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Sökning: WFRF:(Yandell Mark) > Medicin och hälsovetenskap > Amemiya Chris T. > The spotted gar gen...

  • Braasch, IngoUniv Oregon, Inst Neurosci, Eugene, OR 97403 USA.;Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48824 USA. (författare)

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

  • Artikel/kapitelEngelska2016

Förlag, utgivningsår, omfång ...

  • 2016-03-07
  • Springer Science and Business Media LLC,2016
  • electronicrdacarrier

Nummerbeteckningar

  • LIBRIS-ID:oai:DiVA.org:uu-293022
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-293022URI
  • https://doi.org/10.1038/ng.3526DOI

Kompletterande språkuppgifter

  • Språk:engelska
  • Sammanfattning på:engelska

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  • Ämneskategori:ref swepub-contenttype
  • Ämneskategori:art swepub-publicationtype

Anmärkningar

  • Funding: We thank the Broad Institute Genomics Platform for constructing and sequencing gar DNA and RNA libraries and J. Turner-Maier for the gar transcriptome assembly. We thank the teams of the Bayousphere Research Laboratory (Nicholls State University) and the University of Oregon Fish Facility for gar work and husbandry. We thank J. Westlund for the design of the species illustrations. The generation of gar sequences and assemblies by the Broad Institute of MIT and Harvard University was supported by US National Institutes of Health (NIH)/National Human Genome Research Institute grant U54 HG03067. This work was further supported by US NIH grants R01 OD011116 (alias R01 RR020833) and R24 OD01119004 (J.H.P.); a Feodor Lynen Fellowship from the Alexander von Humboldt Foundation and the Volkswagen Foundation Initiative Evolutionary Biology, grant I/84 815 (I.B.); US NIH grant T32 HD055164 and National Science Foundation (NSF) Doctoral Dissertation Improvement Grant 1311436 (A.R.G.); Uehara Memorial Foundation Research Fellowship 2013, Japan Society for the Promotion of Science Postdoctoral Research Fellowship 2012-127 and Marine Biological Laboratory Research Award 2014 (T.N.); Brazilian National Council for Scientific and Technological Development (CNPq) grants 402754/2012-3 and 477658/2012-1 (I.S.); the Brinson Foundation and the University of Chicago Biological Sciences Division (N.H.S.); NSF grant BCS0725227 (K.K.); call 'ARISTEIA I' of the National Strategic Reference Framework 2007-2013 (SPARCOMP, 36), Ministry of Education and Religious Affairs of Greece (T.M.); Agence Nationale de la Recherche (ANR) grant ANR-10-GENM-017 (PhyloFish; J.B.); the Wellcome Trust (grants WT095908 and WT098051) and the European Molecular Biology Laboratory (D.B., S.M.J.S. and B.A.); the Biomedical Research Council of the Agency for Science, Technology and Research (A*STAR), Singapore (B.V.); European Research Council grant 268513 (P.W.H.H. and K.J.M.); the Ministerio de Ciencia e Innovacion (BFU2010-14875 and BFU2015-71340) and the Generalitat de Catalunya, AGAUR (SGR2014-290) (C. C.); US NIH grant R01 AI057559 (G.W.L. and J.A.Y.); US NIH grants R24 OD010922 and R01 GM079492 (C. T. A.); and the National Basic Research Program of China (973 Program) (2012CB947600) and the National Natural Science Foundation of China (NSFC) (31030062) (H.W.).
  • To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

Ämnesord och genrebeteckningar

Biuppslag (personer, institutioner, konferenser, titlar ...)

