130 “Plantae” Emended Based on the Common History of the Primary Plastid Endosymbiosis

Abstract

Phylogenetic relationships between three lineages of the primary photosynthetic eukaryotes (red algae, green plants and glaucophytes) seem to remain unresolved because previous nuclear multigene phylogenies used the highly reduced red algal endosymbiont (nucleomorph) and/or incomplete red algal gene sequences. Here we carried out nuclear multigene phylogeny of various lineages of only mitochondria‐containing eukaryotes, using complete sequences from the red alga Cyanidioschyzon merolae. Cellular slime molds were designated as the outgroup based on concatenated two paralogous tubulin gene sequences. Our phylogenetic analyses based on a 1525‐amino‐acid sequence of four concatenated nuclear genes (actin, elongation factor‐1a, a‐tubulin and b‐tubulin) resolved the presence of two large robust monophyletic groups (Groups A and B) and the basal eukaryotic lineages (Amoebozoa). Group A corresponded to the Opisthokonta (Metazoa and Fungi), whereas Group B included various primary and secondary plastid‐containing lineages (red algae, green plants, glaucophytes, euglenoids, heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, and Heterolobosea. The red algae represented the most basal lineage within Group B. Therefore, the primary plastid endosymbiosis likely occurred once in the common ancestor of Group B, and the primary plastids were subsequently lost in the ancestor(s) of organisms which now lack primary plastids within group B. A new concept of ÒPlantaeÓ is proposed for phototrophic and nonphototrophic organisms belonging to Group B, on the basis of the common history of the primary plastid endosymbiosis. This new scenario of the plastid evolution is discussed in comparison with genome information recently accumulated and plastid genome comparison.