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Genetica

, Volume 132, Issue 2, pp 179–186 | Cite as

Karyotypic characterization and genomic organization of the 5S rDNA in Polypterus senegalus (Osteichthyes, Polypteridae)

  • Maria Alessandra Morescalchi
  • Innocenza Liguori
  • Lucia Rocco
  • Aristea Archimandritis
  • Vincenzo Stingo
Article

Abstract

Polypteridae (Cladistia) is a family of archaic fishes, confined to African freshwaters. On account of their primitiveness in anatomical and morphological characters and mosaic relationships among lower Osteichthyans fishes, they constitute an important subject for the study of evolution in vertebrates. Very little is known about the karyological structure of these species. In this article, a cytogenetic analysis on twenty specimens of Polypterus senegalus (Cuvier, 1829) was performed using both classical and molecular techniques. Karyotype (2n = 36; FN = 72), chromosome location of telomeric sequences (TTAGGG) n , (GATA)7 repeats and ribosomal 5S and 18S rRNA genes were examined by using Ag-NOR, classical C-banding, CMA3 staining and FISH. Staining with Ag-NOR showed the presence of two GC rich NORs on the p arm of the chromosome pair no. 1. CMA3 marked all centromerical and some (no. 1 and no. 14) telomeric regions. FISH with 5S rDNA marked the subtelomeric region of the q arm of the chromosome pair no. 14. FISH with 18S rDNA marked the telomeric region of the p arm of the chromosome pair no. 1, previously marked by Ag-NOR. (GATA)7 repeats marked the subtelomeric regions of all chromosome pairs, with the exclusion of the no. 1, 3 and 14. Hybridization with telomeric probes (TTAGGG) n showed bright signals at the end of all chromosomes. After cloning, the 5SrDNA alignment revealed an organization of sequences made up of two different classes of tandem arrays (5S type I and 5S type II) of different lengths.

