Reconstruction of karyotype evolution in core Glires. I. The genome homology revealed by comparative chromosome painting

Chromosome Research

Volumn 19, Issue 4, 2011, Pages 549-565

  Beklemisheva, Violetta R ^a   Romanenko, Svetlana A ^a   Biltueva, Larisa S ^a   Trifonov, Vladimir A ^a   Vorobieva, Nadezhda V ^a   Serdukova, Natalya A ^a   Rubtsova, Nadezhda V ^b   Brandler, Oleg V ^c   O'Brien, Patricia C M ^d   Yang, Fentang ^e   Stanyon, Roscoe ^f   Ferguson Smith, Malcolm A ^d   Graphodatsky, Alexander S ^a  

^a INSTITUTE OF MOLECULAR AND CELLULAR BIOLOGY   (Russian Federation)

^b INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^c KOL TSOV INSTITUTE OF DEVELOPMENTAL BIOLOGY   (Russian Federation)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^f UNIVERSITY OF FLORENCE   (Italy)

Author keywords

ancestral karyotypes; Castoridae; Lagomorpha; Rodentia; Sciuridae

Indexed keywords

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CHROMOSOME BANDING PATTERN; CHROMOSOME MAP; CHROMOSOME PAINTING; FEMALE; GENOME; KARYOTYPE EVOLUTION; KARYOTYPING; MALE; MOUSE; NONHUMAN; PRIORITY JOURNAL; RABBIT; RAT; SQUIRREL;

ANIMALS; CHROMOSOME BANDING; CHROMOSOME MAPPING; CHROMOSOME PAINTING; CHROMOSOMES, MAMMALIAN; EVOLUTION, MOLECULAR; FEMALE; GENOME; HUMANS; KARYOTYPING; MALE; MAMMALS; RABBITS; SEQUENCE HOMOLOGY;

CASTOR FIBER; CASTORIDAE; EUTHERIA; GLIRES; LAGOMORPHA; LEPORIDAE; LEPUS; LEPUS TIMIDUS; MARMOTA; MARMOTA MONAX; MUROIDEA; OCHOTONIDAE; ORYCTOLAGUS; ORYCTOLAGUS CUNICULUS; RODENTIA; SCIURIDAE; SCIURUS; SPERMOPHILUS; TAMIAS SIBIRICUS;

EID: 79958247374     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-011-9210-y     Document Type: Article

References (64)

