The IL-60 platform, consisting of a disarmed form of tomato yellow leaf curl virus (TYLCV) and auxiliary components, was previously developed as a nontransgenic universal vector system for gene expression and silencing that can express an entire operon in plants. IL-60 does not allow rolling-circle replication; hence, production of viral single-stranded (ss) DNA progeny is prevented. We used this double-stranded (ds) DNA-restricted platform (uncoupled from the dsDNA→ssDNA replication phase of progeny viral DNA) for functional genomics studies of TYLCV. We report that the noncoding 314-bp intergenic region (IR) is the only viral element required for viral dsDNA replication. None of the viral genes are required, suggesting recruitment of host factors that recognize the IR. We further show that IR-carrying reporter genes are also capable of replication but remain confined to the cells into which they were introduced. Only two sense-oriented viral genes (V1 and V2) need to be added to the IR-carrying construct for expression and movement. Hence, any IR-dsDNA construct supplemented with V1 and V2 becomes a replication-competent, mobile and expressing plant plasmid. All viral functions (replication, expression and movement) are determined by the IR and the sense-oriented genes. The complementary-oriented viral genes have auxiliary roles in the late phase of the virus "life cycle". The previously reported involvement of some viral genes in expression and movement is therefore revised.