scholarly journals Taxonomic status of Bhanja and Kismayo viruses (family Bunyaviridae)

2012 ◽  
Vol 17 (4) ◽  
pp. 4-8
Author(s):  
A. S Klimentov ◽  
A. P Gmyl ◽  
A. M Butenko ◽  
L. V Gmyl ◽  
O. V Isaeva ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
The Family ◽  
L Segment

The nucleotide sequence of M= (1398 nucleotides and L= (6186 nucleotides) segments of the genome of Bhanja virus and L-segment (1297 nucleotides) of Kismayo virus has been partially determined. Phylogenetic analysis of deduced amino acid sequences showed that these viruses are novel members of the Flebovirus (Phlebovirus) genus in the family Bunyaviridae

scholarly journals Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot virus isolates

2019 ◽  
Vol 165 (1) ◽  
pp. 21-31 ◽  
Author(s):  
A. M. Dullemans ◽  
M. Botermans ◽  
M. J. D. de Kock ◽  
C. E. de Krom ◽  
T. A. J. van der Lee ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Complete Genome ◽  
New Genus ◽  
Sequence Data ◽  
Amino Acid Sequences ◽  
Ringspot Virus ◽  
Genome Sequences ◽  
The Family ◽  
Virus Isolates

Abstract To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related unassigned viruses be assigned to a new genus within the family Secoviridae, named “Stralarivirus”. Based on the phylogenetic analysis, this genus should include at least three viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.

scholarly journals Complete Nucleotide Sequence of a Partitivirus from Rhizoctonia solani AG-1 IA Strain C24

Viruses ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 703 ◽  
Author(s):  
Chen Liu ◽  
Miaolin Zeng ◽  
Meiling Zhang ◽  
Canwei Shu ◽  
Erxun Zhou
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Rhizoctonia Solani ◽  
Sheath Blight ◽  
Open Reading Frame ◽  
Rice Sheath Blight ◽  
Rna Dependent Rna Polymerase ◽  
Reading Frame ◽  
The Family

The complete genome of a novel double-stranded (ds) RNA mycovirus, named as Rhizoctonia solani partitivirus 5 (RsPV5), isolated from rice sheath blight fungus R. solani AG-1 IA strain C24, was sequenced and analysed. RsPV5 consists of two segments, dsRNA-1 (1899 nucleotides) and dsRNA-2 (1787 nucleotides). DsRNA-1 has an open reading frame (ORF) 1 that potentially codes for a protein of 584 amino acid (aa) containing the conserved motifs of a RNA-dependent RNA polymerase (RdRp), and dsRNA-2 also contains a ORF 2, encoding a putative capsid protein (CP) of 513 aa. Phylogenetic analysis revealed that RsPV5 clustered together with six other viruses in an independent clade of the genus Alphapartitivirus, indicating that RsPV5 was a new member of the genus Alphapartitivirus, within the family Partitiviridae.

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

scholarly journals A novel giant secretion polypeptide in Chironomus salivary glands: implications for another Balbiani ring gene.

1985 ◽  
Vol 101 (3) ◽  
pp. 1044-1051 ◽  
Author(s):  
W Y Kao ◽  
S T Case
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Salivary Glands ◽  
Cyanogen Bromide ◽  
Tryptic Peptide ◽  
Amino Acid Sequences ◽  
The Other ◽  
Balbiani Ring ◽  
Sequence Organization ◽  
Peptide Maps

Chironomus salivary glands contain a family of high Mr (approximately 1,000 X 10(3)) secretion polypeptides thought to consist of three components: sp-Ia, sp-Ib, and sp-Ic. The use of a new extraction protocol revealed a novel high Mr component, sp-Id. Results of a survey of individual salivary glands indicated that sp-Id was widespread in more than a dozen strains of C. tentans and C. pallidivittatus. Sp-Id was phosphorylated at Ser residues, and a comparison of cyanogen bromide and tryptic peptide maps of 32P-labeled polypeptides suggested that sp-Ia, sp-Ib, and sp-Id are comprised of similar but nonidentical tandemly repeated amino acid sequences. We concluded that sp-Id is encoded by an mRNA whose size and nucleotide sequence organization are similar to Balbiani ring (BR) mRNAs that code for the other sp-I components. Furthermore, parallel repression of sp-Ib and sp-Id synthesis by galactose led us to hypothesize that both of their genes exist within Balbiani ring 2.

