Chromosomal distribution and evolution of repetitive DNAs in Fish

Genome Dynamics

Volumn 7, Issue , 2012, Pages 197-221

  Cioffi, M B ^a   Bertollo, L A C ^a  

^a FEDERAL UNIVERSITY OF SÃO CARLOS   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

MICROSATELLITE DNA; REPETITIVE DNA; RIBOSOME DNA; RIBOSOME RNA; SATELLITE DNA;

ARTICLE; CELL DIVISION; CELL NUCLEUS; CHROMOSOMAL LOCALIZATION; CHROMOSOME; CHROMOSOME ANALYSIS; CHROMOSOME REPLICATION; CYTOGENETICS; DNA CONTENT; DNA SEQUENCE; EVOLUTION; FISH; FISH GENETICS; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; GENE FUNCTION; GENE LOCUS; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOME SIZE; KARYOTYPE; KARYOTYPING; NONHUMAN; PRIORITY JOURNAL; SEX CHROMOSOME; TELOMERE; TRANSPOSON; ANIMAL; CHROMOSOME MAP; GENETICS; GENOME; MOLECULAR EVOLUTION; NUCLEOTIDE REPEAT; REVIEW;

PISCES; VERTEBRATA;

ANIMALS; CHROMOSOME MAPPING; CYTOGENETICS; EVOLUTION, MOLECULAR; FISHES; GENETIC HETEROGENEITY; GENOME; IN SITU HYBRIDIZATION, FLUORESCENCE; KARYOTYPING; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SEX CHROMOSOMES;

EID: 84866448739     PISSN: 16609263     EISSN: 16623797     Source Type: Book Series    
DOI: 10.1159/000337950     Document Type: Article

References (101)

