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Vol. 127, No. 2-4, 2009
Issue release date: April 2010
Cytogenet Genome Res 2009;127:79–93

From Reptilian Phylogenomics to Reptilian Genomes: Analyses of c-Jun and DJ-1 Proto-Oncogenes

Katsu Y. · Braun E.L. · Guillette, Jr. L.J. · Iguchi T.
aDivision of Molecular Environmental Endocrinology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, and Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, Okazaki, bDepartment of Biosystems Science, Graduate School of Life Science, Hokkaido University, Sapporo, Japan; cDepartment of Biology, University of Florida, Gainesville, Fla., USA

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Genome projects have revolutionized our understanding of both molecular biology and evolution, but there has been a limited collection of genomic data from reptiles. This is surprising given the pivotal position of reptiles in vertebrate phylogeny and the potential utility of information from reptiles for understanding a number of biological phenomena, such as sex determination. Although there are many potential uses for genomic data, one important and useful approach is phylogenomics. Here we report cDNA sequences for the c-Jun(JUN) and DJ-1(PARK7) proto-oncogenes from 3 reptiles (the American alligator, Nile crocodile, and Florida red-belly turtle), show that both genes are expressed in the alligator, and integrate them into analyses of their homologs from other organisms. With these taxa it was possible to conduct analyses that include all major vertebrate lineages. Analyses of c-Jun revealed an unexpected but well-supported frog-turtle clade while analyses of DJ-1 revealed a topology largely congruent with expectation based upon other data. The conflict between the c-Jun topology and expectation appears to reflect the overlap between c-Jun and a CpG island in most taxa, including crocodilians. This CpG island is absent in the frog and turtle, and convergence in base composition appears to be at least partially responsible for the signal uniting these taxa. Noise reduction approaches can eliminate the unexpected frog-turtle clade, demonstrating that multiple signals are present in the c-Jun alignment. We used phylogenetic methods to visualize these signals; we suggest that examining both historical and non-historical signals will prove important for phylogenomic analyses.

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  1. Aïssani B, Bernardi G: CpG islands: Features and distribution in the genome of vertebrates. Gene 106:173–183 (1991a).
  2. Aïssani B, Bernardi G: CpG islands, genes, isochores in the genome of vertebrates. Gene 106:185–195 (1991b).
  3. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 (1997).
  4. Arndt P, Hwa T: Identification and measurement of neighbor-dependent nucleotide substitution processes. Bioinformatics 21:2322–2328 (2005).
  5. Benton MJ, Donoghue PCJ: Paleontological evidence to date the tree of life. Mol Biol Evol 24:26–53 (2007).
  6. Bernardi G: Isochores and the evolutionary genomics of vertebrates. Gene 241:3–17 (2000).
  7. Bird A: CpG islands as gene markers in the vertebrate nucleus. Trends Genet 3:342–347 (1987).
  8. Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, et al: Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299:1391–1394 (2003).
  9. Braun EL, Grotewold E: Fungal Zuotin proteins evolved from MIDA1-like factors by lineage-specific loss of MYB domains. Mol Biol Evol 18:1401–1412 (2001).
  10. Braun EL, Kimball RT: Examining basal avian divergences with mitochondrial sequences: Model complexity, taxon sampling, and sequence length. Syst Biol 51:614–625 (2002).
  11. Bromham L, Wolfit M, Lee MSY, Rambaut A: Testing the relationship between morphological and molecular rates of change along phylogenies. Evolution 56:1921–1930 (2002).
  12. Brunner B, Grutzner F, Yaspo ML, Ropers HH, Haaf T, Kalscheuer VM: Molecular cloning and characterization of the Fugu rubripesMEST/COPG2 imprinting cluster and chromosomal localization in Fugu and Tetraodon nigroviridis. Chromosome Res 8:465–476 (2000).
  13. Bryant D, Moulton V: NeighborNet: An agglomerative algorithm for the construction of phylogenetic networks. Mol Biol Evol 21:255–265 (2004).
  14. Castoe TA, de Koning AP, Kim HM, Gu W, Noonan BP, et al: Evidence for an ancient adaptive episode of convergent molecular evolution. Proc Natl Acad Sci USA 106:8986–8991 (2009).
  15. Cheung E, Acevedo ML, Cole PA, Kraus WL: Altered pharmacology and distinct coactivator usage for estrogen receptor-dependent transcription through activating protein-1. Proc Natl Acad Sci USA 102:559–564 (2005).
  16. Chojnowski JL, Braun EL: Turtle isochore structure is intermediate between amphibians and other amniotes. Int Comp Biol 48:454–462 (2008).

