scholarly journals Genetic Diversity, Reassortment, and Recombination in Alfalfa mosaic virus Population in Spain

2014 ◽  
Vol 104 (11) ◽  
pp. 1241-1250 ◽  
Author(s):  
María Bergua ◽  
Marisol Luis-Arteaga ◽  
Fernando Escriu
Keyword(s):  
Genetic Diversity ◽  
Mosaic Virus ◽  
Geographic Origin ◽  
Alfalfa Mosaic Virus ◽  
Polymorphism Analysis ◽  
Coding Region ◽  
Coding Regions ◽  
Low Genetic Diversity ◽  
Genetic Types

The variability and genetic structure of Alfalfa mosaic virus (AMV) in Spain was evaluated through the molecular characterization of 60 isolates collected from different hosts and different geographic areas. Analysis of nucleotide sequences in four coding regions—P1, P2, movement protein (MP), and coat protein (CP)—revealed a low genetic diversity and different restrictions to variation operating on each coding region. Phylogenetic analysis of Spanish isolates along with previously reported AMV sequences showed consistent clustering into types I and II for P1 and types I, IIA, and IIB for MP and CP regions. No clustering was observed for the P2 region. According to restriction fragment length polymorphism analysis, the Spanish AMV population consisted of seven haplotypes, including two haplotypes generated by reassortment and one involving recombination. The most frequent haplotypes (types for P1, MP, and CP regions, respectively) were I-I-I (37%), II-IIB-IIB (30%), and one of the reassortants, II-I-I (17%). Distribution of haplotypes was not uniform, indicating that AMV population was structured according to the geographic origin of isolates. Our results suggest that agroecological factors are involved in the maintenance of AMV genetic types, including the reassortant one, and in their geographic distribution.

scholarly journals Identification, Characterization, and Molecular Detection of Alfalfa mosaic virus in Potato

2006 ◽  
Vol 96 (11) ◽  
pp. 1237-1242 ◽  
Author(s):  
H. Xu ◽  
J. Nie
Keyword(s):  
Mosaic Virus ◽  
Gene Sequence ◽  
Alfalfa Mosaic Virus ◽  
Enzyme Linked Immunosorbent Assay ◽  
Polymorphism Analysis ◽  
Rt Pcr ◽  
Potato Leaf ◽  
Simple Method ◽  
Cp Gene ◽  
Nucleotide Sequence Alignment

Alfalfa mosaic virus (AMV) was detected in potato fields in several provinces in Canada and characterized by bioassay, enzyme-linked immunosorbent assay, and reverse-transcription polymerase chain reaction (RT-PCR). The identity of eight Canadian potato AMV isolates was confirmed by sequence analysis of their coat protein (CP) gene. Sequence and phylogenetic analysis indicated that these eight AMV potato isolates fell into one strain group, whereas a slight difference between Ca175 and the other Canadian AMV isolates was revealed. The Canadian AMV isolates, except Ca175, clustered together among other strains based on alignment of the CP gene sequence. To detect the virus, a pair of primers, AMV-F and AMV-R, specific to the AMV CP gene, was designed based on the nucleotide sequence alignment of known AMV strains. Evaluations showed that RT-PCR using this primer set was specific and sensitive for detecting AMV in potato leaf and tuber samples. AMV RNAs were easily detected in composite samples of 400 to 800 potato leaves or 200 to 400 tubers. Restriction analysis of PCR amplicons with SacI was a simple method for the confirmation of PCR tests. Thus, RT-PCR followed by restriction fragment length polymorphism analysis may be a useful approach for screening potato samples on a large scale for the presence of AMV.

scholarly journals Detection and molecular characterization of Pepper mild mottle virus in Serbia

Genetika ◽  
2015 ◽  
Vol 47 (2) ◽  
pp. 651-663 ◽  
Author(s):  
Dragana Milosevic ◽  
Ivana Stankovic ◽  
Aleksandra Bulajic ◽  
Maja Ignjatov ◽  
Zorica Nikolic ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Molecular Characterization ◽  
Great Influence ◽  
Alfalfa Mosaic Virus ◽  
Resistance Breeding ◽  
Elisa Test ◽  
Mottle Virus ◽  
Pepper Mild Mottle Virus ◽  
Das Elisa