1. Charlesworth B, Snlegowski P, Stephan W: The evolutionary dynamics of repetitive DNA in eukary-otes. Nature 1994;371:215-220.
2. Kidwell MG: Transposable elements and the evolution of genome size in eukaryotes. Genetica 2002; 115:49-63.
3. Biémont C: Within-species variation in genome size. Heredity 2008;101:297-298.
4. Biémont C, Vieira C: Junk DNA as an evolutionary force. Nature 2006;443:521-524.
5. Horvath JE, Bailey JA, Locke D P, Eichler EE: Lessons from the human genome: transitions between euchromatin and heterochromatin. Hum Mol Genet 2001;10:2215-2223.
6. Nelson JS: Fishes of the World, ed 4, New Jersey, Inc. Hoboken, 2006.
7. Venkatesh B: Evolution and diversity of fsh genomes. Curr Opin Genet Dev 2003;13:588-592.
8. Gregory TR: Genome size evolution in animals; in Gregory TR (ed): The Evolution of the Genome. San Diego, Elsevier, 2005, pp 3-87.
9. Mayden RL, Tang KL, Conway K W, Freyhof J, Chamberlain S, et al: Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species. J Exp Zool B Mol Dev Evol 2007;308:642-654.
10. Schwarzacher T: DNA, chromosomes, and in situ hybridization. Genome 2003;46:953-962.
11. Dimitri P, Junakovic N: Revising the selfish DNA hypothesis: New evidence on accumulation of trans-posable elements in heterochromatin. Trends Genet 1999;15:123-124.
12. Grewal SI, Jia S: Heterochromatin revisited. Nat Rev Genet 2007;8:35-46.
13. Arnheim N: Concerted evolution of multigene families; in Nei M, Koehn RK (eds): Evolution of Genes and Proteins. Sunderland, Sinauer Associates, 1983, pp 38-61.
14. Ugarkovic D, Plohl M: Variation in satellite DNA profiles-Causes and effects. EMBO J 2002;21:5955-5959.
15. Martins C: Chromosomes and repetitive DNAs: a contribution to the knowledge of fsh genome; in Pisano E, Ozouf-Costaz C, Foresti F, Kapoor BG (eds): Fish Cytogenetics. Enfield, Science Publishers, 2007, pp 421-453.
16. Lanfredi M, Congiu L, Garrido-Ramos MA, de la Herrrán R, Leis M, et al: Chromosomal location and evolution of a satellite DNA family in seven sturgeon species. Chromosome Res 2001;9:47-52.
17. Ferreira IA, Martins C: Physical chromosome mapping of repetitive DNA sequences in Nile tilapia Oreochromis niloticus: Evidences for a differential distribution of repetitive elements in the sex chromosomes. Micron 2008;39:411-418.
18. Volff JN, Bouneau L, Ozouf-Costaz C, Fischer C: Diversity of retrotransposable elements in compact pufferfsh genomes. Trends Genet 2003;19:674-678.
19. Volff JN, Korting C, Sweeney K, Schartl M: The non-LTR retrotransposon Rex3 from the fsh Xiphophorus is widespread among teleosts. Mol Biol Evol 1999;16:1427-1438.
20. Ozouf-Costaz C, Brandt J, Körting C, Pisavo E, Bonillo C, et al: Genome dynamics and chromosomal localization of the non-LTR retrotransposons Rex1 and Rex3 in Antarctic fsh. Antarct Sci 2004;16:51-57.
21. Valente G T, Mazzuchelli J, Ferreira IA, Poletto A, Fantinatti BEA, Martins C: Cytogenetic mapping of the retroelements Rex1, Rex3 and Rex6 among cichlid fish: new insights on the chromosomal distribution of transposable elements. Cytogenet Genome Res 2011;133:34-42.
22. Oliveira C, Chew JSK, Porto-Foresti F, Dobson MJ, Wright JM: A LINE-like repetitive DNA sequence from the cichlid fish, Oreochromis niloticus: sequence analysis and chromosomal distribution. Chromosoma 1999;108:457-468.
23. Gross MC, Schneider CH, Valente GT, Porto JIR, Martins C, Feldberg E: Comparative cytogenetic analysis of the genus Symphysodon (Discus fishes, Cichlidae): chromosomal characteristics of ret-rotransposons and minor ribosomal DNA. Cyto-genet Genome Res 2009;127:43-53.
24. Cioffi MB, Martins C, Bertollo LAC: Chromosomal spreading of associated transposable elements and ribosomal DNA in the fish Erythrinus erythrinus. Implications for genome change and karyoevolu-tion in fish. BMC Evol Biol 2010;10:271.
25. Ferreira DC, Porto-Foresti F, Oliveira C, Foresti F: Transposable elements as a potential source for understanding fish genome. Mob Genet Elements 2011;1:112-117.
26. Hua-Van A, Le Rouzic A, Maisonhaute C, Capy P: Abundance, distribution and dynamics of ret-rotransposable elements and transposons: similarities and differences. Cytogenet Genome Res 2005; 110:426-440.
27. Martins C, Wasko AP: Organization and evolution of 5S ribosomal DNA in the fish genome; in Williams CR (ed): Focus on Genome Research. Hauppauge, Nova Science Publishers, 2004, pp 289-318.
