Studies of the vertebrate origin

2010 Fiscal Year Final Research Report

• Project/Area Number: 17018018
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Kyoto University
• Principal Investigator: SATOH Noriyuki Kyoto University, マリンゲノミックスユニット, 代表研究者 (30025481)
• Project Period (FY): 2005 – 2010
• Keywords: 動物進化 / 脊椎動物の起源 / 脊索動物の進化 / ゲノム解読 / 比較ゲノム / ナメクジウオ / カタユウレイボヤ / ドメインシャフリング

Research Abstract

Vertebrates are one of the three sub-phyletic groups of the phylum Chordata, together with cephalochordates and urochordates. Previously we decoded the genome of a urochordate, Ciona intestinalis. In the present study we succeeded to decode the genome of a cephalochordate, Brachiostoma floridae. Comparative analyses of the three genomes gave us an insight into the evolutionary scenario of chordates and the origin of vertebrates; namely, cephalochordates are most basal, from which vertebrates evolved rather directly.

Research Products

• [Journal Article] Genomic cis-regulatory networks in the early Ciona intestinalis embryo. (2010)
  • Author(s): Kubo, Y., Suzuki, N., Yuan, X., Nakai, K., Satoh, N., Imai, K.S., Satou, Y.
  • Journal Title: Development 137 Pages: 1613-1623
• [Journal Article] Limited functions of Hox genes in the larval development of the ascidian (2010)
  • Author(s): Ikuta, T., Satoh, N., Saiga, H.
  • Journal Title: Ciona intestinalis. Development 137 Pages: 1505-13
• [Journal Article] Regulation of Notochord-Specific Expression of Ci-Bra Downstream Genes in Ciona intestinalis Embryos. (2010)
  • Author(s): Takahashi, H., Hotta, K., Takagi, C., Ueno, N., Satoh N., Shoguchi, E.
  • Journal Title: Zool.Sci. 27 Pages: 110-118
• [Journal Article] An advanced filter-feeder hypothesis for urochordate evolution. (2009)
  • Author(s): Satoh, N.
  • Journal Title: Zoolog.Sci. 26 Pages: 97-111
• [Journal Article] Domain shuffling and the evolution of vertebrates. (2009)
  • Author(s): Kawashima, T., Kawashima, S., Tanaka, C., Murai, M., Yoneda, M., Putnam, N.H., Rokhsar, D.S., Kanehisa, M., Satoh,N., Wada, H.
  • Journal Title: Genome Res. 19 Pages: 1393-1403
• [Journal Article] Evolution and the origin of the visual retinoid cycle in vertebrates. (2009)
  • Author(s): Kusakabe, T.G., Takimoto, N., Jin, M., Tsuda, M.
  • Journal Title: Phil.Trans.R.Soc.Lond. B364 Pages: 2897-2910
• [Journal Article] Tube formation by complex cellular processes in Ciona intestinalis notochord. (2009)
  • Author(s): Dong, B., Horie, T., Denker, E., Kusakabe, T., Tsuda, M., Smith, W.C., Jiang, D.
  • Journal Title: Dev.Biol. 330 Pages: 237-249
• [Journal Article] Structure of the Amphioxus Nebulin Gene and Evolution of the Nebulin Family Genes. (2009)
  • Author(s): Hanashima, A., Kubokawa, K., Kimura, S.
  • Journal Title: Gene 443 Pages: 76-82
• [Journal Article] A Homolog of the Vertebrate Thyrostimulin Glycoprotein Hormone α Subunit (GPA2) is Expressed in Amphioxus Neurons. (2009)
  • Author(s): Tando, Y., Kubokawa, K.
  • Journal Title: Zool.Sci. 26 Pages: 409-414
• [Journal Article] Transcriptional regulation of the retinoic acid receptor in the dorsal midline epidermis in the Ciona intestinalis embryo. (2009)
  • Author(s): Koyano, R., Ishida, S., Fujiwara, S.
