Hop Latent Viroid shares a 19 nucleotide sequence with Cannabis sativa COG7

In the process of sequencing hop latent viroid genomes, we noticed a 19 nucleotide perfect homology of the HpLVd genome to the 5 prime coding region of a Cannabis sativa gene involved in shoot apical meristem (SAM) growth known as COG7. RNA interference has been suggested as the putative mode of pathology with HpLVd. To assess this we designed a RT-qPCR assay to target this region of COG7 in C.sativa and noticed modest but reproducible, (2-5 CT) 4-32 fold decrease in COG7 expression in the infected plant. Both plants were in vegetative state but are of different genetic backgrounds (Jamaican Lion not infected and Strawnana infected). 5 cultivars with public sequence in Kannapedia.net have variants in this 19bp window and should be furthered assessed for gene expression differences in COG7 upon HpLVd infection. We further evaluate the diversity of the publicly available HpLVd genomes and their potential for short sequence homology to 25 cannabis mRNAs.