1932

Abstract

The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-animal-020518-114924
2021-02-15
2024-06-15
Loading full text...

Full text loading...

/deliver/fulltext/animal/9/1/annurev-animal-020518-114924.html?itemId=/content/journals/10.1146/annurev-animal-020518-114924&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Harewood L, Fraser P. 2014. The impact of chromosomal rearrangements on regulation of gene expression. Hum. Mol. Genet. 23:R76–82
    [Google Scholar]
  2. 2. 
    Rieseberg LH. 2001. Chromosomal rearrangements and speciation. Trends Ecol. Evol. 16:351–58
    [Google Scholar]
  3. 3. 
    Harewood L, Chaignat E, Reymond A 2012. Structural variation and its effect on expression. Methods Mol. Biol. 838:173–86
    [Google Scholar]
  4. 4. 
    Raudsepp T, Chowdhary BP. 2016. Chromosome aberrations and fertility disorders in domestic animals. Annu. Rev. Anim. Biosci. 4:15–43
    [Google Scholar]
  5. 5. 
    Hasty P, Montagna C. 2014. Chromosomal rearrangements in cancer: detection and potential causal mechanisms. Mol. Cell. Oncol. 1:e29904
    [Google Scholar]
  6. 6. 
    Weckselblatt B, Hermetz KE, Rudd MK 2015. Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis. Genome Res 25:937–47
    [Google Scholar]
  7. 7. 
    Merot C, Oomen RA, Tigano A, Wellenreuther M 2020. A roadmap for understanding the evolutionary significance of structural genomic variation. Trends Ecol. Evol. 35:561–72
    [Google Scholar]
  8. 8. 
    Miga KH, Koren S, Rhie A, Vollger MR, Gershman A et al. 2020. Telomere-to-telomere assembly of a complete human X chromosome. Nature 585:79–84
    [Google Scholar]
  9. 9. 
    Peichel CL. 2017. Chromosome evolution: molecular mechanisms and evolutionary consequences. J. Hered. 108:1–2
    [Google Scholar]
  10. 10. 
    Makino S. 1951. An Atlas of the Chromosome Numbers in Animals Ames: Iowa State Coll. Press
    [Google Scholar]
  11. 11. 
    Hsu TC, Benirschke K. 1967. An Atlas of Mammalian Chromosomes New York: Springer
    [Google Scholar]
  12. 12. 
    Benirschke K, Hsu TC. 1971. Chromosome Atlas: Fish, Amphibians, Reptiles and Birds New York: Springer
    [Google Scholar]
  13. 13. 
    Sturtevant AH. 1921. A case of rearrangement of genes in Drosophila. PNAS 7:235–37
    [Google Scholar]
  14. 14. 
    Dobzhansky T. 1950. Genetics of natural populations. XIX. Origin of heterosis through natural selection in populations of Drosophila pseudoobscura. Genetics 35:288–302
    [Google Scholar]
  15. 15. 
    Sturtevant A. 1926. A crossover reducer in Drosophila melanogaster due to inversion of a section of the third chromosome. Biol. Zent. 46:697–702
    [Google Scholar]
  16. 16. 
    Painter TS. 1934. A new method for the study of chromosome aberrations and the plotting of chromosome maps in Drosophila melanogaster. Genetics 19:175–88
    [Google Scholar]
  17. 17. 
    Cooper KW. 1945. Normal segregation without chiasmata in female Drosophila melanogaster. Genetics 30:472–84
    [Google Scholar]
  18. 18. 
    Dobzhansky T. 1937. Genetics and the Origin of Species New York: Columbia Univ. Press
    [Google Scholar]
  19. 19. 
    Darwin C. 1859. On the Origin of Species by Means of Natural Selection, or, the Preservation of Favoured Races in the Struggle for Life London: J. Murray
    [Google Scholar]
  20. 20. 
