Genetic Variation and Phylogenetic Analysis of Open Reading Frames 3 and 4 of Various Equine Arteritis Virus Isolates

1998 ◽  
pp. 813-819 ◽  
Author(s):  
D. Archambault ◽  
G. Laganière ◽  
G. St-Laurent
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Open Reading Frames ◽  
Equine Arteritis Virus ◽  
Virus Isolates ◽  
Reading Frames

An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

2021 ◽  
Author(s):  
Juan F Cornejo-Franco ◽  
Francisco Flores ◽  
Dimitre Mollov ◽  
diego fernando quito-avila
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Rna Dependent Rna Polymerase ◽  
Sequence Comparisons ◽  
Genomic Features ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

scholarly journals Genomic Characterization of a New Enamovirus Infecting Common Bean

2021 ◽  
Author(s):  
Ruo-bin Lu ◽  
Ping-xiu Lan ◽  
Ru-jing Kang ◽  
Guan-lin Tan ◽  
Xiao-jiao Chen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Novel Species ◽  
Open Reading Frames ◽  
Amino Acid Sequence Level ◽  
Disease Symptoms ◽  
Bean Plants ◽  
Genomic Characterization ◽  
Pea Enation Mosaic Virus ◽  
Reading Frames

Abstract A novel enamovirus was identified from bean plants with disease symptoms. Its genome of 5,781 nucleotides (nt) encodes five open reading frames. The virus and other species of the genus Enamovirus share identities of 50.4%-68.4% at the complete genome, and 19.9%-51.9% of P0, 24.9%-52.5% of P1, 33.4%-62.9% of P1-P2, 30.6%-81.1% of P3, 32.3%-74.2% of P3-P5 at amino acid sequence level, respectively. Phylogenetic analysis showed that the virus is most closely related to Alfalfa enamovirus 1 and Pea enation mosaic virus 1 in the genus Enamovirus within family Solemoviridae. These results suggest that the virus should be considered as a novel species in the genus Enamovirus and tentatively named as “bean enamovirus 1”.

scholarly journals Complete nucleotide sequence and genome organization of Grapevine leafroll-associated virus 3, type member of the genus Ampelovirus

2004 ◽  
Vol 85 (7) ◽  
pp. 2099-2102 ◽  
Author(s):  
Kai-Shu Ling ◽  
Hai-Ying Zhu ◽  
Dennis Gonsalves
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequence ◽  
Fusion Protein ◽  
Complete Genome Sequence ◽  
Genome Organization ◽  
Complete Nucleotide Sequence ◽  
Open Reading Frames ◽  
The Family ◽  
Mealy Bug ◽  
Reading Frames

This study reports on the complete genome sequence of Grapevine leafroll-associated virus 3, the type member of the genus Ampelovirus. The genome is 17 919 nt in size and contains 13 open reading frames (ORFs). Previously, the sequence of 13 154 nt of the 3′-terminal of the genome was reported. The newly sequenced portion contains a 158 nt 5′ UTR, a single papain-like protease and a methyltransferase-like (MT) domain. ORF1a encodes a large polypeptide with a molecular mass of 245 kDa. With a predicted +1 frameshift, the large fusion protein generated from ORF1a/1b would produce a 306 kDa polypeptide. Phylogenetic analysis using MT domains further supports the creation of the genus Ampelovirus for mealy-bug-transmitted viruses in the family Closteroviridae.

scholarly journals Genetic Analysis of Clinical VZV Isolates Collected in China Reveals a More Homologous Profile

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Longfeng Jiang ◽  
Lin Gan ◽  
Jason Chen ◽  
Mingli Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Open Reading Frames ◽  
Polymorphic Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Varicella Zoster ◽  
Clade B ◽  
The Us ◽  
The World ◽  
Reading Frames