During 2009 and 2010, a survey was conducted in pepper crops to detect the possible presence of Pepper mild mottle virus (PMMoV) in Serbia. A total of 239 pepper samples from 39 crops at 26 localities were collected and analyzed for the presence of PMMoV, Cucumber mosaic virus (CMV), Potato virus Y (PVY), and Alfalfa mosaic virus (AMV), using DAS-ELISA test. Although it was detected in a small percentage, PMMoV could pose a threat to pepper production in Serbia due to its rapid seed-borne spread. Presence of PMMoV was confirmed by serological and biological detection, followed by conventional reverse transcription RT-PCR, using primers specific for the RNA-dependent RNA polymerase (RdRp) and the coat protein (CP) genes. Molecular identification confirmed that the Serbian isolates belong to PMMoV pathotypes P1,2 which do not break the resistance gene L3. Reconstructed phylogenetic tree confirmed the allocation of the Serbian isolates together with the majority of PMMoV isolates which belong to pathotypes P1,2. This study represents the first serological and molecular characterization of PMMoV infection of pepper in Serbia, and provides important data on the population structure. The obtained data could have great influence on pepper production in Serbia as well as future pepper resistance breeding in the country.

Characterization of Pyrenophora tritici-repentis in Tunisia and Comparison with a Global Pathogen Population

Plant Disease ◽  
2021 ◽  
Author(s):  
Marwa Laribi ◽  
Alireza Akhavan ◽  
Sarrah M'Barek ◽  
Amor Yahyaoui ◽  
Stephen Ernest Strelkov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographic Origin ◽  
Tan Spot ◽  
Pcr Analysis ◽  
Group Method ◽  
Region Of Origin ◽  
Pyrenophora Tritici Repentis ◽  
Pair Group ◽  
Necrotrophic Effector

Pyrenophora tritici-repentis (Ptr) causes tan spot, an important foliar disease of wheat. A collection of Ptr isolates from Tunisia, located in one of the main secondary centers of diversification of durum wheat, was tested for phenotypic race classification based on virulence on a host differential set, and for the presence of the necrotrophic effector (NE) genes ToxA, ToxB , and toxb by PCR analysis. While races 2, 4, 5, 6, 7, and 8 were identified according to their virulence phenotypes, PCR testing indicated the presence of ‘atypical’ isolates that induced necrosis on the wheat differential ‘Glenlea’, but lacked the expected ToxA gene, suggesting the involvement of other NEs in the Ptr/wheat interaction. Genetic diversity and the Ptr population structure were explored further by examining 59 Tunisian isolates and 35 isolates from Algeria, Azerbaijan, Canada, Iran, and Syria using 24 simple sequence repeat markers. Average genetic diversity, overall gene flow and percentage polymorphic loci were estimated as 0.58, 2.09 and 87%, respectively. Analysis of molecular variance showed that 81% of the genetic variance occurred within populations and 19% between populations. Cluster analysis by the unweighted pair group method indicated that ToxB- isolates grouped together and were distantly related to ToxB+ isolates. Based on Nei’s analysis, the global collection clustered into two distinct groups according to their region of origin. The results suggest that both geographic origin and the host-specificity imposed by different NEs can lead to differentiation among Ptr populations.

scholarly journals Characterization of a New Alloantigen (SH) on the Human Neutrophil Fcγreceptor IIIb

Blood ◽  
1997 ◽  
Vol 89 (3) ◽  
pp. 1027-1034 ◽  
Author(s):  
Juergen Bux ◽  
Ernst-Ludwig Stein ◽  
Philippe Bierling ◽  
Patricia Fromont ◽  
Mary Clay ◽  
...  
Keyword(s):  
Nucleotide Sequence Analysis ◽  
Polymorphism Analysis ◽  
Mutational Event ◽  
Coding Region ◽  
Specific Pcr ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Antigen Frequency ◽  
Neonatal Neutropenia

