†; corresponding author, *; co-first author


  • Kamikawa R, Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Onuma R, Cenci U, Moog D, Speak S, Sarkozi K, Toseland A, Oosterhout C, Oyama K, Kato M, Kume K, Kayama M, Azuma T, Ishii K, Miyashita H, Henrissat B, Lombard V, Win J, Kamoun S, Kashiyama Y, Mayama S, Miyagishima S, Tanifuji G, Mock T, Nakamura Y. (2022) Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. Science Advances 8: eabi5075
  • Hirooka S, Itabashi T, Ichinose TM, Onuma R, Fujiwara T, Yamashita S, Jong LW, Tomita R, Iwane AH. Miyagishima S. (2022) Life cycle and functional genomics of the unicellular red alga Galdieria for elucidating algal and plant evolution and industrial use. Proceedings of the National Academy of Sciences 119:e2210665119



  • Yamada N, Sakai H, Onuma R, Kroth PG, Horiguchi T. (accepted). Five non-motile dinotom dinoflagellates of the genus Dinothrix. Frontiers in Plant Science11: 1764.
  • Fujiwara T, Hirooka S, Ohbayashi R, Onuma R, Miyagishima S. (2020). Relationship between cell cycle and diel transcriptomic changes in metabolism in a unicellular red alga. Plant Physiology 183: 1484–1501.
  • Onuma R†, Hirooka S, Kanesaki Y, Fujiwara T, Yoshikawa H, Miyagishima S† (2020). Changes in the transcriptome, ploidy, and optimal light intensity of a cryptomonad upon integration into a kleptoplastic dinoflagellate. The ISME Journal 14: 2407–2423.
  • Ohbayashi R, Hirooka S, Onuma R, Kanesaki Y, Hirose Y, Kobayashi Y, Fujiwara T, Furusawa T, Miyagishima, S. (2020). Evolutionary changes in DnaA-dependent chromosomal replication in cyanobacteria. Frontiers in microbiology 11: 786.
  • Harada R, Hirakawa Y, Yabuki A, Kashiyama Y, Maruyama M, Onuma R, Soukal P, Miyagishima S, Hampl V, Tanifuji G, Inagaki, Y. (2020). Inventory and evolution of mitochondrion-localized family A DNA polymerases in euglenozoa. Pathogens 9: 257.


  • Uzuka A*, Kobayashi Y*, Onuma R*, Hirooka S, Kanesaki Y, Yoshikawa H, Fujiwara T, Miyagishima S†. (2019) Responses of unicellular predators to cope with the phototoxicity of photosynthetic prey. Nature Communications 10: 5606.
  • Yamada N, Bolton JJ, Trobajo R, Mann DG, Dąbek P, Witkowski A, Onuma R, Horiguchi T, Kroth PG. (2019). Discovery of a kleptoplastic ‘dinotom’dinoflagellate and the unique nuclear dynamics of converting kleptoplastids to permanent plastids. Scientific Reports 9: 1-13.


  • Yokouchi K, Onuma R, Horiguchi T. (2018). Ultrastructure and phylogeny of a new species of mixotrophic dinoflagellate, Paragymnodinium stigmaticum sp. nov.(Gymnodiniales, Dinophyceae). Phycologia 57: 539-554.


  • Hirooka S, Hirose Y, Kanesaki Y, Higuchi S, Fujiwara T, Onuma R, Era A, Ohbayashi R, Uzuka A, Nozaki H, Yoshikawa H, Miyagishima S. (2017). Acidophilic green algal genome provides insights into adaptation to an acidic environment. Proc. Natl. Acad. Sci. U.S.A., 114: E8304-E8313.
  • Onuma R†, Neha M, Miyagishima S†. (2017) Regulation of chloroplast and nucleomorph replication by the cell cycle in the cryptophyte Guillardia theta. Scientific Reports 7: 2345.


  • Onuma R†, Horiguchi T (2016) Specificity of Chroomonas (Cryptophyceae) as a sourceof kleptochloroplast for Nusuttodinium aeruginosum (Dinophyceae). Phycological Research 64: 35-43.
  • Hagino K, Tomioka N, Young JR, Takano Y, Onuma R, Horiguchi T. (2016). Extracellular calcification of Braarudosphaera bigelowii deduced from electron microscopic observations of cell surface structure and elemental composition of pentaliths. Mar. Micropaleontol. 125: 85-94.


  • Onuma R, Watanabe K, Horiguchi T (2015) Pellucidodinium psammophilum gen. & sp. nov. and Nusuttodinium desymbiontum sp. nov. (Dinophyceae), two novel heterotrophs closely related to kleptochloroplastidic dinoflagellates. Phycologia 54: 192-209.
  • Onuma R, Horiguchi T (2015) Kleptochloroplast enlargement, karyoklepty and the distribution of the cryptomonad nucleus in Nusuttodinium (= Gymnodinium) aeruginosum (Dinophyceae). Protist 166: 177-195.
  • Gómez F, Onuma R, Artigas LF, Horiguchi T. (2015). A new definition of Adenoides eludens, an unusual marine sand-dwelling dinoflagellate without cingulum, and Pseudadenoides kofoidii gen. & comb. nov. for the species formerly known as Adenoides eludens. European Journal of Phycology 50: 125-138.


  • Watanabe K, Miyoshi Y, Kubo F, Onuma R, Murray S, Horiguchi T. (2014). Ankistrodinium armigerum sp. nov.(Dinophyceae), a new species of heterotrophic marine sand‐dwelling dinoflagellate from Japan and Australia. Phycological research 62: 125-135.


  • Onuma R, Horiguchi T. (2013) Morphological transition in kleptochloroplasts after ingestion in the dinoflagellates Amphidinium poecilochroum and Gymnodinium aeruginosum (Dinophyceae). Protist 164: 622–642.
  • Hagino K, Onuma R, Kawachi M, Horiguchi T. (2013). Discovery of an endosymbiotic nitrogen-fixing cyanobacterium UCYN-A in Braarudosphaera bigelowii (Prymnesiophyceae). PloS one 8: e81749.