scholarly journals Full Genome Evolutionary Studies of Wheat Streak Mosaic-Associated Viruses Using High-Throughput Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Carla Dizon Redila ◽  
Savannah Phipps ◽  
Shahideh Nouri
Keyword(s):  
Mosaic Virus ◽  
Rna Sequencing ◽  
Great Plains ◽  
High Throughput ◽  
Phylogenetic Analyses ◽  
Full Genome Sequence ◽  
Mixed Infections ◽  
Full Genome ◽  
Genome Sequences ◽  
Resistance Breaking

Wheat streak mosaic (WSM), a viral disease affecting cereals and grasses, causes substantial losses in crop yields. Wheat streak mosaic virus (WSMV) is the main causal agent of the complex, but mixed infections with Triticum mosaic virus (TriMV) and High plains wheat mosaic emaravirus (HPWMoV) were reported as well. Although resistant varieties are effective for the disease control, a WSMV resistance-breaking isolate and several potential resistance-breaking isolates have been reported, suggesting that viral populations are genetically diverse. Previous phylogenetic studies of WSMV were conducted by focusing only on the virus coat protein (CP) sequence, while there is no such study for either TriMV or HPWMoV. Here, we studied the genetic variation and evolutionary mechanisms of natural populations of WSM-associated viruses mainly in Kansas fields and fields in some other parts of the Great Plains using high-throughput RNA sequencing. In total, 28 historic and field samples were used for total RNA sequencing to obtain full genome sequences of WSM-associated viruses. Field survey results showed WSMV as the predominant virus followed by mixed infections of WSMV + TriMV. Phylogenetic analyses of the full genome sequences demonstrated that WSMV Kansas isolates are widely distributed in sub-clades. In contrast, phylogenetic analyses for TriMV isolates showed no significant diversity. Recombination was identified as the major evolutionary force of WSMV and TriMV variation in KS fields, and positive selection was detected in some encoding genomic regions in the genome of both viruses. Furthermore, the full genome sequence of a second Kansas HPWMoV isolate was reported. Here, we also identified previously unknown WSMV isolates in the Great Plains sharing clades and high nucleotide sequence similarities with Central Europe isolates. The findings of this study will provide more insights into the genetic structure of WSM-associated viruses and, in turn, help in improving strategies for disease management.

scholarly journals Complete Genomic Sequence of Goose-Origin Reovirus from China

2012 ◽  
Vol 86 (18) ◽  
pp. 10257-10257 ◽  
Author(s):  
Tao Yun ◽  
Weicheng Ye ◽  
Zheng Ni ◽  
Liu Chen ◽  
Bin Yu ◽  
...  
Keyword(s):  
New Species ◽  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Full Genome Sequence ◽  
Avian Reovirus ◽  
Complete Genomic Sequence ◽  
Full Genome ◽  
Established Species ◽  
A New Species ◽  
Complete Genomic

We report the full-genome sequence of a goose-origin reovirus (GRV) strain 03G from Zhejiang Province, China. This is the first report of the complete genomic sequence (segments 1 to 10) of GRV. Phylogenetic analyses of the sequence suggest that GRV 03G represents a new species distinct from other established species within the avian reovirus (ARV) group of orthoreoviruses.

Complete nucleotide sequence of a Polish strain of Peanut stunt virus (PSV-P) that is related to but not a typical member of subgroup I.

2008 ◽  
Vol 55 (4) ◽  
pp. 731-739 ◽  
Author(s):  
Aleksandra Obrepalska-Steplowska ◽  
Marta Budziszewska ◽  
Henryk Pospieszny
Keyword(s):  
Phylogenetic Analyses ◽  
The Other ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Satellite Rna ◽  
Protein Coding ◽  
Typical Member ◽  
Rna Analysis ◽  
Nucleotide Homology ◽  
Peanut Stunt Virus

