scholarly journals Biological and Genomic Sequence Characterization of Maize streak virus Isolates from Wheat

2002 ◽  
Vol 92 (1) ◽  
pp. 81-86 ◽  
Author(s):  
J. A. Willment ◽  
D. P. Martin ◽  
E. Van der Walt ◽  
E. P. Rybicki
Keyword(s):  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Maize Streak Virus ◽  
Streak Virus ◽  
Genome Sequences ◽  
Sequence Characterization ◽  
Sequence Identity ◽  
Maize Type ◽  
Barley Genotypes

Maize streak virus (MSV) is best known as the causal agent of maize streak disease. However, only a genetically uniform subset of the viruses within this diverse species is actually capable of producing severe symptoms in maize. Whereas these “maize-type” viruses all share greater than 95% sequence identity, MSV strains isolated from grasses may share as little as 79% sequence identity with the maize-type viruses. Here, we present the complete genome sequences and biological characterization of two MSV isolates from wheat that share ≈89% sequence identity with the maize-type viruses. Clonal populations of these two isolates, named MSV-Tas and MSV-VW, were leafhopper-transmitted to Digitaria sanguinalis and a range of maize, wheat, and barley genotypes. Whereas the two viruses showed some differences in their pathogenicity in maize, they were both equally pathogenic in D. sanguinalis and the various wheat and barley genotypes tested. Phylogenetic analyses involving the genome sequences of MSV-Tas and MSV-VW, a new maize-type virus also fully sequenced in this study (MSV-VM), and all other available African streak virus sequences, indicated that MSV-Tas and MSV-VW are close relatives that together represent a distinct MSV strain. Sequence analyses revealed that MSV-VM has a recombinant genome containing MSV-Tas/VW-like sequences within its movement protein gene.

scholarly journals Virus-derived sequences from the transcriptomes of two snail vectors of schistosomiasis, Biomphalaria pfeifferi and Bulinus globosus from Kenya

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12290
Author(s):  
Sijun Liu ◽  
Si-Ming Zhang ◽  
Sarah K. Buddenborg ◽  
Eric S. Loker ◽  
Bryony C. Bonning
Keyword(s):  
Phylogenetic Analyses ◽  
454 Sequencing ◽  
Genome Sequences ◽  
Bioinformatics Pipeline ◽  
Biomphalaria Pfeifferi ◽  
Rna Sequences ◽  
Positive Sense ◽  
Bulinus Globosus ◽  
Viral Sequences

Schistosomiasis, which infects more than 230 million people, is vectored by freshwater snails. We identified viral sequences in the transcriptomes of Biomphalaria pfeifferi (BP) and Bulinus globosus (BuG), two of the world’s most important schistosomiasis vectors in Africa. Sequences from 26 snails generated using Illumina Hi-Seq or 454 sequencing were assembled using Trinity and CAP3 and putative virus sequences were identified using a bioinformatics pipeline. Phylogenetic analyses were performed using viral RNA-dependent RNA polymerase and coat protein sequences to establish relatedness between virus sequences identified and those of known viruses. Viral sequences were identified from the entire snail holobiont, including symbionts, ingested material and organisms passively associated with the snails. Sequences derived from more than 17 different viruses were found including five near full-length genomes, most of which were small RNA viruses with positive sense RNA genomes (i.e., picorna-like viruses) and some of which are likely derived from adherent or ingested diatoms. Based on phylogenetic analysis, five of these viruses (including BPV2 and BuGV2) along with four Biomphalaria glabrata viruses reported previously, cluster with known invertebrate viruses and are putative viruses of snails. The presence of RNA sequences derived from four of these novel viruses in samples was confirmed. Identification of the genome sequences of candidate snail viruses provides a first step toward characterization of additional gastropod viruses, including from species of biomedical significance.

scholarly journals Isolation and characterization of subgenomic DNAs encapsidated in “single” T = 1 isometric particles of Maize streak virus

Virology ◽  
2004 ◽  
Vol 323 (1) ◽  
pp. 164-171 ◽  
Author(s):  
Carolina G Casado ◽  
G Javier Ortiz ◽  
Eric Padron ◽  
Samantha J Bean ◽  
Robert McKenna ◽  
...  
Keyword(s):  
Maize Streak Virus ◽  
Streak Virus ◽  
Isolation And Characterization

scholarly journals Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae)

