Journal of Molecular Evolution

, Volume 76, Issue 3, pp 83–97 | Cite as

The 5S rDNA High Dynamism in Diplodus sargus is a Transposon-Mediated Mechanism. Comparison with Other Multigene Families and Sparidae Species

  • Manuel A. Merlo
  • Ismael Cross
  • Manuel Manchado
  • Salvador Cárdenas
  • Laureana Rebordinos


There has been considerable discussion in recent years on the evolution of the tandemly repeated multigene families, since some organisms show a concerted model whereas others show a birth-and-death model. This controversial subject extends to several species of fish. In this study, three species of the Sparidae family (Pagrus pagrus, P. auriga and Diplodus sargus) and an interspecific hybrid (P. pagrus (♀) × P. auriga (♂)) have been studied at both molecular and cytogenetic level, taking three different multigene families (5S rDNA, 45S rDNA and U2 snDNA). Results obtained with the 5S rDNA in P. pagrus and P. auriga are characterized by a considerable degree of conservation at the two levels; however, an extraordinary variation was observed in D. sargus at the two levels, which has never been found in other fishes studied to date. As a consequence of this, the evolutionary model of the multigene families is discussed considering the results obtained and others from the bibliography. The result obtained in the hybrid allowed the recombination frequency in each multigene family to be estimated.


Multigene family Sparidae Hybrids Concerted evolution Birth-and-death evolution 



This study has been supported by the AQUAGENET project (SOE2/P1/E287), INTERREG IVB SUDOE program, and by grants from the Junta de Andalucía (Spain) to the PAI BIO-219 group.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

239_2013_9541_MOESM1_ESM.doc (1.8 mb)
Supplementary material 1 (DOC 1893 kb)


  1. Accioly IV, Molina WF (2008) Cytogenetic studies in Brasilian marine Sciaenidae and Sparidae fishes (Perciformes). Genet Mol Res 7(2):358–370PubMedCrossRefGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  3. Bargelloni L, Alarcon JA, Penzo E, Magoulas A, Palma J, Patarnello T (2005) The Atlantic-Mediterranean transition: discordant genetic patterns in two seabream species, Diplodus puntazzo (Cetti) and Diplodus sargus (L.). Mol Phylogenet Evol 36(3):523–535PubMedCrossRefGoogle Scholar
  4. Barzotti R, Pelliccia F, Rocchi A (2003) Identification and characterization of U1 small nuclear RNA genes from two crustacean isopod species. Chromosom Res 11:365–373CrossRefGoogle Scholar
  5. Bauchot ML, Hureau JC (1986) Sparidae. In: Whitehead PJP, Bauchot ML, Hureau JC, Nielsen J, Tortonese E (eds) Fishes of the North-Eastern Atlantic and the Mediterranean, vol 2. UNESCO, Paris, pp 883–907Google Scholar
  6. Boron A, Ozouf-Costaz C, Coutanceau J-P, Woroniecka K (2006) Gene mapping of 28S and 5S rDNA sites in the spined loach Cobitis taenia (Pisces, Cobitidae) from a diploid population and a diploid-tetraploid population. Genetica 128:71–79PubMedCrossRefGoogle Scholar
  7. Boron A, Porycka K, Ito D, Abe S, Kirtiklis L (2009) Comparative molecular cytogenetic analysis of three Leuciscus species (Pisces, Cyprinidae) using chromosome banding and FISH with rDNA. Genetica 135:199–207PubMedCrossRefGoogle Scholar
  8. Boyd DC, Pombo A, Murphy S (2003) Interaction of proteins with promoter elements of the human U2 snRNA genes in vivo. Gene 315:103–112PubMedCrossRefGoogle Scholar