Peanut stunt virus (PSV) is a common legume pathogen present worldwide. It is also infectious for many other plants including peanut and some vegetables. Viruses of this species are classified at present into three subgroups based on their serology and nucleotide homology. Some of them may also carry an additional subviral element - satellite RNA. Analysis of the full genome sequence of a Polish strain - PSV-P - associated with satRNA was performed and showed that it may be classified as a derivative of the subgroup I sharing 83.9-87.9% nucleotide homology with other members of this subgroup. A comparative study of sequenced PSV strains indicates that PSV-P shows the highest identity level with PSV-ER or PSV-J depending on the region used for analysis. Phylogenetic analyses, on the other hand, have revealed that PSV-P is related to representatives of the subgroup I to the same degree, with the exception of the coat protein coding sequence where PSV-P is clustered together with PSV-ER.

scholarly journals Molecular Genetic Analysis of Cucumber mosaic virus Populations Infecting Pepper Suggests Unique Patterns of Evolution in Korea

2014 ◽  
Vol 104 (9) ◽  
pp. 993-1000 ◽  
Author(s):  
Mi-Kyeong Kim ◽  
Jang-Kyun Seo ◽  
Hae-Ryun Kwak ◽  
Jeong-Soo Kim ◽  
Kook-Hyung Kim ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Molecular Genetic ◽  
Purifying Selection ◽  
Molecular Genetic Analysis ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Full Genome Sequencing ◽  
Evolutionary Mechanisms

Studying genetic structure and diversity of viruses is important to understand the evolutionary mechanisms that generate and maintain variations in viral populations. Cucumber mosaic virus (CMV) is endemic in most pepper fields in Korea. Currently, no effective methods for control of CMV are available due to many environmental and biological factors such as the extensive evolutionary capacity of CMV. Thus, analyzing the genetic structure of CMV populations may facilitate the development of strategies for the control of CMV. In this study, 252 pepper (Capsicum annuum) samples showing virus symptoms were collected by field surveys performed throughout Korea in 2007. Reverse-transcription polymerase chain reaction analyses revealed that, in total, 165 collected samples were infected with CMV. Forty-five CMV isolates were randomly selected within each regional subpopulation and analyzed by full-genome sequencing. Analyses of genetic diversity showed that the 2b gene of CMV is under weaker purifying selection than the other genes. Based on the phylogenetic analysis of RNA1, the CMV isolates from pepper were divided into three clusters in subgroup I. Our full-genome sequence-based molecular analyses of the CMV Korean population suggest that the subpopulations of CMV have been geographically localized in pepper fields in Korea.

scholarly journals An Analysis of SARS-CoV-2 Using ViReport

2020 ◽  
Author(s):  
Miranda Song ◽  
Niema Moshiri
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Phylogenetic Analyses ◽  
Full Genome ◽  
Genome Sequences ◽  
Link Type ◽  
Preventative Intervention ◽  
Viral Sequences

AbstractThe ongoing outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of cases and hundreds of thousands of deaths. Given the current lack of treatments or vaccines available, it may be useful to trace the evolu-tion and spread of the virus to better develop methods of preventative intervention. In this study, we analyzed over 4,000 full genome sequences of human SARS-CoV-2 using novel tool ViReport [13], an automated workflow for performing phylogenetic analyses on viral sequences and generating comprehensive molecular epidemiologi-cal reports. The complete ViReport output can be found at https://github.com/mirandajsong/ViReport-SARS-CoV-2.

scholarly journals Full-Genome Sequence of an Enterovirus 71 Strain Isolated from a Throat Swab from a Child with Severe Hand-Foot-and-Mouth Disease in Changzhou, China, in 2017

2018 ◽  
Vol 6 (4) ◽  
Author(s):  
Qiong Li ◽  
Feng-Ming Wang ◽  
Xu-Jian Mao ◽  
Ping Yao ◽  
Xia Jiang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Throat Swab ◽  
Phylogenetic Analyses ◽  
Enterovirus 71 ◽  
Foot And Mouth Disease ◽  
Human Enterovirus ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Human Enterovirus 71 ◽  
Full Length Genome

ABSTRACT The full-length genome sequence of a human enterovirus 71 (EV71) strain (EV71/CZTN01/CHN/2017) was isolated from a throat swab from a child in Changzhou, China, in 2017. According to the phylogenetic analyses, the full-genome sequence in this study belongs to sub-subgenotype C4a.

