Molecular cytogenetic and genomic insights into chromosomal evolution

Heredity

Volumn 108, Issue 1, 2012, Pages 28-36

  Ruiz Herrera, A ^a   Farre M ^a   Robinson, T J ^b  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b STELLENBOSCH UNIVERSITY   (South Africa)

Author keywords

ancestral karyotypes; comparative cytogenetics; conserved syntenies; FISH; phylogenomics; syntenic segmental associations

Indexed keywords

CHROMOSOME; CYTOGENETICS; EVOLUTIONARY BIOLOGY; GENOMICS; HERITABILITY; KARYOTYPE; MOLECULAR ANALYSIS; PHYLOGENY; RECONSTRUCTION; TETRAPOD;

ANIMAL; BIOLOGICAL MODEL; CHROMOSOME; CHROMOSOME ANALYSIS; COMPUTER SIMULATION; GENETICS; GENOME; HUMAN; MOLECULAR EVOLUTION; REVIEW; SYNTENY;

ANIMALS; CHROMOSOMES, MAMMALIAN; COMPUTER SIMULATION; CYTOGENETIC ANALYSIS; EVOLUTION, MOLECULAR; GENOME; HUMANS; MODELS, GENETIC; SYNTENY;

AMNIOTA; ANURA; EUTHERIA; TETRAPODA; VERTEBRATA;

EID: 83655201133     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2011.102     Document Type: Review

References (79)

