Population differentiation and selective constraints in Pelargonium line

[EN] The genomic structure of Pelargonium line pattern virus (PLPV), a tentative member of a proposed new genus within the family Tombusviridae, has been recently determined. However, little is known about the genetic variability and population structure of this pathogen. Here, we have investigated the heterogeneity of PLPV isolates from different origins by sequence analysis of a 1817 nt fragment encompassing the movement (p7 and p9.7) and coat protein genes as well as flanking segments including the complete 3` untranslated region. We have evaluated the selective pressures operating on both viral proteins and RNA genome in order to assess the relative functional and/or structural relevance of different amino acid or nucleotide sites. The results of the study have revealed that distinct protein domains are under different selective constraints and that maintenance of certain primary and/or secondary structures in RNA regulatory sequences might be an important factor limiting viral heterogeneity. We have also performed covariation analyses to uncover potential dependencies among amino acid sites of the same protein or of different proteins. The detection of linked amino acid substitutions has permitted to draw a putative network of intra- and interprotein interactions that are likely required to accomplish the different steps of the infection cycle. Finally, we have obtained phylogenetic trees that support geographical segregation of PLPV sequences. (c) 2010 Elsevier B.V. All rights reserved.We are indebted to Dr. Jan van der Meij (Ball Flora Plant, Chicago) for providing PLPV isolate from USA, and to Dr. Marise Borja (Fundacion Promiva, Madrid) for the Spanish isolates and for valuable comments in the course of this work. We thank to Dr. Selma Gago (IBMCP, Valencia) for critical reading of the manuscript. We are also grateful to Dolores Arocas and Isabella Avellaneda for excellent technical assistance. This research was supported by grants BFU2006-11230 and BFU2009-11699 from Ministerio de Ciencia e Innovacion (MICINN, Spain), ACOM09/040 from Generalitat Valenciana (to C.H.), and by grant BFU2009-06993 (MICINN) (to S.F.E.). A.C. was recipient of predoctoral fellowships from the Generalitat Valenciana and from CSIC-Fundacion Bancaja and L.R. received a postdoctoral contract from the Juan de la Cierva program of MEC.Castaño Sansano, MA.; Ruiz Garcia, ML.; Elena Fito, SF.; Hernandez Fort, C. (2011). Population differentiation and selective constraints in Pelargonium line. Virus Research. 155(1):274-282. doi:10.1016/j.virusres.2010.10.022274282155