    External Resources

  17. Chojnowski JL, Franklin J, Katsu Y, Iguchi T, Guillette Jr LJ, et al: Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes. J Mol Evol 65:259–266 (2007).
  18. Chojnowski JL, Kimball RT, Braun EL: Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene 410:89–96 (2008).
  19. Clay O, Bernardi G: Compositional heterogeneity within and among isochores in mammalian genomes. II. Some general comments. Gene 276:25–31 (2001).
  20. Conant GC, Lewis PO: Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference. Mol Biol Evol 18:1024–1033 (2001).
  21. Costantini M, Cammarano R, Bernardi G: The evolution of isochore patterns in vertebrate genomes. BMC Genomics 10:146 (2009).
  22. Cottage AJ, Edwards YJK, Elgar G: AP1 genes in Fugu indicate a divergent transcriptional control from that of mammals. Mamm Genome 14:514–525 (2003).
  23. Cotton JA, Page RDM: Going nuclear: Gene family evolution and vertebrate phylogeny reconciled. Proc R Soc Lond Ser B 269:1555–1561 (2002).
  24. Crews D: Sex determination: Where environment and genetics meet. Evol Dev 5:50–55 (2003).
  25. Cross S, Kovarik P, Schmidtke J, Bird A: Non-methylated islands in fish genomes are GC-poor. Nucleic Acids Res 19:1469–1474 (1991).
  26. Cuny G, Soriano P, Macaya G, Bernardi G: The major components of the mouse and human genomes. 1. Preparation, basic properties and compositional heterogeneity. Eur J Biochem 115:227–233 (1981).
  27. deBraga M, Rieppel O: Reptile phylogeny and the interrelationships of turtles. Zool J Linn Soc 120:281–354 (1997).
  28. Delsuc F, Brinkmann H, Philippe H: Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6:361–375 (2005).
  29. Duret L, Semon M, Piganeau G, Mouchiroud D, Galtier N: Vanishing GC-rich isochores in mammalian genomes. Genetics 162:1837–1847 (2002).
  30. Eernisse DJ, Kluge AG: Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol Biol Evol 10:1170–1195 (1993).
  31. Eferl R, Wagner EF: AP-1: A double-edged sword in tumorigenesis. Nat Rev Cancer 3:859–868 (2003).
  32. Eisen JA: Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8:163–167 (1998).
  33. Eisen JA, Kaiser D, Myers RL: Gastrogenomic delights: A movable feast. Nat Med 3:1076–1078 (1997).
  34. Fares MA, Byrne KP, Wolfe KH: Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species. Mol Biol Evol 23:245–253 (2006).
  35. Foster PG, Hickey DA: Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol 48:284–290 (1999).
  36. Foster PG, Jermiin LS, Hickey DA: Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol 44:282–288 (1997).
  37. Fujimoto J, Hori M, Ichigo S, Morishita S, Tamaya T: Estrogen induces expression of c-fos and c-jun via activation of protein kinase C in an endometrial cancer cell line and fibroblasts derived from human uterine endometrium. Gynecol Endocrinol 10:109–118 (1996).
  38. Galtier N, Gouy M: Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol Biol Evol 15:871–879 (1998).
  39. Gaucher E, Gu X, Miyamoto M, Benner S: Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci 27:315–321 (2002).
  40. Gauthier J, Kluge AG, Rowe T: Amniote phylogeny and the importance of fossils. Cladistics 4:105–209 (1988).

