The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
Ingo Braasch
(1, 2)
,
Andrew R. Gehrke
(3)
,
Jeramiah J. Smith
(4)
,
Kazuhiko Kawasaki
(5, 6)
,
Tereza Manousaki
(7)
,
Jérémy Pasquier
(8)
,
Angel Amores
(1)
,
Thomas Desvignes
(1)
,
Peter Batzel
(1)
,
Julian Catchen
(9)
,
Aaron M. Berlin
(10)
,
Michael S. Campbell
(11, 12)
,
Daniel Barrell
(13, 14, 15)
,
Kyle J. Martin
(16, 17)
,
John F. Mulley
(18)
,
Vydianathan Ravi
(19)
,
Alison P. Lee
(19)
,
Tetsuya Nakamura
(3)
,
Domitille Chalopin
(20, 21)
,
Shaohua Fan
(4, 21)
,
Dustin Wcisel
(22, 23)
,
Cristian Cañestro
(24, 25)
,
Jason Sydes
(1)
,
Felix E.G. Beaudry
(4)
,
Yi Sun
(26, 27)
,
Jana Hertel
(28, 29)
,
Michael J. Beam
(1)
,
Mario Fasold
(28)
,
Mikio Ishiyama
(30)
,
Jeremy Johnson
(10)
,
Steffi Kehr
(28)
,
Marcia Lara
(10)
,
John H. Letaw
(1)
,
Gary W. Litman
(31)
,
Ronda T. Litman
(31)
,
Masato Mikami
(32)
,
Tatsuya Ota
(33)
,
Nil Ratan Saha
(34)
,
Louise Williams
(10)
,
Peter F. Stadler
(28)
,
Han Wang
(26, 27)
,
John S. Taylor
(4)
,
Quenton Fontenot
(35)
,
Allyse Ferrara
(35)
,
Stephen M.J. Searle
(13)
,
Bronwen Aken
(13, 36)
,
Mark Yandell
(11)
,
Igor Schneider
(37)
,
Jeffrey A Yoder
(38, 23)
,
Jean-Nicolas Volff
(20)
,
Axel Meyer
(4, 39)
,
Chris T Amemiya
(34)
,
Byrappa Venkatesh
(19)
,
Peter W.H. Holland
(16)
,
Yann Guiguen
(8)
,
Julien Bobe
(8)
,
Neil H. Shubin
(3)
,
Federica Di Palma
(10, 40)
,
Jessica Alföldi
(10)
,
Kerstin Lindblad-Toh
(10, 41)
,
John H. Postlethwait
(1)
1
Institute of Neuroscience
2 IB - Department of Integrative Biology [Berkeley]
3 Department of Organismal Biology and Anatomy
4 Department of Biology
5 Department of Anthropology
6 Penn State - Pennsylvania State University
7 HCMR - Hellenic Centre for Marine Research
8 LPGP - Laboratoire de Physiologie et Génomique des Poissons
9 Department of Animal Biology
10 BROAD INSTITUTE - Broad Institute of MIT and Harvard
11 Eccles Institute of Human Genetics
12 Cold Spring Harbor
13 Wellcome Trust Genome Campus
14 EMBL-EBI - European Bioinformatics Institute [Hinxton]
15 The Wellcome Trust Sanger Institute [Cambridge]
16 Department of Zoology
17 Department of Animal and Plant Sciences [Sheffield]
18 School of Biological Sciences [Bangor]
19 A*STAR - Agency for science, technology and research [Singapore]
20 IGFL - Institut de Génomique Fonctionnelle de Lyon
21 Department of Genetics
22 Department of Molecular Biomedical Sciences Raleigh
23 Center for Comparative Medicine and Translational Research
24 Departament de Genètica
25 Institut de Recerca de la Biodiversitat
26 Center for Circadian Clocks
27 School of Biology and Basic Medical Sciences, Medical College
28 Bioinformatics Group, Department of Computer Science
29 Young Investigators Group Bioinformatics and Transcriptomics, Department of Proteomics
30 Department of Dental Hygiene
31 Morsani College of Medicine, Department of Pediatrics
32 Department of Microbiology
33 SOKENDAI - Graduate University for Advanced Studies [Hayama]
34 Molecular Genetics Program
35 Department of Biological Sciences
36 European Molecular Biology Laboratory, Wellcome Trust Genome Campus
37 Instituto de Ciências Biológicas