28. Prokopowich CD, Gregory TR, Crease TJ: The correlation between rDNA copy number and genome size in eukaryotes. Genome 2003;46:48-50.
29. Martins C, Galetti PM Jr: Organization of 5S rDNA in species of the fish Leporinus: Two different genomic locations are characterized by distinct non transcribed spacers. Genome 2001;44:903-910.
30. Sajdak SL, Reed KM, Phillips RB: Intraindividual and interspecies variation in the 5S rDNA of core-gonid fish. J Mol Evol 1998;46:680-688.
31. Cioffi MB, Martins C, Bertollo LAC: Comparative chromosome mapping of repetitive sequences. Implications for genomic evolution in the fish, Hoplias malabaricus. BMC Genetics 2009;10:34.
32. Gromicho M, Coelho M, Alves M, Collares-Pereira M: Cytogenetic analysis of Anaecypris hispanica and its relationship with the paternal ancestor of the diploid-polyploid Squalius alburnoides complex. Genome 2006;49:1621-1627.
33. Foster HA, Bridger JM: The genome and the nucleus: a marriage made by evolution. Genome organization and nuclear architecture. Chromosoma 2005;114:212-229.
34. Poleto AB, Ferreira IA, Martins C: The B chromosomes of the African cichlid fish Haplochromis obliquidens harbour 18S rRNA gene copies. BMC Genetics 2010;11:1.
35. Martins C, Ferreira IA, Oliveira C, Foresti F, Galetti PM Jr: A tandemly repetitive centromeric DNA sequence of the fish Hoplias malabaricus (Characiformes: Erythrinidae) is derived from 5S rDNA. Genetica 2006;127:133-141.
36. Pinhal D, Yoshimura TS, Araki CS, Martins C: The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays. BMC Evol Biol 2011;11:151.
37. Kedes LH: Histone genes and histone messengers. Ann Rev Biochem 1979;48:837-870.
38. Nagoda N, Fukuda A, Nakashima Y, Matsuo Y: Molecular characterization and evolution of the repeating units of histone genes in Drosophila americana: coexistence of quartet and quintet units in a genome. Insect Mol Biol 2005;14:713-717.
39. Albig W, Warthorst U, Drabent B, Prats E, Cornudella L, Doenecke D: My tilus edulis core his-tone genes are organized in two clusters devoid of linker histone genes. J Mol Evol 2003;56:597-606.
40. Pendás AM, Morán P, García-Vázquez E: Organization and chromosomal location of the major histone cluster in brown trout, Atlantic salmon and rainbow trout. Chromosoma 1994;103:147-152.
41. Hashimoto DT, Ferguson-Smith MA, Rens W, Foresti F, Porto-Foresti F: Chromosome mapping of H1 histone and 5S rRNA gene clusters in three species of Astyanax (Teleostei, Characiformes). Cyto-genet Genome Res 2011;134:64-71.
42. Tautz D, Renz M: Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 1984;12:4127-4138.
43. Cioffi MB, Kejnovsky E, Bertollo LAC: The chromosomal distribution of microsatellite repeats in the wolf fish genome Hoplias malabaricus, focusing on the sex chromosomes. Cytogenet Genome Res 2011;132:289-296.
44. 9 microsatellite on chromosomes of some animal and plant species. Cytologia 2002;67:9-13.
45. Shimoda N, Knapik EW, Ziniti J, Sim C, Yamada E, et al: Zebrafish genetic map with 200 microsatellite markers. Genomics 1999;58:219-232.
46. Nanda I, Feichtinger W, Schmid M, Schröder JH, Zischler H, Epplen JC: Simple repetitive sequences are associated with differentiation of the sex chromosomes in the guppy fish. J Mol Evol 1990;30:456-462.
47. Blackburn EH: Telomeres: No end in sight. Cell 1994;77:621-623.
48. Schubert I, Schriever-Schwemmer G, Werner T, Adler ID: Telomeric signals in Robertsonian fusion and fission chromosomes: implications for the origin of pseudoaneuploidy. Cytogenet Cell Genet 1992;59:6-9.
49. Meyne J, Baker RJ, Hobart HH, Hsu TC, Ryder OA, et al: Distribution of nontelomeric sites of the (TTAGGG)n telomeric sequence in vertebrate chromosomes. Chromosoma 1990;99:3-10.
50. n repetitive sequences in the Nile tilapia, Oreochromis niloticus (Teleostei: Cichlidae). Chro-mosoma 2002;111:45-52.
51. 2Y sex chromosome system in this fish group. Heredity 2010;105:554-561.
52. Mota-Velasco JC, Ferreira IA, Cioffi MB, Ocalewicz K, Campos-Ramos R, et al: Characterization of the chromosome fusions in Oreochromis karongae. Chromosome Res 2010;18:575-586.
53. Abuín M, Martínez P, Sánchez L: Localization of the repetitive telomeric sequence (TTAGGG)n in four salmonid species. Genome 1996;39:1035-1038.
