scholarly journals Occurrence and genetic diversity of pigeon circovirus strains in Poland

2014 ◽  
Vol 62 (2) ◽  
pp. 274-283 ◽  
Author(s):  
Tomasz Stenzel ◽  
Daria Pestka
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Capsid Protein ◽  
Immunosuppressive Agent ◽  
Amino Acid Sequences ◽  
Amino Acid Similarity ◽  
Capsid Protein Gene ◽  
Base Fragment ◽  
Polymerase Chain ◽  
Young Pigeon

Pigeon circovirus (PiCV) is an immunosuppressive agent widespread throughout the world, which causes a disease in pigeons called Young Pigeon Disease Syndrome. The aim of the study was to evaluate the prevalence of PiCV in Poland and investigate the genetic diversity relative to other known PiCV isolates. Samples from 152 pigeon flocks (88 flocks of racing pigeons and 64 flocks of fancy pigeons) from various regions of Poland were tested by polymerase chain reaction and an approximately 326-base fragment of the capsid protein gene (Cap gene) of the virus was amplified. The average viral prevalence was found to be 70.3% (76.13% in racing pigeons and 62.5% in fancy pigeons). Among the obtained positive samples, 21 were selected for sequencing and a phylogenetic analysis was performed. It was found that the majority of Polish PiCV isolates, to varying degrees, are related to isolates occurring in Europe. It was also observed that the Cap gene is variable and mutations often occur in it, which impacts the amino acid sequences in the capsid protein (nucleotide similarity averaged 86.57%, amino acid similarity averaged 89.02%).

scholarly journals Identification of a novel bovine enterovirus possessing highly divergent amino acid sequences in capsid protein

2017 ◽  
Vol 17 (1) ◽  
Author(s):  
Shinobu Tsuchiaka ◽  
Sayed Samim Rahpaya ◽  
Konosuke Otomaru ◽  
Hiroshi Aoki ◽  
Mai Kishimoto ◽  
...  
Keyword(s):  
Amino Acid ◽  
Capsid Protein ◽  
Amino Acid Sequences ◽  
Bovine Enterovirus

scholarly journals Genetic Diversity Among Geminiviruses Associated with the Weed Species Sida spp., Macroptilium lathyroides, and Wissadula amplissima from Jamaica

Plant Disease ◽  
1997 ◽  
Vol 81 (11) ◽  
pp. 1251-1258 ◽  
Author(s):  
Marcia E. Roye ◽  
Wayne A. McLaughlin ◽  
Medhat K. Nakhla ◽  
Douglas P. Maxwell
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Mosaic Virus ◽  
Amino Acid Sequences ◽  
Yellow Mosaic Virus ◽  
Weed Species ◽  
Degenerate Primers ◽  
Sequence Comparisons ◽  
The Common ◽  
Macroptilium Lathyroides

Genetic diversity among geminiviruses associated with three common weeds in Jamaica was studied using digoxigenin-labeled geminiviral DNA probes, polymerase chain reaction with degenerate primers for DNA-A and DNA-B, nucleic acid sequencing, and derived amino acid sequences. Geminiviruses with bipartite genomes were found in Sida spp., Macroptilium lathyroides, and Wissadula amplissima. The geminiviruses detected in Sida spp. and M. lathyroides were nearly identical and were both designated Sida golden mosaic geminivirus (SidGMV-JA), whereas the geminivirus in W. amplissima was sufficiently different to be designated Wissadula golden mosaic geminivirus (WGMV). Nucleotide sequence comparisons of the common regions and the N-terminal regions of the AC1 (rep) and AV1 ORFs, together with the derived amino acid sequence comparisons of the N-terminal parts of BC1 and BV1 ORFs were used to determine their similarities to other geminiviruses. SidGMV-JA was most similar to potato yellow mosaic geminivirus (PYMV). We propose that these two geminiviruses (SidGMV-JA and PYMV) define a new geminivirus cluster, the potato yellow mosaic virus (PYMV) cluster. WGMV was most similar to members of the Abutilon mosaic virus cluster but is not likely to be included in the Abutilon phylogenetic group because of the divergent sequence of the common region. These results indicate that geminiviruses infecting some weeds in Jamaica are distinct from crop-infecting geminiviruses in Jamaica and define a new geminivirus cluster.

