| 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, Jérémy; 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; Cañestro, 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; Alföldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H. |
| Contributors: |
Department of Integrative Biology Berkeley (IB); University of California Berkeley (UC Berkeley); University of California (UC)-University of California (UC); Department of Organismal Biology and Anatomy; University of Chicago; Pennsylvania State University State College, PA (Penn State); Penn State System; Hellenic Centre for Marine Research (HCMR); Laboratoire de Physiologie et Génomique des Poissons (LPGP); Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes (Biosit : Biologie - Santé - Innovation Technologique); University of Oregon Eugene; University of Illinois at Urbana-Champaign Urbana (UIUC); University of Illinois System; Broad Institute of MIT and Harvard (BROAD INSTITUTE); Harvard Medical School Boston (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital Boston; Eccles Institute of Human Genetics; University of Utah; European Bioinformatics Institute Hinxton (EMBL-EBI); EMBL Heidelberg; The Wellcome Trust Sanger Institute Cambridge; Department of Animal and Plant Sciences Sheffield; University of Sheffield Sheffield; School of Biological Sciences Bangor; Bangor University; Agency for science, technology and research Singapore (A*STAR); Institut de Génomique Fonctionnelle de Lyon (IGFL); École normale supérieure de Lyon (ENS de Lyon); Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL); Université de Lyon-Centre National de la Recherche Scientifique (CNRS); University of Georgia USA; Department of Molecular Biomedical Sciences Raleigh; North Carolina State University Raleigh (NC State); University of North Carolina System (UNC)-University of North Carolina System (UNC); Center for Comparative Medicine and Translational Research; Universitat de Barcelona (UB); Center for Circadian Clocks; Soochow University; School of Biology and Basic Medical Sciences, Medical College; Graduate University for Advanced Studies Hayama (SOKENDAI); Instituto de Ciências Biológicas; Federal University of Para - Universidade Federal do Pará - UFPA Belém, Brazil (UFPA); Department of Molecular Biomedical Sciences; University of North Carolina System (UNC)-University of North Carolina System (UNC)-College of Veterinary Medicine Raleigh; International Max Planck Research School for Organismal Biology (IMPRS); University of Konstanz; ANR-10-GENM-0017,PhyloFish,Analyse phylogénomique des duplications géniques chez les poissons téléostéens: une approche par RNA-Seq(2010) |
| Source: |
ISSN: 1061-4036. |
| Publisher Information: |
CCSD; Nature Publishing Group |
| Publication Year: |
2016 |
| Collection: |
Institut National de la Recherche Agronomique: ProdINRA |
| Subject Terms: |
genome; regulatory sequence; teleost; human; fish; vertebrates; lépisosté tacheté; évolution du génome; miRNA; lepisosteus oculatus; vertébré; fonction des gènes; duplication des génomes; homme; poisson; teleosteen; interaction animal homme; reproduction; immunité; expression des gènes; analyse phylogénétique; chromosome; analyse du transcriptome; analyse génomique; physiologie animale; séquence régulatrice; [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics; [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry; Molecular Biology/Genomics [q-bio.GN]; [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] |
| Description: |
Corrigendum: Nature Genetics, 2016, 48 (6), pp.700-700 DOI:10.1038/ng0616-700c WOS: 000376744200022 ; 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. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
info:eu-repo/semantics/altIdentifier/pmid/26950095; PRODINRA: 349168; PUBMED: 26950095; PUBMEDCENTRAL: PMC4817229; WOS: 000372908800014 |
| DOI: |
10.1038/ng.3526 |
| Availability: |
https://hal.science/hal-01595410; https://hal.science/hal-01595410v1/document; https://hal.science/hal-01595410v1/file/ng.3526.pdf; https://doi.org/10.1038/ng.3526 |
| Rights: |
https://about.hal.science/hal-authorisation-v1/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.DCFE6845 |
| Database: |
BASE |