Chromosomal evolution in Rattini (Muridae, Rodentia)

Chromosome Research

Volumn 19, Issue 6, 2011, Pages 709-727

  Badenhorst, Daleen ^a   Dobigny, Gauthier ^b,c   Adega, Filomena ^d   Chaves, Raquel ^d   O'Brien, Patricia C M ^e   Ferguson Smith, Malcolm A ^e   Waters, Paul D ^f   Robinson, Terence J ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

^b CENTRE DE BIOLOGIE ET DE GESTION DES POPULATIONS   (France)

^c Centre Regional Agrhymet   (Niger)

^d UNIVERSITY OF TRÁS OS MONTES AND ALTO DOURO   (Portugal)

^e UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^f AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

Ancestral karyotype; BAC FISH; Chromosome painting; Karyotype evolution; Rattini; Satellite DNA

Indexed keywords

SATELLITE DNA;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; AUTOSOME; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME; CHROMOSOME ANALYSIS; CHROMOSOME BANDING PATTERN; CHROMOSOME MAP; CHROMOSOME NOR; CHROMOSOME PAINTING; CHROMOSOME TRANSLOCATION; CLONE; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENOMICS; KARYOTYPE; MALE; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; RAT; RODENT; TAXON;

ANIMALS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; CHROMOSOME BANDING; CHROMOSOME PAINTING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, MAMMALIAN; DNA, SATELLITE; FEMALE; IN SITU HYBRIDIZATION, FLUORESCENCE; KARYOTYPING; MALE; MOLECULAR SEQUENCE DATA; MURINAE; NUCLEOLUS ORGANIZER REGION; RATS; SEQUENCE ALIGNMENT;

BANDICOTA; BANDICOTA SAVILEI; BERYLMYS; LEOPOLDAMYS; MAXOMYS; MAXOMYS SURIFER; MURIDAE; MURINAE; NIVIVENTER; NIVIVENTER FULVESCENS; RATTUS; RATTUS NORVEGICUS; RATTUS TANEZUMI; RODENTIA;

EID: 82955162608     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-011-9227-2     Document Type: Article

References (84)