Abstract Polymorphic structures of the neutrophil Fcγreceptor IIIb (FcγRIIIb) result in alloantibody formation that causes alloimmune neonatal neutropenia and transfusion reactions. Alloantigens located on FcγRIIIb include the antigens NA1 and NA2. In four cases of alloimmune neonatal neutropenia, granulocyte-specific alloantibodies directed against a thus far unknown antigen were detected by granulocyte agglutination and immunofluorescence tests in the maternal sera. By the use of the monoclonal antibody–specific immobilization of granulocyte antigens (MAIGA) assay, the new antigen, termed SH, was located on the FcγRIIIb. Nucleotide sequence analysis of the FcγRIIIb coding region from a SH(+) individual showed a single-base C→A mutation at position 266, which results in an Ala78Asp amino acid substitution. A family study confirmed that this nucleotide difference is inherited, and corresponds to the SH phenotype. Serologic typing of 309 randomly selected individuals showed an antigen frequency of 5% in the white population. The same frequency was found by genotyping, for which a technique based on polymerase chain reaction (PCR) using sequence-specific primers (PCR-SSP) was developed. Typing of all SH(+) individuals for NA1 and NA2, and PCR-restriction fragment length polymorphism analysis of the NA-specific PCR products from five SH(+) individuals using the SH-specific endonuclease SfaN I showed that SH antigen is very probably the result of an additional mutational event in the NA2 form of the FcγRIIIB gene. Immunochemical studies also demonstrated that the SH determinants reside on the 65- to 80-kD NA2 isoform of the FcγRIIIb. Our findings show the existence of an additional polymorphism of the FcγRIIIb, which can result in alloantibody formation causing alloimmune neonatal neutropenia.

scholarly journals Reaction of lettuce genotypes to Lettuce mosaic virus-Most (LMV-Most) and characterization of the translation factor eIF4E

2018 ◽  
Vol 53 (1) ◽  
pp. 125-129
Author(s):  
Mônika Fecury Moura ◽  
Norberto da Silva ◽  
Maria Isabel Motta Hoffmann ◽  
Marcelo Agenor Pavan ◽  
Renate Krause-Sakate
Keyword(s):  
Mosaic Virus ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Coding Region ◽  
Rt Pcr ◽  
Lettuce Mosaic Virus ◽  
Eukaryotic Translation ◽  
Translation Factor ◽  
Eukaryotic Translation Initiation

Abstract: The objective of this work was to evaluate lettuce genotypes for their reaction to Lettuce mosaic virus (LMV; Most-type, isolate AF-199) and variations of the eukaryotic translation initiation factor eIF4E. All inoculated genotypes were susceptible to LMV, which was detected by RT-PCR using specific primer pairs. However, the accessions 169501, 169501C, 172918A, and 162499 showed late development of symptoms that appeared only on the inoculated leaves. Sequencing of the coding region of eIF4E showed that these genotypes have an eIF4E0 (mol 0 ) standard typical for their susceptibility to LMV, indicating that the phenotype found is not correlated to nucleotide variations in this translation factor.

scholarly journals Identification of Six Putative Novel Human Papillomaviruses (HPV) and Characterization of Candidate HPV Type 87

2001 ◽  
Vol 75 (23) ◽  
pp. 11913-11919 ◽  
Author(s):  
Stefano Menzo ◽  
Alessia Monachetti ◽  
Caterina Trozzi ◽  
Andrea Ciavattini ◽  
Guido Carloni ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Biological Data ◽  
Human Papillomaviruses ◽  
The Novel ◽  
Tissue Cultures ◽  
Coding Region ◽  
Coding Regions ◽  
Immunodeficiency Virus ◽  
E6 And E7

ABSTRACT Six putative novel human papillomavirus (HPV) types were detected by using general primers for a conserved L1 HPV region in patients examined in gynecologic centers. One of the isolates, detected in samples from 4 patients with koilocytic atypia at cervical cytology (3 of whom were also infected with human immunodeficiency virus type 1), was completely sequenced, identified as a new HPV genotype, and designated candidate HPV87 (candHPV87) by the Reference Center for Human Papillomavirus. candHPV87 shows the classic HPV genome organization and the absence of a functional E5 coding region. Phylogenetic analysis documented that thecandHPV87 genome clusters within the A3 group of HPVs, together with HPV61, HPV72, HPV83, HPV84 and candHPV86, which have been completely sequenced, and a number of other putative novel genotypes (two of which are described in this work), which have been partially characterized. To address the growth-enhancing potential of candHPV87, the E6 and E7 putative coding regions were cloned and expressed in tissue cultures. The data indicate that both proteins stimulate cell division in tissue cultures more than those of low-risk HPVs, though not as much as those of HPV16. Taken together, the clinical, molecular, and biological data suggest that the novel papillomavirus characterized in the present study is a low- to intermediate-risk HPV.

