The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
| Title: | The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons |
|---|---|
| Authors: | Braasch, Ingo; Gehrke, Andrew R.; Smith, Jeramiah J.; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jeremy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian; Berlin, Aaron M.; Campbell, Michael S.; Barrell, Daniel; Martin, Kyle J.; Mulley, John F.; Ravi, Vydianathan; Lee, Alison P.; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin; Canestro, Cristian; Sydes, Jason; Beaudry, Felix E. G.; Sun, Yi; Hertel, Jana; Beam, Michael J.; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Steffi; Lara, Marcia; Letaw, John H.; Litman, Gary W.; Litman, Ronda T.; Mikami, Masato; Ota, Tatsuya; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F.; Wang, Han; Taylor, John S.; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M. J.; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A.; Volff, Jean-Nicolas; Meyer, Axel; Amemiya, Chris T.; Venkatesh, Byrappa; Holland, Peter W. H.; Guiguen, Yann; Bobe, Julien; Shubin, Neil H.; Di Palma, Federica; Alfoeldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H. |
| Publisher Information: | Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi; Uppsala universitet, Science for Life Laboratory, SciLifeLab; 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.; Univ Kentucky, Dept Biol, Lexington, KY USA.; Penn State Univ, Dept Anthropol, University Pk, PA 16802 USA.; Hellen Ctr Marine Res, Inst Marine Biol Biotechnol & Aquaculture, Iraklion, Greece.; INRA, LPGP, UR1037, Campus Beaulieu, F-35042 Rennes, France.; Univ Oregon, Inst Neurosci, Eugene, OR 97403 USA.; Univ Illinois, Dept Anim Biol, Urbana, IL 61801 USA.; MIT, Broad Inst, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Harvard, Cambridge, MA USA.; Univ Utah, Eccles Inst Human Genet, Salt Lake City, UT USA.;Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA.; Wellcome Trust Sanger Inst, Wellcome Trust Genome Campus, Hinxton, England.;European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Hinxton, England.; Univ Oxford, Dept Zool, Oxford, England.;Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England.; Bangor Univ, Sch Biol Sci, Bangor, Gwynedd, Wales.; ASTAR, Inst Mol & Cell Biol, Comparat Genom Lab, Singapore, Singapore.; Ecole Normale Super Lyon, Inst Genom Fonct Lyon, F-69364 Lyon, France.;Univ Georgia, Dept Genet, Athens, GA 30602 USA.; Univ Konstanz, Dept Biol, Constance, Germany.;Univ Penn, Dept Genet, Philadelphia, PA 19104 USA.; 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.; Univ Barcelona, Dept Genet, Barcelona, Spain.;Univ Barcelona, Inst Recerca Biodiversitat, Barcelona, Spain.; Univ Victoria, Dept Biol, POB 1700, Victoria, BC V8W 2Y2, Canada.; Soochow Univ, Ctr Circadian Clocks, Suzhou, Peoples R China.;Soochow Univ, Coll Med, Sch Biol & Basic Med Sci, Suzhou, Peoples R China.; Univ Leipzig, Dept Comp Sci, Bioinformat Grp, D-04109 Leipzig, Germany.;UFZ Helmholtz Ctr Environm Res, Young Investigators Grp Bioinformat & Transcript, Leipzig, Germany.; Univ Leipzig, Dept Comp Sci, Bioinformat Grp, D-04109 Leipzig, Germany.;ecSeq Bioinformat, Leipzig, Germany.; Nippon Dent Univ Coll Niigata, Dept Dent Hyg, Niigata, Japan.; Univ Leipzig, Dept Comp Sci, Bioinformat Grp, D-04109 Leipzig, Germany.; Univ S Florida, Morsani Coll Med, Dept Pediat, St Petersburg, FL 33701 USA.; Nippon Dent Univ, Sch Life Dent Niigata, Dept Microbiol, Niigata, Japan.; SOKENDAI Grad Univ Adv Studies, Dept Evolutionary Studies Biosyst, Hayama, Japan.; Benaroya Res Inst, Mol Genet Program, Seattle, WA USA.; Nicholls State Univ, Dept Biol Sci, Thibodaux, LA 70310 USA.; Wellcome Trust Sanger Inst, Wellcome Trust Genome Campus, Hinxton, England.; Univ Utah, Eccles Inst Human Genet, Salt Lake City, UT USA.; Fed Univ Para, Inst Ciencias Biol, BR-66059 Belem, Para, Brazil.; Ecole Normale Super Lyon, Inst Genom Fonct Lyon, F-69364 Lyon, France.; Univ Konstanz, Dept Biol, Constance, Germany.;Univ Konstanz, Int Max Planck Res Sch Organismal Biol, Constance, Germany.; Univ Oxford, Dept Zool, Oxford, England.; MIT, Broad Inst, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;Harvard, Cambridge, MA USA.;Genome Anal Ctr, Vertebrate & Hlth Genom, Norwich, Norfolk, England.; 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. |
| Publication Year: | 2016 |
| Collection: | Uppsala University: Publications (DiVA) |
| Subject Terms: | Medical Genetics and Genomics; Medicinsk genetik och genomik |
| Description: | 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. ; 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 ... |
| Document Type: | article in journal/newspaper |
| File Description: | application/pdf |
| Language: | English |
| Relation: | Nature Genetics, 1061-4036, 2016, 48:4, s. 427-437; PMID 26950095; ISI:000372908800014 |
| DOI: | 10.1038/ng.3526 |
| Availability: | http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-293022; https://doi.org/10.1038/ng.3526 |
| Rights: | info:eu-repo/semantics/openAccess |
| Accession Number: | edsbas.CEAB04B9 |
| Database: | BASE |