1. Acosta MJ, Marchal JA, Fernández-Espartero C et al (2010) Characterisation of the satellite DNA Msat-160 from species of Terricola (Microtus) and Arvicola (Rodentia, Arvicolinae). Genetica 138:1085-1098
2. Adega F, Chaves R, Guedes-Pinto H (2008) Suiformes orthologous satellite DNAs as a hallmark of collared and white-lipped peccaries (Tayassuidae) evolutionary rearrangements. Micron 39:1281-1287
3. Aitman TJ, Critser JK, Cuppen E et al (2008) Progress and prospects in rat genetics: a community view. Nat Genet 40:516-522 (Pubitemid 351601225)
4. Aplin KP, Chesser T, Have JT (2003) Evolutionary biology of the genus Rattus: profile of an archetypal rodent pest. In: Singleton GR, Hinds LA, Krebs CJ (eds) Rats, mice and people: rodent biology and management. ACIAR Monograph No. 96. Australian Centre for International Agricultural Research, pp 487-498
5. Avise JC, Robinson TJ (2008) Hemiplasy: a new term in the lexicon of phylogenetics. Syst Biol 57:503-507 (Pubitemid 351882206)
6. Ayala FJ, Coluzzi M (2005) Chromosome speciation: humans, Drosophila, mosquitoes. Proc Natl Acad Sci USA 102:6535-6542 (Pubitemid 40628301)
7. Badenhorst D (2011) Rattini (Rodentia, Murinae) species relationships and involvement as reservoirs for scrub typhus: a comparative molecular cytogenetic and gene expression approach. PhD thesis, University of Stellenbosch: Stellenbosch University Press
8. Badenhorst D, Herbreteau V, Chaval Y et al (2009) New karyotypic data for Asian rodents (Rodentia, Muridae) with the first report of B-chromosomes in the genus Mus. J Zool (Lond) 279:44-56
9. Barch MJ (1997) The AGT cytogenetics laboratory manual. Lippincott-Raven Publishers, Philadelphia, p 301
10. Bastos ADS, Nair D, Taylor PJ et al (2011) Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in South Africa. BMC Genet 12:26
11. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573-580 (Pubitemid 29210025)
12. Bolzan AD, Bianchi MS (2006) Telomeres, interstitial telomeric repeat sequences, and chromosomal aberrations. Mut Res 612:189-214 (Pubitemid 43767088)
13. Bonvicino C, D'Andrea P, Borodin P (2001) Pericentric inversion in natural populations of Oligoryzomys nigripes (Rodentia, Sigmodontinae). Genome 44:791-796 (Pubitemid 33023440)
14. Brown JD, O'Neill RJ (2010) Chromosomes, conflict, and epigenetics: chromosomal speciation revisited. Annu Rev Genomics Hum Genet 11:291-316
15. Cavagna P, Stone G, Stanyon R (2002) Black rat (Rattus rattus) genomic variability characterised by chromosome painting. Mamm Genome 13:157-163 (Pubitemid 34185315)
16. Chaves R, Adega F, Santos S, Guedes-Pinto H, Heslop-Harrison JS (2002) In situ hybridization and chromosome banding in mammalian species. Cytogenet Genome Res 96:113-116 (Pubitemid 37456588)
17. Chaves R, Adega F, Heslop-Harrison JS, Guedes-Pinto H, Wienberg J (2003a) Complex satellite DNA reshuffling in the polymorphic t (1;29) Robertsonian translocation and evolutionary derived chromosomes in cattle. Chromosome Res 11:641-648 (Pubitemid 37323625)
18. Chaves R, Adega F, Wienberg J, Guedes-Pinto H, Heslop-Harrison JS (2003b) Molecular cytogenetic analysis and centromeric satellite organization of a novel 8;11 translocation in sheep: a possible intermediate in biarmed chromosome evolution. Mamm Genome 14:706-710 (Pubitemid 37204881)
19. Coluzzi M, Sabatini A, Della Torre A, Di Deco M, Tetrarca V (2002) A polytene chromosome analysis of the Anopheles gambiae species complex. Science 298:1415-1418 (Pubitemid 35346140)
20. Dobigny G, Aniskin V, Volobouev V (2002a) Explosive chromosome evolution and speciation in the gerbil genus Taterillus (Rodentia, Gerbillinae): a case of two new cryptic species. Cytogenet Genome Res 96:117-124 (Pubitemid 37456589)
