scholarly journals Molecular Population Genetics of Cucumber Mosaic Virus in California: Evidence for Founder Effects and Reassortment

2004 ◽  
Vol 78 (12) ◽  
pp. 6666-6675 ◽  
Author(s):  
Han-Xin Lin ◽  
Luis Rubio ◽  
Ashleigh B. Smythe ◽  
Bryce W. Falk
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Population Analysis ◽  
Single Strand Conformation Polymorphism ◽  
Founder Effects ◽  
Coding Regions ◽  
Nontranslated Region ◽  
Genomic Regions

ABSTRACT The structure and genetic diversity of a California Cucumber mosaic virus (CMV) population was assessed by single-strand conformation polymorphism and nucleotide sequence analyses of genomic regions 2b, CP, MP, and the 3′ nontranslated region of RNA3. The California CMV population exhibited low genetic diversity and was composed of one to three predominant haplotypes and a large number of minor haplotypes for specific genomic regions. Extremely low diversity and close evolutionary relationships among isolates in a subpopulation suggested that founder effects might play a role in shaping the genetic structure. Phylogenetic analysis indicated a naturally occurring reassortant between subgroup IA and IB isolates and potential reassortants between subgroup IA isolates, suggesting that genetic exchange by reassortment contributed to the evolution of the California CMV population. Analysis of various population genetics parameters and distribution of synonymous and nonsynonymous mutations revealed that different coding regions and even different parts of coding regions were under different evolutionary constraints, including a short region of the 2b gene for which evidence suggests possible positive selection.

scholarly journals Evolutionary History of Cucumber Mosaic Virus Deduced by Phylogenetic Analyses

2002 ◽  
Vol 76 (7) ◽  
pp. 3382-3387 ◽  
Author(s):  
Marilyn J. Roossinck
Keyword(s):  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Virus Isolate ◽  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Broad Host Range ◽  
Nontranslated Region ◽  
History Of ◽  
Evolutionary Success ◽  
Reading Frames

ABSTRACT Cucumber mosaic virus (CMV) is an RNA plant virus with a tripartite genome and an extremely broad host range. Previous evolutionary analyses with the coat protein (CP) and 5′ nontranslated region (NTR) of RNA 3 suggested subdivision of the virus into three groups, subgroups IA, IB, and II. In this study 15 strains of CMV whose nucleotide sequences have been determined were used for a complete phylogenetic analysis of the virus. The trees estimated for open reading frames (ORFs) located on the different RNAs were not congruent and did not completely support the subgrouping indicated by the CP ORF, indicating that different RNAs had independent evolutionary histories. This is consistent with a reassortment mechanism playing an important role in the evolution of the virus. The evolutionary trees of the 1a and 3a ORFs were more compact and displayed more branching than did those of the 2a and CP ORFs. This may reflect more rigid host-interactive constraints exerted on the 1a and 3a ORFs. In addition, analysis of the 3′ NTR that is conserved among all RNAs indicated that evolutionary constraints on this region are specific to the RNA component rather than the virus isolate. This indicates that functions other than replication are encoded in the 3′ NTR. Reassortment may have led to the genetic diversity found among CMV strains and contributed to its enormous evolutionary success.

scholarly journals Phylogenetic Analysis of New Isolates of Cucumber mosaic virus from Iran on the Basis of Different Genomic Regions

2012 ◽  
Vol 28 (4) ◽  
pp. 381-389 ◽  
Author(s):  
Sevil Nematollahi ◽  
Nemat Sokhandan-Bashir ◽  
Farshad Rakhshandehroo ◽  
Hamid Reza Zamanizadeh
Keyword(s):  
Phylogenetic Analysis ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Genomic Regions

scholarly journals Genetic Diversity of Watermelon mosaic virus in Slovakia and Iran Shows Distinct Pattern

