The cavefish genome reveals candidate genes for eye loss

Suzanne E. McGaugh (), Joshua B. Gross, Bronwen Aken, Maryline Blin, Richard Borowsky, Domitille Chalopin, Hélène Hinaux, William R. Jeffery, Alex Keene, Li Ma, Patrick Minx, Daniel Murphy, Kelly E. O’Quin, Sylvie Rétaux, Nicolas Rohner, Steve M. J. Searle, Bethany A. Stahl, Cliff Tabin, Jean-Nicolas Volff, Masato Yoshizawa and Wesley C. Warren
Additional contact information
Suzanne E. McGaugh: The Genome Institute, Washington University, Campus Box 8501
Joshua B. Gross: University of Cincinnati
Bronwen Aken: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
Maryline Blin: DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard
Richard Borowsky: New York University
Domitille Chalopin: Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS
Hélène Hinaux: DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard
William R. Jeffery: University of Maryland
Alex Keene: University of Nevada
Li Ma: University of Maryland
Patrick Minx: The Genome Institute, Washington University, Campus Box 8501
Daniel Murphy: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
Kelly E. O’Quin: Centre College
Sylvie Rétaux: DECA group, Neurobiology and Development Laboratory, CNRS-Institut de Neurobiologie Alfred Fessard
Nicolas Rohner: Harvard Medical School Department of Genetics
Steve M. J. Searle: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
Bethany A. Stahl: University of Cincinnati
Cliff Tabin: Harvard Medical School Department of Genetics
Jean-Nicolas Volff: Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS
Masato Yoshizawa: University of Nevada
Wesley C. Warren: The Genome Institute, Washington University, Campus Box 8501

Nature Communications, 2014, vol. 5, issue 1, 1-10

Abstract: 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.

Date: 2014
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DOI: 10.1038/ncomms6307

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