Effects of the broken rps2 gene cluster on evolutionary rates in Campanulaceae

The conserved rps2 gene cluster (rps2-atpI-atpH-atpF-atpA) is broken in the chloroplast genome of Campanulaceae. To explore whether the evolutionary rates of the related genes changed after the cluster was broken, we selected the chloroplast genome sequences of 50 Campanulaceae and two Menyanthaceae species to construct their phylogenetic relationships, and further analyzed the evolutionary rate, selection pressure, and adaptive evolutionary process of the rps2 gene cluster-related genes. Results showed that all species with a broken rps2 gene cluster in Campanulaceae were from Campanuloideae and formed monophyletic branches on the phylogenetic tree. Compared with the unbroken species, the mean evolutionary rate of the related genes decreased in the broken species. There were significant differences in the nonsynonymous substitution rate between genes. In adaptive evolutionary analysis, the site model detected positive-selection sites in the atpI and rps2 genes. Our findings suggest that the fragmentation of the gene cluster holds phylogenetic implications, leading to alterations in evolutionary rates and diverse evolutionary trajectories among individual genes.