    Fuller ZL, Koury SA, Phadnis N, Schaeffer SW 2019. How chromosomal rearrangements shape adaptation and speciation: case studies in Drosophila pseudoobscura and its sibling species Drosophila persimilis. Mol. Ecol 28:1283–301
    [Google Scholar]
  21. 21. 
    Leitwein M, Garza JC, Pearse DE 2017. Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco Bay area: application of adaptive genomic variation to conservation in a highly impacted landscape. Evol. Appl. 10:56–67
    [Google Scholar]
  22. 22. 
    Pettersson ME, Rochus CM, Han F, Chen J, Hill J et al. 2019. A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection. Genome Res 29:1919–28
    [Google Scholar]
  23. 23. 
    Imsland F, Feng C, Boije H, Bed'hom B, Fillon V et al. 2012. The Rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb morphology and defective sperm motility. PLOS Genet 8:e1002775
    [Google Scholar]
  24. 24. 
    Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E et al. 2012. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484:55–61
    [Google Scholar]
  25. 25. 
    Cheng C, Tan JC, Hahn MW, Besansky NJ 2018. Systems genetic analysis of inversion polymorphisms in the malaria mosquito Anopheles gambiae. PNAS 115:E7005–14
    [Google Scholar]
  26. 26. 
    Hughes JF, Skaletsky H, Pyntikova T, Graves TA, van Daalen SK et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463:536–39
    [Google Scholar]
  27. 27. 
    Tuttle EM, Bergland AO, Korody ML, Brewer MS, Newhouse DJ et al. 2016. Divergence and functional degradation of a sex chromosome-like supergene. Curr. Biol. 26:344–50
    [Google Scholar]
  28. 28. 
    Lowry DB, Willis JH. 2010. A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. PLOS Biol 8:e1000500
    [Google Scholar]
  29. 29. 
    Potter S, Bragg JG, Blom MPK, Deakin JE, Kirkpatrick M et al. 2017. Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies. Front. Genet. 8:10
    [Google Scholar]
  30. 30. 
    White MJD. 1978. Modes of Speciation San Francisco, CA: W.H. Freeman
    [Google Scholar]
  31. 31. 
    Faria R, Navarro A. 2010. Chromosomal speciation revisited: rearranging theory with pieces of evidence. Trends Ecol. Evol. 25:660–69
    [Google Scholar]
  32. 32. 
    Farré M, Micheletti D, Ruiz-Herrera A 2013. Recombination rates and genomic shuffling in human and chimpanzee—a new twist in the chromosomal speciation theory. Mol. Biol. Evol. 30:853–64
    [Google Scholar]
  33. 33. 
    Noor MA, Garfield DA, Schaeffer SW, Machado CA 2007. Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions. Genetics 177:1417–28
    [Google Scholar]
  34. 34. 
    Yatabe Y, Kane NC, Scotti-Saintagne C, Rieseberg LH 2007. Rampant gene exchange across a strong reproductive barrier between the annual sunflowers. Helianthus annuus and H. petiolaris. Genetics 175:1883–93
    [Google Scholar]
  35. 35. 
    King M. 1993. Species Evolution: The Role of Chromosome Change Cambridge, UK: Cambridge Univ. Press
    [Google Scholar]
  36. 36. 
    Hadid Y, Tzur S, Pavlíček T, Šumbera R, Šklíba J et al. 2013. Possible incipient sympatric ecological speciation in blind mole rats (Spalax). PNAS 110:2587–92
    [Google Scholar]
  37. 37. 
    White TA, Bordewich M, Searle JB 2010. A network approach to study karyotypic evolution: the chromosomal races of the common shrew (Sorex araneus) and house mouse (Mus musculus) as model systems. Syst. Biol. 59:262–76
    [Google Scholar]
  38. 38. 
    Hubbard TJP, Aken BL, Beal K, Ballester B, Caccamo M et al. 2007. Ensembl 2007. Nucleic Acids Res 35:Suppl. 1D610–17
    [Google Scholar]
  39. 39. 
