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; Wesley C. Warren

doi:10.1038/ncomms6307

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 YoshizawaWesley C. Warren

Biology and Genomics

Research output: Contribution to journal › Article › peer-review

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 language	English (US)
Article number	5307
Journal	Nature communications
Volume	5
DOIs	https://doi.org/10.1038/ncomms6307
State	Published - Oct 20 2014

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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McGaugh, S. E., Gross, J. B., Aken, B., Blin, M., Borowsky, R., Chalopin, D., Hinaux, H., Jeffery, W. R., Keene, A., Ma, L., Minx, P., Murphy, D., O'Quin, K. E., Rétaux, S., Rohner, N., Searle, S. M. J., Stahl, B. A., Tabin, C., Volff, J. N., ... Warren, W. C. (2014). The cavefish genome reveals candidate genes for eye loss. Nature communications, 5, Article 5307. https://doi.org/10.1038/ncomms6307

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

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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.",

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AU - Aken, Bronwen

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AU - Borowsky, Richard

AU - Chalopin, Domitille

AU - Hinaux, Hélène

AU - Jeffery, William R.

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AU - Ma, Li

AU - Minx, Patrick

AU - Murphy, Daniel

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AU - Rétaux, Sylvie

AU - Rohner, Nicolas

AU - Searle, Steve M.J.

AU - Stahl, Bethany A.

AU - Tabin, Cliff

AU - Volff, Jean Nicolas

AU - Yoshizawa, Masato

AU - Warren, Wesley C.

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The cavefish genome reveals candidate genes for eye loss

Abstract

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