  • Journal Title: Dev.Growth Differ. 51 Pages: 777-786
• [Journal Article] Epidermal expression of Hox1 is directly activated by retinoic acid in the Ciona intestinalis embryo. (2009)
  • Author(s): Kanda, M., Wada, H., Fujiwara, S.
  • Journal Title: Dev.Biol. 335 Pages: 454-463
• [Journal Article] Ambulacrarian prototypical Hox and ParaHox gene complements of the indirect-developing hemichordate Balanoglossus simodensis. (2009)
  • Author(s): Ikuta, T., Miyamoto, N., Saito Y., Wada, H., Satoh, N., Saiga, H.
  • Journal Title: Dev.Genes and Evol. 219 Pages: 383-389
• [Journal Article] Evolutionary roots of blastoporal expression and 'organizer' activity of the vertebrate gastrula organizer gene lhx1 and its ancient metazoan paralog lhx3. (2009)
  • Author(s): Yasuoka, Y., Kobayashi, M., Kurokawa, D., Akasaka, K., Saiga, H., Taira, M.
  • Journal Title: Development 136 Pages: 2005-2014
• [Journal Article] Expression of the Gene for Ancestral Glycoprotein Hormone βSubunit in the Nerve Cord of Amphioxus. (2009)
  • Author(s): Tando, Y., Kubokawa, K.
  • Journal Title: Gen.Comp.Endocrinol. 162 Pages: 329-339
• [Journal Article] Delineating metamorphic pathways in the ascidian Ciona intestinalis. (2009)
  • Author(s): Nakayama-Ishimura, A., Chambon, J., Horie, T., Satoh, N., Sasakura, Y.
  • Journal Title: Dev.Biol. 326 Pages: 357-367
• [Journal Article] An aboral-dorsalization hypothesis for chordate origin. (2008)
  • Author(s): Satoh, N.
  • Journal Title: Genesis 46 Pages: 614-622
• [Journal Article] Pigmented and nonpigmented ocelli in the brain vesicle of the ascidian larva. (2008)
  • Author(s): Horie, T., Sakurai, D., Ohtsuki, H., Terakita, A., Shichida, Y., Usukura, J., Kusakabe, T., Tsuda, M.
  • Journal Title: J.Comp.Neurol. 509 Pages: 88-102
• [Journal Article] RNA interference by expressing short hairpin RNA in the Ciona intestinalis embryo. (2008)
  • Author(s): Nishiyama, A., Fujiwara, S.
  • Journal Title: Dev.Growth Differ. 50 Pages: 521-529
• [Journal Article] Whole-mount observation of pharyngeal and trabecular cartilage development in lampreys. (2008)
  • Author(s): Yao, T., Ohtani, K., Wada, H.
  • Journal Title: Zool.Sci. 25 Pages: 976-981
• [Journal Article] Expression of Sox and fibrillar collagen genes in lamprey larval chondrogenesis with implications for the evolution of vertebrate cartilage. (2008)
  • Author(s): Ohtani, K., Yao, T., Kobayashi, M., Kusakabe, R., Kuratani, S., Wada, H.
  • Journal Title: J.Exp.Zool.Part B Mol.Dev.Evol. 310B Pages: 596-607
• [Journal Article] Evolutionary History of Larval Skeletal Morphology in Sea Urchin Echinometridae (Echinoidea : Echinodermata) as Deduced from Mitochondrial DNA Molecular Phylogeny. (2008)
  • Author(s): Kinjo, S., Shirayama, Y., Wada, H.
  • Journal Title: Evol.Dev. 10 Pages: 632-641
• [Journal Article] Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae. (2008)
  • Author(s): Takatori, N., Butts, T., Candiani, S., Pestarino, M., Ferrier, D.E.K., Saiga, H., Holland, P.W.H.
  • Journal Title: Dev.Genes Evol. 218 Pages: 570-590
• [Journal Article] Evolution of CUT class homeobox genes : insights from the genome of the amphioxus, Branchiostoma floridae. (2008)