    Kocher TD. 2004. Adaptive evolution and explosive speciation: the cichlid fish model. Nat. Rev. Genet. 5:288–98
    [Google Scholar]
  40. 40. 
    Fontana F, Rubini M. 1990. Chromosomal evolution in Cervidae. Biosystems 24:157–74
    [Google Scholar]
  41. 41. 
    Goldschmidt R. 1940. The Material Basis of Evolution New Haven, CT: Yale Univ. Press
    [Google Scholar]
  42. 42. 
    Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO et al. 2002. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. PNAS 99:16144–49
    [Google Scholar]
  43. 43. 
    Coyle S, Kroll E. 2008. Starvation induces genomic rearrangements and starvation-resilient phenotypes in yeast. Mol. Biol. Evol. 25:310–18
    [Google Scholar]
  44. 44. 
    Hoffmann AA, Rieseberg LH. 2008. Revisiting the impact of inversions in evolution: From population genetic markers to drivers of adaptive shifts and speciation. Annu. Rev. Ecol. Evol. Syst. 39:21–42
    [Google Scholar]
  45. 45. 
    Wellenreuther M, Bernatchez L. 2018. Eco-evolutionary genomics of chromosomal inversions. Trends Ecol. Evol. 33:427–40
    [Google Scholar]
  46. 46. 
    Nishikawa H, Iijima T, Kajitani R, Yamaguchi J, Ando T et al. 2015. A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly. Nat. Genet. 47:405–9
    [Google Scholar]
  47. 47. 
    Cheng C, White BJ, Kamdem C, Mockaitis K, Costantini C et al. 2012. Ecological genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach. Genetics 190:1417–32
    [Google Scholar]
  48. 48. 
    Kang Z-J, Liu Y-F, Xu L-Z, Long Z-J, Huang D et al. 2016. The Philadelphia chromosome in leukemogenesis. Chin. J. Cancer 35:48
    [Google Scholar]
  49. 49. 
    Denomy C, Germain S, Haave B, Vizeacoumar FS, Freywald A et al. 2019. Banding together: a systematic comparison of the Cancer Genome Atlas and the Mitelman databases. Cancer Res 79:5181–90
    [Google Scholar]
  50. 50. 
    Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE et al. 2020. Patterns of somatic structural variation in human cancer genomes. Nature 578:112–21
    [Google Scholar]
  51. 51. 
    Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613–17
    [Google Scholar]
  52. 52. 
    Darai-Ramqvist E, Sandlund A, Müller S, Klein G, Imreh S, Kost-Alimova M 2008. Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions. Genome Res 18:370–79
    [Google Scholar]
  53. 53. 
    Berthelot C, Muffato M, Abecassis J, Roest Crollius H 2015. The 3D organization of chromatin explains evolutionary fragile genomic regions. Cell Rep 10:1913–24
    [Google Scholar]
  54. 54. 
    Berg PR, Star B, Pampoulie C, Bradbury IR, Bentzen P et al. 2017. Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions. Heredity 119:418–28
    [Google Scholar]
  55. 55. 
    Peichel CL, Prabhakaran B, Vogt TF 1997. The mouse Ulnaless mutation deregulates posterior HoxD gene expression and alters appendicular patterning. Development 124:3481–92
    [Google Scholar]
  56. 56. 
    Renwick JH. 1972. Human genetics. Proceedings of the Fourth International Congress of Human Genetics, 611 September 1971 J de Grouchy, FJG Ebling, IW Henderson 443–44 Amsterdam: Excerpta Med.
    [Google Scholar]
  57. 57. 
    Roderick TH, Lalley PA, Davisson MT, O'Brien SJ, Womack JE et al. 1984. Report of the committee on comparative mapping. Cytogenet. Genome Res. 37:312–39
    [Google Scholar]
  58. 58. 
    O'Brien SJ, Nash WG. 1982. Genetic mapping in mammals: chromosome map of domestic cat. Science 216:257–65
    [Google Scholar]
  59. 59. 
