title: Molecular evolution and phylogeography of potato virus Y based on the CP gene.
abstract: Potato virus Y (PVY) is an important plant pathogen with a wide host range that includes, among others, potato, tobacco, tomato and pepper. The coat protein (CP) of PVY has been commonly used in phylogenetic studies for strain classification. In this study, we used a pool of 292 CP sequences from isolates collected worldwide. After detecting and removing recombinant sequences, we applied Bayesian techniques to study the influence of geography and host species in CP population structure and dynamics. Finally, we performed selection and covariation analyses to identify specific amino acids involved in adaptation. Our results show that PVY CP diversification is significantly accounted for by both geographical and host-driven adaptations. Amino acid positions detected as positively selected concentrate in the N-terminal region of the protein. Some of these selected positions may discriminate among strains, and to a much lesser extent, between potato and non-potato isolates.
authors: Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València 46022, Spain.
authors: José M
authors: JM
authors: Cuevas
authors: INRA-Agrocampus Ouest-Université Rennes 1, UMR1099 BiO3P (Biology of Organisms and Populations Applied to Plant Protection), Le Rheu 35653, France.
authors: Agnès
authors: A
authors: Delaunay
authors: NIB, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia.
authors: Matevz
authors: M
authors: Rupar
authors: INRA-Agrocampus Ouest-Université Rennes 1, UMR1099 BiO3P (Biology of Organisms and Populations Applied to Plant Protection), Le Rheu 35653, France.
authors: Emmanuel
authors: E
authors: Jacquot
authors: The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.|Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València 46022, Spain.
authors: Santiago F
authors: SF
authors: Elena
mesh_terms: D001499:Bayes Theorem; D036022:Capsid Proteins / Q000235:genetics / Q000378:metabolism*; D003062:Codon; D019143:Evolution, Molecular; D015967:Gene Expression Regulation, Viral / Q000502:physiology; D010802:Phylogeny; D058974:Phylogeography; D010935:Plant Diseases / Q000821:virology*; D017800:Potyvirus / Q000235:genetics*; D019657:Solanaceae / Q000821:virology*; D013045:Species Specificity
chemical_list: D036022:Capsid Proteins; D003062:Codon