  9. Brum MJI, Galetti PM Jr (1997) Teleostei ground plan karyotype. J Comput Biol 2(2):91–102Google Scholar
  10. Cabral-de-Mello DC, Valente GT, Nakajima RT, Martins C (2012) Genomic organization and comparative chromosome mapping of the U1 snRNA gene in cichlid fish, with an emphasis in Oreochromis niloticus. Chromosom Res. doi: 10.1007/s10577-10011-19271-y
  11. Campo D, Machado-Schiaffino G, Horreo JL, García-Vázquez E (2009) Molecular organization and evolution of 5S rDNA in the genus Merluccius and their phylogenetic implications. J Mol Evol 68(3):208–216PubMedCrossRefGoogle Scholar
  12. Carrera E, García T, Céspedes A, Gonzáles I, Fernández A, Asensio L, Hernández P, Martín R (2000) Differentiation of smoked Salmo salar, Onchorhynchus mykiss and Brama raii using the nuclear marker 5S rDNA. Int J Food Sci Tech 35:401–406CrossRefGoogle Scholar
  13. Chairi H (2010) Análisis de los parámetros genéticos limitantes en la gestión y conservación de las poblaciones naturales surmediterráneas y atlánticas de la anchoa Engraulis encrasicholus. Universidad de Cádiz, CádizGoogle Scholar
  14. Chiba SN, Iwatsuki Y, Yoshino T, Hanzawa N (2009) Comprehensive phylogeny of the family Sparidae (Perciformes: Teleostei) inferred from mitochondrial gene analyses. Genes Genet Syst 84(2):153–170PubMedCrossRefGoogle Scholar
  15. Chistiakov DA, Hellemans B, Volckaert FAM (2006) Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics. Aquaculture 255:1–29. doi: 10.1016/j.aquaculture.2005.1011.1031 CrossRefGoogle Scholar
  16. Chow S, Ueno Y, Toyokawa M, Oohara I, Takeyama H (2009) Preliminary analysis of length and GC content variation in the ribosomal first Internal Transcribed Spacer (ITS1) of marine animals. Mar Biotechnol 11:301–306PubMedCrossRefGoogle Scholar
  17. Cioffi MB, Martins C, Bertollo LAC (2010) Chromosome spreading of associated transposable elements and ribosomal DNA in the fish Erythrinus erythrinus. Implications for genome change and karyoevolution in fish. BMC Evol Biol 10:271–279PubMedCrossRefGoogle Scholar
  18. Cross I, Rebordinos L (2005) 5S rDNA and U2 snRNA are linked in the genome of Crassostrea angulata and Crassostrea gigas oysters: does the (CT)n·(GA)n microsatellite stabilize this novel linkage of large tandem arrays? Genome 48(6):1116–1119PubMedCrossRefGoogle Scholar
  19. Cross I, Vega L, Rebordinos L (2003) Nucleolar organizing regions in Crassostrea angulata: chromosomal location and polymorphism. Genetica 119:65–74PubMedCrossRefGoogle Scholar
  20. Cross I, Díaz E, Sanchez I, Rebordinos L (2005) Molecular and cytogenetic characterization of Crassostrea angulata chromosomes. Aquaculture 247:135–144CrossRefGoogle Scholar
  21. Cross I, Merlo A, Manchado M, Infante C, Cañavate JP, Rebordinos L (2006) Cytogenetic characterization of the sole Solea senegalensis (Teleostei: Pleuronectiformes: Soleidae): Ag-NOR, (GATA)n, (TTAGGG)n and ribosomal genes by one-color and two-color FISH. Genetica 128:253–259PubMedCrossRefGoogle Scholar
  22. Cuello P, Boyd DB, Dye MJ, Proudfoot NJ, Murphy S (1999) Transcription of the human U2 snRNA genes continues beyond the 3′ box in vivo. EMBO J 18(10):2867–2877PubMedCrossRefGoogle Scholar
  23. de la Herrán R, Ruiz Rejón C, Ruiz Rejón M, Garrido-Ramos MA (2001) The molecular phylogeny of the Sparidae (Pisces, Perciformes) based on two satellite DNA families. Heredity 87:691–697PubMedCrossRefGoogle Scholar