    Graphodatsky A, Ferguson-Smith MA, Stanyon R 2012. A short introduction to cytogenetic studies in mammals with reference to the present volume. Cytogenet. Genome Res. 137:83–96
    [Google Scholar]
  60. 60. 
    Womack JE, Moll YD. 1986. Gene map of the cow: conservation of linkage with mouse and man. J. Hered. 77:2–7
    [Google Scholar]
  61. 61. 
    Solinas-Toldo S, Lengauer C, Fries R 1995. Comparative genome map of human and cattle. Genomics 27:489–96
    [Google Scholar]
  62. 62. 
    Sharma AK, Sharma A. 2001. Chromosome painting—principles, strategies and scope. Methods Cell Sci 23:1–5
    [Google Scholar]
  63. 63. 
    Speicher MR, Carter NP. 2005. The new cytogenetics: blurring the boundaries with molecular biology. Nat. Rev. Genet. 6:782–92
    [Google Scholar]
  64. 64. 
    Froenicke L. 2005. Origins of primate chromosomes—as delineated by Zoo-FISH and alignments of human and mouse draft genome sequences. Cytogenet. Genome Res. 108:122–38
    [Google Scholar]
  65. 65. 
    Larkin DM, Pape G, Donthu R, Auvil L, Welge M, Lewin HA 2009. Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res 19:770–77
    [Google Scholar]
  66. 66. 
    McCarthy LC, Terrett J, Davis ME, Knights CJ, Smith AL et al. 1997. A first-generation whole genome-radiation hybrid map spanning the mousegenome. Genome Res 7:1153–61
    [Google Scholar]
  67. 67. 
    Band MR, Larson JH, Rebeiz M, Green CA, Heyen DW et al. 2000. An ordered comparative map of the cattle and human genomes. Genome Res 10:1359–68
    [Google Scholar]
  68. 68. 
    Nadeau JH, Taylor BA. 1984. Lengths of chromosomal segments conserved since divergence of man and mouse. PNAS 81:814–18
    [Google Scholar]
  69. 69. 
    Everts-van der Wind A, Larkin DM, Green CA, Elliott JS, Olmstead CA et al. 2005. A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. PNAS 102:18526–31
    [Google Scholar]
  70. 70. 
    Lucas JMEX, Roest Crollius H 2017. High precision detection of conserved segments from synteny blocks. PLOS ONE 12:e0180198
    [Google Scholar]
  71. 71. 
    Donthu R, Lewin HA, Larkin DM 2009. SyntenyTracker: a tool for defining homologous synteny blocks using radiation hybrid maps and whole-genome sequence. BMC Res. Notes 2:148
    [Google Scholar]
  72. 72. 
    Grabherr MG, Russell P, Meyer M, Mauceli E, Alfoldi J et al. 2010. Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics 26:1145–51
    [Google Scholar]
  73. 73. 
    Liu D, Hunt M, Tsai IJ 2018. Inferring synteny between genome assemblies: a systematic evaluation. BMC Bioinform 19:26
    [Google Scholar]
  74. 74. 
    Evans BJ, Upham NS, Golding GB, Ojeda RA, Ojeda AA 2017. Evolution of the largest mammalian genome. Genome Biol. Evol. 9:1711–24
    [Google Scholar]
  75. 75. 
    Chen X, Tompa M. 2010. Comparative assessment of methods for aligning multiple genome sequences. Nat. Biotechnol. 28:567–72
    [Google Scholar]
  76. 76. 
    Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J et al. 2018. Earth BioGenome Project: sequencing life for the future of life. PNAS 115:4325–33
    [Google Scholar]
  77. 77. 
    Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S et al. 2018. High-resolution comparative analysis of great ape genomes. Science 360:eaar6343
    [Google Scholar]
  78. 78. 
    Damas J, Kim J, Farré M, Griffin DK, Larkin DM 2018. Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes. Genome Biol 19:155
    [Google Scholar]
  79. 79. 
