scholarly journals Haplotypes of “Candidatus Liberibacter europaeus” also separate by geography and host species

2015 ◽  
Author(s):  
Warrick R Nelson
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Host Species ◽  
Biocontrol Agent ◽  
Intergenic Spacer ◽  
Intergenic Spacer Region ◽  
Scotch Broom ◽  
Candidatus Liberibacter ◽  
Pear Trees ◽  
Historical Accounts

“Candidatus Liberibacter europaeus” (Leu) is one of six currently known Liberibacter species. It is known primarily from pear and related species across Europe, and from Scotch broom and its associated psyllids in New Zealand (introduced from Britain). The psyllids were introduced to New Zealand as a biocontrol agent for broom and it is thought the bacterium may have been introduced as an endosymbiont of the psyllids. No symptoms in apple or pear trees have been reported, but mild symptoms can occur in broom. 16S and 16S–23S intergenic spacer region DNA sequences of this species are available from GenBank. Analysis of these sequences and associated ecological descriptions indicates the occurrence of two haplotypes, LeuA and LeuB, defined not only genetically but also by geographic range as well as by plant/psyllid host species composition. Liberibacter species are new to science and haplotype identifications enable historical accounts of relationships and spread to be generated.

scholarly journals Haplotypes of “Candidatus Liberibacter europaeus” also separate by geography and host species

2014 ◽  
Author(s):  
Warrick R Nelson
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Host Species ◽  
Biocontrol Agent ◽  
Intergenic Spacer ◽  
Intergenic Spacer Region ◽  
Scotch Broom ◽  
Candidatus Liberibacter ◽  
Pear Trees ◽  
Historical Accounts

“Candidatus Liberibacter europaeus” (Leu) is one of six currently known Liberibacter species. It is known primarily from pear and related species across Europe, and from Scotch broom and its associated psyllids in New Zealand (introduced from Britain). The psyllids were introduced to New Zealand as a biocontrol agent for broom and it is thought the bacterium may have been introduced as an endosymbiont of the psyllids. No symptoms in apple or pear trees have been reported, but mild symptoms can occur in broom. 16S and 16S–23S intergenic spacer region DNA sequences of this species have been deposited in GenBank. Analysis of these sequences and associated ecological descriptions indicates the occurrence of two haplotypes, LeuA and LeuB, defined not only genetically but also by geographic range as well as by plant/psyllid host species composition. Liberibacter species are new to science and haplotype identifications enable historical accounts of relationships and spread to be generated.

scholarly journals Haplotypes of “Candidatus Liberibacter europaeus” also separate by geography and host species

2015 ◽  
Author(s):  
Warrick R Nelson
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Host Species ◽  
Biocontrol Agent ◽  
Intergenic Spacer ◽  
Intergenic Spacer Region ◽  
Scotch Broom ◽  
Candidatus Liberibacter ◽  
Pear Trees ◽  
Historical Accounts

“Candidatus Liberibacter europaeus” (Leu) is one of six currently known Liberibacter species. It is known primarily from pear and related species across Europe, and from Scotch broom and its associated psyllids in New Zealand (introduced from Britain). The psyllids were introduced to New Zealand as a biocontrol agent for broom and it is thought the bacterium may have been introduced as an endosymbiont of the psyllids. No symptoms in apple or pear trees have been reported, but mild symptoms can occur in broom. 16S and 16S–23S intergenic spacer region DNA sequences of this species are available from GenBank. Analysis of these sequences and associated ecological descriptions indicates the occurrence of two haplotypes, LeuA and LeuB, defined not only genetically but also by geographic range as well as by plant/psyllid host species composition. Liberibacter species are new to science and haplotype identifications enable historical accounts of relationships and spread to be generated.

scholarly journals Population Structure of Plasmid-Containing Strains of Streptococcus mutans, a Member of the Human Indigenous Biota

2006 ◽  
Vol 189 (4) ◽  
pp. 1238-1243 ◽  
Author(s):  
Page W. Caufield ◽  
Deepak Saxena ◽  
David Fitch ◽  
Yihong Li
Keyword(s):  
Streptococcus Mutans ◽  
Dna Sequences ◽  
Evolutionary History ◽  
Hypervariable Region ◽  
Intergenic Spacer ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Intergenic Spacer Region ◽  
Asian Clade ◽  
History Of