Forty-four varicella-zoster virus (VZV) isolates from China were genotyped by using a scattered single nucleotide polymorphism (SNP) method, including open reading frames (ORFs) 1, 22, 31, 37, 60, 62, 67, and 68. Based on the analysis of the polymorphic markers in the 8 ORFs, all of the 44 isolates can be placed in genotype J defined by the SNP profiles in ORF22 or clade B defined by the SNP profiles in ORFs 31, 37, 60, 62, 67, and 68. The three consecutive nucleotide (CGG) in-frame insertions in ORF 1 were found in 8 (18.2%) isolates, which has not been described in VZV strains from any other part of the world. A novel synonymous A>G substitution in ORF60 was revealed in 4 (9.1%) of the isolates. In addition, a previously described three consecutive nucleotide (ATC) insertion in ORF 60 was found in all the Chinese isolates but not in the US isolate MLS. The results showed all the 44 strains that belong to genotype J/clade B with significantly high homogeneity, and phylogenetic analysis suggested that the 44 Chinese isolates consist of 4 clusters, but interstrain variations also exist. Overall, VZV isolates obtained in China showed significantly higher genetic homogeneity than isolates reported from other countries.

scholarly journals Evidence for Existence of “Mesotogas,” Members of the Order Thermotogales Adapted to Low-Temperature Environments

2006 ◽  
Vol 72 (7) ◽  
pp. 5061-5068 ◽  
Author(s):  
Camilla L. Nesbø ◽  
Marlena Dlutek ◽  
Olga Zhaxybayeva ◽  
W. Ford Doolittle
Keyword(s):  
Phylogenetic Analysis ◽  
Low Temperature ◽  
Polychlorinated Biphenyl ◽  
Enrichment Culture ◽  
Open Reading Frames ◽  
Rrna Gene ◽  
Gene Trees ◽  
16S Rrna Gene Sequences ◽  
Sequence Composition ◽  
Reading Frames

ABSTRACT All cultivated isolates of the bacterial order Thermotogales are either thermophiles or hyperthermophiles, but Thermotogales 16S rRNA gene sequences have been detected in many mesophilic anaerobic and microaerophilic environments, particularly within communities involved in the remediation of pollutants. Here we provide metagenomic evidence for the existence of Thermotogales lineages, which we informally call “mesotoga,” that are adapted to growth at lower temperatures. Two fosmid clones containing mesotoga DNA, originating from a low-temperature enrichment culture that degrades a polychlorinated biphenyl congener, were sequenced. Phylogenetic analysis clearly puts this bacterial lineage within the Thermotogales order, with the rRNA gene trees and 21 of 58 open reading frames strongly supporting this relationship. An analysis of protein sequence composition showed that mesotoga proteins are adapted to function at lower temperatures than are their identifiable homologs from thermophilic and hyperthermophilic members of the order Thermotogales, supporting the notion that this bacterium lives and grows optimally at lower temperatures. The phylogenetic analysis suggests that the mesotoga lineage from which our fosmids derive has used both the acquisition of genes from its neighbors and the modification of existing thermophilic sequences to adapt to a mesophilic lifestyle.

Phylogenetic analysis reveals Stowaway-like elements may represent a fourth family of the IS630-Tc1-mariner superfamily

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 82-90 ◽  
Author(s):  
Kime Turcotte ◽  
Thomas Bureau
Keyword(s):  
Phylogenetic Analysis ◽  
Inverted Repeat ◽  
Evolutionary Relationship ◽  
Open Reading Frames ◽  
Published Data ◽  
Terminal Inverted Repeat ◽  
Predominant Type ◽  
Sequence Signature ◽  
Eukaryotic Organisms ◽  
Reading Frames

The genomes of plants, like virtually all other eukaryotic organisms, harbor a diverse array of mobile elements, or transposons. In terms of numbers, the predominant type of transposons in many plants is the miniature inverted-repeat transposable element (MITE). There are three archetypal MITEs, known as Tourist, Stowaway, and Emigrant, each of which can be defined by a specific terminal inverted-repeat (TIR) sequence signature. Although their presence was known for over a decade, only recently have open reading frames (ORFs) been identified that correspond to putative transposases for each of the archetypes. We have identified two Stowaway elements that encode a putative transposase and are similar to members of the previously characterized IS630–Tc1-mariner superfamily. In this report, we provide a high-resolution phylogenetic analysis of the evolutionary relationship between Stowaway, Emigrant, and members of the IS630–Tc1-mariner superfamily. We show that although Emigrant is closely related to the pogo-like family of elements, Stowaway may represent a novel family. Integration of our results with previously published data leads to the conclusion that the three main types of MITEs have different evolutionary histories despite similarity in structure.Key words: Stowaway, Emigrant, MITE, mariner, transposon.

