Molecular adaptation within the coat protein-encoding gene of Tunisian almond isolates of Prunus necrotic ringspot virus

The sequence alignments of five Tunisian isolates of Prunus necrotic ringspot virus (PNRSV) were searched for evidence of recombination and diversifying selection. Since failing to account for recombination can elevate the false positive error rate in positive selection inference, a genetic algorith...

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Bibliographic Details
Published in:Journal of genetics 2013-04, Vol.92 (1), p.11-24
Main Authors: BOULILA, MONCEF, TIBA, SAWSSEN BEN, JILANI, SAOUSSEN
Format: Article
Language:English
Subjects:
Adaptation
Adaptation, Biological - genetics
Algorithms
almonds
Animal Genetics and Genomics
Base Sequence
Biomedical and Life Sciences
capsid
Capsid Proteins - genetics
Ethylenediaminetetraacetic acid
Evolution, Molecular
Evolutionary Biology
Genes
Genetic algorithms
Genetic polymorphisms
Genetic Variation
Ilarvirus - genetics
Ilarvirus - isolation & purification
Life Sciences
Microbial Genetics and Genomics
Molecular biology
Molecular Sequence Data
Phylogeny
Plant Diseases - virology
Plant Genetics and Genomics
Plant Shoots - virology
Povidone
Proteins
Prunus - virology
Prunus dulcis
Prunus necrotic ringspot virus
Recombination, Genetic
Research Article
Selection, Genetic
Sequence Analysis, DNA
Tunisia
Viruses
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Description
Summary:The sequence alignments of five Tunisian isolates of Prunus necrotic ringspot virus (PNRSV) were searched for evidence of recombination and diversifying selection. Since failing to account for recombination can elevate the false positive error rate in positive selection inference, a genetic algorithm (GARD) was used first and led to the detection of potential recombination events in the coat protein-encoding gene of that virus. The Recco algorithm confirmed these results by identifying, additionally, the potential recombinants. For neutrality testing and evaluation of nucleotide polymorphism in PNRSV CP gene, Tajima’s D, and Fu and Li’s D and F statistical tests were used. About selection inference, eight algorithms (SLAC, FEL, IFEL, REL, FUBAR, MEME, PARRIS, and GA branch) incorporated in HyPhy package were utilized to assess the selection pressure exerted on the expression of PNRSV capsid. Inferred phylogenies pointed out, in addition to the three classical groups (PE-5, PV-32, and PV-96), the delineation of a fourth cluster having the new proposed designation SW6, and a fifth clade comprising four Tunisian PNRSV isolates which underwent recombination and selective pressure and to which the name Tunisian outgroup was allocated.
ISSN:0022-1333
0973-7731
DOI:10.1007/s12041-013-0211-9