Publication 2018

(a) Developmental and Evolutionary Genomics

  1. Luo, Y.J., Kanda, M., Koyanagi, R., Hisata, K., Akiyama, T., Sakamoto, H., Sakamoto, T., Satoh, N.
    Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads.
    Nature Ecology & Evolution 2, 141–151 (2018), doi:10.1038/s41559-017-0389-y.LINK PUBMED
  2. Inoue, J., Satoh, N.
    Deuterostome Genomics: Lineage-specific Protein Expansions that Enabled Chordate Muscle Evolution
    Molecular Biology and Evolution. 35(4):914-924. (2018)LINK PUBMED
  3. Nakano, H., Miyazawa, H., Maeno, A., Shiroishi, T., Kakui, K., Koyanagi, R., Kanda, M., Satoh, N., Omori, A., Kohtsuka, H.
    Correction to: A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella.
    BMC Evolutionary Biology. 18:83. doi:10.1186/s12862-018-1190-5. (2018)LINK PUBMED
  4. Gerdol, M., Luo, Y.J., Satoh, N., Pallavicini, A.
    Genetic and molecular basis of the immune system in the brachiopod Lingula anatina
    Developmental and Comparative Immunology. 82: 7-30. (2018)LINK PUBMED
  5. Tominaga, H., Satoh, N., Ueno, N., Takahashi, H.
    Enhancer activities of amphioxus Brachyury genes in embryos of the ascidian, Ciona intestinalis.
    genesis. 56(8):e23240. (2018)LINK PUBMED
  6. Horie, T., Horie, R., Chen, K., Cao, C., Nakagawa, M., Kusakabe, T.G., Satoh, N., Sasakura, Y., Levine, M.
    Regulatory cocktail for dopaminergic neurons in a proto-vertebrate identified by whole embryo single cell transcriptomics
    Genes and Development, 32(19-20):1297-1302. doi: 10.1101/gad.317669.118. (2018)LINK PUBMED
  7. Irie, N., Satoh, N., Kuratani, S.
    The phylum Vertebrata: a case for zoological recognition
    Zoological Letters, 2018 4:32. (2018)LINK PUBMED
  8. Nakashima, K.
    A comparative approach to decipher intestinal animal-microbe associations.
    Microbial Cell. 5: 522-524. (2018) PUBMED

(b) Environmental Genomics

  1. Hamada, M., Schröder, K., Bathia, J., Kürn, U., Fraune, S., Khalturina, M., Khalturin, K., Shinzato, C., Satoh, N., Bosch, T.C.G
    Metabolic co-dependence drives the evolutionary ancient Hydra-Chlorella symbiosis
    eLife. 31;7. pii: e35122. doi: https://doi.org/10.1101/234757 (2018)LINK PUBMED
  2. Shoguchi, E., Beedessee, G., Tada, I., Hisata, K., Kawashima, T., Takeuchi, T., Arakaki, N., Fujie, M., Koyanagi, R., Roy, M.C., Kawachi, M., Hidaka, M., Satoh, N., Shinzato, C.
    Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes
    BMC Genomics. 19:458. doi:10.1186/s12864-018-4857-9. (2018)LINK PUBMED
  3. Zayasu, Y., Satoh, N., Shinzato, C.
    Genetic diversity of farmed and wild populations of the reef building coral, Acropora tenuis. 
    Restoration Ecology. 26(6):1195-1202. doi: 10.1111/rec.12687 (2018) LINK 
  4. Shinzato, C., Zayasu, Y., Kanda, M., Kawamitsu, M., Satoh, N., Yamashita, H., Go Suzuki, G.
    Using seawater to document coral-zoothanthella diversity: A new approach to coral reef monitoring using environmental DNA
    Front. Mar. Sci. 5:28. doi: 10.3389/fmars.2018.00028 (2018) LINK 
  5. Guzman, C., Han, X., Shoguchi, E., Nic Chormaic, S.
    Fluorescence from a single Symbiodinium cell.
    Methods Appl Fluoresc. 8(1): 8397. doi: 10.1088/2050-6120/aaba89. (2018)PUBMED
  6. Guzman, C., Shinzato, C., Lu, T.M., Conaco, C.
    Transcriptome analysis of the reef-building octocoral, Heliopora coerulea
    Scientific Reports 8:8397. DOI:10.1038/s41598-018-26718-5 (2018)LINK PUBMED
  7. Mohamed, A., Cumbo, V., Harii, S., Shinzato, C., Chan, C.X., Ragan, M., Satoh, N., Ball, E., Miller, D.
    Deciphering the nature of the coral-Chromera association.
    The ISME Journal. 12(3): 776-790 (2018) PUBMED
  8. Higa, Y., Shinzato, C., Zayasu, Y., Nagata, T., Nakamura, R., Yokokura, A., Shanado, S., Ohmori M.
    Flexible development of techniques for coral reef restoration using asexual reproduction in the Coral Reef Preservation and Rehabilitation Project by Okinawa Prefectural Government, Japan (in Japanese)
    Journal of the Japanese Coral Reef Society, 20: 21-37 (2018) LINK
  9. Mao, Y.F., Economo, E.P., Satoh, N.
    The roles of introgression and climate change in the rise to dominance of Acropora corals.
    Current Biology. 28(21):3373-3382.e5. doi: 10.1016/j.cub.2018.08.061. (2018)LINK PUBMED
  10. Maeda, K., Saeki, T.
    Revision of species in Sicyopterus (Gobiidae: Sicydiinae) described by de Beaufort (1912), with a first record of Sicyopterus longifilis from Japan
    Species Diversity 23: 253–262 (2018) LINK 
  11. Nakajima, Y., Shinzato, C., Khalturina, M., Nakamura, M., Watanabe, H.K., Nakagawa, S., Satoh, N., Mitarai, S.
    Isolation and characterization of novel polymorphic microsatellite loci for the deep-sea hydrothermal vent limpet, Lepetodrilus nux, and the vent-associated squat lobster, Shinkaia crosnieri
    Mar Biodiv 48: 677-684. (2018) LINK
  12. Maeda, K., Saeki, T., Shinzato, C., Koyanagi, R., Satoh, N.
    Review of Schismatogobius (Gobiidae) from Japan, with the description of a new species
    Ichthyol Res 65: 56-77. (2018) LINK