21. Dobigny G, Ozouf-Costaz C, Bonillo C, Volobouev V (2002b) "Ag-NORs" are not always true NORs, new evidence in mammals. Cytogenet Genome Res 98:75-77 (Pubitemid 37499924)
22. Dobigny G, Ducroz J, Robinson TJ, Volobouev V (2004a) Cytogenetics and cladistics. Syst Biol 53:470-484 (Pubitemid 38946909)
23. Dobigny G, Ozouf-Costaz C, Bonillo C (2004b) Viability of X autosome translocations in mammals: an epigenomic hypothesis from a rodent case-study. Chromosoma 113:34-41 (Pubitemid 39236720)
24. Dobigny G, Aniskin V, Granjon L, Cornette R, Volobouev V (2005) Recent radiation inWest African Taterillus (Rodentia, Gerbillinae): the concerted role of chromosome and climatic changes. Heredity 95:358-368 (Pubitemid 41548411)
25. Gadi IK, Sharma T (1983) Cytogenetic relationships in Rattus, Cremnomys, Millardia, Nesokia and Bandicota (Rodentia: Muridae). Genetica 61:21-40
26. Gilbert C, O'Brien PCM, Bronner G et al (2006) Chromosome painting and molecular dating indicate a low rate of chromosomal evolution in golden moles (Mammalia, Chrysochloridae). Chromosome Res 14:793-803 (Pubitemid 46144225)
27. Goodpasture C, Bloom SE (1975) Visualization of nucleolar organizer regions in mammalian chromosmes using silver stain. Chromosoma 53:37-50
28. Grutzner F, Himmelbauer H, Paulsen M, Ropers HH, Haaf T (1999) Comparative mapping of mouse and rat chromosomes by fluorescence in situ hybridization. Genomics 55:306-313 (Pubitemid 29096132)
29. Guilly M, Fouchet P, de Chamisso P, Schmitz A, Dutrillaux B (1999) Comparative karyotype of rat and mouse using bidirectional chromosome painting. Chromosome Res 7:213-221 (Pubitemid 29259586)
30. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucl Acids Symp Ser 41:95-98
31. Hamta A, Adamovic T, Samuelson E, Helou K, Behboudi A, Levan G (2006) Chromosome ideograms of the laboratory rat (Rattus norvegicus) based on high-resolution banding, and anchoring of the cytogenetic map to the DNA sequence by FISH in sample chromosomes. Cytogenet Genome Res 115:158-168 (Pubitemid 44622522)
32. Helou K, Walentinsson A, Levan G, Stahl F (2001) Between rat and mouse zoo-FISH reveals 49 chromosomal segments that have been conserved in evolution. Mamm Genome 12:765-771 (Pubitemid 32913021)
33. Hoffman AA, Sgro CM, Weeks AR (2004) Chromosomal inversion polymorphisms and adaptation. Trends Ecol Evol 19:483-488
34. Ijdo JW, Wells RA, Baldini A, Reeders ST (1991) Improved telomere detection using a telomere repeat probe (TTAGGG) n generated by PCR. Nucleic Acids Res 19:4780
35. Jansa SA, Weksler M (2004) Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences. Mol Phylogenet Evol 31:256-276 (Pubitemid 38403336)
36. Kodama Y, Yoshida M, Sasaki M (1980) An improved silver staining technique for nucleolus organizer regions by using nylon cloth. Jap J Human Genet 25:229-233 (Pubitemid 11166114)
37. Lecompte E, Aplin K, Denys C, Catzeflis F, Chades M, Chevret P (2008) Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences,with a new tribal classification of the subfamily. BMC Evol Biol 8:199
38. Lee MR, Elder FFB (1980) Yeast stimulation of bone marrow mitosis for cytogenetic investigations. Cytogenet Cell Genet 26:36-40 (Pubitemid 10128692)
39. Li T, O'Brien PCM, Biltueva L et al (2004) Evolution of genome organizations of squirrels (Sciuridae) revealed by cross-species chromosome painting. Chromosome Res 12:317-335 (Pubitemid 38932373)
40. Li T,Wang J, SuW, NieW, Yang F (2006) Karyotypic evolution of the family Sciuridae: inferences from the genome organizations of ground squirrels. Cytogenet Genome Res 112:270-276 (Pubitemid 43260756)
41. Louzada S, Paco A, Kubickova S et al (2008) Different evolutionary trails in the related genomes Cricetus cricetus and Peromyscus eremicus (Rodentia, Cricetidae) uncovered by orthologous satellite DNA repositioning. Micron 39:1149-1155
