, Volume 141, Issue 7–9, pp 329–336 | Cite as

Chromosomal organization of repetitive DNA sequences in Astyanax bockmanni (Teleostei, Characiformes): dispersive location, association and co-localization in the genome

  • Duílio M. Z. A. SilvaEmail author
  • José Carlos Pansonato-Alves
  • Ricardo Utsunomia
  • Sandro Natal Daniel
  • Diogo Teruo Hashimoto
  • Claudio Oliveira
  • Fabio Porto-Foresti
  • Fausto Foresti


Repetitive DNA sequences constitute a great portion of the genome of eukaryotes and are considered key components to comprehend evolutionary mechanisms and karyotypic differentiation. Aiming to contribute to the knowledge of chromosome structure and organization of some repetitive DNA classes in the fish genome, chromosomes of two allopatric populations of Astyanax bockmanni were analyzed using classic cytogenetics techniques and fluorescent in situ hybridization, with probes for ribosomal DNA sequences, histone DNA and transposable elements. These Astyanax populations showed the same diploid number (2n = 50), however with differences in chromosome morphology, distribution of constitutive heterochromatin, and location of 18S rDNA and retroelement Rex3 sites. In contrast, sites for 5S rDNA and H1, H3 and H4 histones showed to be co-located and highly conserved. Our results indicate that dispersion and variability of 18S rDNA and heterochromatin sites are not associated with macro rearrangements in the chromosome structure of these populations. Similarly, distinct evolutionary mechanisms would act upon histone genes and 5S rDNA, contributing to chromosomal association and co-location of these sequences. Data obtained indicate that distinct mechanisms drive the spreading of repetitive DNAs in the genome of A. bockmanni. Also, mobile elements may account for the polymorphism of the major rDNA sites and heterochromatin in this genus.


Cytogenetics Genome organization Multigene families FISH Evolution 



This study was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brazil.


