The cavefish genome reveals candidate genes for eye loss.
Suzanne E Mcgaugh
(1, 2)
,
Joshua B Gross
(3)
,
Bronwen Aken
(4)
,
Maryline Blin
(5, 6)
,
Richard Borowsky
(7)
,
Domitille Chalopin
(8)
,
William R Jeffery
(9)
,
Alex Keene
(10)
,
Li Ma
(9)
,
Patrick Minx
(2)
,
Kelly E O'Quin
(11)
,
Sylvie Rétaux
(6, 5)
,
Nicolas Rohner
(12)
,
Steve M J Searle
(4)
,
Bethany A Stahl
(3)
,
Cliff Tabin
,
Jean-Nicolas Volff
(8)
,
Masato Yoshizawa
(10)
,
Wesley C Warren
(2)
,
Hélène Hinaux
(6, 5)
,
Daniel V. Murphy
(4)
1
EEB -
Department of Ecology, Evolution and Behavior
2 WUSTL - Washington University in Saint Louis
3 UC - University of Cincinnati
4 The Wellcome Trust Sanger Institute [Cambridge]
5 INAF - Institut de Neurobiologie Alfred Fessard
6 N&eD - Neurobiologie et Développement
7 Department of Biology [New York]
8 IGFL - Institut de Génomique Fonctionnelle de Lyon
9 Department of Biology
10 University of Nevada [Reno]
11 Centre College
12 Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School
2 WUSTL - Washington University in Saint Louis
3 UC - University of Cincinnati
4 The Wellcome Trust Sanger Institute [Cambridge]
5 INAF - Institut de Neurobiologie Alfred Fessard
6 N&eD - Neurobiologie et Développement
7 Department of Biology [New York]
8 IGFL - Institut de Génomique Fonctionnelle de Lyon
9 Department of Biology
10 University of Nevada [Reno]
11 Centre College
12 Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School
Domitille Chalopin
- Fonction : Auteur
- PersonId : 773875
- IdHAL : domitille-chalopin
- ORCID : 0000-0003-0588-9630
- IdRef : 179263013
Sylvie Rétaux
- Fonction : Auteur
- PersonId : 753474
- IdHAL : sylvie-retaux
Cliff Tabin
- Fonction : Auteur
Jean-Nicolas Volff
- Fonction : Auteur
- PersonId : 763540
- ORCID : 0000-0003-3406-892X
- IdRef : 10913480X
Résumé
Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genetic interrogation; however, lack of a reference genome has hampered efforts to identify genes responsible for changes in cave forms of A. mexicanus. Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences. We expect the cavefish genome to advance understanding of the evolutionary process, as well as, analogous human disease including retinal dysfunction.