  • Gehrke, Andrew R.Univ Chicago, Dept Organismal Biol & Anat, 1025 E 57Th St, Chicago, IL 60637 USA. (författare)
  • Smith, Jeramiah J.Univ Kentucky, Dept Biol, Lexington, KY USA. (författare)
  • Kawasaki, KazuhikoPenn State Univ, Dept Anthropol, University Pk, PA 16802 USA. (författare)
  • Manousaki, TerezaHellen Ctr Marine Res, Inst Marine Biol Biotechnol & Aquaculture, Iraklion, Greece. (författare)
  • Pasquier, JeremyINRA, LPGP, UR1037, Campus Beaulieu, F-35042 Rennes, France. (författare)
  • Amores, AngelUniv Oregon, Inst Neurosci, Eugene, OR 97403 USA. (författare)
  • Desvignes, ThomasUniv Oregon, Inst Neurosci, Eugene, OR 97403 USA. (författare)
  • Batzel, PeterUniv Oregon, Inst Neurosci, Eugene, OR 97403 USA. (författare)
  • Catchen, JulianUniv Illinois, Dept Anim Biol, Urbana, IL 61801 USA. (författare)
  • Berlin, Aaron M.MIT, Broad Inst, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Harvard, Cambridge, MA USA. (författare)
  • Campbell, Michael S.Univ Utah, Eccles Inst Human Genet, Salt Lake City, UT USA.;Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA. (författare)
  • Barrell, DanielWellcome Trust Sanger Inst, Wellcome Trust Genome Campus, Hinxton, England.;European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Hinxton, England. (författare)
  • Martin, Kyle J.Univ Oxford, Dept Zool, Oxford, England.;Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England. (författare)
  • Mulley, John F.Bangor Univ, Sch Biol Sci, Bangor, Gwynedd, Wales. (författare)
  • Ravi, VydianathanASTAR, Inst Mol & Cell Biol, Comparat Genom Lab, Singapore, Singapore. (författare)
  • Lee, Alison P.ASTAR, Inst Mol & Cell Biol, Comparat Genom Lab, Singapore, Singapore. (författare)
  • Nakamura, TetsuyaUniv Chicago, Dept Organismal Biol & Anat, 1025 E 57Th St, Chicago, IL 60637 USA. (författare)
  • Chalopin, DomitilleEcole Normale Super Lyon, Inst Genom Fonct Lyon, F-69364 Lyon, France.;Univ Georgia, Dept Genet, Athens, GA 30602 USA. (författare)
  • Fan, ShaohuaUniv Konstanz, Dept Biol, Constance, Germany.;Univ Penn, Dept Genet, Philadelphia, PA 19104 USA. (författare)
  • Wcisel, DustinN Carolina State Univ, Dept Mol Biomed Sci, Raleigh, NC 27695 USA.;N Carolina State Univ, Ctr Comparat Med & Translat Res, Raleigh, NC 27695 USA. (författare)
  • Canestro, CristianUniv Barcelona, Dept Genet, Barcelona, Spain.;Univ Barcelona, Inst Recerca Biodiversitat, Barcelona, Spain. (författare)
  • Sydes, JasonUniv Oregon, Inst Neurosci, Eugene, OR 97403 USA. (författare)
  • Beaudry, Felix E. G.Univ Victoria, Dept Biol, POB 1700, Victoria, BC V8W 2Y2, Canada. (författare)
  • Sun, YiSoochow Univ, Ctr Circadian Clocks, Suzhou, Peoples R China.;Soochow Univ, Coll Med, Sch Biol & Basic Med Sci, Suzhou, Peoples R China. (författare)
  • Hertel, JanaUniv Leipzig, Dept Comp Sci, Bioinformat Grp, D-04109 Leipzig, Germany.;UFZ Helmholtz Ctr Environm Res, Young Investigators Grp Bioinformat & Transcript, Leipzig, Germany. (författare)
  • Beam, Michael J.Univ Oregon, Inst Neurosci, Eugene, OR 97403 USA. (författare)
  • Fasold, MarioUniv Leipzig, Dept Comp Sci, Bioinformat Grp, D-04109 Leipzig, Germany.;ecSeq Bioinformat, Leipzig, Germany. (författare)
  • Ishiyama, MikioNippon Dent Univ Coll Niigata, Dept Dent Hyg, Niigata, Japan. (författare)
  • Johnson, JeremyMIT, Broad Inst, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Harvard, Cambridge, MA USA. (författare)
  • Kehr, SteffiUniv Leipzig, Dept Comp Sci, Bioinformat Grp, D-04109 Leipzig, Germany. (författare)
  • Lara, MarciaMIT, Broad Inst, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Harvard, Cambridge, MA USA. (författare)
  • Letaw, John H.Univ Oregon, Inst Neurosci, Eugene, OR 97403 USA. (författare)