ABSTRACT There are suggestions that the phylogeny of Streptococcus mutans, a member of the human indigenous biota that is transmitted mostly mother to child, might parallel the evolutionary history of its human host. The relatedness and phylogeny of plasmid-containing strains of S. mutans were examined based on chromosomal DNA fingerprints (CDF), a hypervariable region (HVR) of a 5.6-kb plasmid, the rRNA gene intergenic spacer region (IGSR), serotypes, and the genotypes of mutacin I and II. Plasmid-containing strains were studied because their genetic diversity was twice as great as that of plasmid-free strains. The CDF of S. mutans from unrelated human hosts were unique, except those from Caucasians, which were essentially identical. The evolutionary history of the IGSR, with or without the serotype and mutacin characters, clearly delineated an Asian clade. Also, a continuous association with mutacin II could be reconstructed through an evolutionary lineage with the IGSR, but not for serotype e. DNA sequences from the HVR of the plasmid produced a well-resolved phylogeny that differed from the chromosomal phylogeny, indicating that the horizontal transfer of the plasmid may have occurred multiple times. The plasmid phylogeny was more congruent with serotype e than with mutacin II evolution, suggesting a possible functional correlation. Thus, the history of this three-tiered relationship between human, bacterium, and plasmid supported both coevolution and independent evolution.

scholarly journals First Report of the Causal Agent of Huanglongbing (“Candidatus Liberibacter asiaticus”) Infecting Kumquat in Taiwan

Plant Disease ◽  
2006 ◽  
Vol 90 (10) ◽  
pp. 1360-1360 ◽  
Author(s):  
C.-H. Tsai ◽  
H.-J. Su ◽  
Y.-C. Liao ◽  
T.-H. Hung
Keyword(s):  
16S Rrna ◽  
Lateral Roots ◽  
Severe Disease ◽  
Intergenic Spacer ◽  
Sieve Tube ◽  
Causal Agent ◽  
Candidatus Liberibacter Asiaticus ◽  
Intergenic Spacer Region ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

Huanglongbing (greening) disease caused by a nonculturable, phloem-limited bacterium is a severe disease of citrus. On the basis of the influence of temperature on host symptoms and the causal agent, this disease can be categorized as Asian caused by “Candidatus Liberibacter asiaticus”, African caused by “Ca. L. africanus”, and American caused by “Ca. L. americanus”. Kumquat (Fortunella margarita (Lour.) Swingle), a member of the Rutaceae is an economically important crop for export and local consumption in Taiwan. Recently, a Huanglongbing-like disease was found on kumquat in Yilan County, the largest kumquat-producing area in northeastern Taiwan. Even though the disease has been reported on Citrus spp. from Taiwan, it has never been reported on kumquat. Symptoms of infected kumquat were mottling, yellowing, hardening, and curling of leaves followed by premature defoliation, twig dieback, decay of feeder rootlets and lateral roots, and ultimately the death of the entire plant. Typical sieve-tube-restricted bacteria were observed in kumquat cells by electron microscopy (1). In addition, psyllid-transmission tests demonstrated that the Asian psyllid (Diaphorina citri) could transmit this bacterium to healthy kumquats. Positive bud graft transmissions were obtained to F. margarita, F. japonica (Thunb.) Swingle, F. obovata Hort. ex Tanaka, Luchen sweet orange (Citrus sinensis (L.) Osb.), and Wentan pummelo (C. maxima f. sp. butan Hay.). These inoculated plants showed symptoms in 3 to 8 months, and bacteria could be detected by polymerase chain reaction (PCR) using a common primer pair that amplified a 226-bp specific DNA fragment (2). For further molecular identification, the bacterial DNA was extracted from the inoculated plants and PCR was performed by using two sets of primers selected from the 16S rRNA region (GenBank Accession No. L22532) and 16S/23S intergenic spacer region (GenBank Accession No. AB019793). The expected DNA fragments of 1,389 bp and 862 bp were, respectively, amplified from symptomatic plants but not from healthy plants. The PCR products were cloned and sequenced (GenBank Accession Nos. DQ302750 and DQ207841). The 16S rRNA has 98 to 99% identity and 16S/23S intergenic spacer region has 99% identity to the corresponding region of “Ca. L. asiaticus” in GenBank. These molecular analyses confirm the presence of “Ca. L. asiaticus” in kumquat. Since Huanglongbing has been rarely reported naturally on kumquat, further analysis of this bacterium as a special strain of “Ca. L. asiaticus” is needed. References: (1) M. Garnier et al. Ann. Microbiol. 135A:169, 1984. (2) T. H. Hung et al. J. Phytopathol. 147:599, 1999.

scholarly journals Identification of Porphyromonas gingivalis Strains by Heteroduplex Analysis and Detection of Multiple Strains

