Kuraku Shigehiro

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Kuraku
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Shigehiro
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  • Article
    The Earth BioGenome Project 2020: starting the clock
    (National Academy of Sciences, 2022-01-18) Lewin, Harris A. ; Richards, Stephen ; Miguel L. Allende ; Lieberman Aiden, Erez ; Archibald, John M. ; Bálint, Miklós ; Barker, Katharine B. ; Baumgartner, Bridget ; Belov, Katherine ; Bertorelle, Giorgio ; Blaxter, Mark ; Cai, Jing ; Caperello, Nicolette D. ; Carlson, Keith ; Castilla-Rubio, Juan Carlos ; Chaw, Shu-Miaw ; Chen, Lei ; Childers, Anna K. ; Coddington, Jonathan ; Conde, Dalia A. ; Corominas, Montserrat ; Crandall, Keith A. ; Crawford, Andrew J. ; DiPalma, Federica ; Durbin, Richard ; Ebenezer, ThankGod E. ; Edwards, Scott V. ; Fedrigo, Olivier ; Flicek, Paul ; Formenti, Giulio ; Gibbs, Richard A. ; Gilbert, M. Thomas P. ; Goldstein, Melissa M. ; Graves, Jennifer Marshall ; Greely, Henry T. ; Grigoriev, Igor V. ; Hackett, Kevin J. ; Hall, Neil ; Haussler, David ; Helgen, Kristofer M. ; Hogg, Carolyn J. ; Isobe, Sachiko ; Jakobsen, Kjetill S. ; Janke, Axel ; Jarvis, Erich ; Johnson, Warren E. ; Jones, Steven J. M. ; Karlsson, Elinor K. ; Kersey, Paul J. ; Kim, Jin-Hyoung ; Kress, W. John ; Kuraku, Shigehiro ; Lawniczak, Mara K. N. ; Leebens-Mack, James H. ; Li, Xueyan ; Lindblad-Toh, Kerstin ; Liu, Xin ; Lopez, Jose V. ; Marques-Bonet, Tomas ; Mazard, Sophie ; Mazet, Jonna A. K. ; Mazzoni, Camila J. ; Myers, Eugene ; O’Neill, Rachel J. ; Paez, Sadye ; Park, Hyun ; Robinson, Gene E. ; Roquet, Cristina ; Ryder, Oliver A. ; Sabir, Jamal S. M. ; Shaffer, H. Bradley ; Shank, Timothy M. ; Sherkow, Jacob S. ; Soltis, Pamela S. ; Tang, Boping ; Tedersoo, Leho ; Uliano-Silva, Marcela ; Wang, Kun ; Wei, Xiaofeng ; Wetzer, Regina ; Wilson, Julia L. ; Xu, Xun ; Yang, Huanming ; Yoder, Anne D. ; Zhang, Guojie
    November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP’s major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP.
  • Article
    The African coelacanth genome provides insights into tetrapod evolution
    (Nature Publishing Group, 2013-04-17) Amemiya, Chris T. ; Alfoldi, Jessica ; Lee, Alison P. ; Fan, Shaohua ; Philippe, Herve ; MacCallum, Iain ; Braasch, Ingo ; Manousaki, Tereza ; Schneider, Igor ; Rohner, Nicolas ; Organ, Chris ; Chalopin, Domitille ; Smith, Jeramiah J. ; Robinson, Mark ; Dorrington, Rosemary A. ; Gerdol, Marco ; Aken, Bronwen ; Assunta Biscotti, Maria ; Barucca, Marco ; Baurain, Denis ; Berlin, Aaron M. ; Blatch, Gregory L. ; Buonocore, Francesco ; Burmester, Thorsten ; Campbell, Michael S. ; Canapa, Adriana ; Cannon, John P. ; Christoffels, Alan ; De Moro, Gianluca ; Edkins, Adrienne L. ; Fan, Lin ; Fausto, Anna Maria ; Feiner, Nathalie ; Forconi, Mariko ; Gamieldien, Junaid ; Gnerre, Sante ; Gnirke, Andreas ; Goldstone, Jared V. ; Haerty, Wilfried ; Hahn, Mark E. ; Hesse, Uljana ; Hoffmann, Steve ; Johnson, Jeremy ; Karchner, Sibel I. ; Kuraku, Shigehiro ; Lara, Marcia ; Levin, Joshua Z. ; Litman, Gary W. ; Mauceli, Evan ; Miyake, Tsutomu ; Mueller, M. Gail ; Nelson, David R. ; Nitsche, Anne ; Olmo, Ettore ; Ota, Tatsuya ; Pallavicini, Alberto ; Panji, Sumir ; Picone, Barbara ; Ponting, Chris P. ; Prohaska, Sonja J. ; Przybylski, Dariusz ; Ratan Saha, Nil ; Ravi, Vydianathan ; Ribeiro, Filipe J. ; Sauka-Spengler, Tatjana ; Scapigliati, Giuseppe ; Searle, Stephen M. J. ; Sharpe, Ted ; Simakov, Oleg ; Stadler, Peter F. ; Stegeman, John J. ; Sumiyama, Kenta ; Tabbaa, Diana ; Tafer, Hakim ; Turner-Maier, Jason ; van Heusden, Peter ; White, Simon ; Williams, Louise ; Yandell, Mark ; Brinkmann, Henner ; Volff, Jean-Nicolas ; Tabin, Clifford J. ; Shubin, Neil ; Schartl, Manfred ; Jaffe, David B. ; Postlethwait, John H. ; Venkatesh, Byrappa ; Di Palma, Federica ; Lander, Eric S. ; Meyer, Axel ; Lindblad-Toh, Kerstin
    The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.