Shinichiro Maruyama

Summary

Affiliation: Dalhousie University
Country: Canada

Publications

  1. pmc Treetrimmer: a method for phylogenetic dataset size reduction
    Shinichiro Maruyama
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
    BMC Res Notes 6:145. 2013
  2. pmc Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo, Japan
    BMC Evol Biol 11:105. 2011
  3. doi request reprint Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes
    Hisayoshi Nozaki
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Mol Phylogenet Evol 53:872-80. 2009
  4. pmc A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae
    Hisayoshi Nozaki
    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
    BMC Biol 5:28. 2007
  5. pmc Cyanobacterial contribution to the genomes of the plastid-lacking protists
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113 0033, Japan
    BMC Evol Biol 9:197. 2009
  6. ncbi request reprint The minimal eukaryotic ribosomal DNA units in the primitive red alga Cyanidioschyzon merolae
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo, Tokyo 113 0033, Japan
    DNA Res 11:83-91. 2004
  7. pmc Origins of a cyanobacterial 6-phosphogluconate dehydrogenase in plastid-lacking eukaryotes
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo, Tokyo 113 0033, Japan
    BMC Evol Biol 8:151. 2008
  8. pmc Centromere structures highlighted by the 100%-complete Cyanidioschyzon merolae genome
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo, Japan
    Plant Signal Behav 3:140-1. 2008
  9. pmc A case study for effects of operational taxonomic units from intracellular endoparasites and ciliates on the eukaryotic phylogeny: phylogenetic position of the haptophyta in analyses of multiple slowly evolving genes
    Hisayoshi Nozaki
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
    PLoS ONE 7:e50827. 2012
  10. doi request reprint Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo, Tokyo 113 0033, Japan
    Mol Biol Evol 27:1070-6. 2010

Detail Information

Publications14

  1. pmc Treetrimmer: a method for phylogenetic dataset size reduction
    Shinichiro Maruyama
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
    BMC Res Notes 6:145. 2013
    ..There is a need for bioinformatic tools with which to objectively carry out such pruning procedures...
  2. pmc Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo, Japan
    BMC Evol Biol 11:105. 2011
    ..However, the impact of endosymbiosis on the euglenophyte nuclear genome is not fully understood due to its complex nature as a 'hybrid' of a non-photosynthetic host cell and a secondary endosymbiont...
  3. doi request reprint Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes
    Hisayoshi Nozaki
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Mol Phylogenet Evol 53:872-80. 2009
    ..The close relationship between green plants and Chromalveolata is further supported by the common replacement in two plastid-targeted genes...
  4. pmc A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae
    Hisayoshi Nozaki
    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
    BMC Biol 5:28. 2007
    ..Therefore, we aimed to complete all previous gaps and sequence all remaining chromosomal ends, and now report the first nuclear-genome sequence for any eukaryote that is 100% complete...
  5. pmc Cyanobacterial contribution to the genomes of the plastid-lacking protists
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113 0033, Japan
    BMC Evol Biol 9:197. 2009
    ..Although recent genomic surveys demonstrated the presence of cyanobacterial and algal ancestry genes in the genomes of plastid-lacking protists, comparative analyses on the origin and distribution of those genes are still limited...
  6. ncbi request reprint The minimal eukaryotic ribosomal DNA units in the primitive red alga Cyanidioschyzon merolae
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo, Tokyo 113 0033, Japan
    DNA Res 11:83-91. 2004
    ..They consist of only 3 single units of rRNA genes distributed on separate chromosomal loci, representing an implication for concerted evolution. Based on these results, the origin and evolution of the nucleolus are discussed...
  7. pmc Origins of a cyanobacterial 6-phosphogluconate dehydrogenase in plastid-lacking eukaryotes
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo, Tokyo 113 0033, Japan
    BMC Evol Biol 8:151. 2008
    ....
  8. pmc Centromere structures highlighted by the 100%-complete Cyanidioschyzon merolae genome
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo, Japan
    Plant Signal Behav 3:140-1. 2008
    ..No centromere-like A+T-rich repetitive sequence have been found within these regions, implying that the C. merolae centromeres may be 'point' centromeres, or be comprised of nonrepetitive heterogeneous DNA sequences...
  9. pmc A case study for effects of operational taxonomic units from intracellular endoparasites and ciliates on the eukaryotic phylogeny: phylogenetic position of the haptophyta in analyses of multiple slowly evolving genes
    Hisayoshi Nozaki
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
    PLoS ONE 7:e50827. 2012
    ....
  10. doi request reprint Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo, Tokyo 113 0033, Japan
    Mol Biol Evol 27:1070-6. 2010
    ..Taken together, our data demonstrate that permuted tRNA is an evolutionarily conserved and fundamental element in tiny eukaryotic genomes...
  11. ncbi request reprint Centromere dynamics in the primitive red alga Cyanidioschyzon merolae
    Shinichiro Maruyama
    Institute of Molecular and Cellular Biosciences, University of Tokyo, 1 1 1 Yayoi, Bunkyo, Tokyo 113 0032, Japan
    Plant J 49:1122-9. 2007
    ..These results demonstrate dynamic centromere reconstitution during the cell cycle in an organism in which the chromosomes do not condense at metaphase...
  12. ncbi request reprint Sequence and intranuclear location of the extrachromosomal rDNA plasmid of the amoebo-flagellate Naegleria gruberi
    Shinichiro Maruyama
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo, Tokyo 113 0033, Japan
    J Eukaryot Microbiol 54:333-7. 2007
    ..The N. gruberi rDNA plasmid has a unique high-order cluster structure that provides both a molecular basis for understanding chromosomal organization in basal eukaryotes, and a vehicle for constructing stable transgenic vectors...
  13. pmc An extended phylogenetic analysis reveals ancient origin of "non-green" phosphoribulokinase genes from two lineages of "green" secondary photosynthetic eukaryotes: Euglenophyta and Chlorarachniophyta
    Yi Yang
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo, Tokyo 113 0033, Japan
    BMC Res Notes 4:330. 2011
    ..abstract:..
  14. ncbi request reprint Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D
    Motomichi Matsuzaki
    Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nature 428:653-7. 2004
    ..These results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells...