Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas

Ciezarek AG, Dunning LT, Jones CS, Noble LR, Humble E, Stefanni SS, Savolainen V (2016)
Genome Biology and Evolution 8(9): 3011-3021.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Ciezarek, Adam G.; Dunning, Luke T.; Jones, Catherine S.; Noble, Leslie R.; Humble, EmilyUniBi ; Stefanni, Sergio S.; Savolainen, Vincent
Erscheinungsjahr
2016
Zeitschriftentitel
Genome Biology and Evolution
Band
8
Ausgabe
9
Seite(n)
3011-3021
ISSN
1759-6653
Page URI
https://pub.uni-bielefeld.de/record/2906089

Zitieren

Ciezarek AG, Dunning LT, Jones CS, et al. Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas. Genome Biology and Evolution. 2016;8(9):3011-3021.
Ciezarek, A. G., Dunning, L. T., Jones, C. S., Noble, L. R., Humble, E., Stefanni, S. S., & Savolainen, V. (2016). Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas. Genome Biology and Evolution, 8(9), 3011-3021. doi:10.1093/gbe/evw211
Ciezarek, A. G., Dunning, L. T., Jones, C. S., Noble, L. R., Humble, E., Stefanni, S. S., and Savolainen, V. (2016). Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas. Genome Biology and Evolution 8, 3011-3021.
Ciezarek, A.G., et al., 2016. Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas. Genome Biology and Evolution, 8(9), p 3011-3021.
A.G. Ciezarek, et al., “Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas”, Genome Biology and Evolution, vol. 8, 2016, pp. 3011-3021.
Ciezarek, A.G., Dunning, L.T., Jones, C.S., Noble, L.R., Humble, E., Stefanni, S.S., Savolainen, V.: Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas. Genome Biology and Evolution. 8, 3011-3021 (2016).
Ciezarek, Adam G., Dunning, Luke T., Jones, Catherine S., Noble, Leslie R., Humble, Emily, Stefanni, Sergio S., and Savolainen, Vincent. “Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas”. Genome Biology and Evolution 8.9 (2016): 3011-3021.

96 References

Daten bereitgestellt von Europe PubMed Central.

ExaBayes: massively parallel bayesian tree inference for the whole-genome era.
Aberer AJ, Kobert K, Stamatakis A., Mol. Biol. Evol. 31(10), 2014
PMID: 25135941
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
FastML: a web server for probabilistic reconstruction of ancestral sequences
Ashkenazy H., 2012
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Benjamini Y, Hochberg Y.., 1995
Comparative studies of high performance swimming in sharks II. Metabolic biochemistry of locomotor and myocardial muscle in endothermic and ectothermic sharks.
Bernal D, Smith D, Lopez G, Weitz D, Grimminger T, Dickson K, Graham JB., J. Exp. Biol. 206(Pt 16), 2003
PMID: 12847128

AUTHOR UNKNOWN, 2012
Analysis of the evolutionary convergence for high performance swimming in lamnid sharks and tunas [Review]
Bernal D, Dickson KA, Shadwick RE, Graham JB.., 2001
Comparative studies of high performance swimming in sharks I. Red muscle morphometrics, vascularization and ultrastructure.
Bernal D, Sepulveda C, Mathieu-Costello O, Graham JB., J. Exp. Biol. 206(Pt 16), 2003
PMID: 12847127
Evidence for temperature elevation in the aerobic swimming musculature of the common thresher shark
Bernal D, Sepulveda CA.., 2005
Influence of swimming speed on metabolic rates of juvenile pacific bluefin tuna and yellowfin tuna.
Blank JM, Farwell CJ, Morrissette JM, Schallert RJ, Block BA., Physiol. Biochem. Zool. 80(2), 2007
PMID: 17252513
Endothermy in fishes: a phylogenetic analysis of constraints, predispositions, and selection pressures
Block BA, Finnerty JR.., 1994
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Canestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alfoldi J, Lindblad-Toh K, Postlethwait JH., Nat. Genet. 48(4), 2016
PMID: 26950095
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T., Bioinformatics 25(15), 2009
PMID: 19505945
Warm-bodied Fish
Carey FG, Teal JM, Kanwish JW, Lawson KD, Beckett JS.., 1971
Adaptive evolution and functional redesign of core metabolic proteins in snakes.
Castoe TA, Jiang ZJ, Gu W, Wang ZO, Pollock DD., PLoS ONE 3(5), 2008
PMID: 18493604
Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis.
Chaikuad A, Froese DS, Berridge G, von Delft F, Oppermann U, Yue WW., Proc. Natl. Acad. Sci. U.S.A. 108(52), 2011
PMID: 22160680
Isolation, nucleotide sequence, and physiological relevance of the gene encoding triose phosphate isomerase from Kluyveromyces lactis.
Compagno C, Boschi F, Daleffe A, Porro D, Ranzi BM., Appl. Environ. Microbiol. 65(9), 1999
PMID: 10473437
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M., Bioinformatics 21(18), 2005
PMID: 16081474
Differences between glycogen biogenesis in fast- and slow-twitch rabbit muscle.
Cusso R, Lerner LR, Cadefau J, Gil M, Prats C, Gasparotto M, Krisman CR., Biochim. Biophys. Acta 1620(1-3), 2003
PMID: 12595075
RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas.
Diaz-Arce N, Arrizabalaga H, Murua H, Irigoien X, Rodriguez-Ezpeleta N., Mol. Phylogenet. Evol. 102(), 2016
PMID: 27286653
Locomotor muscle of high performance fishes: What do comparisons of tunas with ectothermic sister taxa reveal?
Dickson KA.., 1996
Evolution and consequences of endothermy in fishes.
Dickson KA, Graham JB., Physiol. Biochem. Zool. 77(6), 2004
PMID: 15674772
Convergent evolution in mechanical design of lamnid sharks and tunas
Donley JM, Supelveda CA, Konstanidis P, Gemballa S, Shadwick RE.., 2004
Positive selection in glycolysis among Australasian stick insects.
Dunning LT, Dennis AB, Thomson G, Sinclair BJ, Newcomb RD, Buckley TR., BMC Evol. Biol. 13(), 2013
PMID: 24079656
Respiratory metabolism: glycolysis, the TCA cycle and mitochondrial electron transport.
Fernie AR, Carrari F, Sweetlove LJ., Curr. Opin. Plant Biol. 7(3), 2004
PMID: 15134745
Protein function at thermal extremes: balancing stability and flexibility [Review]
Fields PA.., 2001
Pfam: the protein families database.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24288371
The sarcoplasmic reticulum and the control of muscle contraction.
Franzini-Armstrong C., FASEB J. 13 Suppl 2(), 1999
PMID: 10619141
CD-HIT: accelerated for clustering the next-generation sequencing data.
Fu L, Niu B, Zhu Z, Wu S, Li W., Bioinformatics 28(23), 2012
PMID: 23060610
Evolution of high-performance swimming in sharks: transformations of the musculotendinous system from subcarangiform to thunniform swimmers.
Gemballa S, Konstantinidis P, Donley JM, Sepulveda C, Shadwick RE., J. Morphol. 267(4), 2006
PMID: 16429422
MaxAlign: maximizing usable data in an alignment.
Gouveia-Oliveira R, Sackett PW, Pedersen AG., BMC Bioinformatics 8(), 2007
PMID: 17725821
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A., Nat. Biotechnol. 29(7), 2011
PMID: 21572440
Role of glycerol 3-phosphate dehydrogenase in glyceride metabolism. Effect of diet on enzyme activities in chicken liver.
Harding JW Jr, Pyeritz EA, Copeland ES, White HB 3rd., Biochem. J. 146(1), 1975
PMID: 167714
Peroxisome proliferator-induced long chain acyl-CoA thioesterases comprise a highly conserved novel multi-gene family involved in lipid metabolism.
Hunt MC, Nousiainen SE, Huttunen MK, Orii KE, Svensson LT, Alexson SE., J. Biol. Chem. 274(48), 1999
PMID: 10567408
The mitochondrial carnitine/acylcarnitine carrier: function, structure and physiopathology.
Indiveri C, Iacobazzi V, Tonazzi A, Giangregorio N, Infantino V, Convertini P, Console L, Palmieri F., Mol. Aspects Med. 32(4-6), 2011
PMID: 22020112