  24. Diniz D, Moreira Filho O, Bertollo LAC (2008) Molecular cytogenetics and characterization of a ZZ/ZW sex chromosome system in Triportheus nematurus (Characiformes, Characidae). Genetica 133:85–91PubMedCrossRefGoogle Scholar
  25. Domingues VS, Santos RS, Brito A, Alexandrou M, Almada VC (2007) Mitochondrial and nuclear markers reveal isolation by distance and effects of Pleistocene glaciations in the northeastern Atlantic and Mediterranean populations of the white seabream (Diplodus sargus, L.). J Exp Mar Biol Ecol 346:102–113CrossRefGoogle Scholar
  26. Eickbush HE, Eickbush DG (2007) Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics 175:477–485. doi: 410.1534/genetics.1107.071399 PubMedCrossRefGoogle Scholar
  27. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791. doi: 710.2307/2408678 CrossRefGoogle Scholar
  28. Fontdevila A (2005) Hybrid genome evolution by transposition. Cytogenet Genome Res 110:49–55PubMedCrossRefGoogle Scholar
  29. Frank DN, Roiha H, Guthrie C (1994) Architecture of the U5 small nuclear RNA. Mol Cell Biol 14(3):2180–2190PubMedGoogle Scholar
  30. Freire R, Arias A, Insua A, Méndez J, Eirín-López JM (2010) Evolutionary dynamics of the 5S rDNA gene family in the mussel Mytilus: mixed effects of birth-and-death and concerted evolution. J Mol Evol 70:413–426PubMedCrossRefGoogle Scholar
  31. Garrido-Ramos MA (1994) Evolución del ADN satélite y estudios cromosómicos en la familia Sparidae (Pisces). Tesis Doctoral, Universidad de Granada, GranadaGoogle Scholar
  32. Garrido-Ramos MA, de la Herrán R, Ruiz Rejón C, Ruiz Rejón M (1998) A satellite DNA of Sparidae family (Pisces, Perciformes) associated with telomeric sequences. Cytogene Cell Genet 83:3–9CrossRefGoogle Scholar
  33. Garrido-Ramos MA, de la Herrán R, Jamilena M, Lozano R, Ruiz Rejón C, Ruiz Rejón M (1999) Evolution of centromeric satellite DNA and its use in phylogenetic studies of the sparidae family (Pisces, Perciformes). Mol Phylogenet Evol 12(2):200–204PubMedCrossRefGoogle Scholar
  34. González-Wangüemert M, Pérez-Ruzafa Á, García-Charton JA, Marcos C (2006) Genetic differentiation and gene flow of two sparidae subespecies, Diplodus sargus sargus and Diplodus sargus cadenati in Atlantic and south-west Mediterranean populations. Biol J Linnean Soc 89:705–717CrossRefGoogle Scholar
  35. Gornung E, Colangelo P, Annesi F (2007) 5S ribosomal RNA genes in six species of Mediterranean grey mullets: genomic organization and phylogenetic inference. Genome 50:787–795PubMedCrossRefGoogle Scholar
  36. Gromicho M, Coutanceau J-P, Ozouf-Costaz C, Collares-Pereira MJ (2006) Contrast between extensive variation of 28S rDNA and stability of 5S rDNA and telomeric repeats in the diploid-polyploid Squalius alburnoides complex and in its maternal ancestor Squalius pyrenaicus (Teleostei, Cyprinidae). Chromosom Res 14:297–306CrossRefGoogle Scholar
  37. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  38. Joazeiro CAP, Kassavetis GA, Geiduschek EP (1994) Identical components of yeast transcription factor IIIB are required and sufficient for transcription of TATA box-containing and TATA-less genes. Mol Cel Biol 14(4):2798–2808CrossRefGoogle Scholar
  39. Johansen T, Repolho T, Hellebo A, Raae AJ (2006) Strict conservation of the ITS regions of the ribosomal RNA genes in Atlantic cod (Gadus morhua L.). DNA Seq 17(2):107–114PubMedGoogle Scholar