    External Resources

  41. Genome 10K Community of Scientists: Genome 10K: A proposal to obtain whole-genome sequences for 10,000 vertebrate species. J Hered 100:659–674 (2009).
  42. Georgelis N, Braun EL, Hannah LC: Duplication and functional divergence of ADP-glucose pyrophosphorylase genes in plants. BMC Evol Biol 8:232 (2008).
  43. Gerhart J, Bronner-Fraser M, Edwards S, Holland P: Evolution of the human proteome: Completing the chordate nodes. NIH White Paper available from under ‘The Large-Scale Genome Sequencing Program’ (2005).
  44. Gorr TA, Mable BK, Kleinschmidt T: Phylogenetic analysis of reptilian hemoglobins: trees, rates, and divergences. J Mol Evol 47:471–485 (1998).
  45. Hackett SJ, Kimball RT, Reddy S, Bowie RCK, Braun EL, et al: A phylogenomic study of birds reveals their evolutionary history. Science 320:1763–1768 (2008).
  46. Hamada K, Horiike T, Kanaya S, Nakamura H, Ota H, et al: Changes in body temperature pattern in vertebrates do not influence the codon usages of alpha-globin genes. Genes Genet Syst 77:197–207 (2002).
  47. Harshman J, Huddleston CJ, Bollback JP, Parsons TJ, Braun MJ: True and false gharials: A nuclear gene phylogeny of crocodylia. Syst Biol 52:386–402 (2003).
  48. Heath TA, Hedtke SM, Hillis DM: Taxon sampling and the accuracy of phylogenetic analyses. J Syst Evol 46:239–257 (2008).
  49. Hedges SB, Poling LL: A molecular phylogeny of reptiles. Science 283:998–1001 (1999).
  50. Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, et al: Ensembl 2009. Nucleic Acids Res 37:D690–697 (2009).
  51. Hugall AF, Foster R, Lee MSY: Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Syst Biol 56:543–563 (2007).
  52. Hughes S, Mouchiroud D: High evolutionary rates in nuclear genes of squamates. J Mol Evol 53:70–76 (2001).
  53. Hughes S, Zelus D, Mouchiroud D: Warm-blooded isochore structure in Nile crocodile and turtle. Mol Biol Evol 16:1521–1527 (1999).
  54. Hughes S, Clay O, Bernardi G: Compositional patterns in reptilian genomes. Gene 295:323–329 (2002).
  55. Huson DH, Bryant D: Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267 (2006).
  56. Hyder SM, Nawaz Z, Chiappetta C, Yokoyama K, Stancel GM: The protooncogene c-jun contains an unusual estrogen-inducible enhancer within the coding sequence. J Biol Chem 270:8506–8513 (1995).
  57. International Chicken Genome Sequencing Consortium: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716 (2004).
  58. International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 409:860–921 (2001).
  59. Iwabe N, Hara Y, Kumazawa Y, Shibamoto K, Saito Y, et al: Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins. Mol Biol Evol 22:810–813 (2005).
  60. Jabbari K, Cacciò S, Païs de Barros JP, Desgrès J, Bernardi G: Evolutionary changes in CpG and methylation levels in the genome of vertebrates. Gene 205:109–118 (1997).
  61. Jabbari K, Clay O, Bernardi G: GC3 heterogeneity and body temperature in vertebrates. Gene 317:161–163 (2003).
  62. Janssen P, Goldovsky L, Kunin V, Darzentas N, Ouzounis CA: Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. EMBO Rep 6:397–399 (2005).
  63. Jeffroy O, Brinkmann H, Delsuc F, Philippe H: Phylogenomics: the beginning of incongruence? Trends Genet 22:225–231 (2006).
  64. Jiang ZJ, Castoe TA, Austin CC, Burbrink FT, Herron MD, et al: Comparative mitochondrial genomics of snakes: Extraordinary substitution rate dynamics and functionality of the duplicate control region. BMC Evol Biol 7:123 (2007).
  65. Kent J, Coriat AM, Sharpe PT, Hastie ND, van Heyningen V: The evolution of WT1 sequence and expression pattern in the vertebrates. Oncogene 11:1781–1792 (1995).
  66. Kim RH, Smith PD, Aleyasin H, Hayley S, Mount MP, et al: Hypersensitivity of DJ-1-deficient mice to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrindine (MPTP) and oxidative stress. Proc Natl Acad Sci USA 102:5215–5220 (2005).
  67. Lang JW, Andrews HV: Temperature-dependent sex determination in crocodilians. J Exp Zool 270:28–44 (1994).
  68. Lau CK, Subramaniam M, Rasmussen K, Spelsberg TC: Rapid inhibition of the c-jun proto-oncogene expression in avian oviduct by estrogen. Endocrinology 127:2595–2597 (1990).
  69. Lau CK, Subramaniam M, Rasmussen K, Spelsberg TC: Rapid induction of the c-jun protooncogene in the avian oviduct by the antiestrogen tamoxifen. Proc Natl Acad Sci USA 88:829–833 (1991).
  70. Leão LI, Ho PL, Junqueira-de-Azevedo I de LM: Transcriptomic basis for an antiserum against Micrurus corallinus (coral snake) venom. BMC Genomics 10:112 (2009).
  71. Lee MSY: Molecules, morphology, and the monophyly of diapsid reptiles. Contrib Zool 70:1–22 (2001).

