Publications in 2015-2019

Yazaki E†, Kume K, Shiratori T, Eglit Y, Tanifuji G, Harada R, Simpson AGB, Ishida K, Hashimoto T, Inagaki Y†. Barthelonids represent a deep-branching Matamonad clade with mitochondrion-related organelles generating no ATP. 2019  bioRχiv website (doi: 10.1101/805762v1)  The updated version of this work was published in Proc Roy Soc B in 2020.

Matsuo M, Katahara A, Tachikawa M, Minakuchi Y, Noguchi H, Toyoda A, Fujiyama A, Suzuki Y, Hata T, Satoh S, Nakayama T, Kamikawa R, Nomura M, Inagaki Y, Ishida K, Obokata J†. Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote. 2019  bioRχiv website (doi: 10.1101/809541)

Sarai C*, Tanifuji G*†, Nakayama T*, Kamikawa R*, Takahashi K, Miyashita H, Ishida K, Iwataki M†, Inagaki Y†. Dinoflagellates with relic endosymbiont nuclei as novel models for elucidating organellogenesis. 2019 bioRχiv website  (doi: 10.1101/702274)  The updated version of this work was published in Proc Nat Acad Sci USA in 2020.

Nakayama T†, Nomura M, Takano Y, Tanifuji G, Shiba K, Inaba K, Inagaki Y, Kawata M. Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host. 2019 Proceedings of the National Academy of Sciences of the United States of America 116(32):15973-15978. pubmed. (doi: 10.1073/pnas.1902538116) プレスリリース. A commentary on our PNAS paper. Picked up by The Scientist as "Image of the Day".

Sakamoto K, Kayanuma M†, Inagaki Y, Hashimoto T, Shigeta Y†. In silico structural modeling and analysis of elongation factor-1alpha and elongation factor-like protein. 2019 ACS Omega 4(4):7308-7316. website (doi: 10.1021/acsomega.8b03547)

Nishimura Y†, Shiratori T, Ishida K, Hashimoto T, Ohkuma M, Inagaki Y. Horizontally-acquired genetic elements in the mitochondrial genome of a centrohelid Marophyris sp. SRT127. 2019 Scientific Reports 9:4850. pubmed. (doi: 10.1038/s41598-019-41238-6)

Kamikawa R*,†, Yazaki E*, Tahara M, Sakura T, Matsuo E, Nagamune K, Hashimoto T, Inagaki Y†. Fates of evolutionarily distinct, plastid-type glyceraldehyde 3-phosphate dehydrogenase genes in kareniacean dinoflagellates. 2018 Journal of Eukaryotic Microbiology 65(5):669-678. pubmed.  (doi: https://dx.doi.org/10.1111/jeu.12512)

Matsuo E, Inagaki Y†. Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates. 2018 PeerJ 6:e5345. pubmed. (doi: https://doi.org/10.7717/peerj.5345)  Preprint version is available at https://doi.org/10.7287/peerj.preprints.3488v2

Matsuo M, Katahata A, Satoh S, Matsuzaki M, Nomura M, Ishida K, Inagaki Y, Obokata J†. Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer. 2018 PLOS One 13(7):e0200961. pubmed. (doi: https://doi.org/10.1371/journal.pone.0200961)

Tanifuji G, Takabayashi S, Kume K, Takagi M, Nakayama T, Kamikawa R, Inagaki Y, Hashimoto T†. The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites. 2018 PLOS One 13(3): e0194487. pubmed. (doi: http://doi.org/10.1371/journal.pone.0194487)

Záhonová K, Petrželková R, Valach M, Yazaki E, Tikhonenkov DV, Butenko A, Janouškovec J, Hrdá Š, Klimeš V, Burger G, Inagaki Y, Keeling PJ, Hampl V, Flegontov P, Yurchenko V, Eliáš M†. Extensive molecular tinkering in the evolution of the membrane attachment mechanisms of the Rheb GTPase. 2018 Scientific Reports 8:5239. pubmed (doi:10.1038/s41598-018-23575-0)

Brown MB, Heiss A, Kamikawa R, Inagaki Y, Yabuki A, Tice AK, Shiratori T, Ishida K, Hashimoto T, Simpson AGB†, Roger AJ†. Phylogenomics places orphan protistan lineages in a novel candidate super-group. 2018 Genome Biology and Evolution 10(2):427-433. pubmed. (doi: 10.1093/gbe/evy014)

Nakayama T†, Inagaki Y. Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms. 2017 Scientific Reports 7:13075. pubmed. (doi: 10.1038/s41598-017-13578-8)

Tanifuji G, Curtis BA,Cenci U, David V, Dean S, Fiala I, Flegontov P, Johnson-MacKinnon J, Kelly S, McPhee M, Moog D, Nakayama T, Tanifuji-Onodera N, Sibbald S, Inagaki Y, Hashimoto T, Gull K, Lukeš J, Archibald JM†. Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis. 2017 Scientific Reports 7:111688. pubmed. (doi: 10.1038/s41598-017-11866-x)

Kamikawa R†, Moog D, Zauner S, Tanifuji G, Ishida K, Miyashita H, Mayama S, Hashimoto T, Maier UG, Archibald JA, Inagaki Y. A non-photosynthetic diatom reveals early steps of reductive evolution in plastids. 2017 Molecular Biology and Evolution 34(9):2355-2366. pubmed. (doi: 10.1093/molbev/msx172)

Leger MM*, Kolisko M*, Kamikawa R*, Stairs CW, Kume K, Čepička I, Silberman JD, Andersson JO, Xu F, Yabuki A, Takishita K, Inagaki Y, Simpson AGB, Hashimoto T†, Roger AJ†. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. 2017 Nature Ecology & Evolution 1(4):0092. pubmed. *Equally contributed. (doi :10.1038/s41559-017-0092)

Yazaki Y, Ishikawa SA†, Kume K, Kumagai A, Kamaishi T, Tanifuji G, Hashimoto T, Inagaki Y†. Global Kinetoplastea phylogeny inferred from a large-scale multigene alignment including parasitic species for better understanding transitions from a free-living to a parasitic lifestyle. 2017 Genes & Genetic Systems 92(1):35-42. pubmed. (doi:10.1266/ggs.16-00056)

Nishimura Y, Tanifuji G, Kamikawa R, Yabuki A, Hashimoto T, Inagaki Y†. Mitochondrial genome of Palpitomonas bilix: Derived genome structure and ancestral system for cytochrome c maturation. 2016 Genome Biology and Evolution 8(10):3090-3098. pubmed (doi: 10.1093/gbe/evw217)

稲垣祐司，中山卓郎． 第17章 現在も続く細胞内共生細菌のオルガネラ化．2016 共生微生物（化学同人）大野博司編 p190-201. ISBN 9784759817287

Nishimura Y†, Amagasa T, Inagaki Y, Hashimoto T, Kitagawa H. A system for supporting phylogenetic analyses over alignments of next generation sequence data. 2016 Proceedings for the 10th International Conference on Complex, Intelligent, and Software Intensive Systems (CISIS-2016) 230-237. IEEE Xplore (doi: 10.1109/CISIS.2016.51)

Templeton T, Asada M, Jiratanh M, Ishikawa SA, Tiawsirisup S, Sivakumar T, Namangala B, Takeda M, Mohkaew K†, Ngamjituea S, Inoue N, Sugimoto C, Inagaki Y, Suzuki Y, Yokoyama N, Kaewthamasorn M†, Kaneko O†. Ungulate malaria parasites. 2016 Scientific Reports 6:23230. pubmed  (doi:10.1038/srep23230)

Harada R, Inagaki Y, Shigeta Y†. Protein folding and evolution. 2016 Reference Module in Materials Science and Materials Engineering.  website  (doi: 10.1016/B978-0-12-803581-8.09800-3)

中山卓郎，稲垣祐司． シアノバクテリアと真核藻類の細胞統合―「窒素固定オルガネラ」へ続く道？ 2016 生物の科学 遺伝 ［特集：真核細胞の共生由来オルガネラ研究最前線―広がり続ける多様性と機能］ 70(2):176-180.

稲垣祐司． 共生体由来オルガネラにまつわるエトセトラ．2016 生物の科学 遺伝 ［特集：真核細胞の共生由来オルガネラ研究最前線―広がり続ける多様性と機能］ 70(2):156-160.

Noguchi F, Shimamura S, Nakayama T, Yazaki Y, Yabuki A, Hashimoto T, Inagaki Y, Fujikura K, Takishita K†. Metabolic capacity of mitochondrion-related organelles in the free-living anaerobic stramenopile Cantina marsupialis. 2015 Protist 166(5):534-550. pubmed (doi: 10.1016/j.protis.2015.08.002)

Kamikawa R†, Tanifuji G, Ishikawa SA, Onodera NT, Ishida K, Hashimoto T, Miyashita H, Mayama S, Inagaki Y. Proposal of a Twin-arginine translocator system-mediated constraint against loss of ATP synthase genes from nonphotosynthetic plastid genomes. 2015 Molecular Biology and Evolution 32(10):2598-2604. pubmed  (doi: 10.1093/molbev/msv134)

Ishikawa SA, Kamikawa R, Inagaki Y†. Multiple conversion between the genes encoding bacterial class-I release factors. 2015 Scientific Reports 5:12406. pubmed  (doi: 10.1038/srep12406)

Takeuchi F†, Sekizuka T, Ogasawara Y, Yokoyama H, Kamikawa R, Inagaki Y, Nozaki T, Sugita-Konish Y, Ohnishi T, Kuroda M. The mitochondria genomes of Kudoa species are extremely diverged among Metazoa. 2015 PLOS ONE 10(7):e30132030. pubmed  (doi: 10.01371/journal.pone.0132030)

Yubuki N†, Pánek T, Yabuki A, Čepička I, Takishita K, Inagaki Y, Leander BS. Morphological identities of two different marine stramenopile environmental sequence clades: Bicosoeca kenaiensis (Hilliard 1971) and Cantina marsupialis (Larson and Patterson, 1990) gen. nov., comb. nov. 2015 Journal of Eukaryotic Microbiology 62(4): 532-542. pubmed (doi: 10.1111/jeu.12207) 

Kamikawa R†, Tanifuji G, Kawachi M, Miyashita H, Hashimoto T, Inagaki Y. Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum. 2015 Genome Biology and Evolution 7(4): 1133-1140. pubmed  (doi: 10.1093/gbe/ew060)

Kamikawa R†, Yubuki N, Yoshida M, Taira M, Ishida K, Leander BS, Miyashita H, Hashimoto T, Mayama S, Inagaki Y. Multiple losses of photosynthesis in Nitzschia (Bachillariophyceae). 2015 Phycological Research 63(1):19-28. abstract  (doi: 10.1111/pre.12072)