Molecular Evidence for Recombination in Prunus Necrotic Ringspot Virus

Genetic RNA recombination plays an important role in viral evolution. The evolutionary history of Prunus necrotic ringspot virus (PNRSV) has been extensively studied, but knowledge of recombination in its genome is still lacking. To investigate the recombination events in this virus, 67 accessions c...

Full description

Saved in:
Bibliographic Details
Published in:Plant molecular biology reporter 2009-06, Vol.27 (2), p.189-198
Main Author: Boulila, Moncef
Format: Article
Language:English
Subjects:
Algorithms
Bioinformatics
Biological evolution
Biomedical and Life Sciences
Breakpoints
Clonal deletion
Coat protein
Cost analysis
evolution
Evolutionary genetics
Genetic diversity
genetic recombination
genome
Genomes
Insertion
Life Sciences
Metabolomics
Movement protein
phylogeny
Plant Breeding/Biotechnology
Plant Sciences
plant viruses
Proteomics
Prunus necrotic ringspot virus
Recombination
Ribonucleic acid
RNA
RNA viruses
Subgroups
Viruses
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Genetic RNA recombination plays an important role in viral evolution. The evolutionary history of Prunus necrotic ringspot virus (PNRSV) has been extensively studied, but knowledge of recombination in its genome is still lacking. To investigate the recombination events in this virus, 67 accessions composed by 62 isolates retrieved from the databanks and five Tunisian isolates described in this study were analyzed. The use of RECCO algorithm which is based on cost minimization allowed us to detect several breakpoints in the coat protein gene (CP) of three out of five isolates from Tunisia and one from Poland. Moreover, a recombination signal was also detected in the putative cell-to-cell movement protein-encoding gene of an isolate from the USA. Tajima Neutrality test implemented in MEGA4 program indicated the occurrence of a high level of deletion/insertion events in the sequences. The evolutionary historical relationships were determined by constructing a dendrogram using neighbor joining, minimum evolution, maximum parsimony, maximum likelihood, and unweighted pair group method with arithmetic mean (UPGMA). The first four analyses gave similar results. Three classical groups (PE 5, PV 32, and PV 96) were delineated. The recombinant isolates from Tunisia clustered in a distinct clade except for one nonrecombinant (Ghernghezel) which revealed to be a member of PV 32 group. In contrast, UPGMA algorithm divided the Tunisian isolates in three distinct subgroups. Apart from recombination, reassortment is still an open question among many others and may also represent another way to explore the genetic diversity of PNRSV.
ISSN:0735-9640
1572-9818
DOI:10.1007/s11105-008-0071-2