Isolation and characterization of an expressed napin gene fromBrassica rapa

1991 ◽  
Vol 1 (4) ◽  
pp. 209-219 ◽  
Author(s):  
Jean C. Kridl ◽  
David W. McCarter ◽  
Ronald E. Rose ◽  
Donna E. Scherer ◽  
Deborah S. Knutzon ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Storage Protein ◽  
Protein Gene ◽  
Coding Region ◽  
Coding Regions ◽  
Endogenous Expression ◽  
Isolation And Characterization ◽  
Glucuronidase Reporter ◽  
Transgenic Rapeseed

AbstractAn expressed napin storage protein gene fromBrassica rapa, BcNA1, has been cloned and sequenced. The gene is a member of a family of four to seven napin genes inB. rapaand is highly expressed in developing seeds. An expression cassette containing the DNA flanking the napin coding region of BcNA1 has been engineered and demonstrated to function appropriately, as compared with the gene's endogenous expression, in transgenic rapeseed using the β-glucuronidase reporter gene. TheB. rapaBcNA1 gene and aB. napusnapin gene, gNa, share extremely high nucleotide homology not only throughout their coding regions, but over a DNA locus comprising 4.3 kb. We suggest the gNa gene was contributed by the originalB. rapaprogenitor of the amphidiploidB. napus.

scholarly journals Characterization of Trichodesmium spp. by Genetic Techniques

2002 ◽  
Vol 68 (5) ◽  
pp. 2236-2245 ◽  
Author(s):  
K. M. Orcutt ◽  
U. Rasmussen ◽  
E. A. Webb ◽  
J. B. Waterbury ◽  
K. Gundersen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Natural Populations ◽  
Sargasso Sea ◽  
Closely Related Species ◽  
Trichodesmium Erythraeum ◽  
Low Genetic Diversity ◽  
Gradient Gel Electrophoresis ◽  
Genetic Techniques

ABSTRACT The genetic diversity of Trichodesmium spp. from natural populations (off Bermuda in the Sargasso Sea and off North Australia in the Arafura and Coral Seas) and of culture isolates from two regions (Sargasso Sea and Indian Ocean) was investigated. Three independent techniques were used, including a DNA fingerprinting method based on a highly iterated palindrome (HIP1), denaturing gradient gel electrophoresis of a hetR fragment, and sequencing of the internal transcribed spacer (ITS) of the 16S-23S rDNA region. Low genetic diversity was observed in natural populations of Trichodesmium spp. from the two hemispheres. Culture isolates of Trichodesmium thiebautii, Trichodesmium hildebrandtii, Trichodesmium tenue, and Katagnymene spiralis displayed remarkable similarity when these techniques were used, suggesting that K. spiralis is very closely related to the genus Trichodesmium. The largest genetic variation was found between Trichodesmium erythraeum and all other species of Trichodesmium, including a species of Katagnymene. Our data obtained with all three techniques suggest that there are two major clades of Trichodesmium spp. The HIP1 fingerprinting and ITS sequence analyses allowed the closely related species to be distinguished. This is the first report of the presence of HIP1 in marine cyanobacteria.

scholarly journals Biological and Genetic Diversity of Wheat yellow mosaic virus (Genus Bymovirus)

2014 ◽  
Vol 104 (3) ◽  
pp. 313-319 ◽  
Author(s):  
Takehiro Ohki ◽  
Osamu Netsu ◽  
Hisayo Kojima ◽  
Junichi Sakai ◽  
Masatoshi Onuki ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Mosaic Virus ◽  
Fragment Length Polymorphism ◽  
Wheat Cultivar ◽  
Yellow Mosaic Virus ◽  
Polymorphism Analysis ◽  
Wheat Yellow Mosaic Virus ◽  
Northern Areas ◽  
Polymerase Chain

The biological and genetic diversity of Wheat yellow mosaic virus (WYMV) isolates in Japan was characterized. On the basis of wheat cultivar reactions, 14 WYMV isolates from various places were classified into pathotypes I, II, or III. These were distributed in central, northern, and southern areas of Japan, respectively. WYMV isolates comprised three genotypes (A, A′ and B) based on amino acid differences in RNA1 and two genotypes (a and b) based on amino acid differences in RNA2. A correlation was found between the WYMV RNA1-based genotype and pathotype, suggesting that factors associated with pathogenicity map to RNA1. Genotype Aa and A′a were distributed mainly in the central to southern areas of Japan, and genotype Bb was found in northern areas of Japan, as shown by reverse-transcription polymerase chain reaction restriction fragment length polymorphism analysis. Chinese isolates YA and YZ were closely related to genotypes Bb and Aa, respectively. Wheat was introduced from China to Japan in the 4th and 5th centuries, and the two genotypes of WYMV might also have been introduced with the crop from China and later adapted to local wheat cultivars in Japan.

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