scholarly journals Isolation and Phylogenetic Analysis of Novel Viruses Infecting the Phytoplankton Phaeocystis globosa (Prymnesiophyceae)

2004 ◽  
Vol 70 (6) ◽  
pp. 3700-3705 ◽  
Author(s):  
C. P. D. Brussaard ◽  
S. M. Short ◽  
C. M. Frederickson ◽  
C. A. Suttle
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Polymerase ◽  
Coastal Waters ◽  
Common Ancestor ◽  
Genetic Relatedness ◽  
Amino Acid Sequences ◽  
Polymerase Gene ◽  
Phaeocystis Globosa ◽  
The Family ◽  
Algal Host

ABSTRACT Viruses infecting the harmful bloom-causing alga Phaeocystis globosa (Prymnesiophyceae) were readily isolated from Dutch coastal waters (southern North Sea) in 2000 and 2001. Our data show a large increase in the abundance of putative P. globosa viruses during blooms of P. globosa, suggesting that viruses are an important source of mortality for this alga. In order to examine genetic relatedness among viruses infecting P. globosa and other phytoplankton, DNA polymerase gene (pol) fragments were amplified and the inferred amino acid sequences were phylogenetically analyzed. The results demonstrated that viruses infecting P. globosa formed a closely related monophyletic group within the family Phycodnaviridae, with at least 96.9% similarity to each other. The sequences grouped most closely with others from viruses that infect the prymnesiophyte algae Chrysochromulina brevifilum and Chrysochromulina strobilus. Whether the P. globosa viruses belong to the genus Prymnesiovirus or form a separate group needs further study. Our data suggest that, like their phytoplankton hosts, the Chrysochromulina and Phaeocystis viruses share a common ancestor and that these prymnesioviruses and their algal host have coevolved.

Complete Genome Sequence of a Novel Ourmia-like Mycovirus Infecting the Phytopathogenic Fungus Botryosphaeria Dothidea

2021 ◽  
Author(s):  
Liying Sun ◽  
Ziqian Lian ◽  
Subha Das ◽  
Jingxian Luo ◽  
Ida Bagus Andika
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Amino Acid Sequences ◽  
Shanxi Province ◽  
Phytopathogenic Fungus ◽  
Botryosphaeria Dothidea ◽  
Reading Frame ◽  
Ring Rot ◽  
Ssrna Virus ◽  
The Family

Abstract In this study, we describe the full-length genome sequence of a novel ourmia-like mycovirus, tentatively designated Botryosphaeria dothidea ourmia-like virus 1 (BdOLV1), isolated from the phytopathogenic fungus, Botryosphaeria dothidea strain P8, associated with apple ring rot in Shanxi province, China. The complete BdOLV1 genome is comprised of 2797 nucleotides, a positive-sense (+) single-stranded RNA (ssRNA) with a single open reading frame (ORF). The ORF putatively encodes a 642-amino acid polypeptide with conserved RNA-dependent RNA polymerase (RdRp) motifs, related to viruses of the family Botourmiaviridae. Phylogenetic analysis based on the RdRp amino acid sequences showed that BdOLV1 is grouped with oomycete-infecting unclassified viruses closely related to the genus Botoulivirus in Botourmiaviridae. This is the first report of a novel (+)ssRNA virus in B. dothidea related to the genus Botoulivirus in the family Botourmiaviridae.

scholarly journals Molecular characterization and phylogenetic analysis of NBS-LRR genes in wild relatives of eggplant (Solanum melongena L