Plant Disease ◽  
2011 ◽  
Vol 95 (1) ◽  
pp. 38-42 ◽  
Author(s):  
Miroslav Glasa ◽  
Kaveh Bananej ◽  
Lukáš Predajňa ◽  
Aisan Vahdat
Keyword(s):  
Genetic Diversity ◽  
Mosaic Virus ◽  
Genomic Region ◽  
Distinct Pattern ◽  
Watermelon Mosaic Virus ◽  
Worldwide Distribution ◽  
Geographical Regions ◽  
Group 2 ◽  
Genomic Regions ◽  
Group 1

Although Watermelon mosaic virus (WMV) is one of the main cucurbit pathogens and has a worldwide distribution, reliable data on its molecular variability is still limited to some geographical regions. The genetic diversity of 36 WMV isolates from Slovakia and Iran were studied by sequence analysis targeting two opposite genomic regions (P1 and NIb-CP). Phylogenetic analysis using partial sequences of the P1 gene showed that Slovak WMV isolates had greater diversity, representing two groups (group 1 and group 2), whereas all Iranian isolates belonged to a single group (group 2), with relatively low divergeance. Interestingly, in the NIb-CP region, all analyzed Slovak and Iranian isolates clustered within the group 1, thereby illustrating the phylogenetic discrepancies between the two analyzed genomic regions. Based on these data, one-half of analyzed Slovak isolates and all Iranian WMV isolates showed a switch in affiliation based on considered genomic region, clearly indicating their recombinant nature. This work provides further evidence of the significant contribution of recombination to the evolutionary history of WMV and outlines the necessity to target more than a single genome fragment for accurate typing of WMV isolates.

Assessing the genetic diversity and resistance to Cucumber mosaic virus and Tobacco etch virus of tobacco cultivars in China

2015 ◽  
Vol 44 (4) ◽  
pp. 365-374 ◽  
Author(s):  
W. Chen ◽  
Z. P. Luo ◽  
W. T. Liu ◽  
H. Liu ◽  
D. F. Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Tobacco Etch Virus

Population genetics of cucumber mosaic virus infecting medicinal, aromatic and ornamental plants from northern Italy

2012 ◽  
Vol 157 (4) ◽  
pp. 739-745 ◽  
Author(s):  
Salvatore Davino ◽  
Stefano Panno ◽  
Ezequiel A. Rangel ◽  
Mario Davino ◽  
Maria Grazia Bellardi ◽  
...  
Keyword(s):  
Population Genetics ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Ornamental Plants ◽  
Northern Italy

scholarly journals Genetic Diversity, Reassortment, and Recombination in Alfalfa mosaic virus Population in Spain

2014 ◽  
Vol 104 (11) ◽  
pp. 1241-1250 ◽  
Author(s):  
María Bergua ◽  
Marisol Luis-Arteaga ◽  
Fernando Escriu
Keyword(s):  
Genetic Diversity ◽  
Mosaic Virus ◽  
Geographic Origin ◽  
Alfalfa Mosaic Virus ◽  
Polymorphism Analysis ◽  
Coding Region ◽  
Coding Regions ◽  
Low Genetic Diversity ◽  
Genetic Types

The variability and genetic structure of Alfalfa mosaic virus (AMV) in Spain was evaluated through the molecular characterization of 60 isolates collected from different hosts and different geographic areas. Analysis of nucleotide sequences in four coding regions—P1, P2, movement protein (MP), and coat protein (CP)—revealed a low genetic diversity and different restrictions to variation operating on each coding region. Phylogenetic analysis of Spanish isolates along with previously reported AMV sequences showed consistent clustering into types I and II for P1 and types I, IIA, and IIB for MP and CP regions. No clustering was observed for the P2 region. According to restriction fragment length polymorphism analysis, the Spanish AMV population consisted of seven haplotypes, including two haplotypes generated by reassortment and one involving recombination. The most frequent haplotypes (types for P1, MP, and CP regions, respectively) were I-I-I (37%), II-IIB-IIB (30%), and one of the reassortants, II-I-I (17%). Distribution of haplotypes was not uniform, indicating that AMV population was structured according to the geographic origin of isolates. Our results suggest that agroecological factors are involved in the maintenance of AMV genetic types, including the reassortant one, and in their geographic distribution.

scholarly journals Comparative genomics suggests limited variability and similar evolutionary patterns between major clades of SARS-CoV-2