  40. Kohany O, Gentles AJ, Hankus L, Jurka J (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinf 25(7):474CrossRefGoogle Scholar
  41. Kuriiwa K, Hanzawa N, Yoshino T, Kimura S, Nishida M (2007) Phylogenetic relationships and natural hybridization in rabbitfishes (Teleostei: Siganidae) inferred from mitochondrial and nuclear DNA analyses. Mol Phylogenet Evol 45:69–80PubMedCrossRefGoogle Scholar
  42. Libertini A, Sola L, Rampin M, Rossi AR, Iijima K, Ueda T (2008) Classical and molecular cytogenetic characterization of allochthonous European bitterling Rhodeus amarus (Cyprinidae, Acheilognathinae) from Northern Italy. Genes Genet Syst 83:417–422PubMedCrossRefGoogle Scholar
  43. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452PubMedCrossRefGoogle Scholar
  44. Manchado M, Ponce M, Asensio E, Infante C, de la Herrán R, Robles F, Garrido-Ramos MA, Ruiz Rejón M, Cárdenas S (2005) Pagurta, híbrido interespecífico de pargo Pagrus pagrus (L., 1758) (H) x hurta Pagrus auriga Valenciennes, 1843 (M): caracterización fenotípica y molecular. Bol Inst Esp Oceanogr 21(1–4):219–224Google Scholar
  45. Manchado M, Rebordinos L, Infante C (2006a) U1 and U2 small nuclear RNA genetic linkage: a novel molecular tool for identification of six sole species (Soleidae, Pleuronectiformes). J Agric Food Chem 54:3765–3767PubMedCrossRefGoogle Scholar
  46. Manchado M, Zuasti E, Cross I, Merlo A, Infante C, Rebordinos L (2006b) Molecular characterization and chromosomal mapping of the 5S rRNA gene in Solea senegalensis: a new linkage to the U1, U2, and U5 small nuclear RNA genes. Genome 49(1):79–86PubMedCrossRefGoogle Scholar
  47. Mantovani M, dos Douglas Santos Abel L, Moreira-Filho O (2005) Conserved 5S and variable 45S rDNA chromosomal localization revealed by FISH in Astyanax scabripinnis (Pisces, Characidae). Genetica 123:211–216PubMedCrossRefGoogle Scholar
  48. Martins C, Wasko AP (2004) Organization and evolution of 5S ribosomal DNA in the fish genome. In: Williams CR (ed) Focus on genome research. Nova Science Publisher, Inc., Hauppauge, pp 335–363Google Scholar
  49. McNamara-Schroeder KJ, Hennessey RF, Harding GA, Jensen RC, Stumph WE (2001) The Drosophila U1 and U6 gene proximal sequence elements act as important determinants of the RNA polymerase specificity of small nuclear RNA gene promoters in vitro and in vivo. J Biol Chem 276:31786–31792PubMedCrossRefGoogle Scholar
  50. Merlo A, Cross I, Palazón JL, Sarasquete C, Rebordinos L (2007) Chromosomal mapping of the major and minor ribosomal genes, (GATA)n and (TTAGGG)n by one-color and double-color FISH reveals three chromosomal markers in the toadfish Halobatrachus didactylus (Teleostei: Batrachoididae). Genetica 131:195–200PubMedCrossRefGoogle Scholar
  51. Merlo MA, Cross I, Chairi H, Manchado M, Rebordinos L (2010) Analysis of three multigene families as useful tools in species characterization of two closely-related species, Dicentrarchus labrax, Dicentrarchus punctatus and their hybrids. Genes Genet Syst 85:341–349PubMedCrossRefGoogle Scholar
  52. Merlo MA, Pacchiarini T, Portela-Bens S, Cross I, Manchado M, Rebordinos L (2012a) Genetic characterization of Plectorhinchus mediterraneus yields important clues about genome organization and evolution of multigene families. BMC Genet 13:33. doi: 10.1186/1471-2156-1113-1133 PubMedCrossRefGoogle Scholar
