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چکیده
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Turkey is one of the leading producers and exporter for pomegranate trees. Total production in Turkey reached 445.750 tons in 2015 that corresponds to one of the largest pomegranate economies in the World. Plant viruses have an enormous negative impact on agricultural crop production however, there are not many reports on the virus and virus-like diseases affecting pomegranates worldwide. To date, only Cucumber mosaic virus (CMV) and some putative viroid-like RNAs have been reported in pomegranate trees from ex-Yugoslavia and Spain, respectively. In the last several years, suspected "virus-like" symptoms such as vein clearing, oak-leaf appearance and leaf deformations have been observed in the local pomegranate cultivars grown in Hatay province of Turkey and Grapevine leafroll associated virus-1 (GLRaV-1) was first time detected in the symptomatic trees but no correlation was discovered between this virus and symptoms. Therefore three GLRaV-1 positive pomegranate samples were pooled for NGS analysis. TRIzol Reagent was used for total RNA extraction and the small RNAs with size from 15 to 30 nt were purified from total RNAs. The sRNAs with adaptors were transcribed to cDNA which was used for library construction. The NGS run was performed on HiSeq 2000 Illumina platform and resulted in 56,614,811 reads of 51bp. The reads were trimmed by removing the adaptor sequences and low quality bases, then de novo assembled into larger contigs using Velvet Software 0.7.31 with k-mer values of 15, 17, 19 and 21. The contigs obtained were subsequently screened for homologous sequences by BLASTN and BLASTX on the GenBank Virus Reference Sequence Database. Blast analyses results identified 33 contigs virus associated contigs, which most of them (31 contigs) were matched to viruses belong to caulimoviridae. The blueberry red ringspot virus related contigs were prevailing (12 contigs), followed by Cestrum yellow leaf curling virus (8 contigs) and Soybean chlorotic mottle virus (4 cont
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