Journal Article

The cavefish genome reveals candidate genes for eye loss

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., Retaux, S., Rohner, N., Searl, S.M., Stahl, B.A., Tabin, C., Volff, J.N., Yoshizawa M, Warren WC.

Record Number:
2923
Year:
2014
Journal:
Nature Communications
Pages:
5307
Volume:
5
Short 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.
Times Cited:
1
Related Records:
Hubbs, C.L. and Innes, W.T. (1936)Bridges, W. (1940)Gresser, E. B. and Breder, C. M. (1940)Breder, C. M. and Gresser, E. B. (1941)Breder, C. M. and Gresser, E. B. (1941)Breder, C. M. and Gresser, E. B. (1941)Breder, C. M. (1942)Breder, C. M. (1943)Breder, C. M. (1943)Osorio Tafall, B. F. (1943)Breder, C. M. (1944)Alvarez, J. (1946)Breder, C. M. and Rasquin, P. (1947)Breder, C. M. and Rasquin, P. (1947)Schlagel, S. R. and Breder, C. M. (1947)Alvarez, J. (1947)Rasquin, P. (1949)Luling, K. H. (1953)Luling, K. H. (1953)Luling, K. H. (1953)Luling, K. H. (1954)Luling, K. H. (1954)Thines, G. (1954)Stefanelli, A. (1954)Rasquin, P. and Rosenbloom, L. (1954)Stefanelli, A. (1954)Luling, K. H. (1955)Luling, K. H. (1955)Sadoglu, P. (1956)Sadoglu, P. (1957)Thines, G. and Kahling, J. (1957)Sadoglu, P. (1957)Cahn, P. H. (1958)Grobbel, G. and Hahn, G. (1958)Kahling, J. (1961)Luling, K. H. (1962)Burgers, A. C. J., Bennink, P. J. H. and van Oordt, G. J. (1963)Franck, A. (1964)Thines, G., Wolff-Van Ermengem, F., Boucquey, C. and Soffie, M. (1965)Boucquey, C., Thines, G. and Van Der Borght, C. (1965)Peters, N. and Peters, G. (1966)Thines, G., Soffie, M. and Vandenbussche, E. (1966)Carmignani, M. P. A. (1966)Cavicchioli, G. and Guarnieri, P. (1966)Reed, M. (1966)Sadoglu, P. (1967)Schemmel, C. (1967)Pfeiffer, W. (1967)Pfeiffer, W. (1967)Popper, A. N. and Tavolga, W. N. (1967)Walters, V. and Liu, R. K. (1967)Mattheij, J. A. (1968)Mattheij, J. A. (1968)Carmignani, M. P. A. (1968)Wilkens, H. (1968)Sadoglu, P. and McKee, A. (1969)Mattheij, J. A. (1969)Mattheij, J. A. and Sprangers, J. A. P. (1969)Weiss, B. A. (1969)Mattheij, J. A. (1970)Mattheij, J. A. (1970)Popper, A. N. (1970)Weiss, B. and Martini, J. (1970)Whitt, G. S. and Maeda, F. S. (1970)Wilkens, H. (1970)Gertychowa, R. (1970)Wilkens, H. (1970)Gertychowa, R. (1970)Wilkens, H. (1970)Popper, A. N. (1971)Wiley, S. and Mitchell, R. W. (1971)Wiley, S. and Mitchell, R. W. (1971)Zaccone, G. (1971)Gertychowa, R. (1971)Wilkens, H. (1971)Thines, G. and Wissocq, N. (1972)Wilkens, H. and Burns, R. J. (1972)Avise, J. C. and Selander, R. K. (1972)Zaccone, G. (1972)Wilkens, H. (1972)Wilkens, H. (1972)Wilkens, H. (1972)Thines, G. and LeGrain, J. M. (1973)Schemmel, C. (1973)Voneida, T. J. (1973)Yasuda, K. (1973)Durand, J. P. (1973)Mitchell, R. W. (1973)Zeitlin, S. M. (1973)Zeitlin, S. M. and