Distribution of repetitive DNAs and the hybrid origin of the red vizcacha rat (Octodontidae)

Genome

Volumn 55, Issue 2, 2012, Pages 105-117

  Suarez Villota E Y ^a   Vargas, R A ^a   Marchant, C L ^a   Torres, J E ^a   Kohler N ^a   Nunez J J ^a   De La Fuente, R ^b   Page, J ^b   Gallardo, M H ^a  

^a UNIVERSIDAD AUSTRAL DE CHILE   (Chile)

^b UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

GISH; Hybrid origin; Repetitive DNA; Self GISH; Tympanoctomys barrerae; W CGH

Indexed keywords

ANIMAL; ARTICLE; CHROMOSOME ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; EVOLUTION; GENETICS; GENOME SIZE; HYBRIDIZATION; IN SITU HYBRIDIZATION; NUCLEOTIDE REPEAT; RODENT; SPECIES DIFFERENCE;

ANIMALS; BIOLOGICAL EVOLUTION; COMPARATIVE GENOMIC HYBRIDIZATION; CYTOGENETIC ANALYSIS; GENOME SIZE; HYBRIDIZATION, GENETIC; IN SITU HYBRIDIZATION; REPETITIVE SEQUENCES, NUCLEIC ACID; RODENTIA; SPECIES SPECIFICITY;

EID: 84857221494     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/g11-084     Document Type: Article

References (73)

