Molecular evolution of Coq1 gene family in eukaryotes

Coq1 genes encode polyprenyl diphosphate synthases, which determine the isoprenoid side chain of ubiquinone and plastoquinone in organisms. The biological roles of Coq1 genes have been widely investigated in prokaryotes and eukaryotes. In our study, we analyzed the phylogenetic relationships, structural evolution, selection pressure, and functional divergence of Coq1 genes to comprehensively elucidate the evolutionary fates of these genes after duplication and to understand the evolutionary pattern of the Coq1 family. We surveyed 32 representative sequenced genomes and found 59 Coq1 genes widely distributed in prokaryotic and eukaryotic organisms. Phylogenetic analysis showed that the Coq1 genes have diverged into two clades among eukaryotic lineages. Further evolutionary analysis in intron numbers, evolutionary rates, and degrees of positive selection indicated that the paired clades of Coq1 genes in each eukaryotic lineage were not synchronized, which hinted that their evolutionary processes probably have diverged. Furthermore, functional divergence analysis suggested that different types of subfunctionalization in the Coq1 gene family have occurred. In plants, the paired clades of Coq1 genes only diverged in their localization and expression, whereas the functions of these genes in animals and fungi were partially divided. Therefore, asymmetrical evolutionary processes achieved similar evolutionary fates with different types in the Coq1 gene family among eukaryotes, which might be related to the divergence and conservation of eukaryotic lineages during evolution.