42. MacEachern S, McEwan J, Goddard M (2009) Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae). BMC Genomics 10:177. doi:10.1186/1471-2164-10-177
43. Matisoo-Smith E, Robins JH (2004) Origins and dispersals of Pacific peoples: evidence from mtDNA phylogenies of the Pacific rat. Proc Natl Acad Sci 101:9167-9172 (Pubitemid 38781629)
44. Matsubara K, Nishida-Umehara C, Tsuchiya K, Nukaya D, Matsuda Y (2004) Karyotypic evolution of Apodemus (Muridae, Rodentia) inferred from comparative FISH analyses. Chromosome Res 12:383-395 (Pubitemid 38932378)
45. Meerburg B, Singleton G, Kijlstra A (2009) Rodent-borne diseases and their risks for public health. Crit Rev Microbiol 35:221-270
46. Nguyen TT, Aniskin VM, Gerbault-Seureau M et al (2008) Phylogenetic position of the saola (Pseudoryx nghetinhensis) inferred from cytogenetic analysis of eleven species of Bovidae. Cytogenet Genome Res 122:41-54
47. Nijman IJ, Lenstra JA (2001) Mutation and recombination in cattle satellite DNA: a feedback model for the evolution of satellite DNA repeats. J Mol Evol 52:361-371 (Pubitemid 32368246)
48. Nilsson S, Helou K, Walentinsson A, Szpirer C, Nerman C, Stahl F (2001) Rat-mouse and rat-human comparative maps based on gene homology and high-resolution zoo-FISH. Genomics 74:287-298 (Pubitemid 32675352)
49. Noor MAF, Grams KL, Bertucci LA, Reiland J (2001) Chromosomal inversion and the reproductive isolation of species. Proc Natl Acad Sci USA 98:12084-12088 (Pubitemid 32959830)
50. Pagés M, Chaval Y, Herbreteau V et al (2010) Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries. BMC Evol Biol 10:184
51. Pech M, Igo-Kemenes T, Zachau HG (1979) Nucleotide sequence of a highly repetitive component of rat DNA. Nucleic Acids Res 7:417-432
52. Richard F, Messaoudi C, Bonnet-Garnier A, Lombard M, Dutrillaux B (2003) Highly conserved chromosomes in an Asian squirrel (Menetes berdmorei, Rodentia: Sciuridae) as demonstrated by ZOO-FISH with human probes. Chromosome Res 11:597-603 (Pubitemid 37056162)
53. Robins JH, McLenachan PA, Phillips MJ, Craig L, Ross HA, Matisoo-Smith E (2008) Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes. Mol Phylogenet Evol 49:460-466
54. Robinson TJ, Ropiquet A (2011) Examination of hemiplasy, homoplasy and phylogenetic discordance in chromosomal evolution of the Bovidae. Syst Biol. doi:10.1093/sysbio/syr045
55. Robinson TJ, Ruiz-Herrera A, Avise JC (2008) Hemiplasy and homoplasy in the karyotypic phylogenies of mammals. Proc Natl Acad Sci USA 105:14477-14481
56. Sanchez A, Jimenez R, Burgos M, Stitou S, Zurita F, Diaz de la Guardia R (1995) Cytogenetic peculiarities in the Algerian hedgehog: silver stains not only NORs but also heterochromatic blocks. Heredity 75:10-16
57. Sasaki M, Nishida C, Kodama Y (1986) Characterisation of silver-stained nucleolus organizer regions (Ag-NORs) in 16 inbred strains of the Norway rat, Rattus norvegicus. Cytogenet Cell Genet 41:83-88 (Pubitemid 16183581)
58. Seabright M (1971) A rapid banding technique for human chromosome. Lancet 2:971-972
59. Slamovits CH, Rossi M (2002) Satellite DNA: agent of chromosomal evolution in mammals. A review. J Neotrop Mammal 9:297-308
60. Stanyon R, Yang F, Cavagna P et al (1999) Reciprocal chromosome painting shows that genomic rearrangement between rat and mouse proceeds ten times faster than between humans and cats. Cytogenet Cell Genet 84:150-155 (Pubitemid 29294951)
61. Stanyon R, Stone G, Garcia M, Frönicke L (2003) Reciprocal chromosome painting shows that squirrels, unlike murid rodents, have a highly conserved genome organization. Genomics 82:245-249 (Pubitemid 36808625)
62. Stefansson H, Helgason A, Thorleifsson G et al (2005) A common inversion under selection in Europeans. Nat Rev Genet 37:12-137
63. Sternes KL, Vig BK (1995) Satellite I DNA in transformed rat cells. Cancer Genet Cytogenet 79:64-69
