Small RNA sequencing of a complex of parasitic plant and its host, Cuscuta campestris and Arabidopsis thaliana

Cuscuta campestris is a stem parasitic plant that has a broad host range. It is widely accepted that parasitic plants and host plants exchange various molecules not only water and minerals, but also proteins, peptides, mRNAs and small RNAs. In order to elucidate the biological significance of sRNA exchange, we performed sRNA sequencing of a complex consisting of a parasitic plant, Cuscuta campestris, and a host plant, Arabidopsis thaliana, in order to prioritize sRNAs that were translocated from host to parasite, and vice versa. RNA samples were prepared from the parasitic interface, C. campestris stem distant from the parasitic interface, A. thaliana stem distant from the parasitic junction, non-parasitized C. campestris stem, and non-parasitized A. thaliana stem. Candidates for host-to-parasite mobile sRNAs were identified by mapping C. campestris reads from parasitized stem onto A. thaliana reference transcriptome. On the other hand, candidates for parasite-to-host mobile sRNAs were identified by mapping A. thaliana reads from parasitized stem to C. campestris reference transcriptome.