Yuji Inagaki

Summary

Affiliation: University of Tsukuba
Country: Japan

Publications

  1. ncbi request reprint Phylogenetic estimation under codon models can be biased by codon usage heterogeneity
    Yuji Inagaki
    Center for Computational Sciences, Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki 305 8577, Japan
    Mol Phylogenet Evol 40:428-34. 2006
  2. ncbi request reprint Centrohelida is still searching for a phylogenetic home: analyses of seven Raphidiophrys contractilis genes
    Miako Sakaguchi
    Institute of Biological Sciences, University of Tsukuba, Tsukuba 305 8572, Japan
    Gene 405:47-54. 2007
  3. pmc Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes
    Ryoma Kamikawa
    Graduate School of Global Environmental Studies, Kyoto University, Kyoto 606 8501, Japan
    BMC Evol Biol 13:131. 2013
  4. pmc A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum
    Marianne A Minge
    Centre for Ecological and Evolutionary Synthesis CEES, Department of Biology, University of Oslo, N 0316 Oslo, Norway
    BMC Evol Biol 10:191. 2010
  5. doi request reprint Gene sampling can bias multi-gene phylogenetic inferences: the relationship between red algae and green plants as a case study
    Yuji Inagaki
    Center for Computational Sciences, Tsukuba, Ibaraki, Japan
    Mol Biol Evol 26:1171-8. 2009
  6. doi request reprint Rooting for the root of elongation factor-like protein phylogeny
    Ryoma Kamikawa
    Center for Computational Sciences, University of Tsukuba, 1 1 1 Tennoudai, Tsukuba, 305 8577 Ibaraki, Japan
    Mol Phylogenet Evol 56:1082-8. 2010
  7. doi request reprint Tsukubamonas globosa n. gen., n. sp., a novel excavate flagellate possibly holding a key for the early evolution in "Discoba"
    Akinori Yabuki
    Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305 8572, Japan
    J Eukaryot Microbiol 58:319-31. 2011
  8. doi request reprint Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes
    Ryoma Kamikawa
    Center of Computational Sciences and Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
    Mol Phylogenet Evol 53:565-70. 2009
  9. doi request reprint Green-colored plastids in the dinoflagellate genus Lepidodinium are of core chlorophyte origin
    Takuya Matsumoto
    Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305 8572, Japan
    Protist 162:268-76. 2011
  10. doi request reprint Cercozoa comprises both EF-1α-containing and EFL-containing members
    Ryoma Kamikawa
    Center for Computational Sciences and Institute of Biological Sciences, University of Tsukuba, 1 1 1 Tennoudai, Tsukuba, Ibaraki 305 8577, Japan
    Eur J Protistol 47:24-8. 2011

