scholarly journals Maize (Zea mays L.): A New Host for Ligustrum witches’ Broom Phytoplasma

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 723
Author(s):  
Behçet Kemal Çağlar ◽  
Serkan Pehlivan ◽  
Ekrem Atakan ◽  
Toufic Elbeaino
Keyword(s):  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
Universal Primer ◽  
New Host ◽  
Intergenic Spacer Region ◽  
Distant Relationship ◽  
Molecular Information ◽  
Corn Plants

In the 2019–2020 growing season, two corn fields located in İmamoğlu town (Adana Province, Turkey) were surveyed following the appearance of phytoplasma-like symptoms on maize plants. A total of 40 samples were collected and tested in first-round and nested PCR using universal primer pairs P1/P7 and R16F2n/R16R2, respectively. All maize-diseased plants reacted positively, whilst no PCR amplifications were obtained from asymptomatic plants. Blast sequence analysis of R16F2n/R16R2-primed amplicons from different maize isolates showed 99.2% to 100% of identity with the 16S rRNA gene of Ligustrum witches’ broom phytoplasma (LiWBP). To gain additional molecular information on the 16S ribosomal RNA and 23S rRNA intergenic spacer region of LiWBP, not identified previously, the P1/P7-primed amplicons were also sequenced and analyzed. The results show that maize isolates from Turkey share 99.6% to 100% of identity among them, whereas the highest identity found (91%) was with members of groups 16SrII and 16SrXXV (peanut and tea witches’ broom groups, respectively). This distant relationship between LiWBP and members of 16SrII and XXV was also confirmed by RFLP and phylogenetic analyses. This is the first finding of LiWBP on maize in nature, where it was found responsible for phyllody disease of corn plants in Turkey. The additional molecular information acquired in this study on the 16S–23S rRNA intergenic spacer region of LiWBP further corroborates its distant relationship to any other phytoplasma groups.

Differentiation of group VIII Spiroplasma strains with sequences of the 16S–23S rDNA intergenic spacer region

2004 ◽  
Vol 50 (12) ◽  
pp. 1061-1067 ◽  
Author(s):  
Laura B Regassa ◽  
Kimberly M Stewart ◽  
April C Murphy ◽  
Frank E French ◽  
Tao Lin ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
Analytical Models ◽  
23S Rrna ◽  
Rrna Gene ◽  
Group Viii ◽  
Similarity Coefficients ◽  
Intergenic Spacer Region ◽  
Intergenic Sequences ◽  
The Stability ◽  
The 16S Rrna Gene

Spiroplasma species (Mollicutes: Spiroplasmataceae) are associated with a wide variety of insects, and serology has classified this genus into 34 groups, 3 with subgroups. The 16S rRNA gene has been used for phylogenetic analysis of spiroplasmas, but this approach is uninformative for group VIII because the serologically distinct subgroups generally have similarity coefficients >0.990. Therefore, we investigated the utility of the 16S–23S rRNA spacer region as a means to differentiate closely related subgroups or strains. We generated intergenic sequences and detailed serological profiles for 8 group VIII Spiroplasma strains. Sequence analyses using Maximum Parsimony, Neighbor Joining, and Maximum Likelihood placed the strains into 2 clades. One clade consisted of strains BARC 2649 and GSU5367. The other clade was divided into clusters containing representatives of the 3 designated group VIII subgroups (EA-1, DF-1, and TAAS-1) and 3 previously unclassified strains. The stability of the positions of the strains in various analytical models and the ability to provide robust support for groupings tentatively supported by serology indicates that the 16S–23S intergenic rDNA sequence will prove useful in intragroup analysis of group VIII spiroplasmas.Key words: Mollicutes, Spiroplasma, phylogeny, Tabanidae.

scholarly journals 16S–23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads

2016 ◽  
Vol 7 ◽  
Author(s):  
Sima Tokajian ◽  
Nahla Issa ◽  
Tamara Salloum ◽  
Joe Ibrahim ◽  
Maya Farah
Keyword(s):  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
Intergenic Spacer Region ◽  
23S Rrna Gene

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.

scholarly journals First Report of Oat as Host of a Phytoplasma Belonging to Group 16SrI, Subgroup A

Plant Disease ◽  
2002 ◽  
Vol 86 (4) ◽  
pp. 443-443 ◽  
Author(s):  
R. Jomantiene ◽  
R. E. Davis ◽  
A. Alminaite ◽  
D. Valiunas ◽  
R. Jasinskaite
Keyword(s):  
16S Rdna ◽  
Plant Species ◽  
Nested Pcr ◽  
Sequence Similarity ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
23S Rrna ◽  
Universal Primer ◽  
Intergenic Spacer Region ◽  
Group I