McDevitt, D. S. (1973)Schemmel, C. (1974)Schemmel, C. (1974)Sligar, C. (1974)Chakraborty, R. and Nei, M. (1974)Sadoglu, P. (1975)Peters, N., Scholl, A. and Wilkens, H. (1975)Omura, Y. (1975)Herwig, H. J. (1976)Herwig, H. J. (1976)Voneida, T. J. and Sligar, C. (1976)Sligar, C. and Voneida, T. J. (1976)Durand, J. P. (1976)Erckens, W. and Weber, F. (1976)Wilkens, H. (1976)Wilkens, H. (1977)Kirby, R. F., Thompson, K. W. and Hubbs, C. (1977)Yew, D. T. and Yoshihara, H. M. (1977)Zaccone, G. (1977)Mitchell, R. W., Russell, W. H. and Elliott, W. R. (1977)Thines, G. and Weyers, M. (1978)Durand, J. P. (1978)Sadoglu, P. (1979)Wilkens, H., Peters, H. and Schemmel, C. (1979)Woodhead, A. D. and Achey, P. M. (1979)Durand, J. P. (1979)Wilkens, H. (1980)Wilkens, H. (1980)Schemmel, C. (1980)Quinn, T. P. (1980)Weissert, R. (1980)Herwig, H. J. (1981)Campenhausen, C., Riess, I. and Weissert, R. (1981)Weissert, R. and Campenhausen, C. (1981)Reddell, J. R. (1981)Jankowska, M. and Thines, G. (1982)Lamprecht, G. and Weber, F. (1982)Erckens, W. and Martin, W. (1982)Rose, F. L. and Mitchell, R. W. (1982)Erckens, W. and Martin, W. (1982)Tabata, M. (1982)Parzefall, J. (1983)Romero, A. (1983)Zilles, K., Tillmann, B. and Bennemann, R. (1983)Wilkens, H. (1984)Schuppa, M. (1984)Voneida, T. J. and Fish, S. E. (1984)Romero, A. (1984)Romero, A. (1984)Teyke, T. (1985)Wilkens, H. (1985)Burchards, H., Dolle, A. and Parzefall, J. (1985)Lamprecht, G. and Weber, F. (1985)Romero, A. (1985)Parzefall, J. (1986)Wilkens, H. (1986)Huppop, K. (1986)Wilkens, H. and Huppop, K. (1986)De Fraipont, M. (1986)Fraipont, M. (1986)De Fraipont, M. and Thines, G. (1986)De Fraipont, M. and Thines, G. (1986)Romero, A. (1986)Hassan, E. S. (1986)Wilkens, H. (1987)Huppop, K. (1987)De Fraipont, M. (1987)De Fraipont, M. (1987)Teyke, T. (1988)Huppop, K. (1988)Wilkens, H. (1988)De Fraipont, M. (1988)Fricke, D. (1988)Teyke, T. (1989)Fack, H. and Wilkens, H. (1989)Huppop, K. (1989)Langecker, T. G. (1989)Fricke, D. and Parzefall, J. (1989)Hassan, E. S. (1989)Teyke, T. (1990)Parzefall, J. and Fricke, D. (1990)Peters, N., Schmidt, W. and Fricke, D. (1990)Abdel-Latif, H., Hassan, E. S. and von Campenhausen, C. (1990)Klimpel, B. and Parzefall, J. (1990)Yokoyama, R. and Yokoyama, S. (1990)Yokoyama, R and Yokoyama, S (1990)Langecker, T. G. (1990)Parzefall, J. and Fricke, D. (1991)Huppop, K. and Wilkens, H. (1991)Campenhausen, C. (1991)Huppop, K. (1991)Riedel, G. and Krug, L. (1991)Langecker, T. G., Wilkens, H. and Junge, P. (1991)Parzefall, J. (1992)Parzefall, J. (1992)Wilkens, H. (1992)Wilkens, H. and Meyer, M. (1992)Lamprecht, G. and Weber, F. (1992)De Fraipont, M. (1992)Langecker, T. G. and