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Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA
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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer-Verlag
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079821/ https://www.ncbi.nlm.nih.gov/pubmed/9010139 http://dx.doi.org/10.1007/PL00006124 |
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author | Aranda, Miguel A. Fraile, Aurora Dopazo, Joaquín Malpica, José M. García-Arenal, Fernando |
author_facet | Aranda, Miguel A. Fraile, Aurora Dopazo, Joaquín Malpica, José M. García-Arenal, Fernando |
author_sort | Aranda, Miguel A. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7079821 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Springer-Verlag |
record_format | MEDLINE/PubMed |
spelling | pubmed-70798212020-03-23 Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA Aranda, Miguel A. Fraile, Aurora Dopazo, Joaquín Malpica, José M. García-Arenal, Fernando J Mol Evol Article 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. Springer-Verlag 2014-03-13 1997 /pmc/articles/PMC7079821/ /pubmed/9010139 http://dx.doi.org/10.1007/PL00006124 Text en © Springer-Verlag New York Inc. 1997 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. |
spellingShingle | Article Aranda, Miguel A. Fraile, Aurora Dopazo, Joaquín Malpica, José M. García-Arenal, Fernando Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA |
title | Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA |
title_full | Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA |
title_fullStr | Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA |
title_full_unstemmed | Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA |
title_short | Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA |
title_sort | contribution of mutation and rna recombination to the evolution of a plant pathogenic rna |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079821/ https://www.ncbi.nlm.nih.gov/pubmed/9010139 http://dx.doi.org/10.1007/PL00006124 |
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