1999 ◽  
Vol 37 (12) ◽  
pp. 3906-3911 ◽  
Author(s):  
Eugene J. Leys ◽  
James H. Smith ◽  
Sharon R. Lyons ◽  
Ann L. Griffen
Keyword(s):  
Porphyromonas Gingivalis ◽  
Dna Sequences ◽  
Allelic Variation ◽  
Intergenic Spacer ◽  
Heteroduplex Analysis ◽  
Clinical Samples ◽  
Specific Primers ◽  
Intergenic Spacer Region ◽  
Species Specific ◽  
Multiple Strains

Heteroduplex analysis has been used extensively to identify allelic variation among mammalian genes. It provides a rapid and reliable method for determining and cataloging minor differences between two closely related DNA sequences. We have adapted this technique to distinguish among strains or clonal types of Porphyromonas gingivalis. The ribosomal intergenic spacer region (ISR) was amplified directly from a subgingival plaque sample by PCR with species-specific primers, avoiding the need for culturing the bacteria. The PCR products were then directly compared by heteroduplex analysis with known strains of P. gingivalis for identification. We identified 22 distinct but closely related heteroduplex types ofP. gingivalis in 1,183 clinical samples. Multiple strains were found in 34% of the samples in which P. gingivaliswas detected. Heteroduplex types were identified from these multistrain samples without separating them by culturing or molecular cloning. PCR with species-specific primers and heteroduplex analysis makes it possible to reliably and sensitively detect and identify strains ofP. gingivalis in large numbers of samples.

scholarly journals A Bead-Based Method for Multiplexed Identification and Quantitation of DNA Sequences Using Flow Cytometry

2000 ◽  
Vol 66 (10) ◽  
pp. 4258-4265 ◽  
Author(s):  
Alexander Spiro ◽  
Mary Lowe ◽  
Drew Brown
Keyword(s):  
Flow Cytometry ◽  
Dna Sequences ◽  
Intergenic Spacer ◽  
Polystyrene Spheres ◽  
Intergenic Spacer Region ◽  
Cdna Sequences ◽  
Capture Assay ◽  
Flow Cytometric ◽  
Target Sequences ◽  
Specific Sequences

ABSTRACT A new multiplexed, bead-based method which utilizes nucleic acid hybridizations on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences is described. The method consists of three elements: beads (5.6-μm diameter) with oligomer capture probes attached to the surface, three fluorophores for multiplexed detection, and flow cytometry instrumentation. Two fluorophores are impregnated within each bead in varying amounts to create different bead types, each associated with a unique probe. The third fluorophore is a reporter. Following capture of fluorescent cDNA sequences from environmental samples, the beads are analyzed by flow cytometric techniques which yield a signal intensity for each capture probe proportional to the amount of target sequences in the analyte. In this study, a direct hybrid capture assay was developed and evaluated with regard to sequence discrimination and quantitation of abundances. The target sequences (628 to 728 bp in length) were obtained from the 16S/23S intergenic spacer region of microorganisms collected from polluted groundwater at the nuclear waste site in Hanford, Wash. A fluorescence standard consisting of beads with a known number of fluorescent DNA molecules on the surface was developed, and the resolution, sensitivity, and lower detection limit for measuring abundances were determined. The results were compared with those of a DNA microarray using the same sequences. The bead method exhibited far superior sequence discrimination and possesses features which facilitate accurate quantitation.

scholarly journals Identification of Bifidobacterium Animalis Ssp. Lactis from Egyptian Women Breast Milk and Feces of Breast Fed Infant Based On 16S-23S rRNA Gene

2016 ◽  
Vol 1 (1) ◽  
Keyword(s):  
Dna Sequences ◽  
Patent Protection ◽  
Health Benefit ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Species Discrimination ◽  
Rrna Gene ◽  
Accession Number ◽  
Intergenic Spacer Region ◽  
Breast Fed

Bifidobacterium represent one of the major genera of the intestinal tract of human and animals used as probiotics in dairy and nondairy foods for restore the intestinal microflora which confers a health benefit. The identification of Bifidobacterium by phenotypic features is commonly unreliable, time, money, and effort consuming. We sought to improve the Bifidobacterium identification method based on molecular level to identify probiotic bacteria in complex microbial communities. The application of 16S-23S rRNA oligonucleotide primers is the best and most reliable, rapid, and precise species and sub species identification approach. The ribosomal intergenic spacer region (ISR) located between the highly conserved 16S rRNA and 23S rRNA shows a high degree of variation in length and sequence and potential for intra species discrimination and providing the phylogenetic Relationship of the Genus Bifidobacterium spp. Results showed that one of the two primer sets Bflac2-Bflac5 species specific gives positive results differentiating between B. animalis ssp. Lactis isolated from breast fed infants milk of human and that isolated from feces of breast fed infant and detecting reference strain for B. animalis ssp. Lactis DSM10140. DNA sequences of the two strains were submitted to the Genbank NCBI under accession number (KT758845) named as B. animalis ssp. Lactis Egm1 (Egyptian milk) and accession number (KT758846) named as Egf1 Egyptian feces while the second primer give false positive result. Also, we aim to obtain patent protection under Intellectual property rights (IPRs) for B. animalis ssp. Lactis which was isolated from Egyptian resources to be used for a better and healthier food and dairy products.

