Abstract
Background: Starch is the main source of carbon storage in theArchaeplastida. The Starch Biosynthesis Pathway(SBP) emerged from cytosolic glycogen metabolism shortly after plastid endosymbiosis and was redirected to theplastid stroma during the green lineage divergence. The SBP is a complex network of genes, most of which aremembers of large multigene families. While some gene duplications occurred in theArchaeplastidaancestor, mostwere generated during the SBP redirection process, and the remaining few paralogs were generated throughcompartmentalization or tissue specialization during the evolution of the land plants. In the present study, wetested models of duplicated gene evolution in order to understand the evolutionary forces that have led to thedevelopment of SBP in angiosperms. We combined phylogenetic analyses and tests on the rates of evolution alongbranches emerging from major duplication events in six gene families encoding SBP enzymes.Results: We found evidence of positive selection along branches following cytosolic or plastidial specialization intwo starch phosphorylases and identified numerous residues that exhibited changes in volume, polarity or charge.Starch synthases, branching and debranching enzymes functional specializations were also accompanied byaccelerated evolution. However, none of the sites targeted by selection corresponded to known functionaldomains, catalytic or regulatory. Interestingly, among the 13 duplications tested, 7 exhibited evidence of positiveselection in both branches emerging from the duplication, 2 in only one branch, and 4 in none of the branches.Conclusions: The majority of duplications were followed by accelerated evolution targeting specific residues alongboth branches. This pattern was consistent with the optimization of the two sub-functions originally fulfilled by theancestral gene before duplication. Our results thereby provide strong support to the so-called“Escape fromAdaptive Conflict”(EAC) model. Because none of the residues targeted by selection occurred in characterizedfunctional domains, we propose that enzyme specialization has occurred through subtle changes in affinity, activityor interaction with other enzymes in complex formation, while the basic function defined by the catalytic domainhas been maintained.