Journal Article

An Integrated Transcriptome-Wide Analysis of Cave and Surface Dwelling Astyanax mexicanus

Gross, J.B., Furterer, A., Carlson, B.M. and Stahl, B.A.

Record Number:
2536
Year:
2013
Journal:
Plos One
Volume:
8:e55659
Short Title:
An Integrated Transcriptome-Wide Analysis of Cave and Surface Dwelling Astyanax mexicanus
Alternate Journal:
Plos One
Notes:
092wj
URL:
://WOS:000315153400134
Date:
Feb 6
Accession Number:
WOS:000315153400134
Language:
English
Issue:
2
Abstract:
Numerous organisms around the globe have successfully adapted to subterranean environments. A powerful system in which to study cave adaptation is the freshwater characin fish, Astyanax mexicanus. Prior studies in this system have established a genetic basis for the evolution of numerous regressive traits, most notably vision and pigmentation reduction. However, identification of the precise genetic alterations that underlie these morphological changes has been delayed by limited genetic and genomic resources. To address this, we performed a transcriptome analysis of cave and surface dwelling Astyanax morphs using Roche/454 pyrosequencing technology. Through this approach, we obtained 576,197 Pachon cavefish-specific reads and 438,978 surface fish-specific reads. Using this dataset, we assembled transcriptomes of cave and surface fish separately, as well as an integrated transcriptome that combined 1,499,568 reads from both morphotypes. The integrated assembly was the most successful approach, yielding 22,596 high quality contiguous sequences comprising a total transcriptome length of 21,363,556 bp. Sequence identities were obtained through exhaustive blast searches, revealing an adult transcriptome represented by highly diverse Gene Ontology ( GO) terms. Our dataset facilitated rapid identification of sequence polymorphisms between morphotypes. These data, along with positional information collected from the Danio rerio genome, revealed several syntenic regions between Astyanax and Danio. We demonstrated the utility of this positional information through a QTL analysis of albinism in a surface x Pachon cave F-2 pedigree, using 65 polymorphic markers identified from our integrated assembly. We also adapted our dataset for an RNA-seq study, revealing many genes responsible for visual system maintenance in surface fish, whose expression was not detected in adult Pachon cavefish. Conversely, several metabolism-related genes expressed in cavefish were not detected in surface fish. This resource will enable powerful genetic and genomic analyses in the future that will better clarify the heritable genetic changes governing adaptation to the cave environment.
ISSN:
1932-6203
Times Cited:
1
Author Address:
Univ Cincinnati, Dept Biol Sci, Cincinnati, OH 45221 USA
Related Records:
