Existence and Integration of Chromosomal Viral Elements in The Genome of Medicago sativa in Iraq

Alfalfa (Medicago sativa L.) is widely planted in Iraq and hosts a number of plant viruses. However, endogenous viral elements in the alfalfa genome have not been thoroughly explored. The Illumina-HTS platform and bioinformatics approaches were utilized to identify endogenous pararetroviruses in the local alfalfa genome. The platform generated 106,688,286 and 57,460,428 reads from entire DNA and RNA data, respectively. RepeatExplorer results and mapping to reference revealed that three viral elements from the Caulimovirus genus were discovered in the alfalfa genome, namely Caulimovirus-MSa1, Caulimovirus-MSa2, and Caulimovirus-MSa3. The entire lengths of the three caulimoviruses were 7935, 8234 and 7945 bp respectively. The viruses have domains from plant genes and retrotransposons in their sequences. The Caulimovirus-MSa1, -MSa2 and -MSa3 encode seven, eight and seven coding regions respectively.  Caulimovirus-MSa2 is more abundant than Caulimovirus-MSa1 and Caulimovirus-MSa3 in terms of genome proportion and copy number. The sequences were also present in RNA transcripts, albeit at low levels of expression. Caulimovirus-MSa1 was absent from the chromosomes of diploid and tetraploid alfalfa. Our data also included Soybean chlorotic mottle virus (SBCMV) and Figwort mosaic virus (FMV), confirming results from previous works.