Longley, G. (1992)Hassan, E. S., Abdel-Latif, H. and Biebricher, R. (1992)Hoffman, S. and Hausberg, C. (1993)Parzefall, J. (1993)Peters, N., Schacht, V., Schmidt, W. and Wilkens, H. (1993)Langecker, T. G. (1993)Langecker, T. G., Schmale, H. and Wilkens, H. (1993)Langecker, T. G., Schmale, H. and Wilkens, H. (1993)Teyke, T. and Schaerer, S. (1994)Borowsky, R. (1994)Yokoyama, S., Meany, A., Wilkens, H. and Yokoyama, R. (1995)Langecker, T. G., Neumann, B., Hausberg, C. and Parzefall, J. (1995)Langecker, T. G., Wilkens, H. and Schmale, H. (1995)Borowsky, R. (1996)Behrens, M., Langecker, T.G., Wilkens, H. and Schmale, H. (1997)Riedel, G. (1997)Riedel, G. and Krug, L. (1997)Borowsky, R. and Espinasa, L. (1997)Wilkens, H. (1998)Jeffery, WR and Martasian, DP (1998)Behrens, M, Wilkens, H and Schmale, H (1998)Contreras-Balderas, S. and Lozano-Vilano, M.D.L. (1998)Kullander, S. O. (1999)Baker, CF and Montgomery, J (1999)Espinasa, L. and Borowsky, R. (2000)Jeffery, W. R., Strickler, A.G., Guiney, S., Heyser, D.G. and Tomarev, S.I. (2000)Yamamoto, Y. and Jeffery, W. R. (2000)Ford, D.C. (2000)Espinasa, L. and Borowsky, R. (2001)Jeffery, W. R. (2001)Strickler, A.G., Yamamoto, Y. and Jeffery, W. R. (2001)Montgomery, J.C., Coombs, S. and Baker, C.F. (2001)Boudriot, F and Reutter, K (2001)Romero, A., Jeffery, W.R. and Yamamoto, Y. (2002)Berg, A. and Watson, G.M. (2002)Dowling, TE, Martasian, DP and Jeffery, WR (2002)Krejca, J. (2002)Borowsky, RL and Wilkens, H (2002)Strickler, AG, Famuditimi, K and Jeffery, WR (2002)Sarma, SSS, Lopez-Romulo, A and Nandini, S (2003)Wilkens, H. and Strecker, U. (2003)Contreras-Balderas, S, Almada-Villela, P, Lozano-Vilano, M de L and Garcia-Ramirez, ME (2003)Porter, M.L. and Crandall, K.A. (2003)Strecker, U. (2003)Strecker, U., Bernatchez, L. and Wilkens, H. (2003)McCauley, DW, Hixon, E and Jeffery, WR (2004)Protas ME, Hersey C, Kochanek D, Zhou Y, Wilkens H, Jeffery WR, Zon LI, Borowsky R, Tabin CJ. (2006)Protas, M., Conrad, M., Gross, J.B., Tabin, C. and Borowsky, R.L. (2007)Protas, M, Tabansky, I, Conrad, M, Gross, JB, Vidal, O, Tabin, C and Borowsky, RL (2008)Gross, JB, Protas, M, Conrad, M, Scheid, PE, Vidal, O and others (2008)Kowalko, J, Gross, JB, Protas, M, Borowsky, RL and Tabin, C (2009)Jeffery, WR (2009)Esquivel-Bobadilla, S (2011)Kowalko, J, Rohner, N, Borowsky, RL and Tabin, C (2011)Bradic, M, Beerli, P and Borowsky, RL (2011)Gross, J.B. (2012)Protas, M. and Jeffery, W. R. (2012)Bradic, M., Beerli, P., Garcia-de Leon, F. J., Esquivel-Bobadilla, S. and Borowsky, R. L. (2012)Wilkens, H. (2012)Trontelj, P. (2012)Dufton, M, Hall, BK and Franz-Odendaal, T. (2012)Jeffery, W.R. (2012)Elliott, William