1. OV Brandler 2003 On species status of the forest-steppe marmota Marmota kastschenkoi (Rodentia, Marmotinae) Zool Zh 82 1498 1505 (Pubitemid 38225214)
2. C Chantry-Darmon M Bertaud C Urien 2005 Expanded comparative mapping between man and rabbit and detection of a new conserved segment between HSA22 and OCU4 Cytogenet Genome Res 111 2 134 139 16103654 10.1159/000086382 1:CAS:528:DC%2BD2MXnvFynsb0%3D (Pubitemid 41161031)
3. C Chantry-Darmon C Urien H de Rochambeau 2006 A first-generation microsatellite-based integrated genetic and cytogenetic map for the European rabbit (Oryctolagus cuniculus) and localization of angora and albino Anim Genet 37 4 335 341 16879342 10.1111/j.1365-2052.2006.01462.x 1:CAS:528: DC%2BD28XhtVCmsbfK (Pubitemid 44091657)
4. G Churakov JO Kriegs R Baertsch, et al. 2009 Mosaic retroposon insertion patterns in placental mammals Genome Res 19 868 875 19261842 10.1101/gr.090647.108 1:CAS:528:DC%2BD1MXlsFyku7s%3D
5. G Churakov MK Sadasivuni KR Rosenbloom, et al. 2010 Rodent evolution: back to the root Mol Biol Evol 27 6 1315 1326 20100942 10.1093/molbev/msq019 1:CAS:528:DC%2BC3cXmsVCqtbs%3D
6. MA Ferguson-Smith 1997 Genetic analysis by chromosome sorting and painting: phylogenetic and diagnostic applications Eur J Hum Genet 5 253 265 9412781 1:CAS:528:DyaK2sXnvF2qsr4%3D (Pubitemid 27503672)
7. MA Ferguson-Smith V Trifonov 2007 Mammalian karyotype evolution Nat Rev 8 950 963 10.1038/nrg2199 1:CAS:528:DC%2BD2sXhtlajtrbM (Pubitemid 350129170)
8. L Froenicke J Muller-Navia K Romanakis H Scherthan 1997 Chromosomal homeologies between human, harbor seal (Phoca vitulina) and the putative ancestral carnivore karyotype revealed by Zoo-FISH Chromosoma 106 2 108 113 10.1007/s004120050230 1:CAS:528:DyaK2sXkslGnu74%3D (Pubitemid 27395550)
9. L Froenicke J Wienberg G Stone L Adams R Stanyon 2003 Towards the delineation of the ancestral eutherian genome organization: comparative genome maps of human and the African elephant (Loxodonta africana) generated by chromosome painting Proc Biol Sci 270 1522 1331 1340 10.1098/rspb.2003.2383 (Pubitemid 36833290)
10. L Froenicke 2005 Origins of primate chromosomes-as delineated by Zoo-FISH and alignments of human and mouse draft genome sequences Cytogenet Genome Res 108 122 138 15545724 10.1159/000080810 1:CAS:528:DC%2BD2cXhtVSitLzM (Pubitemid 39551775)
11. L Froenicke MG Caldés A Graphodatsky, et al. 2006 Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes? Genome Res 16 306 310 16510895 10.1101/gr.3955206 1:CAS:528:DC%2BD28Xit1Knsbs%3D (Pubitemid 43327498)
12. AS Graphodatsky F Yang PL Perelman, et al. 2002 Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree Cytogenet Genome Res 96 1-4 137 145 12438790 10.1159/000063032 1:CAS:528:DC%2BD38Xns1ejsbY%3D (Pubitemid 37456592)
13. Graphodatsky AS, Sablina OV (2006) Selected karyotypes. In: O'Brien SJ, Nash WG, Menninger JS (eds) Atlas of mammalian karyotypes. John Wiley, Chichester, pp 188, 177-179
14. AS Graphodatsky OV Sablina MN Meyer, et al. 2000 Comparative cytogenetics of hamsters of the genus Calomyscus Cytogenet Cell Genet 88 296 304 10828614 10.1159/000015513 1:CAS:528:DC%2BD3cXkvFOnsrc%3D (Pubitemid 30311610)
15. AS Graphodatsky F Yang G Dobigny, et al. 2008 Tracking genome organization in rodents by Zoo-FISH Chromosome Res 16 261 274 18266061 10.1007/s10577-007-1191-5 1:CAS:528:DC%2BD1cXisl2htLY%3D
16. AS Graphodatsky F Yang PC O'Brien, et al. 2001 Phylogenetic implications of the 38 putative ancestral chromosome segments for four canid species Cytogenet Cell Genet 92 243 247 11435696 10.1159/000056911 1:CAS:528: DC%2BD3MXlvVygtb8%3D (Pubitemid 32642002)
