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 & 1 others Wesley C. Warren

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number5307
JournalNature Communications
Volume5
DOIs
StatePublished - Oct 20 2014

Fingerprint

genome
genes
Genes
Genome
caves
Caves
Taste Buds
taste
Retinal Diseases
degeneration
Quantitative Trait Loci
interrogation
loci
pigments
organs
Population
assembly
Pressure
shift
Pigments

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemistry(all)
  • Physics and Astronomy(all)

Cite this

McGaugh, S. E., Gross, J. B., Aken, B., Blin, M., Borowsky, R., Chalopin, D., ... Warren, W. C. (2014). The cavefish genome reveals candidate genes for eye loss. Nature Communications, 5, [5307]. https://doi.org/10.1038/ncomms6307

The cavefish genome reveals candidate genes for eye loss. / McGaugh, Suzanne E.; Gross, Joshua B.; Aken, Bronwen; Blin, Maryline; Borowsky, Richard; Chalopin, Domitille; Hinaux, Hélène; Jeffery, William R.; Keene, Alex; Ma, Li; Minx, Patrick; Murphy, Daniel; O'Quin, Kelly E.; Rétaux, Sylvie; Rohner, Nicolas; Searle, Steve M J; Stahl, Bethany A.; Tabin, Cliff; Volff, Jean Nicolas; Yoshizawa, Masato; Warren, Wesley C.

In: Nature Communications, Vol. 5, 5307, 20.10.2014.

Research output: Contribution to journalArticle

McGaugh, SE, Gross, JB, Aken, B, Blin, M, Borowsky, R, Chalopin, D, Hinaux, H, Jeffery, WR, Keene, A, Ma, L, Minx, P, Murphy, D, O'Quin, KE, Rétaux, S, Rohner, N, Searle, SMJ, Stahl, BA, Tabin, C, Volff, JN, Yoshizawa, M & Warren, WC 2014, 'The cavefish genome reveals candidate genes for eye loss', Nature Communications, vol. 5, 5307. https://doi.org/10.1038/ncomms6307
McGaugh, Suzanne E. ; Gross, Joshua B. ; Aken, Bronwen ; Blin, Maryline ; Borowsky, Richard ; Chalopin, Domitille ; Hinaux, Hélène ; Jeffery, William R. ; Keene, Alex ; Ma, Li ; Minx, Patrick ; Murphy, Daniel ; O'Quin, Kelly E. ; Rétaux, Sylvie ; Rohner, Nicolas ; Searle, Steve M J ; Stahl, Bethany A. ; Tabin, Cliff ; Volff, Jean Nicolas ; Yoshizawa, Masato ; Warren, Wesley C. / The cavefish genome reveals candidate genes for eye loss. In: Nature Communications. 2014 ; Vol. 5.
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