2018 ◽  
Author(s):  
Sona. S Dev ◽  
P. Poornima ◽  
Akhil Venu
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Sequence Similarity ◽  
Interleukin 1 ◽  
Preliminary Investigation ◽  
Solanum Melongena ◽  
Wild Relatives ◽  
Amino Acid Sequences ◽  
R Genes ◽  
Multiple Sequence

Eggplantor brinjal (Solanum melongena L.), is highly susceptible to various soil-borne diseases. The extensive use of chemical fungicides to combat these diseases can be minimized by identification of resistance gene analogs (RGAs) in wild species of cultivated plants.In the present study, degenerate PCR primers for the conserved regions ofnucleotide binding site-leucine rich repeat (NBS-LRR) were used to amplify RGAs from wild relatives of eggplant (Black nightshade (Solanum nigrum), Indian nightshade (Solanumviolaceum)and Solanu mincanum) which showed resistance to the bacterial wilt pathogen, Ralstonia solanacearumin the preliminary investigation. The amino acid sequence of the amplicons when compared to each other and to the amino acid sequences of known RGAs deposited in Gen Bank revealed significant sequence similarity. The phylogenetic analysis indicated that they belonged to the toll interleukin-1 receptors (TIR)-NBS-LRR type R-genes. Multiple sequence alignment with other known R genes showed significant homology with P-loop, Kinase 2 and GLPL domains of NBS-LRR class genes. There has been no report on R genes from these wild eggplants and hence the diversity analysis of these novel RGAs can lead to the identification of other novel R genes within the germplasm of different brinjal plants as well as other species of Solanum.

Identification of mariner-like elements in Sitodiplosis mosellana (Diptera: Cecidomyiidae)

2006 ◽  
Vol 138 (2) ◽  
pp. 138-146 ◽  
Author(s):  
O. Mittapalli ◽  
R.H. Shukle ◽  
I.L. Wise
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Blot Analysis ◽  
Copy Number ◽  
Southern Blot Analysis ◽  
Pcr Primers ◽  
Amino Acid Sequences ◽  
Degenerate Pcr ◽  
Sitodiplosis Mosellana ◽  
Wheat Midge

AbstractMariner-like element sequences were recovered from the genome of the orange wheat midge, Sitodiplosis mosellana (Géhin), with degenerate PCR primers designed to conserved regions of mariner transposases. The deduced amino acid sequences of the mariner-like transposases from S. mosellana showed 67% to 78% identity with the peptide sequences of other mariner transposases. A phylogenetic analysis revealed that the mariner-like elements from S. mosellana grouped in the mauritiana subfamily of mariner transposons. Results from Southern blot analysis suggest mariner-like elements are at a moderate copy number in the genome of S. mosellana.

Nucleotide sequence of the carboxy-terminal portion of a lodgepole pine actin gene

1988 ◽  
Vol 18 (12) ◽  
pp. 1595-1602 ◽  
Author(s):  
J. R. Kenny ◽  
B. P. Dancik ◽  
L. Z. Florence ◽  
F. E. Nargang
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Intron Position ◽  
Amino Acid Sequences ◽  
Pairwise Comparisons ◽  
Actin Gene ◽  
Terminal Portion ◽  
The Third ◽  
Actin Genes ◽  
Carboxy Terminal

We have determined the nucleotide sequence of the carboxy-terminal portion of an actin gene (PAc1-A) isolated from Pinuscontorta var. latifolia (Engelm.). Pairwise comparisons of both nucleotide and deduced amino acid sequences were made among PAc1-A, the soybean actins SAc3 and SAc1, maize actin MAc1, chicken β-actin, and yeast β-actin. Of the other actins SAc3 was most similar to the PAc1-A amino acid sequence (91.3% identity) and yeast actin the least similar (78.3% identity). The intron in PAc1-A is present at the same location as the third intron found in MAc1, SAc1, and SAc3 actin genes. This conservation of intron position is unusual when compared with nonplant actin genes.

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