Figure 2.

Schematic genome organization of smacoviruses. Representative genomes were selected from each genogroup for their genome size, ORFs (Rep, replication initiator protein; Cap, capsid protein) intergenic regions, (LIR, long intergenic region; SIR, small intergenic region), and predicted stem loop structure. Stem loop structures were predicted by mfold (Zuker 2003). Three categories of stem loop configurations, stem loop type L, S, and SL, were detected in these smacovirus genomes (for example: type L, genogroup D; type S, genogroup E; type SL, genogroup C). Nucleotide motif sequence NANNNTTAC in the stem-loop in stem loop type L, homologous to those involved in the initiation of DNA replication, were labeled with black dots.