1. Alekseyev MA, Pevzner PA (2009). Breakpoint graphs and ancestral genome Reconstructions. Genome Res 19: 943-957.
2. Asher RJ, Helgen KM (2010). Nomenclature and placental mammal phylogeny. BMCEvol Biol 10: 102.
3. Bailey JA, Eichler EE (2006). Primate segmental duplications: crucibles of evolution, diversityand disease. Nat Rev Genet7: 552-564. (Pubitemid 43943572)
4. Bourque G (2009). Transposable elements in gene regulation and in the evolution of vertebrate genomes. Curr Opin Genet Dev 19: 607-612.
5. Bourque G, Pevzner PA (2002). Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res 12: 26-36. (Pubitemid 34065587)
6. Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G (2005). Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrange- ments across different lineages. Genome Res 15: 98-110.
7. Brown JD, Strbuncelj M, Giardina C, O'Neill RJ (2002). Interspecific hybridization induced amplification of Mdm2 on double minutes in a Mus hybrid. Cytogenet Genome Res98: 184-188. (Pubitemid 37465013)
8. Butlin RK (2010). Population genomics and speciation. Genetica 138: 409-418.
9. Carbone L, Harris RA, Vessere GM, Mootnick AR, Humphray S, Rogers J et al. (2009). Evolutionary breakpoints in the gibbon suggest association between cytosine methyla- tion and karyotype evolution. PLo S Genet5: e1000538.
10. Carbone L, Vessere GM, ten Hallers BF, Zhu B, Osoegawa K, Mootnick AR et al. (2006). A high-resolution map of synteny disruptions in gibbon and human genomes. PLo S Genet 2: 223.
11. Chowdhary BP, Raudsepp T, Fronicke L, Scherthan H (1998). Emerging patterns of comparative genome organization in some mammalian species as revealed by Zoo-FISH. Genome Res 8: 577-589. (Pubitemid 28334133)
12. Churakov G, Kriegs JO, Baertsch R, Zemann A, Brosius J, Schmitz J (2009). Mosaic retroposon insertion patterns in placental mammals. Genome Res 19: 868-875.
13. De Smet WHO (1981). The nuclear Feulgen-DNA content of the vertebrates (especially reptiles), as measured by fluorescence cytophotometry, with notes on the cell and chromosome size. Acta Zool Pathol Antverpiensia 76: 119-167.
14. Delprat A, Negre B, Puig M, Ruiz A (2009). The transposon Galileo generates natural chromosomal inversions in Drosophila by ectopic recombination. PLo S One 4: e7883.
15. Donthu R, Lewin HA, Larkin DM (2009). Synteny Tracker: a tool for defining homologous synteny blocks using radiation hybrid maps and whole-genome sequence. BMC Res Notes 2: 148.
16. Ellegren H (2010). Evolutionarystasis: the stablechromosomes of birds. Trends Ecol Evol 25: 283-291.
17. Ferguson-Smith MA, Trifonov V (2007). Mammalian karyotypeevolution. Nat Rev Genet8: 950-962.
18. Feuk L, Mac Donald JR, Tang T, Carson AR, Li M, Rao G et al. (2005). Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies. PLo S Genet 1: e56.
19. Froenicke L (2005). Origins of primate chromosomes - as delineated by Zoo-FISH and alignmentsof human and mousedraftgenomesequences. Cytogenet Genome Res 108: 122-138. (Pubitemid 39551775)
20. Froenicke L, Caldes MG, Graphodatsky A, Muller S, Lyons LA, Robinson TJ et al. (2006). Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes? Genome Res 16: 306-310. (Pubitemid 43327498)
21. Froenicke L, Wienberg J, Stone G, Adams L, Stanyon R (2003). Towards the delineation of the ancestral eutherian genome organization: comparative genome maps of the human and the African elephant (Loxodonta africana) generated by chromosome painting. Proc RSoc Lond B270: 1331-1340. (Pubitemid 36833290)
22. Glas R, Marshall Graves JA, Toder R, Ferguson-Smith M, O'Brien PC (1999). Cross-species chromosome painting between human and marsupial directly demonstrates the ancient region of the mammalian X. Mamm Genome 10: 1115-1116. (Pubitemid 29513896)
23. Gregory TR (2011). Animal Genome Size Database. http://www.genomesize. com.
24. Griffin DK, Robertson LB, Tempest HG, Skinner BM (2007). The evolution of the avian genome as revealed by comparative molecular cytogenetics. Cytogenet Genome Res 117: 64-77. (Pubitemid 47202666)
25. Hallström BM, Janke A (2010). Mammalian evolution may not be strictly bifurcating. Mol Biol Evol27: 2804-2816.
26. Haussler D, O'Brien SJ, Ryder OA, Barker FK, Clamp M, Crawford AJ, Hanner R, Hanotte O, Johnson WE, Mc Guire JA et al. (2009). Genome 10K: a proposal to obtain whole- genome sequence for 10 000 vertebrate species. J Hered 100: 659-674.