Korsmeyer KE, Dewar H.., 2001
The aerobic capacity of tunas: adaptation for multiple metabolic demands
Korsmeyer KE, Dewar H, Lai NC, Graham JB.., 1996
Effects of exercise on GLUT-4 and glycogenin gene expression in human skeletal muscle.
Kraniou Y, Cameron-Smith D, Misso M, Collier G, Hargreaves M., J. Appl. Physiol. 88(2), 2000
PMID: 10658052
An algorithm for progressive multiple alignment of sequences with insertions.
Loytynoja A, Goldman N., Proc. Natl. Acad. Sci. U.S.A. 102(30), 2005
PMID: 16000407
Assessing niche width of endothermic fish from genes to ecosystem.
Madigan DJ, Carlisle AB, Gardner LD, Jayasundara N, Micheli F, Schaefer KM, Fuller DW, Block BA., Proc. Natl. Acad. Sci. U.S.A. 112(27), 2015
PMID: 26100889
Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families
Miya M., 2013
Using new tools to solve an old problem: the evolution of endothermy in vertebrates.
Nespolo RF, Bacigalupe LD, Figueroa CC, Koteja P, Opazo JC., Trends Ecol. Evol. (Amst.) 26(8), 2011
PMID: 21571391
Molecular pathogenesis of a new glycogenosis caused by a glycogenin-1 mutation.
Nilsson J, Halim A, Moslemi AR, Pedersen A, Nilsson J, Larson G, Oldfors A., Biochim. Biophys. Acta 1822(4), 2011
PMID: 22198226
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Notredame C, Higgins DG, Heringa J., J. Mol. Biol. 302(1), 2000
PMID: 10964570
Genome-wide signatures of convergent evolution in echolocating mammals.
Parker J, Tsagkogeorga G, Cotton JA, Liu Y, Provero P, Stupka E, Rossiter SJ., Nature 502(7470), 2013
PMID: 24005325
GUIDANCE: a web server for assessing alignment confidence scores.
Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T., Nucleic Acids Res. 38(Web Server issue), 2010
PMID: 20497997
jModelTest: phylogenetic model averaging.
Posada D., Mol. Biol. Evol. 25(7), 2008
PMID: 18397919
Scombroid fishes provide novel insights into the trait/rate associations of molecular evolution.
Qiu F, Kitchen A, Burleigh JG, Miyamoto MM., J. Mol. Evol. 78(6), 2014
PMID: 24810994

Rambaut A, Suchard M, Drummond AJ.., 2013
Characterization of the heart transcriptome of the white shark (Carcharodon carcharias).
Richards VP, Suzuki H, Stanhope MJ, Shivji MS., BMC Genomics 14(), 2013
PMID: 24112713
Patterns of positive selection in seven ant genomes.
Roux J, Privman E, Moretti S, Daub JT, Robinson-Rechavi M, Keller L., Mol. Biol. Evol. 31(7), 2014
PMID: 24782441
First molecular scombrid timetree (Percomorpha: Scombridae) shows recent radiation of tunas following invasion of pelagic habitat
Santini FG, Carnevale G, Sorenson L.., 2013
The Atlantic Bonito (Sarda sarda, Bloch 1793) transcriptome and detection of differential expression during larvae development.
Sarropoulou E, Moghadam HK, Papandroulakis N, De la Gandara F, Ortega Garcia A, Makridis P., PLoS ONE 9(2), 2014
PMID: 24503907
Elevated red myotomal muscle temperatures in the most basal tuna species, Allothunnus fallai
Sepulveda CA, Dickson KA, Bernal D, Graham JB.., 2008
The effect of habitat on modern shark diversification.
Sorenson L, Santini F, Alfaro ME., J. Evol. Biol. 27(8), 2014
PMID: 24890604
A rapid bootstrap algorithm for the RAxML Web servers.
Stamatakis A, Hoover P, Rougemont J., Syst. Biol. 57(5), 2008
PMID: 18853362
Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trachiuridae): Tissue-Specific Expression Patterns and characterization of depth-related functional genes
Stefanni S., 2014
The genetic causes of convergent evolution.
Stern DL., Nat. Rev. Genet. 14(11), 2013
PMID: 24105273
Red muscle function in stiff-bodied swimmers: there and almost back again.
Syme DA, Shadwick RE., Philos. Trans. R. Soc. Lond., B, Biol. Sci. 366(1570), 2011
PMID: 21502122
UniProt: a hub for protein information.
UniProt Consortium, Bateman A, Martin MJ, O'Donovan C, Magrane M, Apweiler R, Alpi E, Antunes R, Arganiska J, Bely B, Bingley M, Bonilla C, Britto R, Bursteinas B, Chavali G, Cibrian-Uhalte E, Silva AD, De Giorgi M, Dogan T, Fazzini F, Gane P, Castro LG, Garmiri P, Hatton-Ellis E, Hieta R, Huntley R, Legge D, Liu W, Luo J, MacDougall A, Mutowo P, Nightingale A, Orchard S, Pichler K, Poggioli D, Pundir S, Pureza L, Qi G, Rosanoff S, Saidi R, Sawford T, Shypitsyna A, Turner E, Volynkin V, Wardell T, Watkins X, Zellner H, Cowley A, Figueira L, Li W, McWilliam H, Lopez R, Xenarios I, Bougueleret L, Bridge A, Poux S, Redaschi N, Aimo L, Argoud-Puy G, Auchincloss A, Axelsen K, Bansal P, Baratin D, Blatter MC, Boeckmann B, Bolleman J, Boutet E, Breuza L, Casal-Casas C, de Castro E, Coudert E, Cuche B, Doche M, Dornevil D, Duvaud S, Estreicher A, Famiglietti L, Feuermann M, Gasteiger E, Gehant S, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, Jungo F, Keller G, Lara V, Lemercier P, Lieberherr D, Lombardot T, Martin X, Masson P, Morgat A, Neto T, Nouspikel N, Paesano S, Pedruzzi I, Pilbout S, Pozzato M, Pruess M, Rivoire C, Roechert B, Schneider M, Sigrist C, Sonesson K, Staehli S, Stutz A, Sundaram S, Tognolli M, Verbregue L, Veuthey AL, Wu CH, Arighi CN, Arminski L, Chen C, Chen Y, Garavelli JS, Huang H, Laiho K, McGarvey P, Natale DA, Suzek BE, Vinayaka C, Wang Q, Wang Y, Yeh LS, Yerramalla MS, Zhang J., Nucleic Acids Res. 43(Database issue), 2014
PMID: 25348405
PDBe: Protein Data Bank in Europe.
Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19858099
Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes).
Velez-Zuazo X, Agnarsson I., Mol. Phylogenet. Evol. 58(2), 2010
PMID: 21129490
A Cluster algorithm for graphs
Van S.., 2000
Elephant shark genome provides unique insights into gnathostome evolution.
Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC., Nature 505(7482), 2014
PMID: 24402279
Comparative analyses of animal-tracking data reveal ecological significance of endothermy in fishes.
Watanabe YY, Goldman KJ, Caselle JE, Chapman DD, Papastamatiou YP., Proc. Natl. Acad. Sci. U.S.A. 112(19), 2015
PMID: 25902489
Mammalian metabolite flux rates in a teleost: lactate and glucose turnover in tuna.
Weber JM, Brill RW, Hochachka PW., Am. J. Physiol. 250(3 Pt 2), 1986
PMID: 3953854
The horizontal septum: mechanisms of force transfer in locomotion of scombrid fishes (Scombridae, Perciformes)
Westneat MW, Hoese W, Pell CA, Wainwright SA.., 1993

