Cucumber (Cucumis sativus) is widely planted and hosted many plant viruses in Iraq. However, endogenous papraretroviruses (EPRVs) have not been studied in details in the genome of cucumber. In this study, next generation sequencing (NGS) and bioinformatics techniques were used to diagnose endogenous Pararetroviruses in the cucumber genome. The illumine platform produced 89.893.674 and 53.458.772 short clean reads with a length of 151 and 101 bases for total DNA and RNA data respectively. The results from Repeat Explorer and mapping to reference revealed that two viral elements belong to Florendovirus genus found in the examined genome, named CsatAV-Iraq and CsatBV -Iraq. The full length of CsatAV-Iraq and CsatBV-Iraq were 7147 and 7390 bp respectively. The CsatAV-Iraq encodes seven coding domains; MP, PTZ00440, antiphage_ZorA_4, two RT_LTRs, RT_RNaseH_2, RNase_HI. The CsatBV-Iraq has seven domains of DUF5864, reverse transcriptase (RT_LTR and RVT_1), three domains of RNaseH (RH), and RVT_2. Some plant genes were found to be involved in the two Florendo viruses, which predicted their integration and position in the genome. Genome proportion and copy number values showed that CsatBV-Iraq is more abundant than CsatAV-Iraq. The sequences were existed in RNA transcripts with low expression level. The phylogeny revealed the close relationship between the two EPRVs with their related ones.
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