  53. Merlo MA, Cross I, Palazón JL, Úbeda-Manzanaro M, Sarasquete C, Rebordinos L (2012b) Evidence for 5S rDNA Horizontal Transfer in the toadfish Halobatrachus didactylus (Schneider, 1801) based on the analysis of three multigene families. BMC Evol Biol (accepted)Google Scholar
  54. Merlo MA, Cross I, Rodríguez-Rúa A, Manchado M, Rebordinos L (2012c) First approach to studying the genetics of the meagre (Argyrosomus regius; Asso, 1801) using three multigene families. Aquac Res. doi: 10.1111/j.1365-2109.2012.03103
  55. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New YorkGoogle Scholar
  56. Nei M, Rooney AP (2005) Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39:121–152PubMedCrossRefGoogle Scholar
  57. Nelson JS (2006) Fishes of the world, 4th edn. Wiley, HobokenGoogle Scholar
  58. Ocalewicz K, Woznicki P, Jankun M (2008) Mapping of rRNA genes and telomeric sequences in Danube salmon (Hucho hucho) chromosomes using primed in situ labeling technique (PRINS). Genetica 134:199–203PubMedCrossRefGoogle Scholar
  59. Parry HD, Tebb G, Mattaj IW (1989) The Xenopus U2 gene PSE is a single, compact, element required for transcription initiation and 3′ end formation. Nucleic Acids Res 17(10):3633–3644PubMedCrossRefGoogle Scholar
  60. Pasolini P, Costagliola D, Rocco L, Tinti F (2006) Molecular organization of 5S rDNAs in Rajidae (Chondrichthyes): structural features and evolution of Piscine 5S rRNA gene and nontranscribed intergenic spacers. J Mol Evol 62:564–574PubMedCrossRefGoogle Scholar
  61. Pendás AM, Morán P, Freije JP, García-Vazquez E (1994) Chromosomal mapping and nucleotide sequence of two tandem repeats of Atlantic salmon 5S rDNA. Cytogenet Cell Genet 67:31–36PubMedCrossRefGoogle Scholar
  62. Pérez M, Vieites JM, Presa P (2005) ITS1-rDNA-based methodology to identify world-wide hake species of the genus Merluccius. J Agric Food Chem 53:5239–5247PubMedCrossRefGoogle Scholar
  63. Pinhal D, Yoshimura TS, Araki CS, Martins C (2011) The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays. BMC Evol Biol 11:151–164PubMedCrossRefGoogle Scholar
  64. Rocco L, Costagliola D, Fiorillo M, Tinti F, Stingo V (2005) Molecular and chromosomal analysis of ribosomal cistrons in two cartilaginous fish, Taeniura lymma and Raja montagui (Chondrichthyes, Batoidea). Genetica 123:245–253PubMedCrossRefGoogle Scholar
  65. Rosenthal DS, Doering JL (1983) The genomic organization of dispersed tRNA and 5S RNA genes in Xenopus laevis. J Biol Chem 258:7402–7410PubMedGoogle Scholar
  66. Schuler GD, Altschul SF, Lipman DJ (1991) A workbench for multiple alignment construction and analysis. Proteins Struct Funct Genet 9:180–190PubMedCrossRefGoogle Scholar
  67. Sola L, Rossi AR, Annesi F, Gornung E (2003) Cytogenetic studies in Sparus auratus (Pisces, Perciformes): molecular organization of 5S rDNA and chromosomal mapping of 5S and 45S ribosomal genes and of telomeric repeats. Hereditas 139:232–236PubMedCrossRefGoogle Scholar
  68. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739. doi: 2710.1093/molbev/msr2121 PubMedCrossRefGoogle Scholar
  69. Tebb G, Mattaj IW (1989) The Xenopus laevis U2 gene Distal Sequence Element (enhancer) is composed of four subdomains that can act independently and are partly functionally redundant. Mol Cell Biol 9(4):1682–1690PubMedGoogle Scholar