    External Resources

  72. Li W, Bernaola-Galvan P, Carpena P, Oliver JL: Isochores merit the prefix ‘iso’. Comput Biol Chem 27:5–10 (2003).
  73. Lockhart PJ, Steel MA, Hendy MD, Penny D: Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol 11:605–612 (1994).
  74. Loomis WF, Smith DW: Molecular phylogeny of Dictyostelium discoideum by protein sequence comparison. Proc Natl Acad Sci USA 87:9093–9097 (1990).
  75. Losos J, Braun E, Brown D, Clifton S, Edwards S, et al: Proposal to sequence the first reptilian genome: The green anole lizard, Anolis carolinensis. NIH White Paper available from under ‘The Large-Scale Genome Sequencing Program’ (2005).
  76. Løvtrup S: The Phylogeny of Vertebrata (John Wiley, London 1977).
  77. Maddison D, Maddison W: MacClade (Sinauer Associates, Sunderland 2002).
  78. Maddison WP: Gene trees in species trees. Syst Biol 46:523–536 (1997).

    External Resources

  79. Mannen H, Li SS-L: Molecular evidence for a clade of turtles. Mol Phylogenet Evol 13:144–148 (1999).
  80. Marcourt L, Cordier C, Couesnon T, Dodin G: Impact of C5-cytosine methylation on the solution structure of d(GAAAACGTT TTC)2. An NMR and molecular modelling investigation. Eur J Biochem 265:1032–1042 (1999).
  81. Modi WS, Crews D: Sex chromosomes and sex determination in reptiles. Curr Opin Genet Dev 15:660–665 (2005).
  82. Morishita S, Niwa K, Ichigo S, Hori M, Murase T, et al: Overexpressions of c-fos/jun mRNA and their oncoproteins (Fos/Jun) in the mouse uterus treated with three natural estrogens. Cancer Lett 97:225–231 (1995).
  83. Murphy WJ, Eizirik E, O’Brien SJ, Madsen O, Scally M, et al: Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348–2351 (2001).
  84. Niki T, Takahashi-Niki K, Taira T, Iguchi-Ariga SMM, Ariga H: DJBP: A novel DJ-1-binding protein, negatively regulates the androgen receptor by recruiting histone deacetylase complex, and DJ-1 antagonizes this inhibition by abrogation of this complex. Mol Cancer Res 1:247–261 (2003).
  85. Olmo E: Trends in the evolution of reptilian chromosomes. Integr Comp Biol 48:486–493 (2008).

    External Resources

  86. Omland KE: Correlated rates of molecular and morphological evolution. Evolution 51:1381–1393 (1997).
  87. Organ CL, Janes DE: Evolution of sex chromosomes in Sauropsida. Integr Comp Biol 48:512–519 (2008).

