Begomoviruses have small genomes (2.5-2.7 x 103 nucleotides) that are packaged as ssDNA into virions and occur as double-stranded DNA (dsDNA) in nuclei of infected plant cells. Their genomes can consist of one DNA molecule or two DNA components (DNA-A and DNA-B), both of which are required for systemic infection (Fig. 1A). The circular genomes contain divergent transcription units separated by a 5’ intergenic sequence (IR, ca. 200 nt) that contains an origin of replication and promoters for viral gene transcription. Begomovirus genomes encode 5-8 proteins involved in viral replication (Rep and REn), transcription (TrAP), movement (NSP and MP), encapsidation/transmission (CP), and countering host defenses (TrAP, AC4 and AV2). These proteins are involved in every aspect of viral infection and impact a wide range of plant processes, including DNA replication, cell cycle regulation, gene expression, programmed cell death, macromolecular trafficking, hormone signaling and host defenses. A recent review listed over 60 plant proteins that are known partners of begomovirus proteins. Maintenance of all of these interactions is likely to be a significant constraint on begomovirus evolution.