Keywords

FISH (GATA)n repeats Polypteridae Ribosomal genes Telomere 

References

  1. Almeida-Toledo LF, Ozouf-Costaz C, Foresti F, Bonillo C, Porto-Foresti F, Daniel-Silva M (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. Arnason U, Gulberg A, Janke A (2001) Molecular phylogenetics of gnatosthomous (jawed) fishes: old bones, new cartilage. Zool Scr 30:249–259CrossRefGoogle Scholar
  4. Arratia G, Cloutier R (1996) Reassessment of the morphology of Cheirolepis canadensis (Actinopterygii). In: Shultze HP, Cloutier R (eds) Devonia fishes and plants of Miguasha Quebec, Canada. Verlag Dr. Pfeil. Munchen, pp 165–197Google Scholar
  5. Bartsch P, Gemballa S, Piotrowski T (1997) The embryonic and larval development of Polypterus senegalus Cuvier, 1829: ist staging with reference to external and skeletal features, behaviour and locomotory habits. Acta Zool 78:309–328CrossRefGoogle Scholar
  6. Bi CP, Benham CJ (2004) WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA. Bioinformatics 20(9):1477–1479PubMedCrossRefGoogle Scholar
  7. Britz R, Bartsch P (2003) The myth of dorsal ribs in gnathostome vertebrates. Proc R Soc Lond B 270(Suppl):S1–S4CrossRefGoogle Scholar
  8. Britz R, Johnson GD (2003) On the homology of the posterior most gill arch in polypterids (Cladistia, Actinopterygii). Zool J Linn Soc 138(4):495–530CrossRefGoogle Scholar
  9. Cao Y, Waddel PJ, Okada N, Hasegawa M (1998) The complete mitochondrial sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates. Mol Biol Evol 15:1637–1646PubMedGoogle Scholar
  10. Capanna E, Cataudella S (1973) The chromosomes of Calamoichthys calabaricus (Pisces, Polypteriformes). Experientia 29:491–492PubMedCrossRefGoogle Scholar
  11. Cataudella S, Sola L, Capanna E (1978) Remarks on the karyotype of the Polypteriformes. The chromosomes of Polypterus delhezi, P. endlicheri congicus and P. palmas. Experientia 34(8):999–1000PubMedCrossRefGoogle Scholar
  12. Chiu C, Dewar K, Wagner GP, Takahashi K, Ruddle F, Ledje C, Bartsh P, Scemama JL, Stellwag E, Fried C, Prohaska SJ, Stadler PF, Amemiya CT (2006) Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome Res 14:11–17CrossRefGoogle Scholar
  13. Cross I, Diaz E, Sanchez I, Rebordinos L (2005) Molecular and cytogenetic characterization of Crassostrea angulata chromosomes. Acquaculture 247:135–144CrossRefGoogle Scholar
  14. Cross I., Merlo A, Manchado M, Infante C, Canavate 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
  15. Daget J, Gayet M, Meunier FJ, Sire JY (2001) Major discoveries on the dermal skeleton of fossil and recent polypteriforms: a review. Fish Fisheries 2:113–122CrossRefGoogle Scholar
  16. Deiana AM, Cau A, Salvadori S (2000) Major and 5S ribosomal sequences of the largemouth bass Micropterus salmoides (Perciformes, Centrarchidae) are localized in GC-rich regions of the genome. Chromosome Res 8:213–218PubMedCrossRefGoogle Scholar
  17. Denton TE, Howell WM (1973) Chromosomes of the African Polypterid fishes, Polypterus palmas and Calamoichthys calabaricus (Pisces: Brachiopterygii). Experientia 29:122–124CrossRefGoogle Scholar
  18. Fontana F, Tagliavini J, Congiu L (2001) Sturgeon genetics and citogenetics: recent advancements and perspectives. Genetica 111:359–373PubMedCrossRefGoogle Scholar
  19. Gallardo-Escàrate C, Alvarez-Borrego J, Del Rio-Portilla MA, Cross I, Merlo MA, Rebordinos L (2005) Fluorescence in situ hybridization of rDNA, telomeric (TTAGGG)n and (GATA)n repeats in the red abalone Haliotis rufescens (Archaeogasteropoda: Haliotidae). Hereditas 142:73–79PubMedCrossRefGoogle Scholar
  20. Gardiner B (1984) The relationships of the palaeoniscid fishes, a review based on new specimens of Mimia and Moythomasia from the Upper Devonia of Western Australia. Bulletin of the British Museum (Natural History). Geology 37:175–428Google Scholar
  21. Gardiner B, Schaeffer B, Masserie J (2004) A review of the lower actinopterygian phylogeny. Zool J Linn Soc 144:511–525CrossRefGoogle Scholar
  22. Gayet M, Meunier F, Werner C (2002) Diversification in Polypteriformes and special comparison with the Lepisosteiformes. Palaeontology 45:361–376CrossRefGoogle Scholar
  23. Gemballa S, Hagen K, Roder K, Rolf M, Treiber K (2003) Structure and evolution of the horizontal septum in vertebrates. J Evol Biol 16:966–975PubMedCrossRefGoogle Scholar
  24. Gosse JP (1984) Polypteridae. In: Daget J, Gosse JP, Thys van den Audernaerde DFE (eds) Check-list of the freshwater fishes of Africa. Cloffa I, Paris, ORSTOM Tervuren MRAC, pp 18–29Google Scholar
  25. Greenwood PH (1984) Polypterus and Erpetoichtys. Anachronistic Osteichthyans. In: Eldredge N, Stanley S (eds) Living fossils. Springer – Verlag, Berlin, pp 143–147Google Scholar