27. Hayman DL (1990). Marsupial cytogenetics. Aust JZool37: 331-349.
28. Hayman DL, Martin PG (1969). Cytogenetics of marsupials. In: Benirschke K (ed.). Comparative Mammalian Cytogenetics. Springer-Verlag: New York.
29. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V et al. (2010). The genome of the Western clawed frog Xenopus tropicalis. Science 328: 633-636.
30. Kehrer-Sawatzki H, Cooper DN (2008). Molecular mechanisms of chromosomal rearrange- ment during primate evolution. Chromosome Res 16: 41-56. (Pubitemid 351294783)
31. Kehrer-Sawatzki H, Sandig CA, Goidts V, Hameister H (2005). Breakpoint analysis of the pericentric inversion between chimpanzee chromosome 10 and the homologous chro- mosome 12 in humans. Cytogenet Genome Res 108: 91-97. (Pubitemid 39551771)
32. Kirkpatrick M (2010). How and why chromosome inversions evolve. PLo S Biol 8: e1000501.
33. Kirkpatrick M, Barton N (2006). Chromosome inversions, local adaptation and speciation. Genetics 173: 419-434. (Pubitemid 43800212)
34. Kohn M, Hogel J, Vogel W, Minich P, Kehrer-Sawatzki H, Graves JA et al. (2006). Reconstruction of a 450-My-old ancestral vertebrate protokaryotype. Trends Genet 22: 203-210.
35. Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, Schmitz J (2006). Retroposed elements as archives for the evolutionary history of placental mammals. PLo S Biol 4: e91.
36. Lee J, Han K, Meyer TJ, Kim HS, Batzer MA (2008). Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons. PLo S One 3: e4047.
37. Lin CH, Zhao H, Lowcay SH, Shahab A, Bourque G (2010). web MGR: an onlinetool for the multiple genome rearrangement problem. Bioinformatics 26: 408-410.
38. Longo MS, Carone DM, , Green ED, O'Neill MJ, O'Neill RJ (2009). Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty. BMC Genomics 10: 334.
39. Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ et al. (2006). Reconstructing contiguous regions of an ancestral genome. Genome Res 16: 1557-1565. (Pubitemid 44878494)
40. Matthey R (1945). L'evoltion de la formule chromosomiale chez les Vertebres. Experentia 1: 78-86.
41. Matthey R (1958). Chromosomes & systematic position of various African Murinae (Mammalia, Rodentia). Acta Trop 15: 97-117.
42. Murphy W, Froenicke L, O'Brien SJ, Stanyon R (2003). Theorigin of human chromosome 1 and its homologues in placental mammals. Genome Res 13: 1880-1888. (Pubitemid 36987194)
43. Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ (2001b). Molecular phylogenetics and the origins of placental mammals. Nature 409: 614-618. (Pubitemid 32154812)
44. Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ et al. (2001a). Resolution of the early placental mammalian radiation using Bayesian phylogenetics. Science294: 2348-2351. (Pubitemid 33140557)
45. Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L et al. (2005). Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science309: 613-617. (Pubitemid 41033645)
46. Nakatani Y, Takeda H, Kohara Y, Morishita S (2007). Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res 17: 1254-1265. (Pubitemid 47360900)
47. Nanda I, Benisch P, Fetting D, Haaf T, Schmid M (2011). Synteny conservation of chicken macrochromosomes 1-10 in different avian lineages revealed bycross-species chromo- some painting. Cytogenet Genome Res 132: 165-181.
48. Naruse K, Hori H, Shimizu N, Kohara Y, Takeda H (2004). Medaka genomics: a bridge between mutant phenotype and gene function. Mech Dev 121: 619-628. (Pubitemid 38813122)
49. Nie W, O'Brien PC, Ng BL, Fu B, Volobouev V, Carter NP et al. (2009). Avian comparative genomics: reciprocal chromosome painting between domestic chicken (Gallus gallus) and the stone curlew (Burhinus oedicnemus, Charadriiformes an atypical species with lowdiploid number. Chromosome Res 17: 99-113.
50. Nilsson MA, Churakov G, Sommer M, Tran NV, Zemann A, Brosius J et al. (2010). Tracking marsupial evolution using archaic genomic retroposon insertions. PLo S Biol 8: e1000436.
51. Nishihara H, Satta Y, Nikaido M, Thewissen JG, Stanhope MJ, Okada N (2005). A retroposon analysis of Afrotherian phylogeny. Mol Biol Evol 22: 1823-1833. (Pubitemid 41191509)
52. O'Brien SJ, Menninger JC, Nash WG (2006). An Atlas of Mammalian Chromosomes. John Wiley & Sons, Inc: Hoboken, NJ.
