Endogenous viruses
The genomics era has revealed an abundance of viruses in
many genomes, and plants are no exception. Integration of plant
pararetroviruses has been known for a long time, as well as the
presence of retrotransposons that were likely originally derived
from viruses. Recent data shows that plant genomes have an
abundance of these and other endogenous viral elements, including
ones derived from both nuclear and cytoplasmic viruses.
Geminivirus sequences were discovered in several Nicotiana genomes
many years ago (Ashby et al., 1997). More recently, cytoplasmic
RNA viruses have been found integrated in plant genomes
(Chiba et al., 2011; Kondo et al., 2013; Liu et al., 2010). In many
cases these integrated elements are transcriptionally active, implying
a possible function for these genes. Overall the flow of genes is
from viruses to host cells, and not the other way around (Koonin
and Dolja, 2014) and viruses have ultimately been the source of
many host genes