scholarly journals Genetic Diversity of Babesia bovis MSA-1, MSA-2b and MSA-2c in China

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 473
Author(s):  
Jinming Wang ◽  
Jifei Yang ◽  
Shandian Gao ◽  
Xiaoxing Wang ◽  
Hao Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Immune Responses ◽  
Nested Pcr ◽  
Phylogenetic Analyses ◽  
Apicomplexan Parasite ◽  
Amino Acid Sequences ◽  
Babesia Bovis ◽  
Chain Reaction ◽  
Merozoite Surface Antigen ◽  
Polymerase Chain

The apicomplexan parasite Babesia bovis is a tick-borne intracellular hemoprotozoan parasite that is widespread across China. Genetic diversity is an important strategy used by parasites to escape the immune responses of their hosts. In our present study, 575 blood samples, collected from cattle in 10 provinces, were initially screened using a nested PCR (polymerase chain reaction) for detection of B. bovis infection. To perform genetic diversity analyses, positive samples were further amplified to obtain sequences of three B. bovis merozoite surface antigen genes (MSA-1, MSA-2b, MSA-2c). The results of the nested PCR approach showed that an average of 8.9% (51/575) of cattle were positive for B. bovis infection. Phylogenetic analyses of the predicted amino acid sequences revealed that unique antigen variants were formed only by Chinese isolates. Our findings provide vital information for understanding the genetic diversity of B. bovis in China.

scholarly journals A superfamily of Arabidopsis thaliana retrotransposons.

Genetics ◽  
1991 ◽  
Vol 127 (4) ◽  
pp. 801-809 ◽  
Author(s):  
A Konieczny ◽  
D F Voytas ◽  
M P Cummings ◽  
F M Ausubel
Keyword(s):  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Reverse Transcriptase ◽  
Amino Acid Identity ◽  
Rnase H ◽  
Amino Acid Sequences ◽  
Nucleotide Sequence Analysis ◽  
Degenerate Primers ◽  
Hybridization Probes ◽  
Polymerase Chain

Abstract We describe a superfamily of Arabidopsis thaliana retrotransposable elements that consists of at least ten related families designated Ta1-Ta10. The Ta1 family has been described previously. Two genomic clones representing the Ta2 and Ta3 elements were isolated from an A. thaliana (race Landsberg erecta) lambda library using sequences derived from the reverse transcriptase region of Ta1 as hybridization probes. Nucleotide sequence analysis showed that the Ta1, Ta2 and Ta3 families share greater than 75% amino acid identity in pairwise comparisons of their reverse transcriptase and RNase H genes. In addition to Ta1, Ta2 and Ta3, we identified seven other related retrotransposon families in Landsberg erecta, Ta4-Ta10, using degenerate primers and the polymerase chain reaction to amplify a highly conserved region of retrotransposon-encoded reverse transcriptase. One to two copies of elements Ta2-Ta10 are present in the genomes of the A. thaliana races Landsberg erecta and Columbia indicating that the superfamily comprises at least 0.1% of the A. thaliana genome. The nucleotide sequences of the reverse transcriptase regions of the ten element families place them in the category of copia-like retrotransposons and phylogenetic analysis of the amino acid sequences suggests that horizontal transfer may have played a role in their evolution.

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.

scholarly journals A Single Amino Acid Mutation in theCarnation Ringspot Virus Capsid Protein Allows Virion Formation but Prevents Systemic Infection

2001 ◽  
Vol 75 (19) ◽  
pp. 9538-9542 ◽  
Author(s):  
Tim L. Sit ◽  
Patrick R. Haikal ◽  
Anton S. Callaway ◽  
Steven A. Lommel
Keyword(s):  
Amino Acid ◽  
Capsid Protein ◽  
Protein Gene ◽  
Systemic Infection ◽  
Ringspot Virus ◽  
Single Amino Acid ◽  
Capsid Protein Gene ◽  
Virus Capsid ◽  
Virion Formation ◽  
Virus Capsid Protein

