Journal of Molecular Evolution

, Volume 57, Issue 4, pp 377–382 | Cite as

Phylogeny of Plastids Based on Cladistic Analysis of Gene Loss Inferred from Complete Plastid Genome Sequences

  • Hisayoshi Nozaki
  • Njij Ohta
  • Motomichi Matsuzaki
  • Osami Misumi
  • Tsuneyoshi Kuroiwa


Based on the recent hypothesis on the origin of eukaryotic phototrophs, red algae, green plants, and glaucophytes constitute the “primary photosynthetic eukaryotes” (whose plastids may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis), whereas the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary or tertiary endosymbiotic events (involving a phototrophic eukaryote and a host cell). Although phylogenetic analyses using multiple plastid genes from a wide range of eukaryotic lineages have been carried out, some of the major phylogenetic relationships of plastids remain ambiguous or conflict between different phylogenetic methods used for nucleotide or amino acid substitutions. Therefore, an alternative methodology to infer the plastid phylogeny is needed. Here, we carried out a cladistic analysis of the “loss of plastid genes” after primary endosymbiosis using complete plastid genome sequences from a wide range of eukaryotic phototrophs. Since it is extremely unlikely that plastid genes are regained during plastid evolution, we used the irreversible Camin-Sokal model for our cladistic analysis of the loss of plastid genes. The cladistic analysis of the 274 plastid protein-coding genes resolved the 20 operational taxonomic units representing a wide range of eukaryotic lineages (including three secondary plastid-containing groups) into two large monophyletic groups with high bootstrap values: one corresponded to the red lineage and the other consisted of a large clade composed of the green lineage (green plants and Euglena) and the basal glaucophyte plastid. Although the sister relationship between the green lineage and the Glaucophyta was not resolved in recent phylogenetic studies using amino acid substitutions from multiple plastid genes, it is consistent with the rbcL gene phylogeny and with a recent phylogenetic study using multiple nuclear genes. In addition, our analysis robustly resolved the conflicting/ambiguous phylogenetic positions of secondary plastids in previous phylogenetic studies: the Euglena plastid was sister to the chlorophycean (Chlamydomonas) lineage, and the secondary plastids from the diatom (Odontiella) and cryptophyte (Guillardia) were monophyletic within the red lineage.


Evolution Camin-Sokal model Cladistic analysis Gene loss Phylogeny Plastids Plastid genes Primary plastid Secondary plastid 



This study was supported by Grant-in-Aid for Scientific Research on Priority Areas (c) “Genome Biology” from the Ministry of Education, Culture, Sports, Science and Technology, Japan (No. 1320611 to TK), and by the Program for the Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN; to TK and HN).


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Copyright information

© Springer-Verlag New York Inc. 2003

Authors and Affiliations

  • Hisayoshi Nozaki
    • 1
  • Njij Ohta
    • 2
  • Motomichi Matsuzaki
    • 3
  • Osami Misumi
    • 1
    • 4
  • Tsuneyoshi Kuroiwa
    • 5
  1. 1.Department of Biological SciencesGraduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033Japan
  2. 2.Department of Molecular Biology, Faculty of ScienceSaitama University, Shimo-Ohkubo, Saitama-shi, Saitama 338-8570Japan
  3. 3.Department of Biomedical ChemistryGraduate School of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033Japan
  4. 4.Bio-oriented Technology Research Advancement Institution (BRAIN), Toranomon, Minato-ku, Tokyo 105-0001Japan
  5. 5.Department of Life ScienceCollege of Science, Rikkyo (St.Paul’s) University, Nishiikebukuro, Toshima-ku, Tokyo 171-8501Japan

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