  1. Almeida-Toledo LF, Ozouf-Costaz C, Foresti F, Bonillo C, Porto-Foresti F, Daniel-Silva MFZ (2002) Conservation of the 5S-bearing chromosome pair and co-localization with major rDNA clusters in five species of Astyanax (Pisces, Characidae). Cytogenet Genome Res 97:229–233PubMedCrossRefGoogle 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. Barzotti R, Pelliccia F, Bucciarelli E, Rocchi A (2000) Organization, nucleotide sequence, and chromosomal mapping of a tandemly repeated unit containing the four core histone genes and a 5S rRNA gene in an isopod crustacean species. Genome 43:341–345PubMedCrossRefGoogle Scholar
  4. Cabral-de-Mello DC, Martins C, Souza MJ, Moura RC (2011) Cytogenetic mapping of 5S and 18S rRNAs and H3 histone genes in 4 ancient proscopiidae grasshopper species: contribution to understanding the evolutionary dynamics of multigene families. Cytogenet Genome Res 132:89–93PubMedCrossRefGoogle Scholar
  5. Cabrero J, López-León MD, Teruel M, Camacho JPM (2009) Chromosome mapping of H3 and H4 histone gene clusters in 35 species of acridid grasshoppers. Chromosome Res 17:397–404PubMedCrossRefGoogle Scholar
  6. Charlesworth B, Sniegowski P, Stephan W (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371:215–220PubMedCrossRefGoogle Scholar
  7. 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 10:271PubMedCrossRefGoogle Scholar
  8. Colgan D, McLauchlan A, Wilson G, Livingston S (1998) Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Aust J Zool 46:419–437CrossRefGoogle Scholar
  9. Eickbush TH, Furano AV (2002) Fruit flies and humans respond differently to retrotransposons. Curr Opin Genet Dev 12:669–674PubMedCrossRefGoogle Scholar
  10. Eirín-López JM, Ruiz MF, González-Tizón AM, Martínez A, Sánchez L, Méndez J (2004) Molecular evolutionary characterization of the mussel Mytilus histone multigene family: first record of a tandemly repeated unit of five histone genes containing an H1 subtype with ‘orphon’ features. J Mol Evol 58:131–144PubMedCrossRefGoogle Scholar
  11. Fantinatti BE, Mazzuchelli J, Valente GT, Cabral-de-Mello DC, Martins C (2011) Genomic content and new insights on the origin of the B chromosome of the cichlid fish Astatotilapia latifasciata. Genetica 139:273–282CrossRefGoogle Scholar
  12. Ferreira DC, Oliveira C, Foresti F (2011a) Chromosome mapping of retrotransposable elements Rex1 and Rex3 in three fish species in the subfamily Hypoptopomatinae (Teleostei, Siluriformes, Loricariidae). Cytogenet Genome Res 132:64–70PubMedCrossRefGoogle Scholar
  13. Ferreira DC, Porto-Foresti F, Oliveira C, Foresti F (2011b) Transposable elements as a potential source for understanding fish genome. Mob Genet Elem 2:1–6Google Scholar
  14. Ferro DAM, Néo DM, Moreira-Filho O, Bertollo LAC (2001) Nucleolar organizing regions, 18S and 5S rDNA in Astyanax scabripinnis (Pisces, Characidae): populations distribution and functional diversity. Genetica 110:55–62CrossRefGoogle Scholar
  15. Fischer C, Bouneau L, Coutenceau JP, Weissenbach J, Volff JN, Ozouf-Costaz C (2004) Global heterochromatic colocalization of transposable elements with minisatellites in the compact genome of the pufferfish Tetraodon nigroviridis. Gene 336:175–183PubMedCrossRefGoogle Scholar
  16. Foresti F, Almeida-Toledo LF, Toledo SA (1981) Polymorphic nature of nucleolus organizer regions in fishes. Cytogenet Cell Genet 31:137–144PubMedCrossRefGoogle Scholar
  17. Hadjiolov AA (1985) The nucleolus and ribosome biogenesis. Springer, New York, p 263CrossRefGoogle Scholar
  18. Hall TA (1999) Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium 41:95–98Google Scholar
  19. Hashimoto DT, Porto-Foresti F (2010) Chromosome polymorphism and heterochromatin and nucleolar regions in two populations of the fish Astyanax bockmanni (Teleostei: Characiformes). Neotrop Ichth 8:861–866CrossRefGoogle Scholar