ABSTRACT A Carnation ringspot virus (CRSV) variant (1.26) was identified that accumulates virions but is incapable of forming a systemic infection. The 1.26 capsid protein gene possesses a Ser→Pro mutation at amino acid 282. Conversion of 1.26 amino acid 282 to Ser restored systemic infection, while the reciprocal mutation in wild-type CRSV abolished systemic infection. Similar mutations introduced into the related Red clover necrotic mosaic virus capsid protein gene failed to induce the packaging but nonsystemic movement phenotype. These results provide additional support for the theory that virion formation is necessary but not sufficient for systemic movement with the dianthoviruses.

scholarly journals Phylogeny of North American Powassan virus

2001 ◽  
Vol 82 (7) ◽  
pp. 1657-1665 ◽  
Author(s):  
Gregory D. Ebel ◽  
Andrew Spielman ◽  
Sam R. Telford
Keyword(s):  
Genetic Diversity ◽  
New York ◽  
Amino Acid ◽  
North America ◽  
Adaptive Evolution ◽  
Envelope Protein ◽  
Amino Acid Sequences ◽  
Ixodid Ticks ◽  
Genetic Lineages ◽  
Powassan Virus

To determine whether Powassan virus (POW) and deer tick virus (DTV) constitute distinct flaviviral populations transmitted by ixodid ticks in North America, we analysed diverse nucleotide sequences from 16 strains of these viruses. Two distinct genetic lineages are evident, which may be defined by geographical and host associations. The nucleotide and amino acid sequences of lineage one (comprising New York and Canadian POW isolates) are highly conserved across time and space, but those of lineage two (comprising isolates from deer ticks and a fox) are more variable. The divergence between lineages is much greater than the variation within either lineage, and lineage two appears to be more diverse genetically than is lineage one. Application of McDonald–Kreitman tests to the sequences of these strains indicates that adaptive evolution of the envelope protein separates lineage one from lineage two. The two POW lineages circulating in North America possess a pattern of genetic diversity suggesting that they comprise distinct subtypes that may perpetuate in separate enzootic cycles.

Diversity of the trifunctional histidine biosynthesis gene (his) in cerealPhaeosphaeriaspecies

Genome ◽  
2007 ◽  
Vol 50 (6) ◽  
pp. 595-609 ◽  
Author(s):  
Chih-Li Wang ◽  
Arkadiusz Malkus ◽  
Sabina M. Zuzga ◽  
Pi-Fang Linda Chang ◽  
Barry M. Cunfer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Meiotic Recombination ◽  
Pcr Amplification ◽  
Amino Acid Sequences ◽  
Histidine Biosynthesis ◽  
Leaf Blotch ◽  
Rates Of Evolution ◽  
Biosynthesis Gene ◽  
Histidinol Dehydrogenase

Phaeosphaeria species are important causal agents of Stagonospora leaf blotch diseases in cereals. In this study, the nucleotide sequence and deduced polypeptide of the trifunctional histidine biosynthesis gene (his) are used to investigate the phylogenetic relationships and provide molecular identification among cereal Phaeosphaeria species. The full-length sequences of the his gene were obtained by PCR amplification and compared among cereal Phaeosphaeria species. The coding sequence of the his gene in wheat-biotype P. nodorum (PN-w) was 2697 bp. The his genes in barley-biotype P. nodorum (PN-b), two P. avenaria f. sp. triticea isolates (homothallic Pat1 and Pat3), and Phaeosphaeria species from Polish rye and dallis grass were 2694 bp. The his gene in heterothallic isolate Pat2, however, was 2693 bp because the intron had one fewer base. In P. avenaria f. sp. avenaria (Paa), the his gene was only 2670 bp long. The differences in the size of the his gene contributed to the variation in amino acid sequences in the gap region located between the phosphoribosyl-ATP pyrophosphohydrolase and histidinol dehydrogenase sub-domains. Based on nucleotide and deduced amino acid sequences of the his gene, Pat1 was not closely related to either PN-w or the Paa clade. It appears that rates of evolution of the his gene were fast in cereal Phaeosphaeria species. The possible involvement of meiotic recombination in genetic diversity of the his gene in P. nodorum is discussed.

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