Collaborators

Detail Information

Publications39

  1. ncbi request reprint Phylogenetic estimation under codon models can be biased by codon usage heterogeneity
    Yuji Inagaki
    Center for Computational Sciences, Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki 305 8577, Japan
    Mol Phylogenet Evol 40:428-34. 2006
    ..We advise that homogeneity in codon usage across taxa in a data set be confirmed before codon model-based phylogenetic estimation is attempted...
  2. ncbi request reprint Centrohelida is still searching for a phylogenetic home: analyses of seven Raphidiophrys contractilis genes
    Miako Sakaguchi
    Institute of Biological Sciences, University of Tsukuba, Tsukuba 305 8572, Japan
    Gene 405:47-54. 2007
    ..We concluded that larger scale multi-gene phylogenies are necessary to elucidate the origin and evolution of Centrohelida...
  3. pmc Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes
    Ryoma Kamikawa
    Graduate School of Global Environmental Studies, Kyoto University, Kyoto 606 8501, Japan
    BMC Evol Biol 13:131. 2013
    ..To date, however, just one diatom and one fungus have been found to have both EF-1α and EFL (dual-EF-containing species)...
  4. pmc A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum
    Marianne A Minge
    Centre for Ecological and Evolutionary Synthesis CEES, Department of Biology, University of Oslo, N 0316 Oslo, Norway
    BMC Evol Biol 10:191. 2010
    ....
  5. doi request reprint Gene sampling can bias multi-gene phylogenetic inferences: the relationship between red algae and green plants as a case study
    Yuji Inagaki
    Center for Computational Sciences, Tsukuba, Ibaraki, Japan
    Mol Biol Evol 26:1171-8. 2009
    ..We also address the validity of fast-evolving gene exclusion in multi-gene phylogenetic analyses, in light of this gene sampling bias...
  6. doi request reprint Rooting for the root of elongation factor-like protein phylogeny
    Ryoma Kamikawa
    Center for Computational Sciences, University of Tsukuba, 1 1 1 Tennoudai, Tsukuba, 305 8577 Ibaraki, Japan
    Mol Phylogenet Evol 56:1082-8. 2010
    ..Finally, the relative timing of the first emergence of EFL gene in eukaryotes was contemplated based on the current EF-1alpha/EFL distribution...
  7. doi request reprint Tsukubamonas globosa n. gen., n. sp., a novel excavate flagellate possibly holding a key for the early evolution in "Discoba"
    Akinori Yabuki
    Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305 8572, Japan
    J Eukaryot Microbiol 58:319-31. 2011
    ..globosa possessed a novel set of morphological features, and could not be classified into any taxa in the Discoba clade. Instead we classified T. globosa into Tsukubamonadidae n. fam. under Tsukubamonadida n. ord...
  8. doi request reprint Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes
    Ryoma Kamikawa
    Center of Computational Sciences and Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
    Mol Phylogenet Evol 53:565-70. 2009
    ..Various scenarios of MAT and MATX gene family evolution in diatoms are re-evaluated in light of the new data...
  9. doi request reprint Green-colored plastids in the dinoflagellate genus Lepidodinium are of core chlorophyte origin
    Takuya Matsumoto
    Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305 8572, Japan
    Protist 162:268-76. 2011
    ..All the analyses of the 11-protein data set robustly grouped L. chlorophorumwith members of the "core chlorophytes." Thus, we here propose that Lepidodiniumplastids are of core chlorophyte origin...
  10. doi request reprint Cercozoa comprises both EF-1α-containing and EFL-containing members
    Ryoma Kamikawa
    Center for Computational Sciences and Institute of Biological Sciences, University of Tsukuba, 1 1 1 Tennoudai, Tsukuba, Ibaraki 305 8577, Japan
    Eur J Protistol 47:24-8. 2011
    ..Based on the results, we postulate that cercozoan EF-1α genes have been vertically inherited, and the current EFL-containing species may have secondarily lost their EF-1α genes...
  11. doi request reprint Prasinoxanthin is absent in the green-colored dinoflagellate Lepidodinium chlorophorum strain NIES-1868: pigment composition and 18S rRNA phylogeny
    Takuya Matsumoto
    Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305 8572, Japan
    J Plant Res 125:705-11. 2012
    ....
  12. doi request reprint Tracing back EFL gene evolution in the cryptomonads-haptophytes assemblage: separate origins of EFL genes in haptophytes, photosynthetic cryptomonads, and goniomonads
    Miako Sakaguchi
    Institute of Biological Sciences, University of Tsukuba, Tsukuba 305 8572, Japan
    Gene 441:126-31. 2009
    ....
  13. doi request reprint A deviant genetic code in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum
    Takuya Matsumoto
    Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305 8572, Japan
    Mol Phylogenet Evol 60:68-72. 2011
    ..chlorophorum plastid and the green algal plastids considered in this study. Finally, the possible evolutionary events required for the reassignment of AUA from Ile to Met in Lepitodinium plastids were discussed...
  14. pmc Separate origins of group I introns in two mitochondrial genes of the katablepharid Leucocryptos marina
    Yuki Nishimura
    Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
    PLoS ONE 7:e37307. 2012
    ....
  15. doi request reprint Spheroid bodies in rhopalodiacean diatoms were derived from a single endosymbiotic cyanobacterium
    Takuro Nakayama
    Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305 8577, Japan
    J Plant Res 124:93-7. 2011
    ..sorex, and Rhopalodia gibba. Phylogenetic analyses considering these new sequences clearly indicate that the SBs were acquired by a common ancestor of rhopalodiacean diatoms and have been retained during host speciation...
  16. doi request reprint Split introns in the genome of Giardia intestinalis are excised by spliceosome-mediated trans-splicing
    Ryoma Kamikawa
    Center for Computational Sciences and Institute of Biological Sciences, University of Tsukuba, Ibaraki 305 8577, Japan
    Curr Biol 21:311-5. 2011
    ..These split introns have properties that distinguish them from other trans-splicing systems known within eukaryotes, suggesting that Giardia independently evolved a unique system to splice split introns...
  17. pmc RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity
    Sohta A Ishikawa
    Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305 8572, Japan
    Evol Bioinform Online 8:357-71. 2012
    ..The performance of a non-homogeneous analysis was also validated by analyzing a real-world sequence data set with significant base heterogeneity...
  18. ncbi request reprint Ultrastructure and ribosomal RNA phylogeny of the free-living heterotrophic flagellate Dysnectes brevis n. gen., n. sp., a new member of the Fornicata
    Naoji Yubuki
    Graduate School of Life and Environmental Sciences, University of Tsukuba, 1 1 1 Tennodai, Tsukuba, Ibaraki 305 8572, Japan
    J Eukaryot Microbiol 54:191-200. 2007
    ..Combining both morphological and molecular phylogenetic analyses, D. brevis is classified as a new free-living excavate in the Fornicata incertae sedis...
  19. doi request reprint Palpitomonas bilix gen. et sp. nov.: A novel deep-branching heterotroph possibly related to Archaeplastida or Hacrobia
    Akinori Yabuki
    Graduate School of Life and Environmental Sciences, University of Tsukuba, 1 1 1 Tennoudai, Tsukuba, Ibaraki 305 8572, Japan
    Protist 161:523-38. 2010
    ..On the basis of the results of both morphological and molecular studies, we discuss the possibility that P. bilix might provide key information on the early evolution of major groups of photosynthetic eukaryotes...
  20. doi request reprint Phylogeny of Asian primate malaria parasites inferred from apicoplast genome-encoded genes with special emphasis on the positions of Plasmodium vivax and P. fragile
    Hideya Mitsui
    Institute of Biological Sciences, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305 8572, Japan
    Gene 450:32-8. 2010
    ..The present analyses place P. fragile in a position that is incongruent with the early branching status of P. fragile amongst P-vivax-related primate Plasmodium species propose by Escalante et al. (Proc Natl Acad Sci USA 2005 102: 1980)...
  21. pmc Recombination between elongation factor 1alpha genes from distantly related archaeal lineages
    Yuji Inagaki
    Center for Computational Sciences and Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki 305 8577, Japan
    Proc Natl Acad Sci U S A 103:4528-33. 2006
    ..Although difficult to detect by standard whole-gene phylogenetic analyses, interspecific HR in highly conserved genes may occur at an appreciable frequency, potentially confounding deep phylogenetic inference and hypothesis testing...
  22. ncbi request reprint Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes
    Alastair G B Simpson
    Canadian Institute for Advanced Research, Program in Evolutionary Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 23:615-25. 2006
    ....
  23. ncbi request reprint On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled
    Edward Susko
    Genome Atlantic, Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 21:1629-42. 2004
    ..The focus is on distance methods, but previous simulation results suggest that the zones of inconsistency for distance methods contain the zones of inconsistency for maximum likelihood methods as well...
  24. ncbi request reprint Capsaspora owczarzaki is an independent opisthokont lineage
    Inaki Ruiz-Trillo
    Curr Biol 14:R946-7. 2004
  25. pmc Evolving genetic code
    Takeshi Ohama
    Kochi University of Technology, Department of Environmental System Engineering, Kochi, Japan
    Proc Jpn Acad Ser B Phys Biol Sci 84:58-74. 2008
    ..Supporting evidence for the theory is presented in this review. A possible evolutionary process from the ancient to the present-day genetic code is also discussed...
  26. ncbi request reprint Lateral transfer of an EF-1alpha gene: origin and evolution of the large subunit of ATP sulfurylase in eubacteria
    Yuji Inagaki
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Curr Biol 12:772-6. 2002
    ..To our knowledge, this is the first unequivocal case of LGT followed by functional modification to be described; this mechanism could be a potentially important force in establishing genes with novel functions in genomes...