  20. Hashimoto DT, Ferguson-Smith MA, Rens W, Foresti F, Porto-Foresti F (2011) Chromosome mapping of H1 histone and 5S RNA gene clusters in three species of Astyanax (Teleostei: Characiformes). Cytogenet Genome Res 134:64–71PubMedCrossRefGoogle Scholar
  21. Hashimoto DT, Ferguson-Smith MA, Rens W, Prado FD, Foresti F, Porto-Foresti F (2013) Cytogenetic mapping of H1 histone and ribosomal RNA genes in hybrids between catfish species Pseudoplatystoma corruscans and Pseudoplatystoma reticulatum. Cytogenet Genome Res 139:102–106PubMedCrossRefGoogle Scholar
  22. Howell WM, Black DA (1980) Controlled silver staining of nucleolus organizer regions with a protective colloidal developer: a 1-step method. Experientia 36:1014–1015PubMedCrossRefGoogle Scholar
  23. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:569–573PubMedCrossRefGoogle Scholar
  24. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462–467PubMedCrossRefGoogle Scholar
  25. Kantek DLZ, Vicari MR, Peres WAM, Cestari MM, Artoni RF, Bertollo LAC, Moreira-Filho O (2009) Chromosomal location and distribution of As51 satellite DNA in five species of the genus Astyanax (Teleostei, Characidae, Incertae sedis). J Fish Biol 75:408–421PubMedCrossRefGoogle Scholar
  26. Kavalco KF, Pazza R, Almeida-Toledo LF (2009) Astyanax bockmanni (Vari and Castro, 2007): an ambiguous karyotype in the Astyanax genus. Genetica 136:135–139PubMedCrossRefGoogle Scholar
  27. Kavalco KF, Pazza R, Brandão KO, Almeida-Toledo LF (2013) Biogeographic patterns in the chromosomal distribution of a satellite DNA in the banded tetra Astyanax fasciatus (Teleostei: Characiformes). Org Divers Evol 13:67–76CrossRefGoogle Scholar
  28. Levan A, Fredga KE, Sandberg HA (1964) Nomenclature for centromeric position on chromosomes. Hereditas 52:201–220CrossRefGoogle Scholar
  29. Lima-Filho PA, Cioffi MB, Bertollo LAC, Molina WF (2012) Chromosomal and morphological divergences in Atlantic populations of the frillfin goby Bathygobius soporator (Gobiidae, Perciformes). J Exp Mar Biol Ecol 434–435:63–70CrossRefGoogle Scholar
  30. Mandrioli M (2000) Mariner-Like transposable elements are interspersed within the rDNA-associated heterochromatin of the pufferfish Tetraodon fluviatilis (Osteichthyes). Chromosome Res 8:177–179PubMedCrossRefGoogle Scholar
  31. Mantovani M, Abel LDS, Mestriner CA, Moreira-Filho O (2000) Accentuated polymorphism of heterochromatin and nucleolar organizer regions in Astyanax scabripinnis (Pisces, Characidae): tools for understanding karyotypic evolution. Genetica 109:161–168PubMedCrossRefGoogle Scholar
  32. Mantovani M, Abel LDS, 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
  33. Maxson R, Cohn R, Kedes L, Mohut T (1983) Expressionand organization of histone genes. Ann Rev Gen 17:239–277CrossRefGoogle Scholar
  34. Mestriner CA, Galetti PM Jr, Valentini SR, Ruiz IRG, Abel LDS, Moreira-Filho O, Camacho JPM (2000) Structural and functional evidence that a B chromosome in the characid fish Astyanax scabripinnis is an isochromosome. Heredity 85:1–9PubMedCrossRefGoogle Scholar
  35. Moreira-Filho O, Bertollo LCA (1991) Astyanax scabripinnis (Pisces, Characidae): a species complex. Brazil J Genet 14:331–357Google Scholar
  36. Pansonato-Alves JC, Oliveira C, Foresti F (2011) Karyotypic conservatism in samples of Characidium cf. zebra (Teleostei, Characiformes, Crenuchidae): physical mapping of ribosomal genes and natural triploidy. Genet Mol Biol 34:208–213PubMedCrossRefGoogle Scholar
  37. Pansonato-Alves JC, Serrano EA, Utsunomia R, Scacchetti PC, Oliveira C, Foresti F (2013) Mapping five repetitive DNA classes in sympatric species of Hypostomus (Teleostei: Siluriformes: Loricariidae): analysis of chromosomal variability. Rev Fish Biol Fisher. doi: 10.1007/s11160-013-9303-0 Google Scholar
  38. Pedersen C, Linde-Laursen I (1994) Chromosomal locations of four minor rDNA loci and a marker microsatellite sequence in barley. Chromosome Res 2:65–71PubMedCrossRefGoogle Scholar