1. Acosta M.J. Marchal J.A. Fernández-Espartero C.H. Bullejos M. Sánchez A. 2008. Retroelements (LINEs and SINEs) in vole genomes: differential distribution in the constitutive heterochromatin. Chromosome Res. 16 (7): 949-959. 10.1007/s10577-008-1253-3 18836842
2. Bacquet C. Imamura T. González C.A. Conejeros I. Kausel G. Neildez-Nguyen T.M.A. et al. 2008. Epigenetic processes in a tetraploid mammal. Mamm. Genome, 19 (6): 439-447. 10.1007/s00335-008-9131-z 18758856
3. Benabdelmouna A. Shi Y. Abirached-Darmency M. Darmency H. 2001. Genomic in situ hybridization (GISH) discriminates between the A and B genomes in diploid and tetraploid Setaria species. Genome, 44 (4): 685-690. 10.1139/g01-032 11550905 (Pubitemid 32773645)
4. Bi K. Bogart J.P. 2006. Identification of intergenomic recombinations in unisexual salamanders of the genus Ambystoma by genomic in situ hybridization (GISH). Cytogenet. Genome Res. 112 (3-4): 307-312. 10.1159/000089885 16484787 (Pubitemid 43260759)
5. Bi K. Bogart J.P. 2010. Probing the meiotic mechanism of intergenomic exchanges by genomic in situ hybridization on lampbrush chromosomes of unisexual Ambystoma (Amphibia: Caudata). Chromosome Res. 18 (3): 371-382. 10.1007/s10577-010-9121-3 20358399
6. Bi K. Bogart J.P. Fu J. 2009. An examination of intergenomic exchanges in A. laterale-dependent unisexual salamanders in the genus Ambystoma. Cytogenet. Genome Res. 124 (1): 44-50. 10.1159/000200087 19372668
7. Charlesworth B. Sniegowski P.E. Stephan W. 1994. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature, 371 (6494): 215-220. 10.1038/371215a0 8078581 (Pubitemid 24293018)
8. Chen Z.J. 2007. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu. Rev. Plant Biol. 58 (1): 377-406. 10.1146/annurev.arplant.58.032806.103835 17280525 (Pubitemid 46986330)
9. Contreras L.C. Torres-Mura J.C. Spotorno A.E. Walker L.I. 1994. Chromosomes of Octomys mimax and Octodontomys gliroides and relationships of octodontid rodents. J. Mammal. 75 (3): 768-774. 10.2307/1382529 (Pubitemid 2137962)
10. Dávila-Rodríguez M.I. Cortés-Gutiérrez E.I. López-Fernández C. Pita M. Mezzanotte R. Gosálvez J. 2009. Whole-comparative genomic hybridization in domestic sheep (Ovis aries) breeds. Cytogenet. Genome Res. 124 (1): 19-26. 10.1159/000200084 19372665
11. Eakin G.S. Behringer R.R. 2003. Tetraploid development of the mouse. Dev. Dyn. 228 (4): 751-766. 10.1002/dvdy.10363 14648853 (Pubitemid 37493995)
12. Eichler E.E. Sankoff D. 2003. Structural dynamics of eukaryotic chromosome evolution. Science, 301 (5634): 793-797. 10.1126/science.1086132 12907789 (Pubitemid 36962611)
13. Ezaz T. Quinn A.E. Miura I. Sarre S.D. Georges A. Marshall-Graves J.A. 2005. The dragon lizard Pogona vitticeps has ZZ/ZW micro-sex chromosomes. Chromosome Res. 13 (8): 763-776. 10.1007/s10577-005-1010-9 16331408 (Pubitemid 41768767)
14. Gallardo M.H. 1992. Karyotypic evolution in octodontid rodents based on C-band analysis. J. Mammal. 73 (1): 89-98. 10.2307/1381869
15. Gallardo M.H. Kirsch J.A.W. 2001. Molecular relationships among Octodontidae (Mammalia: Rodentia: Caviomorpha). J. Mamm. Evol. 8 (1): 73-89. 10.1023/A:1011345000786 (Pubitemid 33310582)
16. Gallardo M.H. Bickham J.W. Honeycutt R.L. Ojeda R.A. Köhler N. 1999. Discovery of tetraploidy in a mammal. Nature, 401 (6751): 341. 10.1038/43815 10517628 (Pubitemid 29454947)
17. Gallardo M.H. Bickham J.W. Kausel G. Köhler N. Honeycutt R.L. 2003. Gradual and quantum genome size shifts in the hystricognath rodents. J. Evol. Biol. 16 (1): 163-169. 10.1046/j.1420-9101.2003.00507.x 14635891 (Pubitemid 36108142)
18. Gallardo M.H. Kausel G. Jiménez A. Bacquet C. González C. Figueroa J. et al. 2004 a. Whole-genome duplications in South American desert rodents (Octodontidae). Biol. J. Linn. Soc. 82 (4): 443-451. 10.1111/j.1095-8312.2004.00331.x (Pubitemid 39123333)
