Molecular characterization of ilarvirus Prunus necrotic ring spot virus (PNRSV) and Prune dwarf virus (PDV) in Spanish autochthonous almond cultivars

Abstract

Traditional almond cultivars are an interesting source of different traits for breeders. These old cultivars have been multiplied by grafting for a long time and usually have been accumulating different viruses. In this work a molecular characterization of the ilarviruses Prunus necrotic ring spot virus (PNRSV) and Prune dwarf virus (PDV) was performed in Spanish autochthonous almond cultivars. Results showed the generalized presence of PNRSV and PDV in the analysed collections with a presence of 90 and 68%, respectively, and a high percentage of coinfection (62%). Despite these viruses do not show noticeable symptoms in the tree nor fruits, this poor phytosanitary state urges to the adoption of new strategies for elimination of virus and cleaning these materials. The nucleotide sequence of the RNA 3 of the almond Spanish isolates of PRNSV (37 isolates) and PDV (23 isolates) revealed a nucleotide sequence identity percentage that ranged between 93.7-99.9% for PNRSV and 87.3-100% for PDV. The amino acid similarity percentage observed for the movement protein and coat protein ranged between 94.7-100% and 93.8-100% for PNRSV and 92.2-100% and 88.1-100% for PDV. Phylogenetic analysis based on the nucleotide sequence of the RNA 3 and the coat protein, grouped all PNRSV isolates into the PV32 (22 isolates) and PV96 (15 isolates) clusters; meanwhile all Spanish PDV isolates were grouped in the main cluster previously described by Pallas et al. (2012).