scholarly journals Human Herpesvirus 6B Genome Sequence: Coding Content and Comparison with Human Herpesvirus 6A

1999 ◽  
Vol 73 (10) ◽  
pp. 8040-8052 ◽  
Author(s):  
Geraldina Dominguez ◽  
Timothy R. Dambaugh ◽  
Felicia R. Stamey ◽  
Stephen Dewhurst ◽  
Naoki Inoue ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Nucleotide Sequence Identity ◽  
Genomic Sequence ◽  
Human Herpesvirus ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Sequence Identity ◽  
T Cell Lines ◽  
The Right

ABSTRACT Human herpesvirus 6 variants A and B (HHV-6A and HHV-6B) are closely related viruses that can be readily distinguished by comparison of restriction endonuclease profiles and nucleotide sequences. The viruses are similar with respect to genomic and genetic organization, and their genomes cross-hybridize extensively, but they differ in biological and epidemiologic features. Differences include infectivity of T-cell lines, patterns of reactivity with monoclonal antibodies, and disease associations. Here we report the complete genome sequence of HHV-6B strain Z29 [HHV-6B(Z29)], describe its genetic content, and present an analysis of the relationships between HHV-6A and HHV-6B. As sequenced, the HHV-6B(Z29) genome is 162,114 bp long and is composed of a 144,528-bp unique segment (U) bracketed by 8,793-bp direct repeats (DR). The genomic sequence allows prediction of a total of 119 unique open reading frames (ORFs), 9 of which are present only in HHV-6B. Splicing is predicted in 11 genes, resulting in the 119 ORFs composing 97 unique genes. The overall nucleotide sequence identity between HHV-6A and HHV-6B is 90%. The most divergent regions are DR and the right end of U, spanning ORFs U86 to U100. These regions have 85 and 72% nucleotide sequence identity, respectively. The amino acid sequences of 13 of the 17 ORFs at the right end of U differ by more than 10%, with the notable exception of U94, the adeno-associated virus type 2 rep homolog, which differs by only 2.4%. This region also includes putative cis-acting sequences that are likely to be involved in transcriptional regulation of the major immediate-early locus. The catalog of variant-specific genetic differences resulting from our comparison of the genome sequences adds support to previous data indicating that HHV-6A and HHV-6B are distinct herpesvirus species.

scholarly journals Complete Genome Sequence of a New Maize-Associated Cytorhabdovirus

2017 ◽  
Vol 5 (31) ◽  
Author(s):  
Kristen Willie ◽  
Lucy R. Stewart
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Nucleotide Sequence Identity ◽  
Open Reading Frames ◽  
Sequence Identity ◽  
Genome Wide ◽  
Maize Sample ◽  
Reading Frames

ABSTRACT A new 11,877-nucleotide cytorhabdovirus sequence with 6 open reading frames has been identified in a maize sample. It shares 50 and 51% genome-wide nucleotide sequence identity with northern cereal mosaic cytorhabdovirus and barley yellow striate mosaic cytorhabdovirus, respectively.

scholarly journals Citrus leprosis virus N: A New Dichorhavirus Causing Citrus Leprosis Disease

2017 ◽  
Vol 107 (8) ◽  
pp. 963-976 ◽  
Author(s):  
Pedro Luis Ramos-González ◽  
Camila Chabi-Jesus ◽  
Orlene Guerra-Peraza ◽  
Aline Daniele Tassi ◽  
Elliot Watanabe Kitajima ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Nucleotide Sequence Identity ◽  
Viral Disease ◽  
Sensu Stricto ◽  
Amino Acid Sequences ◽  
Western Hemisphere ◽  
Open Reading Frames ◽  
Yield Reduction ◽  
Sequence Identity ◽  
Citrus Leprosis