    External Resources

  88. Organ CL, Moreno RG, Edwards SV: Three tiers of genomic evolution in reptiles. Integr Comp Biol 48:494–504 (2008).

    External Resources

  89. Page RDM, Charleston MA: From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Mol Phylogenet Evol 7:231–240 (1997).
  90. Parmley JL, Chamary JV, Hurst LD: Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol 23:301–309 (2006).
  91. Phillips MJ, Penny D: The root of the mammalian tree inferred from whole mitochondrial genomes. Mol Phylogenet Evol 28:171–185 (2003).
  92. Pollock DD, Eisen JA, Doggett NA, Cummings MP: A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Mol Biol Evol 17:1776–1788 (2000).
  93. Qinghua L, Xiaowei Z, Wei Y, Chenji L, Yijun H, et al: A catalog for transcripts in the venom gland of the Agkistrodon acutus: identification of the toxins potentially involved in coagulopathy. Biochem Biophys Res Commun 341:522–531 (2006).
  94. Rest JS, Ast JC, Austin CC, Waddell PJ, Tibbetts EA, et al: Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Mol Phylogenet Evol 29:289–297 (2003).
  95. Rozek D, Pfeifer GP: In vivo protein-DNA interactions at the c-jun promoter: preformed complexes mediate the UV response. Mol Cell Biol 13:5490–5499 (1993).
  96. Ruano-Rubio V, Fares MA: Artifactual phylogenies caused by correlated distribution of substitution rates among sites and lineages: the good, the bad, and the ugly. Syst Biol 56:68–82 (2007).
  97. Saccone S, Federicoa C, Bernardi G: Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene 300:169–178 (2002).
  98. Saint KM, Austin CC, Donnellan SC, Hutchinson MN: c-mos, a nuclear marker useful for squamate phylogenetic analysis. Mol Phylogenet Evol 10:259–263 (1998).
  99. Sanderson MJ, Kim J: Parametric phylogenetics? Syst Biol 49:817–829 (2000).
  100. Sarre SD, Georges A, Quinn A: The ends of a continuum: Genetic and temperature- dependent sex determination in reptiles. BioEssays 26:639–645 (2004).
  101. Shedlock AM, Botka CW, Zhao S, Shetty J, Zhang T, et al: Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci USA 104:2767–2772 (2007).
  102. Simmons MP, Carr TG, O’Neill K: Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters. Mol Phylogenet Evol 32:913–926 (2004).
  103. Stamatakis A: RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690 (2006).
  104. Stancheva I, El-Maarri O, Walter J, Niveleau A, Meehan RR: DNA methylation at promoter regions regulates the timing of gene activation in Xenopus laevis embryos. Dev Biol 243:155–165 (2002).
  105. Strausberg RL, Simpson AJG, Old LJ, Riggins GJ: Oncogenomics and the development of new cancer therapies. Nature 429:469–474 (2004).
  106. Swofford D: PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), ver. 4 (Sinauer Associates, Sunderland 2003).
  107. Takahashi K, Taira T, Niki T, Seino C, Iguchi-Ariga SMM, Ariga H: DJ-1 positively regulates the androgen receptor by impairing the binding of PIASxα to the receptor. J Biol Chem 276:37556–37563 (2001).
  108. Thiery JP, Macaya G, Bernardi G: An analysis of eukaryotic genomes by density gradient centrifugation. J Mol Biol 108:219–235 (1976).
  109. Thomas JW: Comparative vertebrate genomics, in Brown JR (ed): Comparative Genomics: Basic and Applied Research (CRC Press, Boca Raton 2008).
  110. Vogt PK: Jun, the oncoprotein. Oncogene 20:2365–2377 (2001).
  111. Waddell PJ, Kishino H, Ota H: Phylogenetic methodology for detecting protein interactions. Mol Biol Evol 24:650–659 (2007).
  112. Werneburg I, Sánchez-Villagra MR: Timing of organogenesis support basal position of turtles in the amniote tree of life. BMC Evol Biol 9:82 (2009).
  113. Wiens JJ, Kuczynski CA, Smith SA, Mulcahy DG, Sites JWJ, et al: Branch lengths, support, and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes. Syst Biol 57:420–431 (2008).
  114. Yamakoshi K, Shimoda N: De novo DNA methylation at the CpG island of the zebrafish no tail gene. Genesis 37:195–202 (2003).
  115. Zardoya R, Meyer A: The evolutionary position of turtle revised. Naturwissenschaften 88:193–200 (2001).

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