Abstract
The genome sequences of three related endogenous pararetroviruses were obtained by high-throughput genomic sequencing of Medicago sativa. The genomes were found to be integrated within plant genes. The phylogeny revealed that Caulimovirus-MSa3 was closely related to caulimoviruses of petunia, whereas Caulimovirus-MSa1 and Caulimovirus-MSa2 were distinct from constructed clades.