Overview of the transcriptome profiles identified in hagfish, shark, and bichir: current issues arising from some nonmodel vertebrate taxa

Authors

  • Masaki Takechi,

    1. Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan
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      Masaki Takechi, Masaki Takeuchi, Kinya G. Ota, and Osamu Nishimura contributed equally to this work.

  • Masaki Takeuchi,

    1. Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan
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      Masaki Takechi, Masaki Takeuchi, Kinya G. Ota, and Osamu Nishimura contributed equally to this work.

  • Kinya G. Ota,

    1. Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan
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      Masaki Takechi, Masaki Takeuchi, Kinya G. Ota, and Osamu Nishimura contributed equally to this work.

  • Osamu Nishimura,

    1. Genome Resource and Analysis Unit, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan
    2. Department of Biophysics and Global COE Program, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
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      Masaki Takechi, Masaki Takeuchi, Kinya G. Ota, and Osamu Nishimura contributed equally to this work.

  • Makoto Mochii,

    1. Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori Akou, Hyogo, Japan
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  • Kazu Itomi,

    1. Genome Resource and Analysis Unit, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan
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  • Noritaka Adachi,

    1. Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan
    2. Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
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  • Maiko Takahashi,

    1. Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan
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  • Satoko Fujimoto,

    1. Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan
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  • Hiroshi Tarui,

    1. Genome Resource and Analysis Unit, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan
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  • Masataka Okabe,

    1. Department of Anatomy, The Jikei University School of Medicine, Minatoku, Tokyo, Japan
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  • Shinichi Aizawa,

    Corresponding author
    1. Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan
    • Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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  • Shigeru Kuratani

    Corresponding author
    1. Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan
    • Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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Abstract

Because of their crucial phylogenetic positions, hagfishes, sharks, and bichirs are recognized as key taxa in our understanding of vertebrate evolution. The expression patterns of the regulatory genes involved in developmental patterning have been analyzed in the context of evolutionary developmental studies. However, in a survey of public sequence databases, we found that the large-scale sequence data for these taxa are still limited. To address this deficit, we used conventional Sanger DNA sequencing and a next-generation sequencing technology based on 454 GS FLX sequencing to obtain expressed sequence tags (ESTs) of the Japanese inshore hagfish (Eptatretus burgeri; 161,482 ESTs), cloudy catshark (Scyliorhinus torazame; 165,819 ESTs), and gray bichir (Polypterus senegalus; 34,336 ESTs). We deposited the ESTs in a newly constructed database, designated the “Vertebrate TimeCapsule.” The ESTs include sequences from genes that can be effectively used in evolutionary developmental studies; for instance, several encode cartilaginous extracellular matrix proteins, which are central to an understanding of the ways in which evolutionary processes affected the skeletal elements, whereas others encode regulatory genes involved in craniofacial development and early embryogenesis. Here, we discuss how hagfishes, sharks, and bichirs contribute to our understanding of vertebrate evolution, we review the current status of the publicly available sequence data for these three taxa, and we introduce our EST projects and newly developed database. J. Exp. Zool. (Mol. Dev. Evol.) 316:526–546, 2011. © 2011 Wiley Periodicals, Inc.

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