2009 ◽  
Vol 83 (21) ◽  
pp. 11233-11243 ◽  
Author(s):  
Stephanie D. Friedman ◽  
Fred J. Genthner ◽  
Jennifer Gentry ◽  
Mark D. Sobsey ◽  
Jan Vinjé
Keyword(s):  
Complete Genome ◽  
Catalytic Domain ◽  
Phylogenetic Analyses ◽  
Detailed Knowledge ◽  
Genome Sequences ◽  
Virus Family ◽  
Sequence Identity ◽  
The Family ◽  
The Individual ◽  
Male Specific

ABSTRACT Male-specific single-stranded RNA (FRNA) coliphages belong to the family Leviviridae. They are classified into two genera (Levivirus and Allolevivirus), which can be subdivided into four genogroups (genogroups I and II in Levivirus and genogroups III and IV in Allolevivirus). Relatively few strains have been completely characterized, and hence, a detailed knowledge of this virus family is lacking. In this study, we sequenced and characterized the complete genomes of 19 FRNA strains (10 Levivirus strains and 9 Allolevivirus strains) and compared them to the 11 complete genome sequences available in GenBank. Nucleotide similarities among strains of Levivirus genogroups I and II were 75% to 99% and 83 to 94%, respectively, whereas similarities among strains of Allolevivirus genogroups III and IV ranged from 70 to 96% and 75 to 95%, respectively. Although genogroup I strain fr and genogroup III strains MX1 and M11 share only 70 to 78% sequence identity with strains in their respective genogroups, phylogenetic analyses of the complete genome and the individual genes suggest that strain fr should be grouped in Levivirus genogroup I and that the MX1 and M11 strains belong in Allolevivirus genogroup III. Strains within each genus share >50% sequence identity, whereas between the two genera, strains have <40% nucleotide sequence identity. Overall, amino acid composition, nucleotide similarities, and replicase catalytic domain location contributed to phylogenetic assignments. A conserved eight-nucleotide signature at the 3′ end of the genome distinguishes leviviruses (5′ ACCACCCA 3′) from alloleviviruses (5′ TCCTCCCA 3′).

Characterization of Southern African Isolates of Maize Streak Virus: Typing of Three Isolates by Restriction Mapping

Intervirology ◽  
1989 ◽  
Vol 30 (2) ◽  
pp. 86-95 ◽  
Author(s):  
Beverley Ann Clarke ◽  
Edward P. Rybicki ◽  
Fiona L. Hughes ◽  
Ralph Kirby ◽  
Barbara von Wechmar
Keyword(s):  
Maize Streak Virus ◽  
Restriction Mapping ◽  
Streak Virus ◽  
Virus Typing

scholarly journals Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster

2021 ◽  
Vol 7 (6) ◽  
Author(s):  
Preetha Shibu ◽  
Frazer McCuaig ◽  
Anne L. McCartney ◽  
Magdalena Kujawska ◽  
Lindsay J. Hall ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Klebsiella Oxytoca ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type

As part of the ongoing studies with clinically relevant Klebsiella spp., we characterized the genomes of three clinical GES-5-positive ST138 strains originally identified as Klebsiella oxytoca. bla OXY gene, average nucleotide identity and phylogenetic analyses showed the strains to be Klebsiella michiganensis . Affiliation of the strains to ST138 led us to demonstrate that the current multi-locus sequence typing scheme for K. oxytoca can be used to distinguish members of this genetically diverse complex of bacteria. The strains encoded the kleboxymycin biosynthetic gene cluster (BGC), previously only found in K. oxytoca strains and one strain of Klebsiella grimontii . The finding of this BGC, associated with antibiotic-associated haemorrhagic colitis, in K. michiganensis led us to carry out a wide-ranging study to determine the prevalence of this BGC in Klebsiella spp. Of 7170 publicly available Klebsiella genome sequences screened, 88 encoded the kleboxymycin BGC. All BGC-positive strains belonged to the K. oxytoca complex, with strains of four ( K. oxytoca , K. pasteurii , K. grimontii , K. michiganensis ) of the six species of complex found to encode the complete BGC. In addition to being found in K. grimontii strains isolated from preterm infants, the BGC was found in K. oxytoca and K. michiganensis metagenome-assembled genomes recovered from neonates. Detection of the kleboxymycin BGC across the K. oxytoca complex may be of clinical relevance and this cluster should be included in databases characterizing virulence factors, in addition to those characterizing BGCs.

scholarly journals Occurrence, Distribution, and Molecular Characterization of Citrus yellow vein clearing virus in China