Hubbs, C. L. and Innes, W. T. (1936)Gresser, E. B. and Breder, C. M. (1940)Bridges, W. (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)Osorio Tafall, B. F. (1943)Breder, C. M. (1943)Breder, C. M. (1943)Breder, C. M. (1944)Alvarez, J. (1946)Breder, C. M. and Rasquin, P. (1947)Alvarez, J. (1947)Schlagel, S. R. and Breder, C. M. (1947)Breder, C. M. and Rasquin, P. (1947)Rasquin, P. (1949)Luling, K. H. (1953)Luling, K. H. (1953)Luling, K. H. (1953)Luling, K. H. (1954)Luling, K. H. (1954)Stefanelli, A. (1954)Stefanelli, A. (1954)Rasquin, P. and Rosenbloom, L. (1954)Thines, G. (1954)Luling, K. H. (1955)Luling, K. H. (1955)Sadoglu, P. (1956)Sadoglu, P. (1957)Sadoglu, P. (1957)Thines, G. and Kahling, J. (1957)Grobbel, G. and Hahn, G. (1958)Cahn, P. H. (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)Boucquey, C., Thines, G. and Van Der Borght, C. (1965)Thines, G., Wolff-Van Ermengem, F., Boucquey, C. and Soffie, M. (1965)Carmignani, M. P. A. (1966)Peters, N. and Peters, G. (1966)Cavicchioli, G. and Guarnieri, P. (1966)Reed, M. (1966)Thines, G., Soffie, M. and Vandenbussche, E. (1966)Sadoglu, P. (1967)Walters, V. and Liu, R. K. (1967)Schemmel, C. (1967)Pfeiffer, W. (1967)Pfeiffer, W. (1967)Popper, A. N. and Tavolga, W. N. (1967)Carmignani, M. P. A. (1968)Wilkens, H. (1968)Mattheij, J. A. (1968)Mattheij, J. A. (1968)Weiss, B. A. (1969)Sadoglu, P. and McKee, A. (1969)Mattheij, J. A. (1969)Mattheij, J. A. and Sprangers, J. A. P. (1969)Weiss, B. and Martini, J. (1970)Whitt, G. S. and Maeda, F. S. (1970)Wilkens, H. (1970)Wilkens, H. (1970)Wilkens, H. (1970)Popper, A. N. (1970)Mattheij, J. A. (1970)Mattheij, J. A. (1970)Gertychowa, R. (1970)Gertychowa, R. (1970)Gertychowa, R. (1971)Wiley, S. and Mitchell, R. W. (1971)Wiley, S. and Mitchell, R. W. (1971)Zaccone, G. (1971)Wilkens, H. (1971)Popper, A. N. (1971)Avise, J. C. and Selander, R. K. (1972)Zaccone, G. (1972)Wilkens, H. (1972)Wilkens, H. (1972)Wilkens, H. (1972)Wilkens, H. and Burns, R. J. (1972)Thines, G. and Wissocq, N. (1972)Voneida, T. J. (1973)Yasuda, K. (1973)Schemmel, C. (1973)Zeitlin, S. M. (1973)Zeitlin, S. M. and McDevitt, D. S. (1973)Durand, J. P. (1973)Thines, G. and LeGrain, J. M. (1973)Mitchell, R. W. (1973)Schemmel, C. (1974)Chakraborty, R. and Nei, M. (1974)Schemmel, C. (1974)Sligar, C. (1974)Omura, Y. (1975)Sadoglu, P. (1975)Peters, N., Scholl, A. and Wilkens, H. (1975)Voneida, T. J. and Sligar, C. (1976)Herwig, H. J. (1976)Herwig, H. J. (1976)Sligar, C. and Voneida, T. J. (1976)Wilkens, H. (1976)Durand, J. P. (1976)Erckens, W. and Weber, F. (1976)Yew, D. T. and Yoshihara, H. M. (1977)Zaccone, G. (1977)Wilkens, H. (1977)Kirby, R. F., Thompson, K. W. and Hubbs, C. (1977)Mitchell, R. W., Russell, W. H. and Elliott, W. R. (1977)Durand, J. P. (1978)Thines, G. and Weyers, M. (1978)Wilkens, H., Peters, H. and Schemmel, C. (1979)Woodhead, A. D. and Achey, P. M. (1979)Sadoglu, P. (1979)Durand, J. P. (1979)Weissert, R. (1980)Schemmel, C. (1980)Quinn, T. P. (1980)Wilkens, H. (1980)Wilkens, H. (1980)Campenhausen, C., Riess, I. and Weissert, R. (1981)Weissert, R. and Campenhausen, C. (1981)Herwig, H. J. (1981)Reddell, J. R. (1981)Jankowska, M. and Thines, G. (1982)Tabata, M. (1982)Erckens, W. and Martin, W. (1982)Lamprecht, G. and