(c) Functional Genomics

  1. Shibata H., Chijiwa T., Oda-Ueda N., Nakamura H., Yamaguchi K., Hattori S., Matsubara K., Matsuda Y., Yamashita A., Isomoto A., Mori K., Tashiro K., Kuhara S., Yamasaki S., Fujie M., Goto H., Koyanagi R., Takeuchi T., Fukumaki Y., Ohno M., Shoguchi E., Hisata K., Satoh N., Ogawa T.
    The habu genome reveals accelerated evolution of venom protein genes.
    Sci Rep. 26;8(1):11300. doi: 10.1038/s41598-018-28749-4. (2018) PUBMED
  2. Nakashima, K., Kimura, S., Ogawa, Y., Watanabe, S., Soma, S., Kaneko, T., Yamada, L., Sawada, H., Tung, CH., Lu, T.M., Yu, J.K., Villar-Briones, A., Kikuchi, S., Satoh, N.
    Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota.
    Nat Commun. 9(1):3402. doi: 10.1038/s41467-018-05884-0. (2018)LINK PUBMED
  3. Matsuura, A., Yoshimura, K., Kintsu, H., Atsumi, T., Tsuchihashi, Y., Takeuchi, T., Satoh, N., Negishi, L., Sakuda, S., Asakura, T., Imura, Y., Yoshimura, E.
    Structural and functional analyses of calcium ion response factors in the mantle of Pinctada fucata.
    Journal of Structural Biology. 204(2):240-249. (2018)LINK PUBMED
  4. Kawahara, T., Izumikawa, M., Kozone, I., Hashimoto, J., Kagaya, N.,Koiwai, H., Komatsu, M., Fujie, M., Sato, N., Ikeda, H., Shin-ya, K.
    Neothioviridamide, a Polythioamide Compound Produced by Heterologous Expression of a Streptomyces sp. Cryptic RiPP Biosynthetic Gene Cluster
    J. Nat. Prod. 81(2):264-269. (2018) PUBMED
  5. Iwasaka, H., Koyanagi, R., Satoh, R., Nagano, A., Watanabe, K., Hisata, K., Satoh, N., Aki, T.
    A Possible Trifunctional β-Carotene Synthase Gene Identified in the Draft Genome of Aurantiochytrium sp. Strain KH105.
    Genes. 9(4): 200 (2018)LINK PUBMED
  6. Tsutsumi, H., Katsuyama, Y., Izumikawa, M., Takagi, M., Fujie, M., Satoh, N., Shin-ya, K., Ohnishi, Y.
    Unprecedented Cyclization Catalyzed by a Cytochrome P450 in Benzastatin Biosynthesis
    JACS 140(21):6631-6639. (2018) PUBMED
  7. Takeuchi, T., , Plasseraud, L., Ziegler-Devin, I., Brosse, N., Shinzato, C., Satoh, N., Marin, F.
    Biochemical characterization of the skeletal matrix of the massive coral, Porites australiensis - The saccharide moieties and their localization
    Journal of Structural Biology. S1047-8477(18)30135-7. (2018)LINK PUBMED
  8. Zhao, R., Takeuchi, T., Luo, Y.J., Ishikawa, A., Kobayashi, T., Koyanagi, R., Villar-Briones, A., Yamada, L., Sawada, H., Iwanaga, S., Nagai, K., Satoh, N., Endo, K.
    Dual gene repertoires for larval and adult shells reveal molecules essential for molluscan shell formation.
    Molecular Biology and Evolution. msy172. https://doi.org/10.1093/molbev/msy172 (2018)LINK PUBMED
  9. Kubota, K., Kintsu, H., Matsuura, A., Tsuchihashi, Y., Takeuchi, T., Satoh, N., Suzuki, M.
    Functional analyses of MMPs for aragonite crystal formation in the ligament of Pinctada fucata.
    Frontiers in Marine Science, 5:373. doi: 10.3389/fmars.2018.00373 (2018) LINK
  10. Kim, O.T.P., Nguyen, P.T., Shoguchi, E., Hisata, K., Vo, T.T.B., Inoue, J., Shinzato, C., Le, B.T.N, Nishitsuji, K., Kanda, M., Nguyen, V.H., Nong, H.V., Satoh, N.
    A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement.
    BMC Genomics, 19(1):733. doi: 10.1186/s12864-018-5079-x. (2018) PUBMED
  11. Marin, F., Chmiel, A., Takeuchi, T., Bundeleva, I., Durlet, C., Samankassou, E., Medakovic, D.
    Skeletal Organic Matrices in Molluscs: Origin, Evolution, Diagenesis.
    In. Biomineralization. Switzerland: Springer Nature. p. 325-332. (2018) LINK