17. M Hasegawa KH Thorne 2003 Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution Genes Genet Syst 78 267 283 14532706 10.1266/ggs.78.267 1:CAS:528:DC%2BD3sXhtVSqsLfL (Pubitemid 37288258)
18. H Hayes C Rogel-Gaillard C Zijlstra, et al. 2002 Establishment of an R-banded rabbit karyotype nomenclature by FISH localization of 23 chromosome-specific genes on both G- and R-banded chromosomes Cytogenet Genome Res 98 199 205 12698004 10.1159/000069807 1:STN:280:DC%2BD3s7nvVKkuw%3D%3D (Pubitemid 37465016)
19. S Horn W Durka R Wolf, et al. 2011 Mitochondrial genomes reveal slow rates of molecular evolution and the timing of speciation in beavers (Castor), one of the largest rodent species PLoS ONE 6 1 9
20. D Huchon O Madsen M Sibbald, et al. 2002 Rodent phylogeny and a timescale of Glires: evidence from an extensive taxon sampling using three nuclear genes Mol Biol Evol 19 7 1053 1065 12082125 1:CAS:528:DC%2BD38Xlt1aktr0%3D (Pubitemid 34743230)
21. Ivanitskaya E (1991) The comparative analysis of G-banding chromosomes of pikas and superspecies system of the genus Ochotona (Ochotonidae, Lagomorpha). In: Zaitsev EV (ed) Questions of systematics, faunistics and paleontology of small mammals. Zoological Institute USSR, St Petersburg, pp 180-188
22. C Kemkemer M Kohn DN Cooper, et al. 2009 Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution BMC Evol Biol 9 84 19393055 10.1186/1471-2148-9-84
23. R Korstanje PCM O'Brien F Yang, et al. 1999 Complete homology maps of the rabbit (Oryctolagus cuniculus) and human by reciprocal chromosome painting Cytogenet Cell Genet 86 317 322 10575232 10.1159/000015325 1:CAS:528: DC%2BD3cXktV2r
24. JO Kriegs G Churakov J Jurka, et al. 2007 Evolutionary history of 7SL RNA-derived SINEs in Supraprimates Trends Genet 23 158 161 17307271 10.1016/j.tig.2007.02.002 1:CAS:528:DC%2BD2sXjslShtbc%3D (Pubitemid 46497508)
25. HC Lanier LE Olson 2009 Inferring divergence times within pikas (Ochotona ssp.) using mtDNA and relaxed molecular dating techniques Mol Phylogenet Evol 53 1 12 19501176 10.1016/j.ympev.2009.05.035 1:CAS:528:DC%2BD1MXptlyksL8%3D
26. T Li P O'Brien L Biltueva, et al. 2004 Evolution of genome organizations of squirrels (Sciuridae) revealed by cross-species chromosome painting Chomosome Res 12 317 355 10.1023/B:CHRO.0000034131.73620.48 (Pubitemid 38932373)
27. T Li J Wang W Su W Nie F Yang 2006 Karyotypic evolution of the family Sciuridae: inferences from the genome organizations of ground squirrels Cytogenet Gen Res 112 270 276 10.1159/000089881 1:STN:280: DC%2BD28%2Fps1Omug%3D%3D (Pubitemid 43260756)
28. Y Liu J Ye B Fu, et al. 2011 Molecular cytogenetic characterization of the genome organization of the 6-banded armadillo (Euphractus sexcinctus) Cytogenet Genome Res 132 1-2 31 40 20720395 10.1159/000318706 1:STN:280:DC%2BC3cbjs12nsg%3D%3D
29. JM Mercer VL Roth 2003 The effects of Cenozoic global change on squirrel phylogeny Science 299 1568 1572 12595609 10.1126/science.1079705 1:CAS:528:DC%2BD3sXhs1yiurc%3D (Pubitemid 36297705)
30. W Murphy E Eizirik W Johnson J Zhang O Ryder S O'Brien 2001 Molecular phylogenetics and the origins of placental mammals Nature 409 614 618 11214319 10.1038/35054550 1:CAS:528:DC%2BD3MXhtVylt7Y%3D (Pubitemid 32154812)
31. W Murphy E Eizirik S O'Brien, et al. 2001 Resolution of the early placental mammal radiation using Bayesian phylogenetics Science 294 2348 2351 11743200 10.1126/science.1067179 1:CAS:528:DC%2BD3MXptFGrtrg%3D (Pubitemid 33140557)
32. W Murphy R Stanyon S O'Brien 2001 Evolution of mammalian genome organization inferred from comparative gene mapping Genome Biol 2 6 reviews 0005.1 0005.8 10.1186/gb-2001-2-6-reviews0005