Diseased plants of oat (Avena sativa L.) exhibiting abnormal proliferation of spikelets were observed in the field in Raseniai, Lithuania. The possible association of a phytoplasma with the disease, termed oat proliferation (OatP), was determined using polymerase chain reaction (PCR) for amplification of phytoplasmal ribosomal (r) RNA gene (rDNA) sequences from template DNA extracted from the diseased oats. DNA extractions and nested PCRs were conducted as previously described (2). In the nested PCRs, the first reaction was primed by phytoplasma-universal primer pair P1/P7, and the second (nested) PCR was primed by primer pair R16F2n/R16R2 (F2n/R2). Phytoplasmal rDNA was amplified in the nested PCR, indicating that the plants contained a phytoplasma, designated oat proliferation (OatP) phytoplasma. The OatP phytoplasma was identified and classified according to the system of Lee et al. (2) through restriction fragment length polymorphism (RFLP) analysis of 16S rDNA amplified in the PCR primed by F2n/R2. On the basis of collective RFLP patterns of the 16S rDNA, the OatP phytoplasma was classified as a member of group 16SrI (group I, aster yellows phytoplasma group). The RFLP patterns of the 16S rDNA were indistinguishable from those of 16S rDNA from tomato big bud (BB) phytoplasma and other phytoplasmas classified in group I, subgroup A (subgroup I-A, tomato big bud phytoplasma subgroup). The 1.8-kbp rDNA product of PCR primed by primer pair P1/P7 was cloned, and its nucleotide sequence was determined. The sequence was deposited in GenBank under Accession No. AF453416. Results from putative restriction site analysis of the cloned and sequenced rDNA were in excellent agreement with the results from enzymatic RFLP analysis of uncloned rDNA from OatP-diseased oat plants. Sequence similarity between the 1.8-kbp rDNA of OatP phytoplasma and that of BB phytoplasma (GenBank No. AF222064) was 99.2%; 9 of the 14 base changes were in the 16S-23S rRNA intergenic spacer region. The base differences in rDNA may signal that the OatP and BB phytoplasmas are mutually distinct in their biologies. Phytoplasmas classified in subgroup I-A have previously been reported in a broad range of plant species in North America and Europe, although there are no previous definitive reports of oat as a host of a subgroup I-A phytoplasma (3,4). In 1977, Fedotina (1) reported electron microscopy of a mycoplasma-like organism (phytoplasma) in pseudorosette-diseased oat plants in Siberia, but the identity of that phytoplasma remains unknown. Subgroup I-A phytoplasma strains are geographically widespread and have been found in numerous plant species (3,4). The discovery reported here, of a subgroup I-A phytoplasma in diseased oats in Lithuania, provokes questions concerning possible impacts of this phytoplasma on oat cultivation in central Europe and other regions. References: (1) V. L. Fedotina. Arch. Phytopathol. Pflanzenschutz 13:177, 1977. (2) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) C. Marcone et al. Int. J. Syst. Evol. Microbiol. 50:1703, 2000. (4) D. Valiunas et al. Plant Dis. 85:804, 2001.

scholarly journals Identification of Lactobacillus Isolates from the Gastrointestinal Tract, Silage, and Yoghurt by 16S-23S rRNA Gene Intergenic Spacer Region Sequence Comparisons

1999 ◽  
Vol 65 (9) ◽  
pp. 4264-4267 ◽  
Author(s):  
G. W. Tannock ◽  
A. Tilsala-Timisjarvi ◽  
S. Rodtong ◽  
J. Ng ◽  
K. Munro ◽  
...  
Keyword(s):  
Lactobacillus Rhamnosus ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Sequence Comparisons ◽  
Intergenic Spacer Region ◽  
23S Rrna Gene

Lactobacillus isolates were identified by PCR amplification and sequencing of the region between the 16S and 23S rRNA genes (spacer region). The sequences obtained from the isolates were compared to those of reference strains held in GenBank. A similarity of 97.5% or greater was considered to provide identification. To check the reliability of the method, the V2-V3 region of the 16S rRNA gene was amplified and sequenced in the case of isolates whose spacer region sequences were less than 99% similar to that of a reference strain. Confirmation of identity was obtained in all instances. Spacer region sequencing provided rapid and accurate identification ofLactobacillus isolates obtained from gastrointestinal, yoghurt, and silage samples. It had an advantage over 16S V2-V3 sequence comparisons because it distinguished between isolates ofLactobacillus casei and Lactobacillus rhamnosus.

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