scholarly journals Nucleotide sequence, genome organization and phylogenetic analysis of pineapple mealybug wilt-associated virus-2

2001 ◽  
Vol 82 (1) ◽  
pp. 1-7 ◽  
Author(s):  
M. J. Melzer ◽  
A. V. Karasev ◽  
D. M. Sether ◽  
J. S. Hu
Keyword(s):  
Phylogenetic Analysis ◽  
Coat Protein ◽  
Genome Organization ◽  
Open Reading Frames ◽  
Double Stranded Rna ◽  
The Family ◽  
Mealybug Wilt ◽  
Pineapple Mealybug Wilt ◽  
Pineapple Mealybug ◽  
Reading Frames

The genome of pineapple mealybug wilt-associated closterovirus-2 (PMWaV-2) was cloned from double-stranded RNA isolated from diseased pineapple and its sequence determined. The 3′-terminal 14861 nt of the single-stranded RNA genome contains ten open reading frames (ORFs) which, from 5′ to 3′, potentially encode a >204 kDa polyprotein containing papain-like protease, methyltransferase and helicase domains (ORF1a), a 65 kDa RNA-dependent RNA polymerase (ORF1b), a 5 kDa hydrophobic protein (ORF2), a 59 kDa heat shock protein 70 homologue (ORF3), a 46 kDa protein (ORF4), a 34 kDa coat protein (ORF5), a 56 kDa diverged coat protein (ORF6), a 20 kDa protein (ORF7), a 22 kDa protein (ORF8) and a 6 kDa protein (ORF9). A 132 nt untranslated region was present at the 3′ terminus of the genome. This genome organization is typical of the monopartite closteroviruses, including the putative +1 ribosomal frameshift allowing expression of ORF1b. Phylogenetic analysis revealed that within the family Closteroviridae the mealybug-transmitted PMWaV-2 is more closely related to other mealybug-transmitted members than to those which are transmitted by aphids or whiteflies. Within this group, PMWaV-2 shares the greatest sequence identity with grapevine leafroll-associated virus-3, another mealybug-transmitted closterovirus.

scholarly journals Genomic and Morphological Features of a Banchine Polydnavirus: Comparison with Bracoviruses and Ichnoviruses

2007 ◽  
Vol 81 (12) ◽  
pp. 6491-6501 ◽  
Author(s):  
Renée Lapointe ◽  
Kohjiro Tanaka ◽  
Walter E. Barney ◽  
James B. Whitfield ◽  
Jonathan C. Banks ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Size ◽  
Genome Sequence ◽  
Protein Tyrosine Phosphatase ◽  
Size Range ◽  
Tyrosine Phosphatase ◽  
Gene Families ◽  
Open Reading Frames ◽  
Genomic Features ◽  
Reading Frames

ABSTRACT Many ichneumonid and braconid endoparasitoids inject a polydnavirus (PDV) into their caterpillar hosts during oviposition. The viral entities carried by wasps of these families are referred to as “ichnoviruses” (IVs) and “bracoviruses” (BVs), respectively. All IV genomes characterized to date are found in wasps of the subfamily Campopleginae; consequently, little is known about PDVs found in wasps of the subfamily Banchinae, the only other ichneumonid taxon thus far shown to carry these viruses. Here we report on the genome sequence and virion morphology of a PDV carried by the banchine parasitoid Glypta fumiferanae. With an aggregate genome size of ∼290 kb and 105 genome segments, this virus displays a degree of genome segmentation far greater than that reported for BVs or IVs. The size range of its genome segments is also lower than those in the latter two groups. As reported for other PDVs, the predicted open reading frames of this virus cluster into gene families, including the protein tyrosine phosphatase (PTP) and viral ankyrin (ank) families, but phylogenetic analysis indicates that ank genes of the G. fumiferanae virus are not embedded within the IV lineage, while its PTPs and those of BVs form distinct clusters. The banchine PDV genome also encodes a novel family of NTPase-like proteins displaying a pox-D5 domain. The unique genomic features of the first banchine virus examined, along with the morphological singularities of its virions (IV-like nucleocapsids, but enveloped in groups like some of the BVs), suggest that they could have an origin distinct from those of IVs and BVs.

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