber transmissible since approximately 35% of plants produced from infected tubers collected in this study developed symptoms. Transmission via infected tubers may pose a potential threat for disease spread by planting uncertified seed potatoes. To our knowledge, this is the first report of 16SrIII group phytoplasmas-associated diseases in potato. A phytoplasma closely related to the PPT-MT strains has recently been detected in potato seedlings exhibiting purple top, rosette, and stunting in Alaska (GenBank Accession No. FJ376628). 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. (3) I.-M. Lee et al. Int. J. Syst. Evol. Microbiol. 56:1593, 2006. (4) W. Wei et al. Int. J. Syst. Evol. Microbiol. 58:2368, 2008.

scholarly journals Molecular analysis of the mitochondrial markers COI, 12S rDNA and 16S rDNA for six species of Iranian scorpions

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Parisa Soltan-Alinejad ◽  
Javad Rafinejad ◽  
Farrokh Dabiri ◽  
Piero Onorati ◽  
Olle Terenius ◽  
...  
Keyword(s):  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Coi Gene ◽  
Diagnostic Tools ◽  
Morphological Identification ◽  
Species Determination ◽  
Important Species ◽  
Mitochondrial Markers ◽  
12S Rdna ◽  
Rdna Sequences

Abstract Objectives Annually, 1.2 million humans are stung by scorpions and severely affected by their venom. Some of the scorpion species of medical importance have a similar morphology to species with low toxicity. To establish diagnostic tools for surveying scorpions, the current study was conducted to generate three mitochondrial markers, Cytochrome Oxidase I (COI gene), 12S rDNA and 16S rDNA for six species of medically important Iranian scorpions: Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus, M. eupeus, Odontobuthus doriae, and Scorpio maurus. Results Phylogenetic analyses of the obtained sequences corroborated the morphological identification. For the first time, 12S rDNA sequences are reported from Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus and M. eupeus and also the 16S rDNA sequence from Hottentotta saulcyi. We conclude that the mitochondrial markers are useful for species determination among these medically important species of scorpions.

scholarly journals The phylogeny of the genusYersiniabased on 16S rDNA sequences

1993 ◽  
Vol 114 (2) ◽  
pp. 173-177 ◽  
Author(s):  
A. Ibrahim ◽  
B.M. Goebel ◽  
W. Liesack ◽  
M. Griffiths ◽  
E. Stackebrandt
Keyword(s):  
16S Rdna ◽  
Rdna Sequences ◽  
16S Rdna Sequences
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