  • Litman, Gary W.Univ S Florida, Morsani Coll Med, Dept Pediat, St Petersburg, FL 33701 USA. (författare)
  • Litman, Ronda T.Univ S Florida, Morsani Coll Med, Dept Pediat, St Petersburg, FL 33701 USA. (författare)
  • Mikami, MasatoNippon Dent Univ, Sch Life Dent Niigata, Dept Microbiol, Niigata, Japan. (författare)
  • Ota, TatsuyaSOKENDAI Grad Univ Adv Studies, Dept Evolutionary Studies Biosyst, Hayama, Japan. (författare)
  • Saha, Nil RatanBenaroya Res Inst, Mol Genet Program, Seattle, WA USA. (författare)
  • Williams, LouiseMIT, Broad Inst, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Harvard, Cambridge, MA USA. (författare)
  • Stadler, Peter F.Univ Leipzig, Dept Comp Sci, Bioinformat Grp, D-04109 Leipzig, Germany. (författare)
  • Wang, HanSoochow Univ, Ctr Circadian Clocks, Suzhou, Peoples R China.;Soochow Univ, Coll Med, Sch Biol & Basic Med Sci, Suzhou, Peoples R China. (författare)
  • Taylor, John S.Univ Victoria, Dept Biol, POB 1700, Victoria, BC V8W 2Y2, Canada. (författare)
  • Fontenot, QuentonNicholls State Univ, Dept Biol Sci, Thibodaux, LA 70310 USA. (författare)
  • Ferrara, AllyseNicholls State Univ, Dept Biol Sci, Thibodaux, LA 70310 USA. (författare)
  • Searle, Stephen M. J.Wellcome Trust Sanger Inst, Wellcome Trust Genome Campus, Hinxton, England. (författare)
  • Aken, BronwenWellcome Trust Sanger Inst, Wellcome Trust Genome Campus, Hinxton, England.;European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Hinxton, England. (författare)
  • Yandell, MarkUniv Utah, Eccles Inst Human Genet, Salt Lake City, UT USA. (författare)
  • Schneider, IgorFed Univ Para, Inst Ciencias Biol, BR-66059 Belem, Para, Brazil. (författare)
  • Yoder, Jeffrey A.N Carolina State Univ, Dept Mol Biomed Sci, Raleigh, NC 27695 USA.;N Carolina State Univ, Ctr Comparat Med & Translat Res, Raleigh, NC 27695 USA. (författare)
  • Volff, Jean-NicolasEcole Normale Super Lyon, Inst Genom Fonct Lyon, F-69364 Lyon, France. (författare)
  • Meyer, AxelUniv Konstanz, Dept Biol, Constance, Germany.;Univ Konstanz, Int Max Planck Res Sch Organismal Biol, Constance, Germany. (författare)
  • Amemiya, Chris T.Benaroya Res Inst, Mol Genet Program, Seattle, WA USA. (författare)
  • Venkatesh, ByrappaASTAR, Inst Mol & Cell Biol, Comparat Genom Lab, Singapore, Singapore. (författare)
  • Holland, Peter W. H.Univ Oxford, Dept Zool, Oxford, England. (författare)
  • Guiguen, YannINRA, LPGP, UR1037, Campus Beaulieu, F-35042 Rennes, France. (författare)
  • Bobe, JulienINRA, LPGP, UR1037, Campus Beaulieu, F-35042 Rennes, France. (författare)
  • Shubin, Neil H.Univ Chicago, Dept Organismal Biol & Anat, 1025 E 57Th St, Chicago, IL 60637 USA. (författare)
  • Di Palma, FedericaMIT, Broad Inst, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Harvard, Cambridge, MA USA.;Genome Anal Ctr, Vertebrate & Hlth Genom, Norwich, Norfolk, England. (författare)
  • Alfoeldi, JessicaMIT, Broad Inst, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Harvard, Cambridge, MA USA. (författare)
  • Lindblad-Toh, KerstinUppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab,MIT, Broad Inst, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Harvard, Cambridge, MA USA.;Uppsala Univ, Dept Med Biochem & Microbiol, Sci Life Lab, Uppsala, Sweden.(Swepub:uu)kerli865 (författare)
  • Postlethwait, John H.Univ Oregon, Inst Neurosci, Eugene, OR 97403 USA. (författare)
  • Univ Oregon, Inst Neurosci, Eugene, OR 97403 USA.;Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48824 USA.Univ Chicago, Dept Organismal Biol & Anat, 1025 E 57Th St, Chicago, IL 60637 USA. (creator_code:org_t)

Sammanhörande titlar

  • Ingår i:Nature Genetics: Springer Science and Business Media LLC48:4, s. 427-4371061-40361546-1718

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