In May-2016 a Cestrum elegans with virus-like symptoms including chlorotic spots, mosaic and leaf deformation collected from Hatay province of Turkey. In order to analyze the etiology, the sample was subjected to high throughput sequencing (HTS) using small RNA. Small RNAs was extracted from leaves and prepared for NGS using TruSeq RNA Library Prep Kit. The libraries were sequenced using HiSeq 2500 resulted in 60,546,721 single end 51nt reads. The adapter sequences were trimmed from the reads, then low quality and duplicated reads were discarded. Finally, unique reads with length range of 15-30nt (~14M reads) were uploaded to VirusDetect software for virus identification. VirusDetect yielded 1,519 contigs. Blast and mapping analysis of the contigs indicated presence of Tomato chlorosis virus (ToCV). 40 reads (41-111nt) with 99% identity for RNA1 (28.5% coverage) and 46 reads (42-313nt) with 98.8% identity (59% coverage) for RNA2 were mapped to the reference genome of ToCV. For further confirmation, we designed two specific primers and successfully amplified target regions of RNA1 (RdRp) and RNA 2 (CP). To our knowledge, this is the first report of this virus in Cestrum elegans and our studies are in progress to determine its molecular and biological characteristics.