54. Dernburg AF, Sedat J W, Hawley RS: Direct evidence of a role for heterochromatin in meiotic chromosome segregation. Cell 1996;86:135-146.
55. Raskina O, Barber JC, Nevo E, Belyayev A: Repetitive DNA and chromosomal rearrangements: speciation-related events in plant genomes. Cytogenet Genome Res 2008;120:351-357.
56. Le Rouzic A, Capy P: The first steps of transposable elements invasion: parasitic strategy vs. genetic drift. Genetics 2005;169:1033-1043.
57. Haaf T, Schmid M, Steinlein C, Galetti PM Jr, Willard HF: Organization and molecular cytogenet-ics of a satellite DNA family from Hoplias malabari-cus (Pisces, Erythrinidae). Chromosome Res 1993;1:77-86.
58. Ferreira IA, Bertollo LAC, Martins C: Comparative chromosome mapping of 5S rDNA and 5SHindIII repetitive sequences in Erythrinidae fishes (Characiformes) with emphasis on the Hoplias mal-abaricus' species complex. Cytogenet Genome Res 2007;118:78-83.
59. Leggatt RA, Iwama GK: Occurrence of polyploidy in the fshes. Rev Fish Biol Fish 2003;13:237-246.
60. Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y: Genome duplication, a trait shared by 22, 000 species of ray-fnned fsh. Genome Res 2003;13:382-390.
61. Fontana F, Zane L, Pepe A, Congiu L: Polyploidy in Acipenseriformes: cytogenetic and molecular approaches; in Pisano E, Ozouf-Costaz C, Foresti F, Kapoor BG (eds): Fish Cytogenetics. Enfield, Science Publishers, 2007, pp 385-403.
62. Fontana F, Bruch RM, Binkowski F P, Lanfredi M, Chicca M, et al: Karyotype characterization of the lake sturgeon, Acipenser fulvescens (Rafinesque, 1817) by chromosome banding and fluorescent in situ hybridization. Genome 2004;47:742-746.
63. Garrido-Ramos MA, Soriguer MC, de la Herrán R, Jamilena M, Ruiz Rejón C, et al: Morphometric and genetic analysis as proof of the existence of two sturgeon species in the Guadalquivir river. Mar Biol 1997;129:33-39.
64. Charlesworth D, Charlesworth B, Marais G: Steps in the evolution of heteromorphic sex chromosomes. Heredity 2005;95:118-128.
65. Cioffi MB, Camacho JPM, Bertollo LAC: Repetitive DNAs and the differentiation of sex chromosomes in Neotropical fishes. Cytogenet Genome Res 2011; 132:188-194.
66. Dettai A, Bouneau L, Fischer C: FISH analysis of fish transposable elements: tracking down mobile DNA in teleost genomes; in Pisano E, Ozouf-Costaz C, Foresti F, Kapoor BG (eds): Fish Cytogenetics. Enfield, Science Publishers, 2007, pp 361-383.
67. Devlin RH, Nagahama T: Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences. Aquaculture 2002;208:191-364.
68. Tanaka K, Takehana Y, Naruse K, Hamaguchi S, Sakaizumi M: Evidence for different origins of sex chromosomes in closely related medaka fishes: substitution of the master sex-determining gene. Genetics 2007;177:2075-2081.
69. Nanda I, Volff JN, Weis S, Körting C, Froschauer A, et al: Amplification of a long terminal repeat-like element on the Y chromosome of the platyfish, Xiphophorus maculatus. Chromosoma 2000;109:173-180.
70. Molina WF, Schmid M, Galetti PM Jr: Heterochromatin and sex chromosomes in the Neotropical fish genus Leporinus (Characiformes, Anostomidae). Cytobios 1998;94:141-149.
71. Nakayama I, Foresti F, Tewari R, Schartl M, Chourrout D: Sex chromosome polymorphism and heterogametic males revealed by two cloned DNA probes in the ZW/ZZ fish Leporinus elongatus. Chromosoma 1994;103:31-39.
72. Parise-Maltempi P P, Martins C, Oliveira C, Foresti F: Identification of a new repetitive element in the sex chromosomes of Leporinus elongatus (Teleostei: Characiformes: Anostomidae): new insights into the sex chromosomes of Leporinus. Cytogenet Genome Res 2007;116:218-223.
73. Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, et al: The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 2003;423:825-837.
74. Kejnovsky E, Hobza R, Kubat Z, Cermak T, Vyskot B: The role of repetitive DNA in structure and evolution of sex chromosomes in plants. Heredity 2009;102:533-541.
75. Vicente VE, Bertollo LAC, Valentini SR, Moreira-Filho O: Origin and differentiation of a sex chromosome system in Parodon hilarii (Pisces, Parodontidae). Satellite DNA, G-and C-banding. Genetica 2003;119:115-120.
76. Cioffi MB, Martins C, Rebordinos L, Vicari MR, Bertollo LAC: Differentiation of the XX/XY sex chromosome system in the fish Hoplias malabari-cus: Unusual accumulation of repetitive sequences on the X chromosome. Sex Dev 2010;4:176-185.
