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

Ecology, Evolution and Behavior

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

172 Scopus citations

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

Bibliographical note

Funding Information:
This work was supported by NIH grant R24 RR032658-01 to W.C.W. and The Genome Institute at Washington University School of Medicine. Collections were conducted with Mexican Permit Number 040396-213-03 granted to W.R.J. This work was also supported by the Wellcome Trust (grant numbers WT095908 and WT098051) and the European Molecular Biology Laboratory. Shisa2 qPCR work benefited from the facilities and expertise of the QPCR platform of IMAGIF (Centre de Recherche de Gif-www. imagif.cnrs.fr). This work was supported in part by the National Institutes of Health (NIDCR) grant DE022403 to J.B.G. We thank J. Tabin for technical assistance. We are grateful for resources from the University of Minnesota Supercomputing Institute.

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© 2014 Macmillan Publishers Limited. All rights reserved.

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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, [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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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.",

author = "McGaugh, {Suzanne E.} and Gross, {Joshua B.} and Bronwen Aken and Maryline Blin and Richard Borowsky and Domitille Chalopin and H{\'e}l{\`e}ne Hinaux and Jeffery, {William R.} and Alex Keene and Li Ma and Patrick Minx and Daniel Murphy and O'Quin, {Kelly E.} and Sylvie R{\'e}taux and Nicolas Rohner and Searle, {Steve M.J.} and Stahl, {Bethany A.} and Cliff Tabin and Volff, {Jean Nicolas} and Masato Yoshizawa and Warren, {Wesley C.}",

note = "Funding Information: This work was supported by NIH grant R24 RR032658-01 to W.C.W. and The Genome Institute at Washington University School of Medicine. Collections were conducted with Mexican Permit Number 040396-213-03 granted to W.R.J. This work was also supported by the Wellcome Trust (grant numbers WT095908 and WT098051) and the European Molecular Biology Laboratory. Shisa2 qPCR work benefited from the facilities and expertise of the QPCR platform of IMAGIF (Centre de Recherche de Gif-www. imagif.cnrs.fr). This work was supported in part by the National Institutes of Health (NIDCR) grant DE022403 to J.B.G. We thank J. Tabin for technical assistance. We are grateful for resources from the University of Minnesota Supercomputing Institute. Publisher Copyright: {\textcopyright} 2014 Macmillan Publishers Limited. All rights reserved.",

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AU - McGaugh, Suzanne E.

AU - Gross, Joshua B.

AU - Aken, Bronwen

AU - Blin, Maryline

AU - Borowsky, Richard

AU - Chalopin, Domitille

AU - Hinaux, Hélène

AU - Jeffery, William R.

AU - Keene, Alex

AU - Ma, Li

AU - Minx, Patrick

AU - Murphy, Daniel

AU - O'Quin, Kelly E.

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.

N1 - Funding Information: This work was supported by NIH grant R24 RR032658-01 to W.C.W. and The Genome Institute at Washington University School of Medicine. Collections were conducted with Mexican Permit Number 040396-213-03 granted to W.R.J. This work was also supported by the Wellcome Trust (grant numbers WT095908 and WT098051) and the European Molecular Biology Laboratory. Shisa2 qPCR work benefited from the facilities and expertise of the QPCR platform of IMAGIF (Centre de Recherche de Gif-www. imagif.cnrs.fr). This work was supported in part by the National Institutes of Health (NIDCR) grant DE022403 to J.B.G. We thank J. Tabin for technical assistance. We are grateful for resources from the University of Minnesota Supercomputing Institute. Publisher Copyright: © 2014 Macmillan Publishers Limited. All rights reserved.

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N2 - 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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The cavefish genome reveals candidate genes for eye loss

Abstract

Bibliographical note

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