Archivio Journal of Plant Pathology

Abstract:

In 2016, during a survey aimed to assess the health status of tomatoes (Solanum lycopersicum L.) in Slovakia, a sample labelled as T62, collected from cultivated tomato grown in a garden in western Slovakia was analysed by Illumina next-generation sequencing of cDNA libraries prepared from ribosomal-depleted total RNAs isolated from leaves. De novo assembling of ca. 2.8 Mb of reads and subsequent mapping enabled the identification of a single potato virus S variant (PVS, genus Carlavirus). Besides PVS, the T62 tomato showing slight veinal chlorosis on the leaves was found coinfected with cucumber mosaic virus (CMV). Comparative analysis showed that the T62 genome (deposited as MF346599) was 78.7- 95.8% identical to the 21 PVS complete genome sequences available in GenBank. Until now, however, the T62 PVS sequence is the only one originating from tomato. In the phylogenetic analysis, T62 forms a subcluster with Hungarian HF571059 and Ukrainian LN851189 and LN854492-93 isolates, all from potato. To further investigate the presence of PVS in tomato, 66 additional samples from seven localities in western Slovakia were tested by RT-PCR using a set of newly designed primers from PVS sequences retrieved from GenBank (accessed in May, 2016). The primers PVS_7833F (5´-AGGCYATGGGATTTCAATGG-3´, sense) and PVS_8386R (5´-TGGTATCACCTCAGTTACTC-3´, antisense) amplified a 533 nt long 3’ region of the genome spanning the end of the CP and complete 11K protein genes. RT-PCR confirmed the presence of PVS in 21% of tomato plants tested. Comparison of 13 partial sequences obtained by Sanger sequencing of these amplicons (MF346600-MF346613) showed limited genetic variability (3.1%) among Slovak isolates. The phylogenetic analysis of obtained and additional available 47 sequences encompassing the target region showed that PVS isolates cluster in two main groups, previously designated as PVSO (ordinary) and PVSA (Andean) (Cox et al., 2010). All Slovak PVS isolates were assigned to the major PVSO strain, although divided between two distinct subclusters, without correlation to either geographic origin or biological properties.