Identification and genetic characterization of Pseudomonas syringae pv. syringae from sweet cherry in Turkey

Plant Disease ◽  
2021 ◽  
Author(s):  
Cansu Oksel ◽  
Farhat A. Avin ◽  
Mustafa Mirik ◽  
Fulya Baysal-Gurel
Keyword(s):  
Genetic Diversity ◽  
Pseudomonas Syringae ◽  
Sweet Cherry ◽  
Pcr Amplification ◽  
Bacterial Disease ◽  
Broad Host Range ◽  
Marmara Region ◽  
Mlst Analysis ◽  
The Relationship

Pseudomonas syringae pv. syringae (Pss), which causes bacterial canker, is the most polyphagous bacterium in the P. syringae complex due to its broad host range. This pathogen is considered the major bacterial disease in cherry orchards. In this study, several samples were collected from infected sweet cherry trees in different locations of the Marmara region in Turkey between 2016-2018. Sixty-three isolates were identified as Pss by pathogenicity, LOPAT, GATTa, and MALDI-TOF MS tests. Total genomic DNA was extracted to confirm identity, followed by PCR amplification of syrB and cfl genes. Out of 63 isolates, 12 were randomly selected for Repetitive Element Sequence-based PCR (rep-PCR) and Multilocus Sequence Typing (MLST) analysis to gain insight into the relationships of those isolates. The cluster analysis of rep-PCR (ERIC-, REP- and BOX-PCR) could classify the isolates into two distinct clusters. Phylogenetic analysis was carried out to obtain the relation between isolates and the location.The MLST analysis of gyrB, rpoDp, rpoDs, and gltA genes allowed a clear allocation of the isolates into two separate main clusters. The relationship among the isolates were also evaluated by constructing a genealogical median-joining network (MJN). The isolates from six locations produced 11 haplotypes that were illustrated in the MJN. The results of this study proved that location could not be an indicator for showing the genetic diversity of Pss from cherry orchards. As the genetic variability of Pseudomonads has been demonstrated, the current study also showed high diversity among different isolates even within the populations. While more research is recommended, the results of this study contributed to a better understanding of the Pss evolutionary progress and genetic diversity of sweet cherry isolates.

scholarly journals TU-DAMD employment for molecular characterization of Salvia judaica and Salvia palaestina species

2021 ◽  
Vol 65 (1) ◽  
pp. 11-16
Author(s):  
Basel Saleh
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker ◽  
Annealing Temperature ◽  
Polymorphic Information Content ◽  
Pcr Amplification ◽  
Marker Index ◽  
C Cycle ◽  
Separated Sets ◽  
Polymorphism Level

Genetic diversity in perennial Salvia judaica Boiss (Judean sage) and Salvia palaestina Benth (Palestinian sage) species using touch-up directed amplification of minisatellite region DNA (TU-DAMD) has been performed in two separated sets; in the first set (set A) the initial annealing temperature was increased from 50 °C to 55 °C, whereas, in the second one (set B), it increased from 55 °C to 60 °C by 0.5 °C/cycle during the first 10 PCR amplification cycles. Fifteen DAMD primers have been tested for each set. Set (A) produced 89.39% polymorphism level (P%) with polymorphic information content (PIC) average of 0.33 and marker index (MI) average of 3.96. Whereas, in set (B) these values were recorded to be 94.02%, 0.34 and 3.98 for P%, PIC and MI, respectively. Data showed that the two mentioned sets successfully highlighted high polymorphism level between the two studied Salvia sp. This work studies genetic diversity of S. judaica and S. palaestina species using TU-DAMD test as a novel molecular marker.

scholarly journals Characterization of the salA, syrF, and syrG Regulatory Genes Located at the Right Border of the Syringomycin Gene Cluster of Pseudomonas syringae pv. syringae

2002 ◽  
Vol 15 (1) ◽  
pp. 43-53 ◽  
Author(s):  
Shi-En Lu ◽  
Brenda K. Scholz-Schroeder ◽  
Dennis C. Gross
Keyword(s):  
Gene Cluster ◽  
Pseudomonas Syringae ◽  
Binding Motifs ◽  
Right Border ◽  
Dna Binding Motifs ◽  
In Series ◽  
Regulatory Loci ◽  
The Right ◽  
The Relationship

Sequence analysis of the right border of the syr gene cluster of Pseudomonas syringae pv. syringae strain B301D revealed the presence of the salA gene 8,113 bp downstream of syrE. The predicted SalA protein of strain B301D differs by one amino acid from that of strain B728a. Two homologs of salA, designated syrF and syrG, were identified between syrE and salA. All three proteins contain helix-turn-helix DNA-binding motifs at their C termini and exhibit homology to regulatory proteins of the LuxR family. A salA mutant failed to produce syringomycin, whereas syrF and syrG mutants produced 12 and 50%, respectively, of syringomycin relative to the wild-type strain. The salA, syrF, and syrG mutants were significantly reduced in virulence, forming small, nonspreading lesions in immature cherry fruits. Translational fusions to the uidA gene were constructed to evaluate expression of syrB1 in regulatory mutant backgrounds and to determine the relationship among the three regulatory loci. Expression of a syrB1::uidA fusion required functional salA and syrF genes and, in series, the expression of a syrF::uidA fusion required a functional salA gene. These results demonstrate that salA is located upstream of syrF in the regulatory hierarchy controlling syringomycin production and virulence in P. syringae pv. syringae.