53. O'Neill RJ, Eldridge MD, Metcalfe CJ (2004). Centromere dynamics and chromosome evolution in marsupials. J Heredity95: 375-381. (Pubitemid 39304774)
54. O'Neill RJW, O'Neill MJ, Graves JAM (1998). Undermethylation associated with retro- element activation and chromosome remodeling in an interspecific mammalian hybrid. Nature 393: 68-72. (Pubitemid 28240255)
55. Ouangraoua A, Boyer F, Mc Pherson A, Tannier E, Chauve C (2009). Prediction of contiguous regions in the amniote ancestral genome. Lect Notes Comput Sci 5542: 173-185.
56. Peng Z, Elango N, Wildman DE, Yi SV (2009). Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation. BMC Genomics 10: 247.
57. Pham SK, Pevzner PA (2010). DRIMM-Synteny: decomposing genomes into evolutionary conservedsegments. Bioinformatics26: 2509-2516.
58. Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan YL, Kelly PD, Chu F et al. (2000). Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 10: 1890-1902. (Pubitemid 32049135)
59. Rens W, Fu B, O'Brien PC, Ferguson-Smith M (2006). Cross- specieschromosome painting. Nat Protoc 1: 783-790.
60. Rens W, O'Brien PC, Yang F, Solanky N, Perelman P, Graphodatsky AS et al. (2001). Karyotype relationships between distantly related marsupials from South America and Australia. Chromosome Res9: 301-308.
61. Richard F, Lombard M, Dutrillaux B (2003). Reconstruction of the ancestral karyotype of eutherian mammals. Chromosome Res 11: 605-618. (Pubitemid 37056163)
62. Rieseberg LH (2001). Chromosomal rearrangements and speciation. Trends Ecol Evol 16: 351-358. (Pubitemid 32525775)
63. Robinson TJ, Fu B, Ferguson-Smith MA, Yang F (2004). Cross-species chromosome painting in the golden mole and elephant-shrew: support for the mammalian clades Afrotheria and Afroinsectiphillia but not Afroinsectivora. Proc Biol Sci 271: 1477-1484. (Pubitemid 38943075)
64. Robinson TJ, Ruiz-Herrera A (2008). Definingtheancestral eutherian karyotype: a cladistic interpretation of chromosome painting and genome sequence assembly data. Chromosome Res16: 1133-1141.
65. Robinson TJ, Ruiz-Herrera A, Froenicke L (2006). Dissecting the mammalian genome - new insights into chromosomal evolution. Trends Genet 22: 297-301. (Pubitemid 43794924)
66. Robinson TJ, Seiffert E (2004). Afrotherian origins and interrelationships: newviews and future prospects. Curr Top Dev Biol 63: 37-60. (Pubitemid 39752384)
67. Ruiz-Herrera A, Castresana J, Robinson TJ (2006). Is mammalian chromosomal evolution driven by regions of genome fragility? Genome Biol 7: R115.
68. Ruiz-Herrera A, Robinson TJ (2007). Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assem- blies. BMCEvol Biol 7: 199.
69. Svartman M, Stone G, Page JE, Stanyon R (2004). Achromosomepaintingtest of thebasal eutherian karyotype. Chromosome Res 12: 45-53.
70. Svartman M, Stone G, Stanyon R (2006). The ancestral eutherian karyotype is present in Xenarthra. PLo S Genet 2: e109.
71. Voss SR, Kump DK, Putta S, Pauly N, Reynolds A, Henry R et al. (2011). Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Res21: 1306-1312.
72. Waddell PJ, Okada N, Hasegawa M (1999). Towards resolvingthe interordinal relationships of placental mammals. Syst Biol48: 1-5. (Pubitemid 129481119)
73. Waters PD, Dobigny G, Waddell PJ, Robinson TJ (2007). Evolutionary history of LINE-1 in the major clades of placental mammals. PLo S One 2: e158.
74. Westerman M, Meredith RW, Springer MS (2010). Cytogenetics meets phylogenetics: a review of karyotype evolution in diprotodontian marsupials. J Hered 101: 690-702.
75. White MJD (1973). Animal Cytologyand Evolution, 3rd edn. Cambridge University Press: London.
76. Wienberg J (2004). The evolution of eutherian chromosomes. Curr Opin Genet Dev 14: 657-666. (Pubitemid 39505371)
77. Woods IG, Wilson C, Friedlander B, Chang P, Reyes DK, Nix R et al. (2005). Thezebrafish gene map defines ancestral vertebrate chromosomes. Genome Res 15: 1307-1314. (Pubitemid 41247922)
78. Yang F, Alkalaeva EZ, Perelman PL, Pardini AT, Harrison WR, O'Brien PC et al. (2003). Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype. Proc Natl Acad Sci USA 100:1062-1066. (Pubitemid 36183955)
79. Zhao H, Bourque G (2009). Recovering genome rearrangements in the mammalian phylogeny. Genome Res 19: 934-942.