Phylogenetic dissection provides insights into the incongruity in the tree of Archaeplastida between the analyses of nucleus- and plastid-encoded proteins.

Archaeplastida is defined as a taxonomic assemblage comprising three sub-clades, namely Chloroplastida, Glaucophyta, and Rhodophyta plus two non-photosynthetic lineages sister to Rhodophyta (the latter three lineages collectively termed "Rhodozoa" here). The members of Archaeplastida are the descendants of the eukaryote that took up and transformed a cyanobacterial endosymbiont into a primary plastid. Recent phylogenetic analyses of multiple proteins (phylogenomic analyses) stably recovered the monophyly of Archaeplastida, but uncertainty remains in the relationship among the three sub-clades in this assemblage. The phylogenomic analyses of nucleus-encoded proteins (nuc-proteins) grouped Chloroplastida and Glaucophyta together, excluding Rhodozoa in the Archaeplastida clade, albeit the union of Chloroplastida and Rhodophyta was often inferred from the phylogenomic analyses of plastid-encoded proteins (pld-proteins). In this study, we challenged the previously recognized but as-yet-explicitly addressed issue in the tree of Archaeplastida (ToA). The detailed analyses of the nuc-protein and pld-protein supermatrices revealed that taxon sampling can invoke different types of phylogenetic artifacts into the inferences from both supermatrices examined here. In the end, we propose a working hypothesis for the ToA and provide future perspectives toward resolving the ToA.