More importantly, the authors link the head-on replication-transcription conflicts with gene evolution. The ratio of non-synonymous to synonymous mutations is less than 0.025 and more than 0.05 within almost half of genes on the leading strand and lagging strand, respectively. It indicates that the different ratios of the leading- and lagging-strand genes may due in part to negative selection against non-synonymous mutations or positive selection for non-synonymous mutations. To give evidence of positive selection on lagging strand, convergent amino-acid mutations are detected, for they imply positive selection, as well as adaptive evolution. The more convergent mutations in lagging-strand genes suggest that positive selection in part causes high mutation rates and evolution rate of genes on lagging strand is faster. Last, the functions of core genes on the lagging strand are analyzed and most of these genes are associated with stress responses. Thus, the high mutation rates of lagging-strand genes may help the population adapt to rapid changes in the environment.
All of these results suggest that mutation rate of lagging-strand genes is higher due to head-on replication-transcription encounters, which helps adaptive evolution of genes on lagging strand.