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

Journal of genetics

Saoussen Jilani³  Sawssen Ben Tiba²  Moncef Boulila1¹ 

[1] Institut de l’Olivier, B.P. 14, 4061 Sousse Ibn-Khaldoun, Tunisia$$;Institut Supérieur de Biotechnologie de Monastir, Avenue Tahar Hadded. B.P. 74, Monastir 5019, Tunisia$$;Centre Régional de Transfusion Sanguine de Sousse, Centre Hospitalo-Universitaire Farhat Hached, Avenue Ibn El Jazzar-Sousse 4000, Tunisia$$

关键词: bioinformatics;    molecular genetics;    evolution;    sequence;    phylogeny;    Prunus necrotic ringspot virus.;   

DOI  :  

学科分类：生物科学（综合）

来源: Indian Academy of Sciences

【 摘 要 】

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.

【 授权许可】

Unknown