Citrus leprosis (CL) is a viral disease endemic to the Western Hemisphere that produces local necrotic and chlorotic lesions on leaves, branches, and fruit and causes serious yield reduction in citrus orchards. Samples of sweet orange (Citrus × sinensis) trees showing CL symptoms were collected during a survey in noncommercial citrus areas in the southeast region of Brazil in 2013 to 2016. Transmission electron microscopy analyses of foliar lesions confirmed the presence of rod-like viral particles commonly associated with CL in the nucleus and cytoplasm of infected cells. However, every attempt to identify these particles by reverse-transcription polymerase chain reaction tests failed, even though all described primers for the detection of known CL-causing cileviruses and dichorhaviruses were used. Next-generation sequencing of total RNA extracts from three symptomatic samples revealed the genome of distinct, although highly related (>92% nucleotide sequence identity), viruses whose genetic organization is similar to that of dichorhaviruses. The genome sequence of these viruses showed <62% nucleotide sequence identity with those of orchid fleck virus and coffee ringspot virus. Globally, the deduced amino acid sequences of the open reading frames they encode share 32.7 to 63.8% identity with the proteins of the dichorhavirids. Mites collected from both the naturally infected citrus trees and those used for the transmission of one of the characterized isolates to Arabidopsis plants were anatomically recognized as Brevipalpus phoenicis sensu stricto. Molecular and biological features indicate that the identified viruses belong to a new species of CL-associated dichorhavirus, which we propose to call Citrus leprosis N dichorhavirus. Our results, while emphasizing the increasing diversity of viruses causing CL disease, lead to a reevaluation of the nomenclature of those viruses assigned to the genus Dichorhavirus. In this regard, a comprehensive discussion is presented.

scholarly journals Complete Genome Sequence of a Lineage IV Peste des Petits Ruminants Virus from Turkey, 2018

2020 ◽  
Vol 9 (15) ◽  
Author(s):  
Sabri Hacıoğlu ◽  
Simon King ◽  
Şirin Gülsün Çizmeci ◽  
Öznur Yeşil ◽  
John Flannery ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Nucleotide Sequence Identity ◽  
Clinical Signs ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Peste Des Petits Ruminants ◽  
Sequence Identity ◽  
Lineage Iv

We report the whole-genome sequence of a peste des petits ruminants virus (PPRV) from a lamb exhibiting clinical signs in Turkey in September 2018. The genome of PPRV/Turkey/Central_Anatolia/2018 shows the highest nucleotide sequence identity (97.63%) to PPRV isolated in Turkey in 2000.

scholarly journals Complete Genome Sequence of a Lineage II Peste des Petits Ruminants Virus from Sierra Leone

2018 ◽  
Vol 6 (1) ◽  
Author(s):  
William G. Dundon ◽  
Caroline M. Adombi ◽  
Saidu Kanu ◽  
Angelika Loitsch ◽  
Giovanni Cattoli ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Sierra Leone ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Ivory Coast ◽  
Nucleotide Sequence Identity ◽  
Peste Des Petits Ruminants ◽  
Sequence Identity

ABSTRACT The complete genome sequence of a peste des petits ruminants virus (PPRV) from goat samples collected in Sierra Leone in 2011 is reported here. The genome shows a higher nucleotide sequence identity (98.9%) with a lineage II PPRV from Senegal than to PPRVs from neighboring Liberia and Ivory Coast.

scholarly journals Complete Genome Sequence of Novel Polerovirus-Associated RNA Infecting Pepper (Capsicum spp.) in South Africa

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
W. E. W. Schravesande ◽  
J. P. van Wijk ◽  
A. Verhage
Keyword(s):  
South Africa ◽  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Nucleotide Sequence Identity ◽  
Closely Related Species ◽  
Sequence Identity ◽  
Capsicum Spp ◽  
Pepper Vein Yellows Virus

ABSTRACT The complete genome sequence of a novel polerovirus-associated RNA infecting pepper in South Africa was determined. The nucleotide sequence identity of 78.3% with closely related species suggested that this associated RNA was novel, and the name pepper vein yellows virus-associated RNA is proposed for this RNA fragment.

scholarly journals Complete Genome Sequence of Streptomyces Siphophage Sitrop

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Victor Portillo ◽  
Haydee Diaz ◽  
James Clark ◽  
Isla Hernandez ◽  
Mei Liu ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Nucleotide Sequence Identity ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Sequence Identity

ABSTRACT Streptomyces sp. strain Mg1 is a Gram-positive soil bacterium capable of causing cell lysis and degradation of Bacillus subtilis colonies. Here, we report the 48,481-bp genome of Streptomyces sp. Mg1 siphophage Sitrop. With 77 predicted protein-coding genes and one tRNA, Sitrop shares 77% nucleotide sequence identity with the Streptomyces phage Verse.

scholarly journals Genome Sequence of a New Siphoviridae Phage Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain

2018 ◽  
Vol 6 (22) ◽  
Author(s):  
Fabrício S. Campos ◽  
Gil R. Santos ◽  
Vitor L. Nascimento ◽  
Roberto F. T. Corrêia ◽  
Alex S. R. Cangussu ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Nucleotide Sequence Identity ◽  
Fermentation Process ◽  
High Nucleotide Sequence Identity ◽  
Content Type ◽  
Brazilian Strain ◽  
Sequence Identity

