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Tomato spotted wilt orthotospovirus (TSWV, Orthotospovirus tomatomaculae) resistance genes (Tsw, Sw5) have been identified in pepper and tomato plants. The development of resistant cultivars is one of the popular management strategies for overcoming viral infections. However, the breakdown of resistance genes has been documented from many places where resistant cultivars have been developed. This has mainly been due to the emergence of resistance-breaking (RB) lines because of the consecutive use of these cultivars. The development of these isolates may cause great losses in both tomato and pepper plants in Türkiye. To investigate the incidence of TSWV, 150 symptomatic samples were collected from widespread locations of tomato and pepper growing provinces in Türkiye. Samples were inoculated to enhance the virus titer and further confirmed by enzyme-linked immunosorbent assay (ELISA). The ELISA positive samples were confirmed by reverse transcription-polymerase chain reaction. The sequence-characterized amplified region (SCAR) and CAPS markers were used to screen resistance genes in tomato and pepper plants. Positive TSWV-isolates were partially sequenced to determine whether they had the previously reported mutations in NSs or NSm genes for RB isolates. As per the virus characterization, NSm and NSs amino acid sequences showed no previously identified mutations. Resistance gene-carrying isolates were amplified for partial genome sequences. Phylogenetic analyses revealed that both NSs and NSm were distributed in the same genetic pool. The N gene sequence comparison and phylogenetic analysis showed that the Turkish isolates were clustered in a separate clade. These findings provide insight into TSWV infections and resistance genes of pepper and tomato by phylogenetic analysis. [ABSTRACT FROM AUTHOR]

Raspberry bushy dwarf virus (RBDV), recently renamed to Idaeovirus rubi, is one of the most common viruses infecting Rubus species worldwide but there is still a limited number of genome sequences available in the GenBank database and the majority of the sequences include partial sequences of RNA‐1 and RNA‐2. The distribution and incidence of RBDV in main raspberry and blackberry growing provinces in Turkey were monitored during 2015–2019 and 537 Rubus spp. samples were tested by both DAS‐ELISA and RT‐PCR. Among the tested samples, 36 samples tested positive for RBDV by DAS‐ELISA and 67 samples by RT‐PCR. There was relatively low nucleotide diversity among the Turkish isolates. Turkish isolates shared 93%–97.7%, 84.3%–98.9%, and 85%–99.2% nucleotide sequence identities with available sequences in the GenBank, in partial RNA‐1, movement protein (MP) and coat protein (CP) genes, respectively. In the phylogenetic tree constructed for RNA‐1, MP, and CP sequences, all Turkish raspberry isolates were clustered in a distinct clade. However, the blackberry isolates showed considerable variation in nucleotide sequences and were placed in three distinct groups. The divergent blackberry isolates showed high variability in MP (84.5%–89.3%) and CP (85.5%–89.7%) regions and were placed in a distinct group. The rest of blackberry isolates clustered together with sweet cherry RBDV isolates adjacent to the grapevine clade or together with raspberry isolates. The comparative analysis conducted on three RNA segments of RBDV highlighted the high sequence diversity of Turkish RBDV isolates. This study also emphasizes the importance of regular monitoring of RBDV infections in Turkey, with special regard to those Rubus spp. and grapevine accessions employed in conservation and selection programmes. In particular, the presence of new RBDV genetic variants and infection of Rubus species must be taken into account to choose a correct detection protocol and management strategy. [ABSTRACT FROM AUTHOR]