There has been some detection and characterization studies by conventional detection methods like DAS-ELISA and RT-PCR on commonly known viruses in Rubus species in Turkey. Recently the first studies based on metagenomics analyses were performed to characterize better the etiology of diseased samples, leading potentially to the discovery of novel viruses infecting Rubus plants. One raspberry sample showing virus-like symptoms but negative for all known viruses by RT-PCR was selected for Next generation sequencing (NGS). The NGSanalysis was performed on an Illumina Nextseq 500 platform yielding a total of 10,428,288 paired-end reads (2x150 nt). The quality of sequences was analyzed by FASTQC v0.11.7. The Geneious R10 software (https://www.geneious.com) was used for sequence analysis. The reads were trimmed for adapters and then low quality and duplicated reads were discardedThe trimmed reads were then de novo assembled into larger contigs by SPAdes with a k-mer of 55. The generated contigs were annotated using TBLASTX on the refseq database of viral nucleotides sequences downloaded from NCBI (ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral) which revealed a contig (8516nt) with 62.5% identity in 590 amino acid to peach chlorotic mottle virus (PCMV, Foveavirus)Overlapping RT-PCR amplicons were used to sequence full genome of the virus. The preliminary analyses showed that this virus shared 43-50% identity with reference full genome of other members of Foveavirus. Identities at aa level were 38-43% and 17-28% for replicase and CP, respectively. These identities were lower than established threshold for species in Betaflexivirdae.Multiple alignment and phylogenetic analysis confirmed that this virus is a putative new member of the genus Foveavirus in the family Betaflexiviridae. Complementary analyses will be carried out to evaluate its presence in other raspberry samples.