38 Department of Molecular Biomedical Sciences
39 IMPRS - International Max Planck Research School for Organismal Biology
40 Genome Analysis Center
41 Science for Life Laboratory, Department of Medical Biochemistry and Microbiology
2 IB - Department of Integrative Biology [Berkeley]
3 Department of Organismal Biology and Anatomy
4 Department of Biology
5 Department of Anthropology
6 Penn State - Pennsylvania State University
7 HCMR - Hellenic Centre for Marine Research
8 LPGP - Laboratoire de Physiologie et Génomique des Poissons
9 Department of Animal Biology
10 BROAD INSTITUTE - Broad Institute of MIT and Harvard
11 Eccles Institute of Human Genetics
12 Cold Spring Harbor
13 Wellcome Trust Genome Campus
14 EMBL-EBI - European Bioinformatics Institute [Hinxton]
15 The Wellcome Trust Sanger Institute [Cambridge]
16 Department of Zoology
17 Department of Animal and Plant Sciences [Sheffield]
18 School of Biological Sciences [Bangor]
19 A*STAR - Agency for science, technology and research [Singapore]
20 IGFL - Institut de Génomique Fonctionnelle de Lyon
21 Department of Genetics
22 Department of Molecular Biomedical Sciences Raleigh
23 Center for Comparative Medicine and Translational Research
24 Departament de Genètica
25 Institut de Recerca de la Biodiversitat
26 Center for Circadian Clocks
27 School of Biology and Basic Medical Sciences, Medical College
28 Bioinformatics Group, Department of Computer Science
29 Young Investigators Group Bioinformatics and Transcriptomics, Department of Proteomics
30 Department of Dental Hygiene
31 Morsani College of Medicine, Department of Pediatrics
32 Department of Microbiology
33 SOKENDAI - Graduate University for Advanced Studies [Hayama]
34 Molecular Genetics Program
35 Department of Biological Sciences
36 European Molecular Biology Laboratory, Wellcome Trust Genome Campus
37 Instituto de Ciências Biológicas
38 Department of Molecular Biomedical Sciences
39 IMPRS - International Max Planck Research School for Organismal Biology
40 Genome Analysis Center
41 Science for Life Laboratory, Department of Medical Biochemistry and Microbiology
Ingo Braasch
- Fonction : Auteur
- PersonId : 1017552
Kazuhiko Kawasaki
- Fonction : Auteur
- PersonId : 784022
- ORCID : 0000-0003-1090-5340
Tereza Manousaki
- Fonction : Auteur
- PersonId : 784023
- ORCID : 0000-0001-7518-0542
Jérémy Pasquier
- Fonction : Auteur
- PersonId : 955496
Tatsuya Ota
- Fonction : Auteur
- PersonId : 784024
- ORCID : 0000-0002-1115-5169
Yann Guiguen
- Fonction : Auteur
- PersonId : 739883
- IdHAL : yann-guiguen
- ORCID : 0000-0001-5464-6219
- IdRef : 094996423
Julien Bobe
- Fonction : Auteur
- PersonId : 739882
- IdHAL : julien-bobe
- ORCID : 0000-0002-9355-8227
- IdRef : 111700884
Résumé
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.
Mots clés
lépisosté tacheté
teleosteen
poisson
homme
duplication des génomes
fonction des gènes
vertébré
lepisosteus oculatus
miRNA
évolution du génome
séquence régulatrice
physiologie animale
analyse génomique
analyse du transcriptome
chromosome
analyse phylogénétique
expression des gènes
immunité
reproduction
interaction animal homme