ABSTRACT During the fermentation process, Bacillus thuringiensis (Bt) phages can result in bacterial death and decreased yield. In this work, we describe the genome of a new phage related to the Siphoviridae viral family from a Brazilian strain of Bt which showed high nucleotide sequence identity to the genomes of phages phi4l1 and BtCS33.

scholarly journals Complete Genome Sequence of a New Strain of Tanay Virus, Isolate YN15_103_01, from Yunnan, China

2018 ◽  
Vol 6 (8) ◽  
Author(s):  
Lu Zhao ◽  
Han Xia ◽  
Yujuan Wang ◽  
Atoni Evans ◽  
Yunzhi Zhang ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Nucleotide Sequence Identity ◽  
Virus Isolate ◽  
The Philippines ◽  
Content Type ◽  
Sequence Identity

ABSTRACT We report here the complete genome sequence of a new strain of Tanay virus, isolate YN15_103_01, which was isolated from Anopheles sinensis mosquitoes caught in China. Sequence analysis showed that it shares a 79% nucleotide sequence identity with the only other previously reported strains of Tanay virus, which were isolated from the Philippines.

scholarly journals Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in Escherichia coli

2007 ◽  
Vol 189 (22) ◽  
pp. 8206-8214 ◽  
Author(s):  
Sophie Zuber ◽  
Catherine Ngom-Bru ◽  
Caroline Barretto ◽  
Anne Bruttin ◽  
Harald Brüssow ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Open Reading Frames ◽  
High Sequence Identity ◽  
E Coli ◽  
Sequence Identity ◽  
Shared Identity ◽  
Wastewater Samples ◽  
The Right ◽  
Nonstructural Genes

ABSTRACT Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene (g23) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of E. coli T4-like phages. We conducted an analysis of the 169-kb JS98 genome sequence. Overall, 198 of the 266 JS98 open reading frames (ORFs) shared amino acid sequence identity with the reference T4 phage, 41 shared identity with other T4-like phages, and 27 ORFs lacked any database matches. Genes on the plus strand encoded virion proteins, which showed moderate to high sequence identity with T4 proteins. The right genome half of JS98 showed a higher degree of sequence conservation with T4 and RB69, even for the nonstructural genes, than did the left genome half, containing exclusively nonstructural genes. Most of the JS98-specific genes were found in the left genome half. Two came as a hypervariability cluster, but most represented isolated genes, suggesting that they were acquired separately in multiple acquisition events. No evidence for DNA exchange between JS98 phage and the E. coli host genome or coliphages other than T4 was observed. No undesired genes which could compromise its medical use were detected in the JS98 genome sequence.

scholarly journals Sequence identity in an early chorion multigene family is the result of localized gene conversion.

Genetics ◽  
1991 ◽  
Vol 128 (3) ◽  
pp. 595-606
Author(s):  
B L Hibner ◽  
W D Burke ◽  
T H Eickbush
Keyword(s):  
Nucleotide Sequence ◽  
Gene Conversion ◽  
Nucleotide Sequence Identity ◽  
Early Period ◽  
Gene Families ◽  
Multigene Families ◽  
Coding Regions ◽  
Sequence Identity ◽  
Isolation And Characterization ◽  
Sequence Exchange

Abstract The multigene families that encode the chorion (eggshell) of the silk moth, Bombyx mori, are closely linked on one chromosome. We report here the isolation and characterization of two segments, totaling 102 kb of genomic DNA, containing the genes expressed during the early period of choriogenesis. Most of these early genes can be divided into two multigene families, ErA and ErB, organized into five divergently transcribed ErA/ErB gene pairs. Nucleotide sequence identity in the major coding regions of the ErA genes was 96%, while nucleotide sequence identity for the ErB major coding regions was only 63%. Selection pressure on the encoded proteins cannot explain this difference in the level of sequence conservation between the ErA and ErB gene families, since when only fourfold redundant codon positions are considered, the divergence within the ErA genes is 8%, while the divergence within the ErB genes (corrected for multiple substitutions at the same site) is 110%. The high sequence identity of the ErA major exons can be explained by sequence exchange events similar to gene conversion localized to the major exon of the ErA genes. These gene conversions are correlated with the presence of clustered copies of the nucleotide sequence GGXGGX, encoding paired glycine residues. This sequence has previously been correlated with gradients of gene conversion that extend throughout the coding and noncoding regions of the High-cysteine (Hc) chorion genes of B. mori. We suggest that the difference in the extent of the conversion tracts in these gene families reflects a tendency for these recombination events to become localized over time to the protein encoding regions of the major exons.

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