  26. Hoegg S, Brinkmann H, Taylor JS, Meyer A, (2004) Phylogenetic timing of the fish-specific Genome Duplication correlates with the diversification of Teleost fish. J Mol Evol 59:190–203PubMedCrossRefGoogle Scholar
  27. 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
  28. Inafuku J, Nabeyama M, Kikuma Y, Saitoh J, Kubota S, Kohno S (2000) Chromosomal location and nucleotide sequences of 5S ribosomal DNA of two cyprinid species (Osteichthyes, Pisces). Chromosome Res 8:193–199PubMedCrossRefGoogle Scholar
  29. Kikugawa K, Katoh K, Kuraku S, Sakurai H, Ishida O, Iwabe N, Miyata T (2004) Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes. BMC Biol 2(3):1–11Google Scholar
  30. Lund R (2000) The new Actinopterygian order Guildayichthyiformes from the Lower Carboniferous of Montana (USA). Geodiversitas 22:171–206Google Scholar
  31. Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbour Laboratory Press, New YorkGoogle Scholar
  32. Martins C, Galetti PM Jr (1999) Chromosomal localization of 5S rDNA genes in Leporinus fish (Anostomidae, Characiformes). Chromosome Res 7:363–367PubMedCrossRefGoogle Scholar
  33. Martins C, Galetti PM Jr (2000) Conservative distribution of 5S rDNA loci in Schizodon (Pisces, Anostomidae) chromosomes. Chromosome Res 8:353–355CrossRefGoogle Scholar
  34. Martins C, Galetti PM Jr (2001a) Organization of 5S rDNA in species of the fish Leporinus: two different genomic locations are characterized by distinct nontranscribed spacers. Genome 44:903–910PubMedCrossRefGoogle Scholar
  35. Martins C, Galetti PM Jr (2001b) Two 5S array in Neotropical fish species: is it a general rule for fishes? Genetica 111:439–446PubMedCrossRefGoogle Scholar
  36. Martins C, Wasko AP, Oliveira C (2002) Dynamics of 5S rDNA in the tilapia (Oreochromis niloticus) genome: repeat units, inverted sequences, pseudogenes and chromosome loci. Cytogenet Gen Res 98:78–85CrossRefGoogle Scholar
  37. Martins C, Wasko AP, Oliveira C, Wright JM (2000) Nucleotide sequence of 5S rDNA and localization of ribosomal RNA genes to metaphase chromosomes of the tilapiine cichlid fish, Oreochromis niloticus. Hereditas 133:39–46PubMedCrossRefGoogle Scholar
  38. Mayne J, Baker RJ, Hobart HH, Hsu TC, Ryder OA, Ward OG, Wiley JE, Wurster-Hill DH, Yates TL, Moyzis RK (1990) Distribution of non-telomeric sites of the (TTAGGG)n telomeric sequence in vertebrate chromosomes. Chromosoma 99(1):3–10CrossRefGoogle Scholar
  39. Messias LH, Ferreira DC, Wasko AP, Oliveira C, Foresti F, Martins C (2003) 5S rDNA organization in the fish Synbrancus marmoratus (Symbranchidae; Symbranchiformes). Hereditas 139(3):228–231PubMedCrossRefGoogle Scholar
  40. Mezzanotte R, Ferrucci L, Vanni R, Bianchi U (1983) Selective digestion of human metaphase chromosomes by AluI restriction endonuclease. J Histochem Cytochem 31:553–556PubMedGoogle Scholar
  41. Morescalchi MA, Rocco L, Stingo V (2001) New karyological and molecular data in three species of ancient Osteichthyes. 14th International Chromosome Conference, 4–8 Sept. 2001, Wurzburg, Germany, p 73Google Scholar
  42. Morescalchi MA, Rocco L, Stingo V (2002) Cytogenetic and molecular studies in a lungfish, Protopterus annectens (Osteichthyes, Dipnoi). Gene 295:279–287PubMedCrossRefGoogle Scholar
  43. Morescalchi MA (2005) Karyotype, molecular characterization and phylogenetic implications in the Sarcopterygian and Polypteriformes fishes: a review. Recent Res Dev Genes Genomes 1:35–60Google Scholar
  44. Morescalchi MA, Liguori I, Rocco L, Stingo V (2006) Karyotypic characterization and genomic organization of the 5S rDNA in Erpetoichthys calabaricus (Osteichthyes, Polypteridae). Genetica, Nov 30, ISSN 0016–6707Google Scholar
  45. Negi MS, Rajagopal J, Chauhan N, Cronn R, Lakshmikumaran M (2002) Length and sequence heterogeneity in 5S rDNA of Populus deltoides. Genome 45:1181–1188PubMedCrossRefGoogle Scholar
  46. Ozouf-Costaz C, Pisano E, Bonillo C, Williams R (1997) Ribosomal RNA location in the Antarctic fish Champsocephalus gunnari (Notothenioidei, Channichthyidae) using banding and fluorescence in situ hybridization. Chromosome Res 4(8):557–561CrossRefGoogle Scholar
  47. 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 genes and nontrascribed intergenic spacers. J Mol Evol 62:564–574PubMedCrossRefGoogle Scholar
  48. Patterson C (1982) Morphology and interrelationships of primitive actinopterygian fishes. Am Zool 22:9759–9774Google Scholar
  49. Pendas AM, Moran P, Freije JP, Garcia-Vasquez E (1994) Chromosomal mapping and nucleotide sequence of two tandem repeats of Atlantic salmos 5S rDNA. Cytogenet Cell Genet 67:31–36PubMedGoogle Scholar