  39. Pendás AM, Morán P, García-Vázquez E (1994a) Organization and chromosomal location of the major histone cluster in brown trout, Atlantic salmon and rainbow trout. Chromosoma 103:147–152PubMedCrossRefGoogle Scholar
  40. Pendás AM, Moran P, Freije JP, Garcia-Vazquez E (1994b) Chromosomal mapping and nucleotide sequence of two tandem repeats of Atlantic salmon 5S rDNA. Cytogenet Cell Genet 67:31–36PubMedCrossRefGoogle Scholar
  41. Pineau P, Henry M, Suspène R, Marchio A, Dettai A, Debruyne R, Petit T, Lécu A, Moisson P, Dejean A, Wain-Hobson S, Vartanian JP (2005) A universal primer set for PCR amplification of nuclear histone H4 genes from all animal species. Mol Biol Evol 22:582–588PubMedCrossRefGoogle Scholar
  42. Pinkel D, Straume T, Gray JW (1986) Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Natl Acad Sci 83:2934–2938PubMedCrossRefGoogle Scholar
  43. Raskina O, Barber JC, Nevo E, Belyayev A (2008) Repetitive DNA and chromosomal rearrangements: speciation-related events in plant genomes. Cytogenet Genome Res 120:351–357PubMedCrossRefGoogle Scholar
  44. Scacchetti PC, Pansonato-Alves JC, Utsunomia R, Claro FL, Almeida-Toledo LF, Oliveira C, Foresti F (2012) Molecular characterization and physical mapping of two classes of 5S rDNA in the genomes of Gymnotus sylvius and G. inaequilabiatus (Gymnotiformes, Gymnotidae). Cytogenet Genome Res 136:131–137PubMedCrossRefGoogle Scholar
  45. Schweizer D, Loidl JA (1987) Model of heterochromatin dispersion and the evolution of C banding patterns. Chrom Today 9:61–74CrossRefGoogle Scholar
  46. Sumner AT (1972) A simple technique for demonstrating centromeric heterocromatin. Expl Cell Res 75:304–306CrossRefGoogle Scholar
  47. Valente G, Mazzuchelli J, Ferreira IA, Poletto AB, Fantinatti BEA, Martins C (2011) Cytogenetic mapping of the retroelements Rex1, Rex3 and Rex6 among cichlid fish : New insights on the chromosomal distribution of transposable elements. Cytogenet Genome Res 133:34–42PubMedCrossRefGoogle Scholar
  48. Vicari MR, Artoni RF, Moreira-Filho O, Bertollo LAC (2008a) Colocalization of repetitive DNAs and silencing of major rRNA genes. A case report of the fish Astyanax janeiroensis. Cytogenet Genome Res 122:67–72PubMedCrossRefGoogle Scholar
  49. Vicari MR, Noleto RB, Artoni RF, Moreira-Filho O, Bertollo LCA (2008b) Comparative cytogenetics among species of the A. scabripinnis complex. Evolutionary and biogeographical inferences. Genet Mol Biol 31:173–179CrossRefGoogle Scholar
  50. Volff JN, Körting C, Sweeney K, Schartl M (1999) The non-LTR retrotransposon Rex3 from the fish Xiphophorus is widespread among teleosts. Mol Biol Evol 16:1427–1438PubMedCrossRefGoogle Scholar
  51. Ward RD, Zemiak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia’s fish species. Phil Trans R Soc B 360:1847–1857PubMedCrossRefGoogle Scholar
  52. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols: a guide to methods and applications. Academic Press Inc, London, New York, pp 312–315Google Scholar
  53. Zhang X, Eickbush MT, Eickbush TH (2008) Role of recombination in the longterm retention of transposable elements in rRNA gene loci. Genetics 180:1617–1626PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Duílio M. Z. A. Silva
    • 1
    Email author
  • José Carlos Pansonato-Alves
    • 1
  • Ricardo Utsunomia
    • 1
  • Sandro Natal Daniel
    • 2
  • Diogo Teruo Hashimoto
    • 3
  • Claudio Oliveira
    • 1
  • Fabio Porto-Foresti
    • 2
  • Fausto Foresti
    • 1
  1. 1.Departamento de Morfologia, Instituto de BiociênciasUniversidade Estadual PaulistaBotucatuBrazil
  2. 2.Departamento de Ciências Biológicas, Faculdade de CiênciasUniversidade Estadual PaulistaBauruBrazil
  3. 3.CAUNESPUniversidade Estadual PaulistaJaboticabalBrazil

Personalised recommendations