  70. Thomas J, Lea K, Zucker-Aprison E, Blumenthal T (1990) The spliceosomal snRNAs of Caenorhabditis elegans. Nucleic Acids Res 18(9):2633–2642PubMedCrossRefGoogle Scholar
  71. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alingment aided by quality analysis tools. Nucleic Acids Res 25(24):4876–4882PubMedCrossRefGoogle Scholar
  72. Tortonese E (1975) Fauna d’Italia “Osteichthyes” Pesci Ossei. Calderini, BolognaGoogle Scholar
  73. Úbeda-Manzanaro M, Merlo MA, Palazón JL, Sarasquete C, Rebordinos L (2010a) Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in species of the family Batrachoididae. Genome 53:723–730PubMedCrossRefGoogle Scholar
  74. Úbeda-Manzanaro M, Merlo MA, Palazón JL, Cross I, Sarasquete C, Rebordinos L (2010b) Chromosomal mapping of the ribosomal genes, (GATA)n and U2 snRNA gene by double-colour FISH in species of the Batrachoididae family. Genetica (submitted)Google Scholar
  75. Uguen P, Murphy S (2003) The 3′ ends of human pre-snRNAs are produced by RNA polymerase II CTD-dependent RNA processing. EMBO J 22:4544–4554PubMedCrossRefGoogle Scholar
  76. Vierna J, González-Tizón AM, Martínez-Lage A (2009) Long-term evolution of 5S ribosomal DNA seems to be driven by birth-and-death processes and selection in Ensis razor shells (Mollusca: Bivalvia). Biochem Genet 47:635–644PubMedCrossRefGoogle Scholar
  77. Vierna J, Martínez-Lage A, González-Tizón AM (2010) Analysis of ITS1 and ITS2 sequences in Ensis razor shells: suitability as molecular markers at the population and species levels, and evolution of these ribosomal DNA spacers. Genome 53:23–34PubMedCrossRefGoogle Scholar
  78. Vitturi R, Catalano E, Colomba M, Montagnino L, Pellerito L (1995) Karyotype analysis of Aphanius fasciatus (Pisces, Cyprinodontiformes) Ag-NORs and C-band polymorphism in four populations from Sicily. Biol Zent 114:392–402Google Scholar
  79. Vitturi R, Libertini A, Mazzola A, Colomba MS, Sara G (1996) Characterization of mitotic chromosomes of four species of the genus Diplodus: karyotypes and chromosomal nucleolar organizer region phenotypes. J Fish Biol 49:1128–1137Google Scholar
  80. Vizoso M, Vierna J, González-Tizón AM, Martínez-Lage A (2011) The 5S rDNA gene family in mollusks: Characterization of transcriptional regulatory regions, prediction of secondary structures, and long-term evolution, with special attention to Mytilidae mussels. J Hered 102(4):433–447PubMedCrossRefGoogle Scholar
  81. Wang Y, Guo X (2008) ITS length polymorphism in oysters and its use in species identification. J Shellfish Res 27(3):489–493CrossRefGoogle Scholar
  82. Wasko AP, Martins C, Wright JM, Galetti PM Jr (2001) Molecular organization of 5S rDNA in fishes of the genus Brycon. Genome 44(5):893–902PubMedGoogle Scholar
  83. Yu YT, Schart EC, Smith CM, Seitz JA (1999) The growing world of small nuclear ribonucleoproteins. In: Gesteland RF, Cech T, Atkins JF (eds) The RNA world: the nature of modern RNA suggests a prebiotic RNA. Cold Spring Harbor Press, New York, pp 487–524Google Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Manuel A. Merlo
    • 1
  • Ismael Cross
    • 1
  • Manuel Manchado
    • 2
  • Salvador Cárdenas
    • 2
  • Laureana Rebordinos
    • 1
  1. 1.Laboratorio de Genética, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizCádizSpain
  2. 2.Centro IFAPA, Junta de AndaluciaCádizSpain

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