Publications

†, corresponding author(s); *, equally contributed authors

• Yazaki E†., Isogai R, Inagaki Y. Colponemidia questions the ancestry of an ATG10-lacking ATG8–ATG12 conjugation system in Alveolata. Journal of Protistology in press.

• PREPRINT Isogai R*, Wei M*, Harada R, Yazaki E, Nakayama T, Gawryluk RMR, Inagaki Y†. 2026 Diversity and evolution of DNA polymerase θ in eukaryotes and the origin of mitochondrion-localized DNA polymerase PolIA in Euglenozoa. SSRN (doi: 10.2139/ssrn.6190616)

• Yazaki E†, Shiratori T, Inagaki Y. 2025 Protists with uncertain phylogenetic affiliations for resolving the deep tree of eukaryotes. Microorganisms 13(8):1926. PubMed (doi: https://doi.org/10.3390/microorganisms13081926)

• Prokina KI†, Yubuki N, Galindo LJ, Torruella G, Inagaki Y, Iwamoto K, López-García P, Moreira D. 2025 A deeply branching lineage in Heterolobosea (Discoba) with multiflagellated and multigrooved life stages.  Journal of Eukaryotic Microbiology 72(5):e70037. PubMed (doi: 10.1111/jeu.70037)

• Nakayama T†, Harada R, Yabuki A, Nomura M, Shiba K, Inaba K, Inagaki Y.  2025 Marked genome reduction driven by a parasitic lifestyle: Two complete genomes of endosymbiotic bacteria possibly hosted by a dinoflagellate. Microbes and Environments 40(2):ME250005. PubMed (doi: 10.1264/jsme2.ME25005)

• Yazaki E†, Harada R, Isogai R, Bamba K, Ishida K, Inagaki Y, Shiratori T†. 2025 Glissandra oviformis n. sp.: A novel predatory flagellate illuminates the character evolution within the eukaryotic clade CRuMs. Open Biology 15(6):250057. PubMed (doi: 10.1098/rsob.250057)  プレスリリース

• Harada R†, Shiratori T, Yabuki A, Inagaki Y, Roger AJ, Kamikawa R†. 2025 Complete mitochondrial genomes of ancyromonads provide clues for the gene content and genome structures of ancestral mitochondria. Journal of Eukaryotic Microbiology 72(3):e70012. PubMed (doi: 10.1111/jeu.70012)

• PREPRINT Isogai R, Harada R, Nakayama T, Inagaki Y†. 2025 Phylogenetic dissection provides insights into the incongruity in the tree of Archaeplastida between the analyses of nucleus- and plastid-encoded proteins. bioRχiv  (doi: 10.1101/2025.05.06.652364)

• PREPRINT Harada R, Nishimura Y, Nomura M, Yabuki A, Shiba K, Inaba K, Inagaki Y, Nakayama T†. 2025 A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome. bioRχiv  (doi: 10.1101/2025.05.02.651781) A news article that introduced this work and was published in Science.

• PREPRINT Harada R†, Shiratori T, Yabuki A, Inagaki Y, Roger AJ, Kamikawa R†. 2025 Complete mitochondrial genomes of ancyromonads provide clues for the gene content and genome structures of ancestral mitochondria. bioRχiv (doi: 10.1101/2025.03.26.645259)  The version after peer-review was published in J Eukaryot Microbiol in 2025.

• PREPRINT Yazaki E†, Harada R, Isogai R, Bamba K, Ishida K, Inagaki Y, Shiratori T†. 2025 Glissandra oviformis n. sp.: a novel predatory flagellate illuminates the character evolution within the eukaryotic clade CRuMs. bioRχiv  (doi: 10.1101/2025.02.18.638917v1)  The version after peer-review was published in Open Biol in 2025.

• Pánek T†, Tice AK, Žihala D, Corre P, Hrubá P, Kamikawa R, Mirzoyan S, Jones R, Yazaki E, Shiratori T, Kume K, Hashimoto T, Ishida K, Zadrobílková E, Hradilová M, Silberman JD, Stairs CW, Roger AJ, Inagaki Y, Eliáš M, Brown MW, Čepička I. 2025 An expanded phylogenomic analysis of Heterolobosea reveals the deep relationships, non-canonical genetic codes, and cryptic flagellate stages in the group. Molecular Phylogenetics and Evolution 204:108289. PubMed (doi: 10.1016/j.ympev.2025.108289)

• PREPRINT Nakayama T†, Harada R, Yabuki A, Nomura M, Shiba K, Inaba K, Inagaki Y.  2025 Drastic genome reduction driven by parasitic lifestyle: Two complete genomes of endosymbiotic bacteria possibly hosted by a dinoflagellate. bioRχiv  (doi: 10.1101/2025.01.03.631278)  The version after peer-review was published in Microbes Environ in 2025.