77. Camacho JPM: B chromosomes; in Gregory TR (ed): The Evolution of the Genome. San Diego, Elsevier, 2005, pp 223-286.
78. Oliveira C, Foresti F, Hilsdorf AWS: Genetics of Neotropical fsh: from chromosomes to populations. Fish Physiol Biochem 2009;35:81-100.
79. Carvalho RA, Martins-Santos IC, Dias AL: B chromosomes: an update about their occurrence in freshwater Neotropical fshes (Teleostei). J Fish Biol 2008;72:1907-1932.
80. Alves AL, Porto-Foresti F, Oliveira C, Foresti F: Supernumerary chromosomes in the pufferfish Sphoeroides spengleri-first occurrence in marine Teleostean Tetraodontiformes fish. Genet Mol Biol 2008;31:243-245.
81. Jesus CM, Galetti PM Jr, Valentini SR, Moreira-Filho O: Molecular characterization and chromosomal localization of two families of satellite DNA in Prochilodus lineatus (Pisces, Prochilodontidae), a species with B chromosomes. Genética 2003;116:1-8.
82. Schartl M, Nanda I, Schlupp I, Wilde B, Epplen JT, et al: Incorporation of subgenomic amounts of DNA as compensation for mutational load in a gynoge-netic fish. Nature 1995;373:68-71.
83. Sampaio T, Gravena W, Gouveia J, Giuliano-Caetano L, Dias A: B microchromosomes in the family Curimatidae (Characiformes): mitotic and meiotic behavior. Comp Cytogenet 2011;5:301-313.
84. Fenocchio AS, Bertollo LAC: Supernumerary chromosome in a Rhamdia hilarii population (Pisces, Pimelodidae). Genetica 1990;81:193-198.
85. Lui RL, Blanco DR, Margarido VP, Moreira-Filho O: First description of B chromosomes in the family Auchenipteridae, Parauchenipterus galeatus (Siluriformes) of the São Francisco River basin (MG, Brazil). Micron 2009;40:552-559.
86. Maistro EL, Foresti F, Oliveira C, Almeida-Toledo LF: Occurrence of macro B chromosomes in Astyanax scabripinnis paranae (Pisces, Characi-formes, Characidae). Genetica 1992;87:101-106.
87. Ziegler CG, Lamatsch DK, Steinlein C, Engel W, Schartl M, Schmid M: The giant B chromosome of the cyprinid fish Alburnus alburnus harbours a retrotransposon-derived repetitive DNA sequence. Chromosome Res 2003;11:23-35.
88. Alves AL, Martins-Santos IC: Cytogenetics studies in two populations of Astyanax scabripinnis with 2n = 48 chromosomes (Teleostei, Characidae). Cytologia 2002;67:117-122.
89. Mestriner CA, Galetti PM Jr, Valentini S, Ruiz IGR, Abel LDS, et al: Structural and functional evidence that a B chromosome in the characid fsh Astyanax scabripinnis is an isochromosome. Heredity 2000; 85:1-9.
90. McAllister BF, Werren JH: Hybrid origin of a B chromosome (PSR) in the parasitic wasp Nasonia vitripennis. Chromosoma 1997;106:243-253.
91. Franks TK, Houben A, Leach CR, Timmis JN: The molecular organisation of a B chromosome tandem repeat sequence from Brachycome dichromosomat-ica. Chromosoma 1996;105:223-230.
92. Langdon T, Seago C, Jones RN, Ougham H, Thomas H, et al: De novo evolution of satellite DNA on the rye B chromosome. Genetics 2000;154:869-884.
93. Dantas ESO, Vicari MR, Souza IL, Moreira-Filho O, Bertollo LAC, Artoni RF: Cytotaxonomy and kary-otype evolution in Moenkhausia Eigenmann, 1903 (Teleostei, Characidae). Nucleus 2007;50:509-522.
94. Baroni S, Lopes CE, Almeida-Toledo LF: Cytogenetic characterization of Metynnis maculatus (Teleostei; Characiformes): the description in Serrasalminae of a small B chromosome bearing inactive NOR-like sequences. Caryologia 2009;62:95-101.
95. Tjio JH, Levan A: The chromosome number of man. Hereditas 1956;42:1-6.
96. Pinkel D, Straume T, Gray JW: Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Natl Acad Sci USA 1986;83:2934-2938.
97. Speicher MR, Ballard SG, Ward DC: Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 1996;12:368-375.
98. Martins C, Cabral-de-Mello DC, Valente GT, Mazzuchelli J, Oliveira SG, Pinhal D: Animal Genomes under the Focus of Cytogenetics, ed 1. New York, Nova Science Publisher, 2011.
99. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, et al: Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 2004;431:946-957.
100. Kohn M, Högel J, Vogel W, Minich P, Kehrer-Sawatzki H, et al: Reconstruction of a 450-My-old ancestral vertebrate protokaryotype. Trends Genet 2006;22:203-210.
101. Froenicke L, Caldés MG, Graphodatsky A, Müller S, Lyons LA, et al: Are molecular cytogenetics and bio-informatics suggesting diverging models of ancestral mammalian genomes? Genome Res 2006;16:306-310.