19. Gallardo M.H. Garrido O. Bahamonde R. González M. 2004 b. Gametogenesis and nucleotypic effects in the tetraploid red vizcacha rat, Tympanoctomys barrerae (Rodentia, Octodontidae). Biol. Res. 37 (4 Suppl A): 765-775. 10.4067/S0716-97602004000500006 15586825
20. Gallardo M.H. González C.A. Cebrián I. 2006. Molecular cytogenetics and allotetraploidy in the red vizcacha rat, Tympanoctomys barrerae (Rodentia, Octodontidae). Genomics, 88 (2): 214-221. 10.1016/j.ygeno.2006.02. 010 16580173 (Pubitemid 44062269)
21. Gallardo, M.H., Ojeda, R.A., González, C.A., and Ríos, C.A. 2007. The Octodontidae revisited. In The quintessential naturalist: honoring the life and legacy of Oliver P. Pearson. Edited by D.A. Kelt, E.P. Lessa, J. Salazar-Bravo, and J.L. Patton. University of California Publications in Zoology, California. Vol. 134. pp. 695-720.
22. Gosálvez J.F. Crespo J.L. Vega-Pla C. López- Fernández E.I. Cortés-Gutiérrez E.I. Mezzanotte R. 2010. Shared Y chromosome repetitive DNA sequences in stallion and donkey as visualized using whole-genomic comparative hybridization. Eur. J. Histochem. 54 (1): e2. 10.4081/ejh.2010.e2 20353909
23. Goureau A. Yerle M. Schmitz A. Riquet J. Milan D. Pinton P. et al. 1996. Human and porcine correspondence of chromosome segments using bidirectional chromosome painting. Genomics, 36 (2): 252-262. 10.1006/geno.1996.0460 8812451 (Pubitemid 26307487)
24. Guc-Scekic M. Milasin J. Stevanovic M. Stojanov L.J. Djorjevic M. 2002. Tetraploidy in a 26-month-old girl (cytogenetic and molecular studies). Clin. Genet. 61 (1): 62-65. 10.1034/j.1399-0004.2002.610112.x 11903358 (Pubitemid 36372605)
25. Guenatri M. Bailly D. Maison C. Almouzni G. 2004. Mouse centric and pericentric satellite repeats form distinct functional heterochromatin. J. Cell Biol. 166 (4): 493-505. 10.1083/jcb.200403109 15302854 (Pubitemid 39097169)
26. Guichaoua M.R. Devictor M. Hartung M. Luciani J.M. Stahl A. 1986. Random acrocentric bivalent associations in human pachytene spermatocytes. Molecular implications in the occurrence of Robertsonian translocations. Cytogenet. Cell Genet. 42 (4): 191-197. 10.1159/000132277 3463445 (Pubitemid 16026327)
27. Hassold T. Chen N. Funkhouser J. Jooss T. Manuel B. Matsuura J. et al. 1980. A cytogenetic study of 1000 spontaneous abortions. Ann. Hum. Genet. 44 (2): 151-164. 10.1111/j.1469-1809.1980.tb00955.x 7316468
28. Hawkins J.S. Kim H. Nason J.D. Wing R.A. Wendel J.F. 2006. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res. 16 (10): 1252-1261. 10.1101/gr.5282906 16954538 (Pubitemid 44506958)
29. Hegarty M.J. Hiscock S.J. 2008. Genomic clues to the evolutionary success of polyploid plants. Curr. Biol. 18 (10): R435-R444. 10.1016/j.cub.2008.03.043 18492478 (Pubitemid 351672036)
30. Hepperger C. Mayer A. Merz J. Vanderwall D.K. Dietzel S. 2009. Parental genomes mix in mule and human cell nuclei. Chromosoma, 118 (3): 335-347. 10.1007/s00412-008-0200-6 19198867
31. Heslop-Harrison J.S. Chapman V. Bennett M.D. 1985. Heteromorphic bivalent association at meiosis in bread wheat. Heredity, 55 (1): 93-103. 10.1038/hdy.1985.75
32. Kalitsis P. Griffiths B. Choo K.H. 2006. Mouse telocentric sequences reveal a high rate of homogenization and possible role in Robertsonian translocation. Proc. Natl. Acad. Sci. U.S.A. 103 (23): 8786-8791. 10.1073/pnas.0600250103 16731628 (Pubitemid 43878097)
33. Kamstra S.A. Ramanna M.S. De Jeu M.J. Kuipers A.G. Jacobsen E. 1999. Homoeologous chromosome pairing in the distant hybrid Alstroemeria aurea × A. inodora and the genome composition of its backcross derivatives determined by fluorescence in situ hybridization with species-specific probes. Heredity, 82 (1): 69-78. 10.1038/sj.hdy.6884650 10087627 (Pubitemid 29087450)
34. Kato A. Lamb J.C. Birchler J.A. 2004. Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc. Natl. Acad. Sci. U.S.A. 101 (37): 13 554-13 559. 10.1073/pnas.0403659101 15342909 (Pubitemid 39238441)
35. Köhler N. Gallardo M.H. Contreras L.C. Torres-Mura J.C. 2000. Allozymic variation and systematic relationships of the Octodontidae and allied taxa (Mammalia, Rodentia). J. Zool. (Lond.), 252 (2): 243-250.