64. Szabo P, Lee M, Elder F, Prensky W (1978) Localization of 5S RNA and rRNA genes in the Norway rat. Chromosoma 65:161-172 (Pubitemid 8252015)
65. Taylor PJ, Arntzen L, Hayter M, Iles M, Frean J, Belmain SR (2008) Understanding and managing sanitary risks due to rodent zoonoses in an African city: beyond the Boston Model. Integr Zool 3:38-50
66. Telenius H, Pelmear A, Tunnacliffe A et al (1992) Cytogenetic analysis by chromosome painting using DOP-PCR amplified sorted chromosomes. Gene Chromosome Canc 4:257-264
67. Twigger SN, Pruitt KD, Fernández-Suárez XM et al (2008) What everybody should know about the rat genome and its online resources. Nat Genet 40:523-527 (Pubitemid 351601234)
68. Verneau O, Catzeflis F, Furano AV (1997) Determination of the evolutionary relationships in Rattus sensu lato (Rodentia: Muridae) using L1 (LINE-1 amplification events). J Mol Evol 45:424-436 (Pubitemid 27425914)
69. Verneau O, Catzeflis F, Furano AV (1998) Determining and dating recent rodent speciation events by using L1 (LINE-1) retrotransposons. Proc Natl Acad Sci USA 95:11284-11289 (Pubitemid 28450120)
70. Veyrunes F, Dobigny G, Yang F et al (2006) Phylogenomics of the genus Mus (Rodentia; Muridae): extensive genome repatterning is not restricted to the house mouse. Proceedings Proc R Soc B 273:2925-2934 (Pubitemid 46622422)
71. Veyrunes F, Catalan J, Tatard C et al (2010) Mitochondrial and chromosomal insights into karyotypic evolution of the pygmy mouse, Mus minutoides, in South Africa. Chromosome Res 18:563-574
72. Wang J, Zhao X, Koh HS, Deng Y, Qi H (2003) Chromosomal polymorphisms due to heterochromatin growth and pericentric inversions in white-bellied rat, Niviventer confucianus, from China. Hereditas 138:59-64 (Pubitemid 36722192)
73. Wang B, Jiang J, Xie F et al (2009) Molecular Phylogeny and Genetic Identification of Populations of Two Species of Feirana Frogs (Amphibia: Anura, Ranidae, Dicroglossinae, Paini) Endemic to China. Zoolog Sci 26:500-509
74. Waters PD, Dobigny G, Pardini AT, Robinson TJ (2004) LINE-1 distribution in Afrotheria and Xenarthra: implications for understanding the evolution of LINE-1 in eutherian genomes. Chromosoma 113:137-144 (Pubitemid 39386403)
75. Wilson DE, Reeder DAM (2005) Mammal species of the world: a taxonomic and geographic reference. The John Hopkins University Press, Baltimore
76. Wolfe ND, Dunavan CP, Diamond J (2007) Origins of major human infectious diseases. Nature 447:279-283 (Pubitemid 46788835)
77. Yosida TH (1976) Frequencies of chromosome polymorphism (pairs no. 1, 9 and 13) in the black rat, Rattus rattus diardii (Rodentia, Muridae). Chromosoma 36:256-262
78. Yosida TH (1977) Frequencies of chromosome polymorphisms in pairs no. 1, 9, and 13 in three geographical variants of Black rats, Rattus rattus. Chromosoma 60:391-398 (Pubitemid 8082742)
79. Yosida TH (1979) A comparative study on nucleolus organizer regions (NORs) in 7 Rattus species with special emphasis on the organizer differentiation and species evolution. Proc Jap Acad 55:481-486
80. Yosida TH (1980) Cytogenetics of the black rat: Karyotype evolution and species differentiation. University of Tokyo Press, Tokyo, pp 1-255
81. Yosida TH, Sagai T (1975) Variation of C-bands in the chromosomes of several subspecies of Rattus rattus. Chromosoma 50:283-300
82. Yosida TH, Tsuchiya K, Moriwaki K (1971a) Frequency of chromosome polymorphism in Rattus rattus collected in Japan. Chromosoma 33:33-40
83. Yosida TH, Tsuchiya K, Moriwaki K (1971b) Karyotypic differences of Black rats, Rattus rattus, collected in various localities of East and Southeast Asia and Oceania. Chromosoma 33:252-267
84. Zhao S, Shetty J, Hou L et al (2004) Human, mouse, and rat genome large-scale rearrangements: stability versus speciation. Genome Res 14:1851-1860 (Pubitemid 39386498)