33. W Murphy DM Larkin A Everts-van der Wind, et al. 2005 Dynamics of mammalian chromosome evolution inferred multispecies comparative maps Science 309 613 617 16040707 10.1126/science.1111387 1:CAS:528:DC%2BD2MXmsFChsbk%3D (Pubitemid 41033645)
34. W Nie J Wang PC O'Brien B Fu T Ying 2002 The genome phylogeny of domestic cat, red panda and five mustelid species revealed by comparative chromosome painting and GTG-banding Chromosome Res 10 209 222 12067210 10.1023/A: 1015292005631 1:CAS:528:DC%2BD38XksVykurs%3D (Pubitemid 34553495)
35. H Nishihara M Hasegawa N Okada 2006 Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions PNAS 103 9929 9934 16785431 10.1073/pnas.0603797103 1:CAS:528:DC%2BD28XmvVajtb8%3D (Pubitemid 43993600)
36. P Perelman AS Graphodatsky NA Serdukona, et al. 2005 Karyotypic conservatism in the suborder Feliformia (Order Carnivora) Cytogenet Genome Res 108 348 354 15627756 10.1159/000081530 1:STN:280:DC%2BD2M%2FgtF2isQ%3D%3D (Pubitemid 40082274)
37. D Petit J Couturier E Viegas-Pequignot M Lombard B Dutrillaux 1984 Great degree of homeology between the ancestral karyotype of squirrels (Rodents) and that of Primates and Carnivora Ann Génét 27 201 212 6335365 1:STN:280:DyaL2M7itVKktg%3D%3D
38. D Petit B Dutrillaux 1985 Chromosomal phylogeny of the seven species of Sciurinae Ann Génét 28 13 18 3874584 1:STN:280: DyaL2M3ltVaitg%3D%3D (Pubitemid 15144922)
39. F Richard M Lombard B Dutrillaux 2003 Reconstruction of the ancestral karyotype of eutherian mammals Chromosome Res 11 605 618 14516069 10.1023/A:1024957002755 1:CAS:528:DC%2BD3sXlslOksLY%3D (Pubitemid 37056163)
40. F Richard C Messaoudi A Bonnet-Garnier M Lombard B Dutrillaux 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 14516068 10.1023/A:1024905018685 1:CAS:528:DC%2BD3sXlslOksLg%3D (Pubitemid 37056162)
41. TJ Robinson 1980 Comparative chromosome studies in the family Leporidae (Lagomorpha, Mammalia) Cytogenet Cell Genet 28 64 70 7449437 10.1159/000131513 1:STN:280:DyaL3M%2FovFChtw%3D%3D (Pubitemid 10049530)
42. TJ Robinson FFB Elder JA Chapman 1983 Karyotypic conservatism in the genus Lepus (order Lagomorpha) Can J Genet Cytol 25 540 544 6652568 1:STN:280:DyaL2c%2FotFKnsg%3D%3D
43. TJ Robinson FFB Elder JA Chapman 1983 Evolution of chromosomal variation in cottontails, genus Sylvilagus (Mammalia: Lagomorpha): S. aquaticus, S. floridanus, and S. transitionalis Cytogenet Cell Genet 35 216 222 6861527 10.1159/000131869 1:STN:280:DyaL3s3jtlOqtQ%3D%3D
44. TJ Robinson FFB Elder JA Chapman 1984 Evolution of chromosomal variation in cottontails, genus Sylvilagus (Mammalia: Lagomorpha). II. Sylvilagus audubonii, S. idahoensis, S. nuttallii, and S. palustris Cytogenet Cell Genet 38 282 289 6510022 10.1159/000132076 1:STN:280:DyaL2M%2FnsFOkuw%3D%3D (Pubitemid 15221662)
45. Robinson Ruiz-Herrera 2008 Defining the ancestral eutherian karyotype: a cladistic interpretation of chromosome painting and genome sequence assembly data Chromosome Res 16 1133 1141 19067196 10.1007/s10577-008-1264-0 1:CAS:528:DC%2BD1cXhsFarsrbE
46. TJ Robinson F Yang WR Harrison 2002 Chromosome painting refines the history of genome evolution in hares and rabbits (order Lagomorpha) Cytogenet Genome Res 96 223 227 12438803 10.1159/000063034 1:CAS:528:DC%2BD38Xns1ejtL0%3D (Pubitemid 37456603)
47. SA Romanenko PL Perelman NA Serdukova, et al. 2006 Reciprocal chromosome painting between three laboratory rodent species Mamm Genome 17 1183 1192 17143584 10.1007/s00335-006-0081-z (Pubitemid 44915820)
48. SA Romanenko NA Sitnikova VR Beklemisheva PL Perelman NA Serdukova AS Graphodatsky 2010 Comparative cytogenetics of rodents Russ J Genet 46 9 1143 1145 10.1134/S1022795410090334