36. Lammers J.H.M. Offenberg H.H. Van Aalderen M. Vink A.C.G. Dietrich A.J.J. Heyting C. 1994. The gene encoding a major component of the lateral elements of synaptonemal complexes of rat is related to X-linked lymphocyte-regulated genes. Mol. Cell. Biol. 14 (2): 1137-1146. 10.1128/MCB.14.2.1137 8289794 (Pubitemid 24036564)
37. Lapierre J.M. Tachdjian G. 2005. Detection of chromosomal abnormalities by comparative genomic hybridization. Curr. Opin. Obstet. Gynecol. 17 (2): 171-177. 10.1097/01.gco.0000162188.99219.04 15758611 (Pubitemid 40432740)
38. Lim K.Y. Soltis D.E. Soltis P.S. Tate J. Matyasek R. Srubarova H. et al. 2008. Rapid chromosome evolution in recently formed polyploids in Tragopodon (Asteraceae). PLoS ONE, 3 (10): e3353. 10.1371/journal.pone.0003353 18843372
39. Liu B. Wendel J.F. 2003. Epigenetic phenomena and the evolution of plant allopolyploids. Mol. Phylogenet. Evol. 29 (3): 365-379. 10.1016/S1055-7903(03) 00213-6 14615180 (Pubitemid 37491884)
40. Markova M. Vyskot B. 2009. New Horizons of genomic in situ hybridization. Cytogenet. Genome Res. 126 (4): 368-375. 10.1159/000275796 20110676
41. Markova M. Michu E. Vyskot B. Janousek B. Zluvova J. 2007. An interspecific hybrid as a tool to study phylogenetic relationships in plants using the GISH technique. Chromosome Res. 15 (8): 1051-1059. 10.1007/s10577-007-1180-8 18075777
42. Modi W.S. Serdyukova N.A. Vorobieva N.V. Graphodatsky A.S. 2003. Chromosomal localization of six repeated DNA sequences among species of Microtus (Rodentia). Chromosome Res. 11 (7): 705-713. 10.1023/A:1025922813756 14606632 (Pubitemid 37323630)
43. Ohno S. Wolf U. Atkin N.B. 1968. Evolution from fish to mammals by gene duplication. Hereditas, 59 (1): 169-187. 5662632
44. Otto S.P. 2007. The evolutionary consequences of polyploidy. Cell, 131 (3): 452-462. 10.1016/j.cell.2007.10.022 17981114 (Pubitemid 350007701)
45. Otto S.P. Whitton J. 2000. Polyploid incidence and evolution. Annu. Rev. Genet. 34 (1): 401-437. 10.1146/annurev.genet.34.1.401 11092833 (Pubitemid 32065927)
46. Peters A.H.F.M. Plug A.W. Van Vugt M.J. De Boer P. 1997. A drying-down technique for the spreading of mammalian meiocytes from the male and female germline. Chromosome Res. 5 (1): 66-68. 10.1023/A:1018445520117 9088645 (Pubitemid 27129985)
47. Petrov D.A. 2001. Evolution of genome size: new approaches for an old problem. Trends Genet. 17 (1): 23-28. 10.1016/S0168-9525(00)02157-0 11163918 (Pubitemid 32332976)
48. Pikaard C.S. 2000. Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in genetic hybrids. Plant Mol. Biol. 43 (2-3): 163-177. 10.1023/A:1006471009225 10999402
49. Pinkel D. Albertson D.G. 2005. Comparative genomic hybridization. Annu. Rev. Genomics Hum. Genet. 6 (1): 331-354. 10.1146/annurev.genom.6.080604.162140 16124865 (Pubitemid 41397087)
50. Pita M. Fernández J.L. Gosálvez J. 2003. Whole-comparative genomic hybridization (W-CGH): I. The quick overview of repetitive DNA sequences on a genome. Chromosome Res. 11 (7): 673-679. 10.1023/A:1025937726614 14606629 (Pubitemid 37323627)
51. Pita M. Zabal-Aguirre M. Arroyo F. Gosálvez J. López-Fernández C. De la Torre J. 2008 a. Arcyptera fusca and Arcyptera tornosi repetitive DNA families: whole-comparative genomic hybridization (W-CGH) as a novel approach to the study of satellite DNA libraries. J. Evol. Biol. 21 (1): 352-361. 10.1111/j.1420-9101.2007.01436.x 17995950 (Pubitemid 350256614)
52. Pita M. García-Casado P. Toro M.A. Gosálvez J. 2008 b. Differential expansion of highly repeated DNA sequences in the swine subgenomes. J. Zool. Syst. Evol. Res. 46 (2): 186-189. 10.1111/j.1439-0469.2008.00466.x (Pubitemid 351533551)
53. Plohl M. Luchetti A. Mestrović N. Mantovani B. 2008. Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene, 409 (1-2): 72-82. 10.1016/j.gene.2007.11.013 18182173
