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Nat Commun. 2014 Oct 20;5:5307. doi: 10.1038/ncomms6307.

The cavefish genome reveals candidate genes for eye loss.

Author information

1
The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA.
2
Department of Biological Sciences, University of Cincinnati, 711B Rieveschl Hall, 312 College Drive, Cincinnati, Ohio 45221, USA.
3
1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK [2] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
4
DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France.
5
Department of Biology, New York University, New York, New York 10003-6688, USA.
6
Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR 5242, UCBL, 46 allée d'Italie, Lyon F-69364, France.
7
Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
8
Department of Biology, University of Nevada, Reno, Nevada 89557, USA.
9
Department of Biology, Centre College, 600 West Walnut St, Danville, Kentucky 40422, USA.
10
Harvard Medical School Department of Genetics, 77 Avenue Louis Pasteur; NRB 360, Boston, Massachusetts 02115, USA.
11
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

Abstract

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.

PMID:
25329095
PMCID:
PMC4218959
DOI:
10.1038/ncomms6307
[Indexed for MEDLINE]
Free PMC Article
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