First Record of Citrus exocortis viroid (CEVd) on Onions and Determining its Complete Sequence Using Next Generation Sequencing (NGS) Technology in Iraq

This study was conducted at the Research Station of the College of Agriculture, Tikrit University, and aimed to isolate and diagnose a strain of Citrus exocortis viroid (CEVd) on onion plants, describe its pathological symptoms, determine the complete genomic sequence of the Iraqi isolates, and draw its phylogenetic tree using next generation sequencing (NGS) technology and bioinformatics programs. The observed symptoms of infection included twisting and wrinkling of the leaves, stiffening of the top of the leaf, sharp leaf bending, and reduced growth, in addition to causing a change in the natural tubular leaf structure and variation in size. 98,945,112 accurate reads were obtained representing the total RNA sequences in infected onion plant samples. These reads were mapped to the complete viroid reference sequence, with 49,175 accurate reads and a length of 395 base pairs. This viroid strain which infects onion was the first record in Iraq and was given the name Citrus exocortis viroid isolate Aan-Saladin (CEVd Aan-saladin) and deposited in the gene library of the National Center for Biotechnology Information (NCBI) under the accession number OR589765.1, based on the complete genomic sequence. The phylogenetic analysis revealed close relation between the diagnosed isolate CEVd Aan-Saladin and the Najaf OR024670.1, Tikrit OR993891.1 and Baghdad OR343512.1 isolates, with significant divergence from the viroids outside the group. Keywords: Citrus exocortis viroid, onion disease, next generation sequence, complete genome, Phylogenetic tree.