A. Varsani and others Fig. 2. Partial conservation of recombination breakpoint distributions across the family Geminiviridae. (a) Breakpoint distribution plot (solid black line) indicating recombination hot- and cold-spots detectable in African streak virus sequences. Broken lines represent 99 and 95 % confidence intervals for the ‘global’ hot-spot test of Heath et al. (2006). Light and dark shaded regions, respectively, represent 99 and 95 % confidence intervals of the ‘local’ hot- and cold-spot test of Heath et al. (2006). (b) Recombination breakpoint distribution plot for the begomoviruses (after Lefeuvre et al. 2007b). Positions of genomic features are indicated above the plots: horizontal arrows labelled V and C, respectively, represent virion and complementary sense genes; boxes labelled IR, LIR or SIR represent intergenic regions. cp, Coat protein gene; rep, replication-associated protein gene; repA, ORF encoding the N-terminal portion of Rep. Vertical black arrows indicate polyadenylation signals of the complementary-sense genes and white arrows indicate the virion-strand replication origin. to explain non-random recombination breakpoint distri- butions in geminiviruses (Jeske et al., 2001; Lefeuvre et al., 2007a, b). In both the begomoviruses and mastreviruses the recom- bination hot-spots map to complementary-sense gene transcription initiation and termination sites and virion- strand origins of replication. The reason complementary gene transcription initiation and termination sites may be more predisposed to recombination than other sites is possibly that these are the regions where the most frequent 2068 clashes between transcription and replication complexes occur (Lefeuvre et al., 2007a). The absence in mastreviruses of a transcription initiation site and promoter elements in the middle of rep analogous to those found in begomo- viruses (Shung et al., 2006) may explain why there is no detectable recombination hot-spot in this region of mastrevirus genomes. It is also possible that the absence of a short intergenic region in begomoviruses could be the reason for the recombination hot-spot mapping to the 39 end of cp in Journal of General Virology 89