  • Author(s): Takatori, N., Saiga, H.
  • Journal Title: Int.J.Cev.Biol. 52 Pages: 969-977
• [Journal Article] The amphioxus genome and the evolution of the chordate karyotype. (2008)
  • Author(s): Putnam, N.H., Butts, T., Ferrier, D.E.K., Furlong, R.F., Hellsten, U., Kawashima, T., Robinson-Rechavi, M., Shoguchi, E., Terry, A., Yu, J.-K.---Satoh, N., Rohksar
  • Journal Title: Nature 453 Pages: 1064-1071
• [Journal Article] Gneome-wide network of regulatory genes for construction of a chordate embryo. (2008)
  • Author(s): Shoguchi, E., Hamaguchi, M., Satoh, N.
  • Journal Title: Dev.Biol. 316 Pages: 498-509
• [Journal Article] The Amphioxus genome illuminates vertebrate origins and cephalovhordate biology. (2008)
  • Author(s): Holland, L.Z., Albalat, R., Azumi, K., Benito-Gutierrez, E., Blow, M.J., Bronner-Fraser, M., Bruner, F., Butts, T., Candiani, S., Dishaw, L.J., Satoh, N.
  • Journal Title: Genome Res. 18 Pages: 1100-1111
• [Journal Article] Function of Pax1 and Pax9 in the sclerotome of medaka fish (2008)
  • Author(s): Mise, T., Iijima, M., Inohaya, K., Kudo, A., Wada, H.
  • Journal Title: Genesis 46 Pages: 185-192
• [Journal Article] Glutamatergic networks in the Ciona intestinalis larva. (2008)
  • Author(s): Horie, T., Kusakabe, T., Tsuda, M.
  • Journal Title: J.Comp.Neurol. 508 Pages: 249-263
• [Journal Article] Comparative pair-wise domain-combinations for screening the clade specific domain-architectures. (2007)
  • Author(s): Kawashima, S., Kawashima, T., Putnum, N.H., Rokhser, D.S., Wada, H., Kanehisa, M.
  • Journal Title: Genome Informatics 19 Pages: 50-60
• [Journal Article] Dynamic change in the expression of developmental genes in the ascidian central nervous system : revisit to the tripartite model and the origin of the midbrain-hindbrain boundary region. (2007)
  • Author(s): Ikuta, T., Saiga, H.
  • Journal Title: Dev.Biol. 312 Pages: 631-643
• [Journal Article] Nodal regulates neural tube formation in the Ciona intestinalis embryo. (2007)
  • Author(s): Mita, K., Fujiwara, S.
  • Journal Title: Dev.Genes Evol. 217 Pages: 593-601
• [Journal Article] Functional proteomics in Viona intestinalis -A breakthrough in the exploration of the molecular and cellular mechanism of ascidian development. (2007)
  • Author(s): Inaba k, Nomura, M., Nakajima, A., Hozumi, A.
  • Journal Title: Dev.Dyn. 236 Pages: 1782-1789
• [Journal Article] Analysis of large scale expression sequenced tage (ESTs) from the anural ascidian, Molgula tectiformis. (2007)
  • Author(s): Gyoja, F., Satou, Y., Shin-i, T., Kohara, Y., Swalla, B.J., Satoh, N.
  • Journal Title: Dev.Biol. 307 Pages: 460-482
• [Journal Article] Brachyury-downstream notochord genes and convergent extension in Ciona intestinalis embryos. (2007)
  • Author(s): Hotta, K., Yamada, S., Ueno, N., Satoh, N., Takahashi, H.
  • Journal Title: Dev.Growth Differ. 49 Pages: 373-382
• [Journal Article] Cephalochordate melanopsin, Evolutionary linkage between invertebrate visual cells and vertebrate photosensitive retinal ganglion cells. (2005)
  • Author(s): Koyanagi, M., Kubokawa, K., Tsukamoto, H., Shichida, Y., Terakita, A.
  • Journal Title: Cur.Biol. 15 Pages: 1065-1069