Publications in 2005-2009

Burki F, Inagaki Y, Bråte J, Archibald JM, Keeling PJ, Cavalier-Smith T, Sakaguchi M, Hashimoto T, Horak A, Kumar S, Klaveness D, Jakobsen K, Pawlowski J†, Shalchian-Tabrizi K†. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. 2009 Genome Biology and Evolution 1(1):231-238. pubmed

Kamikawa R†, Sanchez-Perez GF, Sako Y, Roger AJ, Inagaki Y. Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes. 2009 Molecular Phylogenetics and Evolution 53(2):565-570. pubmed

Inagaki Y†, Nakajima Y, Sato M, Sakaguchi M, Hashimoto T. Gene sampling can bias multi-gene phylogenetic inferences: the relationship between red algae and green plants as the case study. 2009 Molecular Biology and Evolution 26(5):1171-1178. pubmed

Takishita K†, Yamaguchi H, Maruyama T, Inagaki Y. A hypothesis for the evolution of nuclear-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase genes in "chromalveolate" members. 2009 PLoS One 4(3):e4737. pubmed.

Sakaguchi M†, Takishita K, Matsumoto T, Hashimoto T, Inagaki Y. Tracing back the EFL evolution in the cryptomonads-haptophytes assemblage: Separate origins of EFL genes in haptophytes, photosynthetic cryptomonads, and goniomonads. 2009 Gene 441(1-2): 126-131. 【Published on-line on Jun. 26, 2008】 pubmed

Takishita K, Inagaki Y†. Eukaryotic origin of glyceraldehydes-3-phosphate dehydrogenase genes in Clostridium thermocellum and Clostridium cellulolyticum genomes and putative fates of the exogenous gene in the subsequent genome evolution. 2009 Gene 441(1-2): 22-27.  【Published on-line on Jun. 26, 2008】 pubmed

Kamikawa R, Inagaki Y†, Sako Y. Direct phylogenetic evidence for lateral transfer of elongation factor-like gene. 2008 Proceedings of the National Academy of Sciences of the United States of America 105(19):6965-6969. pubmed 関連新聞記事

Ohama T, Inagaki Y, Bessho Y, Osawa S†. Evolving genetic code. 2008 Proceeding of the Japan Academy Series B 84(2):58-74. pubmed

Takishita K, Kawachi M, Noël, M-H, Matsumoto T, Kakizoe N, Watanabe MM, Inouye I, Ishida K, Hashimoto T, Inagaki Y†. Origins of plastids and glyceraldehydes-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum. 2008 Gene 410(1): 26-36. pubmed

橋本哲男†, 有末伸子, 坂口美亜子, 稲垣祐司. 複数遺伝子の連結データに基づく分子系統樹の推定 — 真核生物の大系統の解析を例として 2008 統計数理 56:145-164. PDF Abstract 

Patron NJ, Inagaki Y, Keeling PJ†. Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. 2007 Current Biology 17(10):887-891. pubmed

Sakaguchi M†, Inagaki Y, Hashimoto T. Centrohelida is still searching for a phylogenetic home: analyses of seven Raphidiophrys contractilis genes. 2007 Gene 405(1-2):47-54. pubmed

Iida K, Takishita K. Ohshima K, Inagaki Y†. Assessing the monophyly of chlorophyll-c containing plastids by multi-gene phylogenies under the unlinked model conditions. 2007 Molecular Phylogenetics and Evolution 45(1):227-238. pubmed

Takishita K†, Yubuki N, Kakizoe N, Inagaki Y, Maruyama T. Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures. 2007 Extremophiles 11(4):563-576. pubmed

Kamikawa R†*, Inagaki Y*, Sako Y. Fragmentation of mitochondrial large subuint rRNA in a dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondria. 2007 Protist 58(2):239-245. 【*Joint 1st authors】. pubmed

Yubuki N, Inagaki Y, Nakayama T, Inouye I†. Ultrastructure and ribosomal RNA phylogeny of the free-living heterotrophic flagellate Dysnectes brevis n. gen., n. sp., a new member of the Fornicata. 2007 Journal of Eukaryotic Microbiology 54(2):191-200. pubmed

Hosoi-Tanabe S†, Honda D, Fukaya S, Inagaki Y, Sako Y. Proposal of Pseudochattonella verruculosa gen. nov., comb. nov. (Dictyochophyceae) for a former raphidophycean alga Chattonella verruculosa, based on 18S rDNA phylogeny and ultrastructural characteristics. 2007 Phycological Research 55(3):185-192. Abstract

稲垣祐司. ロングブランチの誘惑 — 分子系統解析のダークサイド 2007 Japanese Journal of Phycology （藻類） 55:111-116. （日本語総説・査読なし）

Nambu T*, Inagaki Y*, Kutsukake K†. Plasticity of the domain structure in FlgJ, a bacterial protein involved in flagellar rod formation. 2006 Genes & Genetic Systems 81(6):381-389. 【*Joint 1st authors】. PDF pubmed

Inagaki Y†, Roger AJ. Phylogenetic estimation under codon models can be biased by codon usage heterogeneity. 2006 Molecular Phylogenetics and Evolution 40(2): 428-434. pubmed

Inagaki Y, Susko E, Roger AJ†. Recombination between elongation factor 1α genes from distantly related archaeal lineages. 2006 Proceedings of the National Academy of Sciences of the United States of America 103(12):4528-4533. pubmed Faculty-of-1000 Biol.

Simpson AGB†, Inagaki Y, Roger AJ. Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of “primitive” eukaryotes. 2006 Molecular Biology and Evolution 23(3): 614-625. pubmed

Simpson AGB†, Inagaki Y, Roger AJ. The evolutionary relatoinships amongst excavates: a concatenated protein analysis. 2005 Journal of Eukaryotic Microbiology 52:7S-27S.

Takishita K†*, Inagaki Y*, Tsuchiya M, Sakaguchi M, Maruyama T. A close relationship between Cercozoa and Foraminifera supported by phylogenetic analyses based on combined amino acid sequences of three cytoskeletal proteins (actin, α-tubulin, and β-tubulin). 2005 Gene 362(1):153-160. 【*Joint 1st authors】 pubmed