scholarly journals MOLECULAR CHARACTERIZATION OF FIVE SELECTED BRINJAL (Solanum melongena L) GENOTYPES USING SSR MARKERS

2008 ◽  
Vol 21 (1) ◽  
pp. 01-06 ◽  
Author(s):  
A. K. M. Khorsheduzzaman ◽  
M. Z. Alam ◽  
M. M. Rahman ◽  
M. A. K. Mian ◽  
M. I. H. Mian ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Banding Pattern ◽  
Genomic Dna ◽  
Molecular Level ◽  
Narrow Range ◽  
Solanum Melongena ◽  
Pcr Amplification ◽  
Simple Sequence

Five brinjal (Solanum melongena L.) genotypes were selected for characterization using Simple Sequence Repeats (SSR) markers. All the genotypes showed considerable variation in respect of morphological, anatomical and biochemical aspects. For study of relatedness, plant genomic DNA was extracted by CTAB based method using 11 randomly selected primers produced from Calgene Inc. USA. The primers developed 22 bands through PCR amplification out of which 15 from 3 primers and were polymorphic. Genetic similarities of SSR profiles were estimated based on Jaccard’s coefficient value. The dendrogram generated two clusters and they were clearly distinct and separated from each other. Cluster-I consisted of genotypes TURBO and BL009; and cluster-II comprised of genotypes EG058, EG075 and ISD006. Genotype TURBO and BL009 were identified as the diverse genotype and showed a maximum of 17% dissimilarity from EG058, EG075 and ISD006. The similarity value ranged from 0.83 to 1.00 which indicated the presence of narrow range of genetic diversity at molecular level but have still a possibility of crossing among the genotypes of two clusters. The banding pattern of different genotypes could be utilized as reference for further comparisons.DOI: http://dx.doi.org/10.3329/bjpbg.v21i1.17041

scholarly journals Characterization of Pseudomonas syringae pathovars from different sweet cherry cultivars by RAPD analysis

Genetika ◽  
2016 ◽  
Vol 48 (1) ◽  
pp. 285-295 ◽  
Author(s):  
Renata Ilicic ◽  
Jelica Balaz ◽  
Vera Stojsin ◽  
Dragana Josic
Keyword(s):  
Pseudomonas Syringae ◽  
Reference Strain ◽  
Sweet Cherry ◽  
Rapd Analysis ◽  
Plant Organs ◽  
Race 1 ◽  
Pseudomonas Syringae Pathovars ◽  
Sweet Cherry Cultivars

Pseudomonas syringae pvs., isolated from sweet cherry grown on different localities in Serbia, were genetically characterized using RAPD analysis. Four out of eleven tested primers (SPH1, DJP 17, DJ 15, and DJ 16) were selected on the basis of the differences between isolates within two pathovars - syringae and morsprunorum race 1. Cumulative RAPD analysis indicated heterogeneity within the population of both groups of tested isolates, revealing four different patterns in each group. RAPD analysis showed up to 24% differences among pv. syringae isolates, as well as 41% in comparison with the reference strain KFB0103 (pv. syringae), while differences of 15% among isolates pv. morsprunorum 1 race and 36% compared to the reference strain CFBP2119 (pv. morsprunorum 1) were observed. Isolates from locality Selenca exhibited three different genotypic patterns of pv. morsprunorum race 1 and one pattern of pv. syringae. Isolates of pv. morsprunorum collected in the same year from two plant organs (branches and leaves) of the cv. Vanda yielded two different patterns. The pv. morsprunorum on cv. Kordia and pv. syringae on cv. Regina were detected at Mikicevo locality. The same patterns were observed for isolates of pv. syringae from Kanjiza and Selenca, as well as from Gornji Tavankut in two years of isolation. Differences were noted between isolates from the same pathovar originating from Ljutovo and Mikicevo, as well as with respect to all other isolates of same pathovar.

scholarly journals Characterization of Nigerian Sesame (Sesamum Indicum L.) Using Random Polymorphic DNA (RAPD) Marker

2019 ◽  
pp. 77-84
Author(s):  
Alege Gbenga Olorunshola
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Similarity Index ◽  
Pcr Amplification ◽  
Sesamum Indicum ◽  
Uv Illumination ◽  
Sesame Genotypes ◽  
High Level

The assessment of genetic diversity among 23 sesame genotypes (Sesamum indicum L.) obtained from different locations across 10 states in Nigeria was carried out using Random Amplified Polymorphic DNA (RAPD) technique. The field trial tests were carried out on the 23 sesame accessions for two seasons to have uniform genotypes from each accessions. A standard protocol of CTAB with slight modifications was employed for DNA extracted from the harvested seeds. The extracted DNA samples were observed under UV illumination using agarose gel electrophoresis after staining with ethidium bromide. A total of 7 primers were used for PCR amplification, 5 of which have been previously used to discriminate sesame genotypes from other countries. Only 3 of the 7 primers considered produced strong amplification with the selected 23 sesame samples. A total of 47 amplified products were produced by the 3 primers among the 23 accessions all of which are 100% polymorphic. The estimates of similarity index for the 23 accessions ranged from 0.29 to 0.92. Cluster analysis revealed 2 main clusters with some of the accessions from different geographical origin cluster together in the same group which might indicate the involvement of human factor in the spread of sesame varieties in Nigeria. The relevance of RAPD to this study was evident from the high level of polymorphism reported in this study. There is therefore existence of adequate genetic diversity among the 23 Nigerian sesame accessions for sesame breeders to develop improved varieties.