R. (2013)Kowalko, J.E., Rohner, N., Rompani, S.B., Peterson, B.K., Linden, T.A., Yoshizawa, M., Kay, E.H., Weber, J., Hoekstra, H.E., Jeffery, W.R., Borowsky, R. and Tabin, C.J. (2013)Rohner, N., Jarosz, D.F., Kowalko, J.E., Yoshizawa, M., Jeffery, W.R., Borowsky, R.L., Lindquist, S. and Tabin, C.J. (2013)Rohner, N (2013)Kowalko, J., Rohner, N., Linden, T.A., Rompani SB, Warren, W.C., Borowsky, R, Tabin, C.J., Jeffery, W.R. and Yoshizawa M. (2013)Gross, J.B., Furterer, A., Carlson, B.M. and Stahl, B.A. (2013)Bradic, M., Teotonio, H. and Borowsky, R. L. (2013)Stahl, B. A. and Gross, J. B. (2013)Stahl, AL (2013)Pazza, R (2013)Bibliowicz, J., Alie, A., Espinasa, L., Yoshizawa, M., Blin, M., Hinaux, H., Legendre, L., Pere, S. and Retaux, S. (2013)Atukorala, A. D. S., Hammer, C., Dufton, M. and Franz-Odendaal, T. A. (2013)Elliott, W.R. (2014)Espinasa, L., Bartolo, N.D. and Newkirk, C.E. (2014)Atukorallaya, D. and Franz-Odendaal, T. (2014)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., Retaux, S., Rohner, N., Searl, S.M., Stahl, B.A., Tabin, C., Volff, J.N., Yoshizawa M, Warren WC. (2014)Atukorala, A. D. S. and Franz-Odendaal, T. A. (2014)Moran, D., Softley, R. and Warrant, E.J. (2014)McGaugh, S. E. (2015)Dufton, Megan and Franz-Odendaal, Tamara A. (2015)Moran, D., Softley, R. and Warrant, E.J. (2015)Hinaux, Helene, Blin, Maryline, Fumey, Julien, Legendre, Laurent, Heuze, Aurelie, Casane, Didier and Retaux, Sylvie (2015)Fumey, J. (2015)Aspiras, A.C., Rohner, N., Martineau, B., Borowsky, R.L. and Tabin, C.J. (2015)Caballero-Hernandez, O., Hernandez-Patricio, M., Sigala-Regalado, I., Morales-Malacara, J. B. and Miranda-Anaya, M. (2015)Stahl, Bethany A. and Gross, Joshua B. (2015)Stahl, B. A., Ma, L and Gross, J. B. (2015)Bradic, M, Rohner, N, Tabin, C and Borowsky, R. (2015)Rohner, N (2015)Yoshizawa, Masato, Robinson, Beatriz G., Duboue, Erik R., Masek, Pavel, Jaggard, James B., O'Quin, Kelly E., Borowsky, Richard L., Jeffery, William R. and Keene, Alex C. (2015)Jaggard, J. B. (2015)Devos, Lucie, Alie, A. and Retaux, S (2015)Silva, D. M. Z. A., Utsunomia, R., Pansonato-Alves, J.C., Oliveira, C. and Foresti, F. (2015)O'Quin, Kelly and McGaugh, Suzanne E. (2016)Atukorala, A. D. S. and Franz-Odendaal, Tamara A. (2016)Beale, A., Whitmore, D. and Moran, D. (2016)Schmitter-Soto, JJ (2016)Gross, J.B., Stahl, B.A., Powers, A.K. and Carlson, B.M. (2016)Rohner, Nicolas (2016)Yoshizawa, M., Settle, A., Macaspac, C., Fernandes, V. Yoshida, M. and Keene, A. (2016)Aspiras, A., Tabin, C. and Rohner, N. (2016)Keene, A.C., Yoshizawa, M. and McGaugh, S.E. (2016)Retaux, Sylvie, Alie, Alexandre, Blin, Maryline, Devos, Lucie, Elipot, Yannick and Hinaux, Helene (2016)Casane, D and Retaux, S (2016)Fumey J, Hinaux H, Noirot