Identifying losses and expansions of selected gene families in incomplete genomic datasets

Introduction DURING evolution, some eukaryotic lineages have acquired the ability to photosynthesize through endosymbiosis and conversion of the endosymbiont into a plastid. The first endosymbiotic event has involved a phagotrophic eukaryote and a cyanobacterium and has given rise to three monophyletic groups: glaucophytes, green plants and red algae. Red algae have generally smaller genomes with less coding genes compared to the two others (especially green plants). Because the earliest-branching group among red algae (Cyanidiales) is composed of thermoacidophilic organisms, we hypothesize that these missing genes might have been lost by the common ancestor of extant red algal during its adaptation to life in extremophilic conditions.