Eggplant has recently suffered a serious threat from a virus infection that causes mosaic and fruit deformation in egg-plant fields in Iraq. The infection ratio has registered between 1-80% in examined eggplant fields. The Illumina platform has been applied to sequencing genomic DNA and total RNAseq of symptomatic samples in addition to healthy genomic DNA. The analysis of an entire RNA data revealed Eggplant mild leaf mottle virus (EMLMV) as a causal agent of the symptoms. The sequence of EMLMV was composed of 9280 nt encodes ten protein domains and the transcripts per million (TPM) was 9. Two endogenous pararetroviruses registered, Caulimovirus – SMe and SmelV belong to Caulimovirus and Florendovirus genera with lengths of 8233 and 6198 nt respectively, and both were found interestingly in the RNA transcripts. Phylogeny has revealed EMLMV and endogenous elements’ relations to related viruses.
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