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Nat Genet. 2016 Apr;48(4):427-37. doi: 10.1038/ng.3526. Epub 2016 Mar 7.

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

Author information

1
Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA.
2
Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA.
3
Department of Biology, University of Kentucky, Lexington, Kentucky, USA.
4
Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA.
5
Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece.
6
Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France.
7
Department of Animal Biology, University of Illinois, Urbana-Champaign, Illinois, USA.
8
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
9
Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA.
10
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
11
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
12
Department of Zoology, University of Oxford, Oxford, UK.
13
School of Biological Sciences, Bangor University, Bangor, UK.
14
Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.
15
Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France.
16
Department of Biology, University of Konstanz, Konstanz, Germany.
17
Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA.
18
Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA.
19
Departament de Genètica, Universitat de Barcelona, Barcelona, Spain.
20
Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain.
21
Department of Biology, University of Victoria, Victoria, British Columbia, Canada.
22
Center for Circadian Clocks, Soochow University, Suzhou, China.
23
School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, China.
24
Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany.
25
Department of Dental Hygiene, Nippon Dental University College at Niigata, Niigata, Japan.
26
Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA.
27
Department of Microbiology, Nippon Dental University School of Life Dentistry at Niigata, Niigata, Japan.
28
Department of Evolutionary Studies of Biosystems, SOKENDAI (Graduate University for Advanced Studies), Hayama, Japan.
29
Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA.
30
Department of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA.
31
Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Brazil.
32
International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany.
33
Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.

Abstract

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.

PMID:
26950095
PMCID:
PMC4817229
DOI:
10.1038/ng.3526
[Indexed for MEDLINE]
Free PMC Article

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