Sequencing and Characterization of Canna Yellow Mottle Virus

Abstract

Badnaviruses are pararetroviruses that exist as episomal viruses or as integrants in plant chromosomes by illegitimate recombination. Endogenous virus sequences can be a hidden reservoir of infection that emerge when plants are stressed, or a source of small RNAs that contribute to anti-viral defense. Advanced nucleic acid sequencing technology has enabled the discovery of complicated viromes existing in naturally infected plants and provided for new insights into virus synergistic interactions. Such approaches are vital to gaining insight into economically significant diseases. We report the entire Canna yellow mottle badnavirus (CaYMV) genome that exists in naturally infected hybrid cannas. We also identified two subviral DNAs related to CaYMV. One subviral DNA, named EVS-0036, encodes an intact reverse transcriptase and RNase H. Southern analysis identified episomal forms of CaYMV genomes. EVS-0036 transcripts are detected in canna plants naturally infected with Canna yellow streak potyvirus (CaYSV) or CaYMV. The results demonstrate the occurrence of endogenous subviral DNAs which, through evolution is related to badnaviruses, but preferentially occurs alongside an RNA virus. Because they are vegetatively transmitted, CaYMV, CaYSV and EVS-0036 share a long-term association within canna that represents a powerful model to explore the mutualistic-parasitic continuum that can involve virus-host and virus-virus interactions.