C, Thermes C, Re´ taux S, Casane D. (2017)Lyon, A., Powers, A. K., Gross, J. B. and O'Quin, K. E. (2017)Gross, J. B. (2017)Kaplan, S.A., Powers, A.K. and Gross, J.B. (2017)Schmitter-Soto, JJ (2017)Jaggard, J. B., Robinson, B. G., Stahl, B, Oh, I, Masek, P, Yoshizawa, M and Keene, A. (2017)Stahl, B (2017)Yoshizawa, M (2017)Stahl, B.A. and Gross, J.B. (2017)Krishnan, J and Rohner, N (2017)Alvarado, C.G. (2017)Jaggard, J. B. (2017)Wilkens, H. and Strecker, U. (2017)Hinaux, H, Recher, G, Alie, A., Legendre, L, Blin, M. and Retaux, S (2017)Gross, J.B., Weagley, J., Stahl, B.A., Ma, L., Espinasa, L. and McGaugh, S.E. (2018)Devi, A., Atukorala, S. and Franz-Odendaal, T.A. (2018)Retaux, S. (2018)Blin, M., Tine, E., Meister, L., Elipot, Y., Bibliowicz, J., Espinasa, L. and Rétaux, S. (2018)Powers, A.K., Kaplan, S.A., Boggs, T.E. and Gross, J. (2018)Carlson, B.M. and Gross, J.B. (2018)Espinasa, L. (2018)Sears, C.R. and Gross, J.B. (2018)Espinasa, L., Legendre, L., Fumey, J., Blin, M., Rétaux, S. and Espinasa, M. (2018)Stah, B.A., Sears, C.R., Ma, L., Perkins, M. and Gross, J.B. (2018)Mirande, J.M. (2018)Powers, A.K., Boggs, T.E. and Gross, J.B. (2018)Borowsky, R. (2018)Tabin, J.A., Aspiras, A., Martineau, B., Riddle, M., Kowalko, J. Borowsky, R. Rohner, N. and Tabin, C.J. (2018)Borowsky, R., Luk, A., He, X.J. and Kim, R.S. (2018)Yoshizawa, M., Settle, A., Hermosura, M.C., Tuttle, L.J., Cetraro, N., Passow, C.N. and McGaugh, S.E. (2018)Riddle, M.R., Aspiras, A.C., Gaudenz, K., Peuß, R., Sung, J.Y., Martineau, B., Peavey, M., Box, A.C., Tabin, J.A., McGaugh, S., Borowsky, R., Tabin, C.J. and Rohner, N. (2018)Fernandes, V.F.L., Macaspac, C., Lu, L. and Yoshizawa, M. (2018)Rohner, N. (2018)Garita-Alvarado, C.A., Barluenga, M. and Ornelas-García, C.P. (2018)Jaggard, J.B., Stahl, B.A., Lloyd, E., Prober, D.A., Duboue, E.R. and Keene, A.C. (2018)Pazza, R., Dergam, J.A. and Kavalco, K.F. (2018)Kopp, J., Avasthi, S. and Espinasa, L. (2018)Ojha, A. and Watve, M. (2018)Kling, J. (2018)Gore, A., Jeffery, W., Retaux, S. and Rohner, N. (2018)Chin, J.S.R., Gassant, C.E., Amaral, P.M., Lloyd, E., Stahl, B.A., Jaggard, J.B., Keene, A.C. and Duboue, E.R. (2018)Gore, A.V., Rohner, N., Rétaux, S. and Jeffery, W.R. (2018)Alie, A., Devos, L., Torres-Paz, J., Prunier, L., Boulet, F., Blin, M., Elipot, Y. and Retaux, S. (2018)Ma, L., Strickler, A.G., Parkhurst, A., Yoshizawa, M., Shi, J. and Jeffery, W.R. (2018)Stern, D.B and Crandall, K.A. (2018)Xiong, S., Krishnan, J., Peuß, F. and Rohner, N. (2018)Ren, X.Y., Hamilton, N., Müller, F. and Yamamoto, Y. (2018)Elliott, W.R. (2018)Devitsina, G.V. and Golovkina, T.V. (2018)Fumey, J., Hinaux, H., Noirot, C., Thermes, C., Rétaux, S. and Casane, D. (2018)