2020 ◽  
Author(s):  
Matteo Chiara ◽  
David S. Horner ◽  
Carmela Gissi ◽  
Graziano Pesole
Keyword(s):  
Specific Protein ◽  
Phylogenomic Analysis ◽  
Founder Effects ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Geographic Locations ◽  
Coding Regions ◽  
Rapid Spread ◽  
Novel Virus ◽  
Genomic Regions

AbstractPhylogenomic analysis of SARS-CoV-2 as available from publicly available repositories suggests the presence of 3 prevalent groups of viral episomes (super-clades), which are mostly associated with outbreaks in distinct geographic locations (China, USA and Europe). While levels of genomic variability between SARS-CoV-2 isolates are limited, to our knowledge, it is not clear whether the observed patterns of variability in viral super-clades reflect ongoing adaptation of SARS-CoV-2, or merely genetic drift and founder effects. Here, we analyze more than 1100 complete, high quality SARS-CoV-2 genome sequences, and provide evidence for the absence of distinct evolutionary patterns/signatures in the genomes of the currently known major clades of SARS-CoV-2. Our analyses suggest that the presence of distinct viral episomes at different geographic locations are consistent with founder effects, coupled with the rapid spread of this novel virus. We observe that while cross species adaptation of the virus is associated with hypervariability of specific protein coding regions (including the RDB domain of the spike protein), the more variable genomic regions between extant SARS-CoV-2 episomes correspond with the 3’ and 5’ UTRs, suggesting that at present viral protein coding genes should not be subjected to different adaptive evolutionary pressures in different viral strains. Although this study can not be conclusive, we believe that the evidence presented here is strongly consistent with the notion that the biased geographic distribution of SARS-CoV-2 isolates should not be associated with adaptive evolution of this novel pathogen.

Genetic Diversity of Cucumber Mosaic Virus Strain Soybean from Several Areas

2015 ◽  
Vol 9 (1) ◽  
pp. 44-49 ◽  
Author(s):  
TRI ASMIRA DAMAYANTI ◽  
◽  
SURYO WIYONO ◽  
Keyword(s):  
Genetic Diversity ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Virus Strain ◽  
Cucumber Mosaic Virus Strain

scholarly journals Cucumber mosaic virus Isolates from Greek Legumes are Associated with Satellite RNAs that are Necrogenic for Tomato

Plant Disease ◽  
2018 ◽  
Vol 102 (11) ◽  
pp. 2268-2276 ◽  
Author(s):  
Antonis Giakountis ◽  
Iason Tsarmpopoulos ◽  
Elisavet K. Chatzivassiliou
Keyword(s):  
Genetic Diversity ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Protein Sequence ◽  
Coat Protein Sequence ◽  
Tomato Plants ◽  
Satellite Rnas ◽  
Virus Isolates ◽  
Limited Genetic Diversity

Worldwide, Cucumber mosaic virus (CMV) is the causal agent of many economically important diseases. Based on immunological or molecular analysis, three distinct subgroups of CMV isolates can be identified (IA, IB, and II). In addition, some CMV isolates are associated with satellite RNAs (satRNAs), a type of noncoding transcript that may alter the symptoms of CMV infections. This study presents an analysis of CMV isolates occurring in legumes in Greece in respect to their genetic diversity, and the presence and diversity of their satRNA. Phylogenetic analysis of the CMV coat protein sequence of 18 legume and 5 tomato CMV isolates collected throughout Greece classified them within subgroups IA and IB, with a limited genetic diversity. The CMV satRNAs found in nine field legumes exhibiting mild symptoms and in one tomato with a necrotic syndrome contained a functional necrogenic motif; therefore, they were grouped within the necrogenic group of CMV-satRNAs. The necrotic phenotype was expressed in all legume CMV isolates containing necrogenic satRNAs when mechanically inoculated onto tomato plants. To our knowledge, this is the first observation that legumes host necrogenic CMV-satRNAs. The possible role of legumes in the epidemiology of CMV and necrogenic satRNA complex is discussed.

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