Isolation and genetic characterization of Neospora caninum from asymptomatic calves in Spain

Parasitology ◽  
2008 ◽  
Vol 135 (14) ◽  
pp. 1651-1659 ◽  
Author(s):  
J. REGIDOR-CERRILLO ◽  
M. GÓMEZ-BAUTISTA ◽  
J. PEREIRA-BUENO ◽  
G. ADURIZ ◽  
V. NAVARRO-LOZANO ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Characterization ◽  
Neospora Caninum ◽  
Epidemiological Features ◽  
Newborn Calves ◽  
Genetic Profiles ◽  
The Relationship ◽  
Infected Newborn

SUMMARYNeospora caninum is a cyst-forming parasite that causes abortion in cattle. Despite this parasite's ubiquitous distribution and wide host range, the number of N. caninum isolates obtained to date is limited. In vitro isolation of the parasite is arduous and often unsuccessful. In addition, most isolates have been obtained from clinically affected hosts and therefore could be biased towards more virulent isolates. In this report, an improved isolation approach from transplacentally infected newborn calves was undertaken and 9 new isolates were obtained. Moreover, a microsatellite technique was applied to investigate the genetic diversity of these isolates. Most isolates showed specific genetic profiles. However, the Nc-Spain10 isolate was identical to the previously described Nc-Spain1H isolate and Nc-Spain3H was identical to Nc-Spain4H. These isolates were likely to have identical genotypes because they were isolated from distinct calves of the same herd. Future pathogenic characterization of these isolates will contribute to the investigation of the relationship between isolate virulence and the outcome of infection, as well as other epidemiological features, such as transmission.

scholarly journals Characterization of the first double-stranded RNA bacteriophage infecting Pseudomonas aeruginosa

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Yuhui Yang ◽  
Shuguang Lu ◽  
Wei Shen ◽  
Xia Zhao ◽  
Mengyu Shen ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Pseudomonas Syringae ◽  
Broad Host Range ◽  
Genome Sequences ◽  
Detailed Characterization ◽  
Double Stranded Rna ◽  
Dsrna Genome ◽  
Hospital Sewage

Abstract Bacteriophages (phages) are widely distributed in the biosphere and play a key role in modulating microbial ecology in the soil, ocean, and humans. Although the role of DNA bacteriophages is well described, the biology of RNA bacteriophages is poorly understood. More than 1900 phage genomes are currently deposited in NCBI, but only 6 dsRNA bacteriophages and 12 ssRNA bacteriophages genome sequences are reported. The 6 dsRNA bacteriophages were isolated from legume samples or lakes with Pseudomonas syringae as the host. Here, we report the first Pseudomonas aeruginosa phage phiYY with a three-segmented dsRNA genome. phiYY was isolated from hospital sewage in China with the clinical P. aeruginosa strain, PAO38, as a host. Moreover, the dsRNA phage phiYY has a broad host range, which infects 99 out of 233 clinical P. aeruginosa strains isolated from four provinces in China. This work presented a detailed characterization of the dsRNA bacteriophage infecting P. aeruginosa.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

Microstructural Characterization of Au-Ge-Ni based ohmic contacts to GaAs/AlGaAs modfet device

1987 ◽  
Vol 45 ◽  
pp. 326-327
Author(s):  
A.K. Rai ◽  
A.K. Petford-Long ◽  
A. Ezis ◽  
D.W. Langer
Keyword(s):  
Contact Resistance ◽  
Ohmic Contact ◽  
Ohmic Contacts ◽  
Microstructural Characterization ◽  
Almost Everywhere ◽  
Spacer Layer ◽  
Good Contact ◽  
The Relationship ◽  
Lower Contact

Considerable amount of work has been done in studying the relationship between the contact resistance and the microstructure of the Au-Ge-Ni based ohmic contacts to n-GaAs. It has been found that the lower contact resistivity is due to the presence of Ge rich and Au free regions (good contact area) in contact with GaAs. Thus in order to obtain an ohmic contact with lower contact resistance one should obtain a uniformly alloyed region of good contact areas almost everywhere. This can possibly be accomplished by utilizing various alloying schemes. In this work microstructural characterization, employing TEM techniques, of the sequentially deposited Au-Ge-Ni based ohmic contact to the MODFET device is presented.The substrate used in the present work consists of 1 μm thick buffer layer of GaAs grown on a semi-insulating GaAs substrate followed by a 25 Å spacer layer of undoped AlGaAs.

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