title: The cavefish genome reveals candidate genes for eye loss.
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.
authors.affiliation: The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA.
authors.forename: Suzanne E
authors.initials: SE
authors.lastname: McGaugh
authors.affiliation: Department of Biological Sciences, University of Cincinnati, 711B Rieveschl Hall, 312 College Drive, Cincinnati, Ohio 45221, USA.
authors.forename: Joshua B
authors.initials: JB
authors.lastname: Gross
authors.affiliation: 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.
authors.forename: Bronwen
authors.initials: B
authors.lastname: Aken
authors.affiliation: DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France.
authors.forename: Maryline
authors.initials: M
authors.lastname: Blin
authors.affiliation: Department of Biology, New York University, New York, New York 10003-6688, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Borowsky
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR 5242, UCBL, 46 allée d'Italie, Lyon F-69364, France.
authors.forename: Domitille
authors.initials: D
authors.lastname: Chalopin
authors.affiliation: DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Hinaux
authors.affiliation: Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
authors.forename: William R
authors.initials: WR
authors.lastname: Jeffery
authors.affiliation: Department of Biology, University of Nevada, Reno, Nevada 89557, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Keene
authors.affiliation: Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Ma
authors.affiliation: The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Minx
authors.affiliation: 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.
authors.forename: Daniel
authors.initials: D
authors.lastname: Murphy
authors.affiliation: Department of Biology, Centre College, 600 West Walnut St, Danville, Kentucky 40422, USA.
authors.forename: Kelly E
authors.initials: KE
authors.lastname: O'Quin
authors.affiliation: DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard, 91198 Gif-sur-Yvette, France.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Rétaux
authors.affiliation: Harvard Medical School Department of Genetics, 77 Avenue Louis Pasteur; NRB 360, Boston, Massachusetts 02115, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Rohner
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Steve M J
authors.initials: SM
authors.lastname: Searle
authors.affiliation: Department of Biological Sciences, University of Cincinnati, 711B Rieveschl Hall, 312 College Drive, Cincinnati, Ohio 45221, USA.
authors.forename: Bethany A
authors.initials: BA
authors.lastname: Stahl
authors.affiliation: Harvard Medical School Department of Genetics, 77 Avenue Louis Pasteur; NRB 360, Boston, Massachusetts 02115, USA.
authors.forename: Cliff
authors.initials: C
authors.lastname: Tabin
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR 5242, UCBL, 46 allée d'Italie, Lyon F-69364, France.
authors.forename: Jean-Nicolas
authors.initials: JN
authors.lastname: Volff
authors.affiliation: Department of Biology, University of Nevada, Reno, Nevada 89557, USA.
authors.forename: Masato
authors.initials: M
authors.lastname: Yoshizawa
authors.affiliation: The Genome Institute, Washington University, Campus Box 8501, St Louis, Missouri 63108, USA.
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
mesh_terms: D000818:Animals; D017209:Apoptosis; D060126:Characidae / Q000196:embryology / Q000235:genetics*; D004251:DNA Transposable Elements; D004777:Environment; D019143:Evolution, Molecular; D005123:Eye / Q000196:embryology*; D029941:Fish Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D017403:In Situ Hybridization; D008969:Molecular Sequence Data; D010641:Phenotype; D040641:Quantitative Trait Loci; D012160:Retina / Q000196:embryology* / Q000502:physiology
chemical_list: D004251:DNA Transposable Elements; D029941:Fish Proteins