  27. ncbi request reprint Testing for differences in rates-across-sites distributions in phylogenetic subtrees
    Edward Susko
    Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 19:1514-23. 2002
    ..Such methods will be helpful in studying the phylogenetic, structural, and functional bases of changes in evolutionary rates at sites, a phenomenon that has important consequences for deep phylogenetic inference...
  28. pmc Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria
    Yuji Inagaki
    Program in Evolutionary Biology, Canadian Institute for Advanced Research and Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
    Nucleic Acids Res 31:4227-37. 2003
    ..We re-assess the available genetic data for HBS1 in light of our analyses, and propose that this protein may function in stop codon-independent peptide release...
  29. ncbi request reprint Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies
    Yuji Inagaki
    Program in Evolutionary Biology, Canadian Institute for Advanced Research and Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 21:1340-9. 2004
    ....
  30. ncbi request reprint Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study
    Yuji Inagaki
    Department of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, Japan
    Syst Biol 53:582-93. 2004
    ..We suggest that codon usage heterogeneity could be a more general problem for DNA level analyses of protein-coding genes, even when third codon positions are excluded...
  31. pmc A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1alpha
    Patrick J Keeling
    Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
    Proc Natl Acad Sci U S A 101:15380-5. 2004
    ..Altogether, it appears that EFL has replaced eEF-1alpha several times independently. This finding could be an indication of an ancient paralogy or, more likely, eukaryote-to-eukaryote lateral gene transfer...
  32. ncbi request reprint A close relationship between Cercozoa and Foraminifera supported by phylogenetic analyses based on combined amino acid sequences of three cytoskeletal proteins (actin, alpha-tubulin, and beta-tubulin)
    Kiyotaka Takishita
    Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Kanagawa 237 0061, Japan
    Gene 362:153-60. 2005
    ..The Foraminifera+Cercozoa affinity recovered in the latter multi-gene analyses is most likely genuine, and thus our data presented here provide further support for the close relationship between these two protist lineages...
  33. ncbi request reprint Plasticity of the domain structure in FlgJ, a bacterial protein involved in flagellar rod formation
    Takayuki Nambu
    Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga 526 0829, Japan
    Genes Genet Syst 81:381-9. 2006
    ....
  34. ncbi request reprint 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
    Kiyotaka Takishita
    Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Kanagawa 237 0061, Japan
    Extremophiles 11:563-76. 2007
    ..Since these phylotypes were not identified in the raw sediment samples, the approach incorporating a cultivation step successfully found at least a fraction of the "hidden" microeukaryotic diversity in the environment examined...
  35. ncbi request reprint Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages
    Nicola J Patron
    Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Curr Biol 17:887-91. 2007
    ..This relationship demonstrates that loss of nucleomorphs must have taken place in haptophytes independently of any other red alga-containing lineages and that the ancestor of both already contained a red algal endosymbiont...
  36. ncbi request reprint Assessing the monophyly of chlorophyll-c containing plastids by multi-gene phylogenies under the unlinked model conditions
    Kei Iida
    Faculty of Bio Science, Nagahama Institute of Bio Science and Technology, 1266 Tamura, Nagahama, Shiga 526 0829, Japan
    Mol Phylogenet Evol 45:227-38. 2007
    ..Thus, future data analyses of larger multi-gene data sets, preferentially under the unlinked model, are required to conclusively understand Chl-c plastid evolution...
  37. doi request reprint Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum
    Kiyotaka Takishita
    Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Kanagawa, Japan
    Gene 410:26-36. 2008
    ..However, in the light of Lepidodinium GAPDH data, we need to closely examine whether the monophyly of the plastids in the above lineages inferred from plastid-targeted GapC genes truly reflects that of the host lineages...
  38. pmc Direct phylogenetic evidence for lateral transfer of elongation factor-like gene
    Ryoma Kamikawa
    Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
    Proc Natl Acad Sci U S A 105:6965-9. 2008
    ..Finally, based on a reverse transcriptase quantitative PCR assay and the genome information of Thalassiosira and Phaeodactylum, we propose the loss of elongation factor function in Thalassiosira EF-1alpha...
  39. pmc Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity
    Yuji Inagaki
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Nucleic Acids Res 30:532-44. 2002
    ..We assess the feasibility of this alternative binding orientation with a triplet stop codon and the eRF1 domain 1 structures using molecular modeling techniques...