On the stability of sequences inserted into viral genomes

Willemsen, Anouk; Zwart, Mark P

Besides HGT, another mechanism for evolutionary innovation is gene duplication. The effects in the stability on a genetically redundant insert might be variable. On one hand, one would expect the duplicated copy to be rapidly deleted from the genome as it does not confer an additional function. On the other hand, if a duplicated sequence is stable it may act as a stepping stone to the evolution of new biological functions. We have investigated the stability of genetically redundant sequences by generating (TEV) viruses with potentially beneficial gene duplications (Willemsen et al. 2016 ). All gene duplications resulted in a loss of viability or in a significant reduction in viral fitness. Experimental evolution always led to deletion of the duplicated gene copy and maintenance of the ancestral copy. However, the stability of the different duplicated genes was highly divergent, suggesting that passage duration is not the main factor for determining whether the insert will be stable or unstable. The deletion dynamics of the duplicated genes were associated with the passage duration and the size of the duplicated copy. By developing a mathematical model we showed that the fitness effects alone are not enough to predict genomic stability. A context-dependent recombination rate is also required, with the context being the identity of the insert and its position.