Plant Disease ◽  
2017 ◽  
Vol 101 (1) ◽  
pp. 137-143 ◽  
Author(s):  
Y. Zhou ◽  
H. M. Chen ◽  
M. J. Cao ◽  
X. F. Wang ◽  
X. Jin ◽  
...  
Keyword(s):  
Viral Disease ◽  
Yellow Vein ◽  
Genome Sequences ◽  
Sequence Heterogeneity ◽  
Vein Clearing ◽  
Sequence Identity ◽  
Geographic Origins ◽  
The World ◽  
Citrus Orchards

In 2009, a new citrus viral disease caused by Citrus yellow vein clearing virus (CYVCV) was discovered in China. To more effectively monitor the presence of CYVCV, a survey was conducted in 166 citrus orchards from 11 major citrus-growing provinces in China from May 2014 to April 2016. In all, 458 of a total of 2,350 citrus samples tested positive for CYVCV, demonstrating that the virus is widely distributed in China. In this study, the complete genome sequences of 19 CYVCV isolates from different provinces and hosts were sequenced and characterized. Comparisons of the whole-genome sequences of these 19 CYVCV isolates as well as 4 isolates previously reported from around the world revealed that the sequence identity ranged from 97.1 to 99.8%, indicating that there is a very low level of sequence heterogeneity among CYVCV isolates of different geographic origins and hosts. Phylogenetic analysis of these 23 genomic sequences suggested that all of the isolates from China were clustered into the same clade, clearly apart from the CYVCV isolates from Turkey and Pakistan. To our knowledge, this is the first extensive survey conducted in China for CYVCV incidence.

scholarly journals Genomic sequence characterization of Begomovirus infecting soybean and molecular evolutionary genomics of Legume yellow mosaic viruses (LYMVs)

Plant Omics ◽  
2017 ◽  
Vol 10 (02) ◽  
pp. 88-96 ◽  
Author(s):  
Shunmugiah V. Ramesh ◽  
◽  
Bhagat S. Chouhan ◽  
Girish K. Gupta ◽  
Syed M. Husain ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Evolutionary Genomics ◽  
Sequence Characterization

Characterization of maize streak virus: description of strains; symptoms

1988 ◽  
Vol 37 (1) ◽  
pp. 74-87 ◽  
Author(s):  
M. S. PINNER ◽  
P. G. MARKHAM ◽  
R. H. MARKHAM ◽  
L. DEKKER
Keyword(s):  
Maize Streak Virus ◽  
Streak Virus

scholarly journals Distribution of Common Maize Diseases and Molecular Characterization of Maize Streak Virus in Kenya

2019 ◽  
Vol 11 (4) ◽  
pp. 47
Author(s):  
Alice K. Charles ◽  
William M. Muiru ◽  
Douglas W. Miano ◽  
John W. Kimenju
Keyword(s):  
Molecular Characterization ◽  
Maize Streak Virus ◽  
Gray Leaf Spot ◽  
Leaf Blight ◽  
Streak Virus ◽  
Northern Leaf Blight ◽  
Ecological Zones ◽  
Wide Range ◽  
Sequence Similarities

Maize is an important food crop in Kenya and is susceptible to a wide range of diseases. A survey was conducted in 2012 in different agro-ecological zones (AEZ) of Kiambu, Embu and Nakuru counties to determine the distribution of northern leaf blight (NLB), common rust (CR), maize streak disease (MSD), gray leaf spot (GLS), head smut (HS) and common smut (CS). Data collected included prevalence, incidence and severity of each of the diseases. Maize leaf samples infected with MSD were also collected for molecular characterization of Maize streak virus (MSV). Northern leaf blight was reported in all counties surveyed with 100% disease prevalence. Kiambu had the highest incidence (100%) of CR whereas Embu had the highest prevalence (45%) of MSD. The incidences of GLS and HS were very low with averages of below 2.5%. The highest incidence of GLS was in Kiambu (5%). High altitude areas had higher incidences of NLB and GLS while CS and MSD were widespread in the three counties. Comparison of 797 nucleotides from the open reading frame (ORF) C2/C1 of MSV with other sequences from the GenBank showed sequence similarities of 99 to 100% with MSV-A strain. The study revealed that the major foliar diseases of maize are widespread in Kenya and therefore there is need to institute measures to manage these diseases and reduce associated losses. Also, the high percent sequence similarities of MSV indicate low variability which is good for breeders since developed resistant varieties can be adopted over a wider region.

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