Wikström M.., 2010
Orthology inference in non-model organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics
Yang Y, Smith SA.., 2014
PAML 4: phylogenetic analysis by maximum likelihood.
Yang Z., Mol. Biol. Evol. 24(8), 2007
PMID: 17483113
Statistical methods for detecting molecular adaptation.
Yang Z, Bielawski JP., Trends Ecol. Evol. (Amst.) 15(12), 2000
PMID: 11114436
A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis.
Yasuike M, Fujiwara A, Nakamura Y, Iwasaki Y, Nishiki I, Sugaya T, Shimizu A, Sano M, Kobayashi T, Ototake M., Gene 576(2 Pt 1), 2015
PMID: 26477480
Ensembl 2016.
Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Giron CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P., Nucleic Acids Res. 44(D1), 2015
PMID: 26687719
Leiomodin-3 dysfunction results in thin filament disorganization and nemaline myopathy.
Yuen M, Sandaradura SA, Dowling JJ, Kostyukova AS, Moroz N, Quinlan KG, Lehtokari VL, Ravenscroft G, Todd EJ, Ceyhan-Birsoy O, Gokhin DS, Maluenda J, Lek M, Nolent F, Pappas CT, Novak SM, D'Amico A, Malfatti E, Thomas BP, Gabriel SB, Gupta N, Daly MJ, Ilkovski B, Houweling PJ, Davidson AE, Swanson LC, Brownstein CA, Gupta VA, Medne L, Shannon P, Martin N, Bick DP, Flisberg A, Holmberg E, Van den Bergh P, Lapunzina P, Waddell LB, Sloboda DD, Bertini E, Chitayat D, Telfer WR, Laquerriere A, Gregorio CC, Ottenheijm CA, Bonnemann CG, Pelin K, Beggs AH, Hayashi YK, Romero NB, Laing NG, Nishino I, Wallgren-Pettersson C, Melki J, Fowler VM, MacArthur DG, North KN, Clarke NF., J. Clin. Invest. 124(11), 2014
PMID: 25250574
Effect of muscle-fiber type on glycogenin-1 gene expression and its relationship with the glycolytic potential and pH of pork.
Zhang SH, Zhu L, Wu ZH, Zhang Y, Tang GQ, Jiang YZ, Li MZ, Bai L, Li XW., Genet. Mol. Res. 12(3), 2013
PMID: 24065679

Zou Z, Zhang J.., 2015

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 27614233
PubMed | Europe PMC

Suchen in

Google Scholar