About: Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA
Creator	Fraile, Aurora García-Arenal, Fernando Dopazo, Joaquín Malpica, José Aranda, Miguel
Source	Medline; PMC
abstract	The nucleotide sequence of 17 variants of the satellite RNA of cucumber mosaic virus (CMV-satRNA) isolated from field-infected tomato plants in the springs of 1989, 1990, and 1991 was determined. The sequence of each of the 17 satRNAs was unique and was between 334 and 340 nucleotides in length; 57 positions were polymorphic. There was much genetic divergence, ranging from 0.006 to 0.141 nucleotide substitutions per site for pairwise comparisons, and averaging 0.074 for any pair. When the polymorphic positions were analyzed relative to a secondary structure model proposed for CMV-satRNAs, it was found that there were significantly different numbers of changes in base-paired and non–base-paired positions, and that mutations that did not disrupt base pairing were preferred at the putatively paired sites. This supports the concept that the need to maintain a functional structure may limit genetic divergence of CMV-satRNA. Phylogenetic analyses showed that the 17 CMV-satRNA variants clustered into two subgroups, I and II, and evolutionary lines proceeding by the sequential accumulation of mutations were apparent. Three satRNA variants were outliers for these two phylogenetic groups. They were shown to be recombinants of subgroup I and II satRNAs by calculating phylogenies for different molecular regions and by using Sawyer's test for gene conversion. At least two recombination events were required to produce these three recombinant satRNAs. Thus, recombinants were found to be frequent (∼17%) in natural populations of CMV-satRNA, and recombination may make an important contribution to the generation of new variants. To our knowledge this is the first report of data allowing the frequency of recombinant isolates in natural populations of an RNA replicon to be estimated.
has issue date	2014-03-13(xsd:dateTime)
bibo:doi	10.1007/pl00006124
bibo:pmid	9010139
has license	no-cc
sha1sum (hex)	9b94b39b145793cdd8f1725b60722cff0e2aa41c
schema:url	https://doi.org/10.1007/pl00006124
resource representing a document's title	Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA
has PubMed Central identifier	PMC7079821
has PubMed identifier	9010139
schema:publication	J Mol Evol
resource representing a document's body	covid:9b94b39b145793cdd8f1725b60722cff0e2aa41c#body_text
is schema:about of	named entity 'disrupt' named entity 'functional' named entity 'gene' named entity 'clustered' named entity 'relative' named entity 'Mutation' covid:arg/9b94b39b145793cdd8f1725b60722cff0e2aa41c named entity 'lines' named entity 'replicon' named entity 'Thus' named entity 'generation' named entity 'proceeding' named entity 'mutations' named entity 'recombination' named entity 'polymorphic' named entity 'When' named entity 'polymorphic' named entity 'length' named entity 'Evolution' named entity 'CMV' named entity 'RNA' named entity 'base pairing' named entity 'base-paired' named entity 'recombination events' named entity 'CMV' named entity 'nucleotide substitutions' named entity 'CMV' named entity 'recombinants' named entity 'nucleotides' named entity 'genome' named entity 'RNA' named entity 'CMV' named entity 'statistically significant' named entity 'nucleotide' named entity 'CMV' named entity 'molecular biology' named entity 'CMV' named entity 'recombination' named entity 'biological properties' named entity 'plant viruses' named entity 'CMV' named entity 'epidemic' named entity 'nucleotide substitution' named entity 'genetic divergence' named entity 'helper virus' named entity 'sequenced' named entity 'molecular structure' named entity 'EMBL' named entity 'molecular structure' named entity 'replicons' named entity 'nucleotide' named entity 'PCR' named entity 'epidemic' named entity 'RNA' named entity 'polymorphic' named entity 'nucleotides' named entity 'genetic divergence' named entity 'CMV' named entity 'base pairing' named entity 'ribonuclease' named entity 'recombination' named entity 'neighbor-joining method' named entity 'CMV' named entity 'replicon' named entity 'CMV' named entity 'recombination' named entity 'RNA' named entity 'RNA synthesis' named entity 'secondary structure' named entity 'nucleotides' named entity 'encapsidation' named entity 'cDNA' named entity 'CMV' named entity 'parsimony' named entity 'picornaviruses' named entity 'cDNA' named entity 'electrophoretic'

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