  50. Ràb P, Rabova M, Reed KM, Phillips RB (1999) Chromosomal characteristics of ribosomal DNA in the primitive semionotiform fish, longnose gar, Lepisosteus osseus. Chromosome Res 7:475–480PubMedCrossRefGoogle Scholar
  51. Rasmussen AS, Arnason U (1999a) Phylogenetic studies of complete mitochondrial molecules place cartilaginous fishes within the tree of bony fishes. J Mol Evol 48:118–123PubMedCrossRefGoogle Scholar
  52. Rasmussen AS, Arnason U (1999b) Molecular studies suggest that cartilaginous fishes have a terminal position in the piscine tree. Proc Natl Acad Sci USA 96:2177–2182PubMedCrossRefGoogle Scholar
  53. Saitoh K, Hayashizaki K, Yokoyama Y, Asahida T, Toyohara H, Yamashita Y (2000) Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome: structural properties and cue for resolving teleostean relationships. J Hered 91(4):271–278PubMedCrossRefGoogle Scholar
  54. Sambrook J, Russel DW (2001) Molecular cloning. A laboratory manual, 3rd edn. Cold Spring Harbour Laboratory PressGoogle Scholar
  55. Schafer F (2004) Polypterus, Flosselhechte Bichirs. Verlag A.C.S. GmbH (Aqualog.)Google Scholar
  56. Sola L, Rossi AR, Iaselli V, Rasch EM, Monaco PG (1992) Cytogenetics of bisexual/unisexual species of Poecilia II. Analysis of heterochromatin and nucleolar organizer regions in Poecilia mexicana maxicana by C-banding and DAPI, quinacrine, chromomycin A3 and silver staining. Cytogenet Cell Genet 60:229–235PubMedGoogle Scholar
  57. Sola L, Rossi AR, Annesi F, Gornung E (2003b) 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(3):232–236PubMedCrossRefGoogle Scholar
  58. Subramanian S, Mishra RK, Singh L (2003) Genome-wide analysis of Bkm sequences (GATA repeats): predominant association with sex chromosomes and potential role in higher order chromatin organization and function. Bioinformatics 19(6):681–615PubMedCrossRefGoogle Scholar
  59. Tiersh TR, Simco BA, Davis KB, Watchel SS (1992) Molecular genetics of sex determination in channel catfish: studies on SRY, ZFY, Bkm and human telomeric repeats. Biol Reprod 47(2):185–192CrossRefGoogle Scholar
  60. Tigano C, Rocco L, Ferrito V, Costagliola D, Pappalardo AM, Stingo V (2004) Chromosomal mapping and molecular characterization of ribosomal RNA genes in Lebias fasciata (Teleostei, Cyprinodontidae). Genetica 121:95–100PubMedCrossRefGoogle Scholar
  61. Urushido T, Takahashi Y, Taki Y, Kondo N (1977) A karyotype study of polypterid fishes, with notes on their phyletic relationships. Proc Jpn Acad 53:95–98CrossRefGoogle Scholar
  62. Venkatesh B, Ning Y, Brenner S (1999) Late changes in spliceosomal introns define clades in vertebrate evolution. Proc Nat Acad Sci USA 96:10267–10271PubMedCrossRefGoogle Scholar
  63. Venkatesh B, Erdmann MV, Brenner S (2001) Molecular synapomorphyes resolve evolutionary relationships of extant jawed vertebrates. Proc Nat Acad Sci USA 98:11382–11387PubMedCrossRefGoogle Scholar
  64. Vervoort A (1980a) Tetraploidy in Protopterus (Dipnoi). Experientia 36:294–296CrossRefGoogle Scholar
  65. Vervoort A (1980b) Karyotypes and nuclear DNA contents of Polypteridae (Osteichthyes). Experientia 36(6):646–647PubMedCrossRefGoogle Scholar
  66. Volff JN, Schartl M (2001) Variability of genetic sex determination in poeciliid fishes. Genetica 111:101–110PubMedCrossRefGoogle Scholar
  67. Zardoya R, Meyer A (1996) Evolutionary relationships of the coelacanth, lungfishes and tetrapods based on the 28s ribosomal gene. Proc Natl Acad Sci USA 93:5449–5454PubMedCrossRefGoogle Scholar
  68. Zardoya R, Meyer A (2001) Vertebrate phylogeny: limits of inference of mitochondrial genome and nuclear rDNA sequence data due to an adverse phylogenetic signal/noise ratio. In: Ahlberg PE (ed) Major events in early Vertebrate evolution. Taylor & Francis, London, pp 135–155Google Scholar
  69. Zardoya R, Cao Y, Hasegawa M, Meyer A (1998) Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data. Mol Biol Evol 15:506–517PubMedGoogle Scholar
  70. Wachtel S, Demas S, Tiersh T, Pechan P, Shapiro D (1991) Bkm satellite DNA and ZFY in the coral reef fish Anthias squamipinnis. Genome 34(4):612–617PubMedGoogle Scholar
  71. Wasko AP, Martins C, Wright JM, Galetti PM (2001) Molecular organization of 5S rDNA in fishes of the genus Brycon. Genome 44:893–902PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Maria Alessandra Morescalchi
    • 1
  • Innocenza Liguori
    • 1
  • Lucia Rocco
    • 1
  • Aristea Archimandritis
    • 1
  • Vincenzo Stingo
    • 1
  1. 1.Dipartimento di Scienze della VitaSeconda Università degli Studi di NapoliCasertaItaly

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