54. Pontes O. Lawrence R.J. Neves N. Silva M. Lee J.-H. Chen Z.J. et al. 2003. Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 100 (20): 11 418-11 423. 10.1073/pnas.1932522100 14504406 (Pubitemid 37205950)
55. Putnam N.H. Butts T. Ferrier D.E.K. Furlong R.F. Hellsten U. Kawashima T. et al. 2008. The amphioxus genome and the evolution of the chordate karyotype. Nature, 453 (7198): 1064-1071. 10.1038/nature06967 18563158 (Pubitemid 351888243)
56. Raina S.N. Rani V. 2001. GISH technology in plant genome research. Methods Cell Sci. 23 (1-3): 83-104. 10.1023/A:1013197705523 11741146 (Pubitemid 34116337)
57. Rego A. Marec F. 2003. Telomeric and interstitial telomeric sequences in holokinetic chromosomes of Lepidoptera: telomeric DNA mediates association between postpachytene bivalents in achiasmatic meiosis of females. Chromosome Res. 11 (7): 681-694. 10.1023/A:1025937808382 14606630 (Pubitemid 37323628)
58. Schmidt T. Heslop-Harrison J.S. 1998. Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci. 3 (5): 195-199. 10.1016/S1360-1385(98)01223-0 (Pubitemid 28229040)
59. Schwarzacher, T., and Heslop-Harrison, P. 2000. Practical in situ hybridization. BIOS Scientific Publishers Limited, Oxford.
60. Scott L.A. Kuroiwa A. Matsuda Y. Wichman H.A. 2006. X accumulation of LINE-1 retrotransposons in Tokudaia osimensis, a spiny rat with the karyotype XO. Cytogenet. Genome Res. 112 (3-4): 261-269. 10.1159/000089880 16484782 (Pubitemid 43260755)
61. She C. Liu J. Diao Y. Hu Z. Song Y. 2007. The distribution of repetitive DNAs along chromosomes in plants revealed by self-genomic in situ hybridization. J. Genet. Genomics, 34 (5): 437-448. 10.1016/S1673-8527(07)60048-4 17560530 (Pubitemid 46874285)
62. Stebbins, G.L. 1971. Chromosomal evolution in higher plants. Edward Arnold Publishers, London.
63. Stocker H. Hafen E. 2000. Genetic control of cell size. Curr. Opin. Genet. Dev. 10 (5): 529-535. 10.1016/S0959-437X(00)00123-4 10980431
64. Svartman M. Stone G. Stanyon R. 2005. Molecular cytogenetics discards polyploidy in mammals. Genomics, 85 (4): 425-430. 10.1016/j.ygeno.2004.12.004 15780745 (Pubitemid 40386471)
65. Tachdjian G. Aboura A. Lapierre J.M. Viguié F. 2000. Cytogenetic analysis from DNA by comparative genomic hybridization. Ann. Genet. 43 (3-4): 147-154. 10.1016/S0003-3995(00)01028-5 11164197 (Pubitemid 32050071)
66. The French-Italian Public Consortium for Grapevine Genome Characterization. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449 (7161): 463-467. 10.1038/nature06148 17721507 (Pubitemid 47509545)
67. Traut W. Sahara K. Otto T.D. Marec F. 1999. Molecular differentiation of sex chromosomes probed by comparative genomic hybridization. Chromosoma, 108 (3): 173-180. 10.1007/s004120050366 10398846 (Pubitemid 29346647)
68. Traut W. Eickhof U. Schorch J.-C. 2001. Identification and analysis of sex chromosomes by comparative genomic hybridization (CGH). Methods Cell Sci. 23 (1-3): 155-161. 10.1023/A:1013138925996 11741153 (Pubitemid 34116344)
69. Uozu S. Ikehashi H. Ohmido N. Ohtsubo H. Ohtsubo E. Fukui K. 1997. Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol. Biol. 35 (6): 791-799. 10.1023/A:1005823124989 9426599 (Pubitemid 28016938)
70. Ventura M. Archidiacono N. Rocchi M. 2001. Centromere emergence in evolution. Genome Res. 11 (4): 595-599. 10.1101/gr.152101 11282974 (Pubitemid 32331556)
71. Verma, R.S., and Babu, A. 1995. Human chromosomes. Principles and techniques. McGraw-Hill, New York.
72. Yao X.C. Du X.Z. Ge X.H. Chen J.P. Li Z.Y. 2010. Intra-and intergenomic chromosome pairings revealed by dual-color GISH in trigenomic hybrids of Brassica juncea and B. carinata with B. maurorum. Genome, 53 (1): 14-22. 10.1139/G09-082 20130745
73. Zhan, P., Kynast, R., and Bernd, F. 2004. Protocol for GISH, genomic in situ hybridization [online]. Wheat Genetics Resource Center, Kansas State University, Manhattan. Available from http://www.k-state.edu/wgrc/Protocols/ labbook.html. [accessed 19 April 2010].