Phylogenetic studies for construction of a new concept of the kingdom Plantae and a new taxonomic system of the eukaryotes

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Based on the re-examinations and re-analyses of the sequence data previously used for macrophylogeny of eukaryotes as well as on the construction of EST data from the free-living, plastid-lacking euglenoid Peranema, it was suggested that the fast evolving genes from intracellular endoparasites, ciliates etc. may have mislead the nonmonophyly of the primary phototrophs. Since our nuclear genome analyses also demonstrated the possible cryptic secondary or tertiary endosymbiosis of a red alga before the secondary endosymbiosis of a green alga in Chlorarachniophyta or Euglenophyta, respectively, the concept of the secondary phototrophs is now renewing.