Weber, F. (1982)Erckens, W. and Martin, W. (1982)Rose, F. L. and Mitchell, R. W. (1982)Parzefall, J. (1983)Zilles, K., Tillmann, B. and Bennemann, R. (1983)Romero, A. (1983)Voneida, T. J. and Fish, S. E. (1984)Wilkens, H. (1984)Romero, A. (1984)Romero, A. (1984)Burchards, H., Dolle, A. and Parzefall, J. (1985)Teyke, T. (1985)Wilkens, H. (1985)Lamprecht, G. and Weber, F. (1985)Romero, A. (1985)Hassan, E. S. (1986)Parzefall, J. (1986)Huppop, K. (1986)De Fraipont, M. (1986)Fraipont, M. (1986)De Fraipont, M. and Thines, G. (1986)De Fraipont, M. and Thines, G. (1986)Wilkens, H. (1986)Romero, A (1986)Wilkens, H. and Huppop, K. (1986)Huppop, K. (1987)De Fraipont, M. (1987)De Fraipont, M. (1987)Wilkens, H. (1987)Huppop, K. (1988)De Fraipont, M. (1988)Teyke, T. (1988)Wilkens, H. (1988)Fricke, D. (1988)Hassan, E. S. (1989)Huppop, K. (1989)Teyke, T. (1989)Langecker, T. G. (1989)Fricke, D. and Parzefall, J. (1989)Fack, H. and Wilkens, H. (1989)Parzefall, J. and Fricke, D. (1990)Yokoyama, R. and Yokoyama, S. (1990)Peters, N., Schmidt, W. and Fricke, D. (1990)Abdel-Latif, H., Hassan, E. S. and von Campenhausen, C. (1990)Yokoyama, R and Yokoyama, S (1990)Teyke, T. (1990)Klimpel, B. and Parzefall, J. (1990)Langecker, T. G. (1990)Langecker, T. G., Wilkens, H. and Junge, P. (1991)Campenhausen, C. (1991)Parzefall, J. and Fricke, D. (1991)Huppop, K. and Wilkens, H. (1991)Huppop, K. (1991)Riedel, G. and Krug, L. (1991)Wilkens, H. and Meyer, M. (1992)Parzefall, J. (1992)Hassan, E. S., Abdel-Latif, H. and Biebricher, R. (1992)Parzefall, J. (1992)De Fraipont, M. (1992)Lamprecht, G. and Weber, F. (1992)Wilkens, H. (1992)Langecker, T. G. and Longley, G. (1992)Langecker, T. G., Schmale, H. and Wilkens, H. (1993)Langecker, T. G., Schmale, H. and Wilkens, H. (1993)Parzefall, J. (1993)Hoffman, S. and Hausberg, C. (1993)Peters, N., Schacht, V., Schmidt, W. and Wilkens, H. (1993)Langecker, T. G. (1993)Borowsky, R. (1994)Teyke, T. and Schaerer, S. (1994)Langecker, T. G., Neumann, B., Hausberg, C. and Parzefall, J. (1995)Langecker, T. G., Wilkens, H. and Schmale, H. (1995)Yokoyama, S., Meany, A., Wilkens, H. and Yokoyama, R. (1995)Borowsky, R. (1996)Behrens, M., Langecker, T. G., Wilkens, H. and Schmale, H. (1997)Riedel, G. (1997)Borowsky, R. and Espinasa, L. (1997)Riedel, G. and Krug, L. (1997)Contreras-Balderas, S. and Lozano-Vilano, M.D.L. (1998)Behrens, M, Wilkens, H and Schmale, H (1998)Jeffery, WR and Martasian, DP (1998)Wilkens, H. (1998)Baker, CF and Montgomery, J (1999)Kullander, S. O. (1999)Yamamoto, Y. and Jeffery, W. R. (2000)Jeffery, W. R., Strickler, A.G., Guiney, S., Heyser, D.G. and Tomarev, S.I. (2000)Espinasa, L. and Borowsky, R. (2000)Strickler, A.G., Yamamoto, Y. and Jeffery, W. R. (2001)Jeffery, W. R. (2001)Boudriot, F and Reutter, K (2001)Espinasa, L. and Borowsky, R. (2001)Montgomery, J.C., Coombs, S. and Baker, C.F. (2001)Romero, A, Jeffery, WR and Yamamoto, Y (2002)Krejca, J. (2002)Berg, A and Watson, GM (2002)Strickler, AG, Famuditimi, K and Jeffery, WR (2002)Dowling, TE, Martasian, DP and Jeffery, WR (2002)Borowsky, RL and Wilkens, H (2002)Wilkens, H. and Strecker, U. (2003)Porter, M.L. and Crandall, K.A. (2003)Sarma, SSS, Lopez-Romulo, A and Nandini, S (2003)Contreras-Balderas, S, Almada-Villela, P, Lozano-Vilano, M de L and Garcia-Ramirez, ME (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, JB, Tabin, C and Borowsky, RL (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)Jeffery, WR (2009)Kowalko, J, Gross, JB, Protas, M, Borowsky, RL and Tabin, C (2009)Kowalko, J, Rohner, N, Borowsky, RL and Tabin, C (2011)Esquivel-Bobadilla, S (2011)Jeffery, W.R. (2012)Protas, M. and Jeffery, W. R. (2012)Pazza, R (2013)Bibliowicz, J., Alie, A., Espinasa, L., Yoshizawa, M., Blin, M., Hinaux, H., Legendre, L., Pere, S. and Retaux, S. (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)Stahl, B. A. and Gross, J. B. (2013)Stahl, AL (2013)Espinasa, L., Bartolo, N.D. and Newkirk, C.E. (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)Moran, D, Softley, R and Warrant, EJ (2014)Stahl, B. A., Ma, L and Gross, J. B. (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)McGaugh, S. E. (2015)Silva, D. M. Z. A., Utsunomia, R., Pansonato-Alves, J.C., Oliveira, C. and Foresti, F. (2015)Hinaux, Helene, Blin, Maryline, Fumey, Julien, Legendre, Laurent, Heuze, Aurelie, Casane, Didier and Retaux, Sylvie (2015)Moran, D, Softley, R and Warrant, EJ (2015)Fumey, J. (2015)Rohner, N (2015)Aspiras, Ariel C., Rohner, Nicolas, Martineau, Brian, Borowsky, Richard L. and Tabin, Clifford J. (2015)Bradic, M, Rohner, N, Tabin, C and Borowsky, R. (2015)Stahl, Bethany A. and Gross, Joshua B. (2015)Gross, J.B., Stahl, B.A., Powers, A.K. and Carlson, B.M. (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)Schmitter-Soto, JJ (2016)O'Quin, Kelly and McGaugh, Suzanne E. (2016)Casane, D and Retaux, S (2016)Beale, A., Whitmore, D and Moran, D (2016)Rohner, Nicolas (2016)Aspiras, A., Tabin, C. and Rohner, N. (2016)Jaggard, J. B., Robinson, B. G., Stahl, B, Oh, I, Masek, P, Yoshizawa, M and Keene, A. (2017)Wilkens, H. and Strecker, U. (2017)Stahl, B (2017)Stahl, B.A. and Gross, J.B. (2017)Jaggard, J. B. (2017)Hinaux, H, Recher, G, Alie, A., Legendre, L, Blin, M. and Retaux, S (2017)Schmitter-Soto, JJ (2017)Fumey J, Hinaux H, Noirot C, Thermes C, Re´ taux S, Casane D. (2017)Krishnan, J and Rohner, N (2017)Pazza, R., Dergam, J.A. and Kavalco, K.F. (2018)Kling, J. (2018)Chin, J.S.R., Gassant, C.E., Amaral, P.M., Lloyd, E., Stahl, B.A., Jaggarda, J.B., Keenea, A.C. and Duboue, E.R. (2018)Stern, D.B and Crandall, K.A. (2018)Xiong, S., Krishnan, J., Peuß, F. and Rohner, N. (2018)Jaggard, J.B., Stahl, B.A., Lloyd, E., Prober, D.A., Duboue, E.R. and Keene, A.C. (2018)Alie, A., Devos, L., Torres-Paz, J., Prunier, L., Boulet, F., Blin, M., Elipot, Y. and Retaux, S. (2018)Gross, J.B., Weagley, J., Stahl, B.A., Ma, L., Espinasa, L. and McGaugh, S.E. (2018)Elliott, W.R. (2018)Fumey, J., Hinaux, H., Noirot, C., Thermes, C., Rétaux, S. and Casane, D. (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)Rohner, N. (2018)