49. SA Romanenko NA Sitnikova NA Serdukova, et al. 2007 Chromosomal evolution of Arvicolinae (Cricetidae, Rodentia). II. The genome homology of two mole voles (genus Ellobius), the field vole and golden hamster revealed by comparative chromosome painting Chromosome Res 15 891 897 17924201 10.1007/s10577-007-1171-9 1:CAS:528:DC%2BD2sXhtlSlt7fJ (Pubitemid 350160094)
50. SA Romanenko VT Volobuev PL Perelman, et al. 2007 Karyotype evolution and phylogenetic relationships of hamsters (Cricetidae, Muroidea, Rodentia) inferred from chromosomal painting and banding comparison Chromosome Res 15 283 297 17333534 10.1007/s10577-007-1171-9 1:CAS:528:DC%2BD2sXmsV2jsbY%3D (Pubitemid 350160094)
51. M Seabright 1971 A rapid banding technique for human chromosomes Lancet 11 971 972 10.1016/S0140-6736(71)90287-X
52. NA Sitnikova SA Romanenko PCM O'Brien, et al. 2007 Chromosomal evolution of Arvicolinae (Cricetidae, Rodentia). I. The genome homology of tundra vole, field vole, mouse and golden hamster revealed by comparative chromosome painting Chromosome Res 15 447 456 17497247 10.1007/s10577-007-1137-y 1:CAS:528:DC%2BD2sXntFKjsbk%3D (Pubitemid 47025004)
53. R Stanyon G Stone M Garcia L Froenicke 2003 Reciprocal chromosome painting shows that squirrels, unlike murid rodents, have a highly conserved genome organization Genomics 82 2 245 249 12837274 10.1016/S0888-7543(03)00109-5 1:CAS:528:DC%2BD3sXkvFelsrk%3D (Pubitemid 36808625)
54. R Stanyon F Garofalo F Bigoni 2008 Reconstruction of ancestral genomes In Encyclopedia Life Sci 10.1002/9780470015902.a0020752
55. AD Stock 1976 Chromosome banding pattern relationships of hares, rabbits and pikas (order Lagomorpha). A phyletic interpretation Cytogenet Cell Genet 17 78 88 975938 10.1159/000130692 1:STN:280:DyaE2s%2FisFamsQ%3D%3D
56. A Sumner 1972 A rapid technique for demonstrating centromeric heterochromatin Exp Cell Res 75 304 306 4117921 10.1016/0014-4827(72)90558-7 1:STN:280:DyaE3s%2FkslGitA%3D%3D
57. M Svartman G Stone R Stanyon 2006 The ancestral eutherian karyotype is present in Xenarthra PLoS Genet 2 7 e109 16848642 10.1371/journal.pgen.0020109 (Pubitemid 44147405)
58. PJ Waddell N Okada M Hasegawa 1999 Towards resolving the interordinal relationships of placental mammals Syst Biol 48 1 5 12078634 10.1093/sysbio/48.1.1 1:STN:280:DC%2BD38zjslSjsQ%3D%3D (Pubitemid 129481119)
59. OG Ward AS Graphodatsky DH Wurster-Hill, et al. 1991 Cytogenetics of beavers: a case of monobrachial fusions Genome 34 324 328 10.1139/g91-053
60. F Yang E Alkalaeva P Perelman, et al. 2003 Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype Proc Natl Acad Sci USA 100 3 1062 1066 12552116 10.1073/pnas.0335540100 1:CAS:528:DC%2BD3sXhtF2gtr0%3D (Pubitemid 36183955)
61. F Yang NP Carter L Shi Ferguson-Smith 1995 A comparative study of karyotypes of muntjacs by chromosome painting Chromosoma 103 642 652 7587587 10.1007/BF00357691 1:STN:280:DyaK28%2FovVekug%3D%3D
62. F Yang PC O'Brien BS Milne, et al. 1999 A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic map Genomics 62 189 202 10610712 10.1006/geno.1999.5989 1:CAS:528: DyaK1MXotFektLw%3D (Pubitemid 30053934)
63. F Yang PCM O'Brien MA Ferguson-Smith 2000 Comparative chromosome map of the laboratory mouse and Chinese hamster defined by reciprocal chromosome painting Chromosome Res 8 219 227 10841049 10.1023/A:1009200912436 1:CAS:528:DC%2BD3cXjvVSjsrk%3D (Pubitemid 30261215)
64. J Ye W Nie J Wang, et al. 2011 Genome-wide comparative chromosome map between human and the Forrest's pika (Ochotona forresti) established by cross-species chromosome painting: further support for the Glires hypothesis Cytogenet Genome Res 132 1-2 41 46 20664243 10.1159/000317082 1:STN:280:DC%2BC3cbjs1Kruw%3D%3D