New PCR-based assay for the identification of Pectobacterium carotovorum causing potato soft rot

Plant Disease ◽  
2021 ◽  
Author(s):  
M. Belén Suárez ◽  
Marta Diego ◽  
F. J. Feria ◽  
M J Martín-Robles ◽  
Sergio Moreno ◽  
...  
Keyword(s):  
Real Time ◽  
Dna Sequences ◽  
Real Time Pcr ◽  
Bacterial Species ◽  
Intergenic Spacer ◽  
Soft Rot ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Intergenic Spacer Region

Soft rot on potato tuber is a destructive disease caused by pathogenic bacterial species of the genera Pectobacterium and Dickeya. Accurate identification of the causal agent is necessary to ensure adequate disease management, since different species may have distinct levels of aggressiveness and host range. One of the most important potato pathogens is P. carotovorum, a highly heterogeneous species capable of infecting multiple hosts. The complexity of this species, until recently divided into several subspecies, has made it difficult to develop precise diagnostic tests. This study proposes a PCR assay based on the new pair of primers Pcar1F/R to facilitate the identification of potato isolates of P. carotovorum according to the most recent taxonomic description of this species. The new primers were designed on a variable segment of the 16S rRNA gene and the intergenic spacer region (ITS) of available DNA sequences from classical and recently established species in the genus Pectobacterium. The results of the PCR analysis of genomic DNA from 32 Pectobacterium and Dickeya strains confirmed that the Pcar1F/R primers have sufficient nucleotide differences to discriminate between P. carotovorum and other Pectobacterium species associated with damage to potato crops, with the exception of P. versatile, which improves the specificity of the currently available primers. The proposed assay was originally developed as a conventional PCR but was later adapted to the real-time PCR format for application in combination with the existing real-time PCR test for the potato-specific pathogen P. parmentieri. This should be useful for the routine diagnosis of potato soft rot.

Phylogenetic positions of Actites megalocarpa and Sonchus hydrophilus (Sonchinae: Asteraceae) based on ITS and chloroplast non-coding DNA sequences

2004 ◽  
Vol 17 (1) ◽  
pp. 73 ◽  
Author(s):  
Seung-Chul Kim ◽  
Christina T. Lu ◽  
Brendan J. Lepschi
Keyword(s):  
New Zealand ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Intergenic Spacer ◽  
Its Sequences ◽  
Monotypic Genus ◽  
Nuclear Rdna

Phylogenetic positions of the Australian endemic taxa Actites megalocarpa and Sonchus hydrophilus within the subtribe Sonchinae were determined on the basis of ITS sequences of nuclear rDNA and the psbA–trnH(GUG) intergenic spacer of chloroplast DNA. Both ITS and cpDNA phylogenies suggest that the monotypic genus Actites is not closely related to the members of Sonchus section Asperi, as previously suggested. Rather, this study indicates that it is more closely related to the members of Sonchus sections Maritimi (S.�maritimus) and Arvenses (S. arvensis). It also suggests that S. maritimus from section Maritimi is one of the closest relatives of Actites in Australia, although an alternative origin from section Arvenses is possible. Actites and Embergeria, once treated as congeneric taxa, appear to have originated independently in Australia and New Zealand, respectively. Sonchus hydrophilus is closely related to the S. asper complex, S. oleraceus and S. kirkii. This study suggests that S. kirkii may be involved in the origin of S. hydrophilus in Australia.

Accidental introduction of Candidatus Liberibacter europaeus into New Zealand via a weed biocontrol agent from the UK

2021 ◽  
pp. 104697
Author(s):  
Simon V. Fowler ◽  
Claudia Lange ◽  
Sam Beard ◽  
Dagmar F. Cheeseman ◽  
Gary J. Houliston ◽  
...  
Keyword(s):  
New Zealand ◽  
Biocontrol Agent ◽  
Weed Biocontrol ◽  
Candidatus Liberibacter ◽  
The Uk ◽  
Accidental Introduction
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