scholarly journals Full-Genome Sequences and Phylogenetic Analysis of Archived Danish European Bat Lyssavirus 1 (EBLV-1) Emphasize a Higher Genetic Resolution and Spatial Segregation for Sublineage 1a

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 634
Author(s):  
Sten Calvelage ◽  
Conrad M. Freuling ◽  
Anthony R. Fooks ◽  
Dirk Höper ◽  
Denise A. Marston ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Spatial Segregation ◽  
Full Genome ◽  
Genome Sequences ◽  
Genetic Characteristics ◽  
Close Phylogenetic Relationship ◽  
Almost All ◽  
Relationship Of

European bat lyssavirus type 1 (EBLV-1) is the causative agent for almost all reported rabies cases found in European bats. In recent years, increasing numbers of available EBLV-1 full genomes and their phylogenetic analyses helped to further elucidate the distribution and genetic characteristics of EBLV-1 and its two subtypes, namely EBLV-1a and EBLV-1b. Nonetheless, the absence of full-genome sequences from regions with known detections of EBLV-1 still limit the understanding of the phylogeographic relations between viruses from different European regions. In this study, a set of 21 archived Danish EBLV-1 samples from the years 1985 to 2009 was processed for the acquisition of full-genome sequences using a high-throughput sequencing approach. Subsequent phylogenetic analysis encompassing all available EBLV-1 full genomes from databases revealed the Danish sequences belong to the EBLV-1a subtype and further highlighted the distinct, close phylogenetic relationship of Danish, Dutch and German isolates in this region. In addition, the formation of five putative groups nearly exclusively formed by Danish isolates and the overall increased resolution of the EBLV-1a branch indicate a higher genetic diversity and spatial segregation for this sublineage than was previously known. These results emphasize the importance of phylogenetic analyses of full-genome sequences of lyssaviruses for genetic geography.

scholarly journals Long-Term Cocirculation of Two Strains of Pepino Mosaic Virus in Tomato Crops and Its Effect on Population Genetic Variability

2020 ◽  
Vol 110 (1) ◽  
pp. 49-57 ◽  
Author(s):  
C. Alcaide ◽  
M. P. Rabadán ◽  
M. Juárez ◽  
P. Gómez
Keyword(s):  
Genetic Variability ◽  
Mosaic Virus ◽  
Evolutionary Dynamics ◽  
Geographical Area ◽  
Viral Fitness ◽  
Mixed Infections ◽  
Supporting Evidence ◽  
Pepino Mosaic Virus ◽  
Nucleotide Variability

Mixed viral infections are common in plants, and the evolutionary dynamics of viral populations may differ depending on whether the infection is caused by single or multiple viral strains. However, comparative studies of single and mixed infections using viral populations in comparable agricultural and geographical locations are lacking. Here, we monitored the occurrence of pepino mosaic virus (PepMV) in tomato crops in two major tomato-producing areas in Murcia (southeastern Spain), supporting evidence showing that PepMV disease-affected plants had single infections of the Chilean 2 (CH2) strain in one area and the other area exhibited long-term (13 years) coexistence of the CH2 and European (EU) strains. We hypothesized that circulating strains of PepMV might be modulating the differentiation between them and shaping the evolutionary dynamics of PepMV populations. Our phylogenetic analysis of 106 CH2 isolates randomly selected from both areas showed a remarkable divergence between the CH2 isolates, with increased nucleotide variability in the geographical area where both strains cocirculate. Furthermore, the potential virus–virus interaction was studied further by constructing six full-length infectious CH2 clones from both areas, and assessing their viral fitness in the presence and absence of an EU-type isolate. All CH2 clones showed decreased fitness in mixed infections and although complete genome sequencing indicated a nucleotide divergence of those CH2 clones by area, the magnitude of the fitness response was irrespective of the CH2 origin. Overall, these results suggest that although agroecological cropping practices may be particularly important for explaining the evolutionary dynamics of PepMV in tomato crops, the cocirculation of both strains may have implications on the genetic variability of PepMV populations.

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