    Farré M, Bosch M, López-Giráldez F, Ponsà M, Ruiz-Herrera A 2011. Assessing the role of tandem repeats in shaping the genomic architecture of great apes. PLOS ONE 6:e27239
    [Google Scholar]
  80. 80. 
    Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y et al. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491:393–98
    [Google Scholar]
  81. 81. 
    Kemkemer C, Kohn M, Cooper DN, Froenicke L, Hogel J 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
    [Google Scholar]
  82. 82. 
    Armengol L, Marquès-Bonet T, Cheung J, Khaja R, González JR et al. 2005. Murine segmental duplications are hot spots for chromosome and gene evolution. Genomics 86:692–700
    [Google Scholar]
  83. 83. 
    Lemaitre C, Zaghloul L, Sagot MF, Gautier C, Arneodo A et al. 2009. Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation. BMC Genom 10:335
    [Google Scholar]
  84. 84. 
    Everts RE, Chavatte-Palmer P, Razzak A, Hue I, Green CA et al. 2008. Aberrant gene expression patterns in placentomes are associated with phenotypically normal and abnormal cattle cloned by somatic cell nuclear transfer. Physiol. Genom. 33:65–77
    [Google Scholar]
  85. 85. 
    Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE 2004. Hotspots of mammalian chromosomal evolution. Genome Biol 5:R23
    [Google Scholar]
  86. 86. 
    Smagulova F, Gregoretti IV, Brick K, Khil P, Camerini-Otero RD, Petukhova GV 2011. Genome-wide analysis reveals novel molecular features of mouse recombination hotspots. Nature 472:375–78
    [Google Scholar]
  87. 87. 
    Ullastres A, Farré M, Capilla L, Ruiz-Herrera A 2014. Unraveling the effect of genomic structural changes in the rhesus macaque—implications for the adaptive role of inversions. BMC Genom 15:530
    [Google Scholar]
  88. 88. 
    Farré M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI et al. 2019. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Genome Res 29:576–89
    [Google Scholar]
  89. 89. 
    Farré M, Narayan J, Slavov GT, Damas J, Auvil L et al. 2016. Novel insights into chromosome evolution in birds, archosaurs, and reptiles. Genome Biol. Evol. 8:2442–51
    [Google Scholar]
  90. 90. 
    Pevzner P, Tesler G. 2003. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res 13:37–45
    [Google Scholar]
  91. 91. 
    Larkin DM, Everts-van der Wind A, Rebeiz M, Schweitzer PA, Bachman S et al. 2003. A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res 13:1966–72
    [Google Scholar]
  92. 92. 
    Mlynarski EE, Obergfell CJ, O'Neill MJ, O'Neill RJ 2010. Divergent patterns of breakpoint reuse in Muroid rodents. Mamm. Genome 21:77–87
    [Google Scholar]
  93. 93. 
    Peng Q, Pevzner PA, Tesler G 2006. The fragile breakage versus random breakage models of chromosome evolution. PLOS Comput. Biol. 2:e14
    [Google Scholar]
  94. 94. 
    Pevzner P, Tesler G. 2003. Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. PNAS 100:7672–77
    [Google Scholar]
  95. 95. 
    Alekseyev MA, Pevzner PA. 2007. Are there rearrangement hotspots in the human genome. PLOS Comput. Biol. 3:e209
    [Google Scholar]
  96. 96. 
    Bourque G, Pevzner PA, Tesler G 2004. Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res 14:507–16
    [Google Scholar]
  97. 97. 
    Drier Y, Lawrence MS, Carter SL, Stewart C, Gabriel SB et al. 2013. Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Genome Res 23:228–35
    [Google Scholar]
  98. 98. 
    Hinsch H, Hannenhalli S. 2006. Recurring genomic breaks in independent lineages support genomic fragility. BMC Evol. Biol. 6:90
    [Google Scholar]
  99. 99. 
    Damas J, O'Connor R, Farré M, Lenis VPE, Martell HJ et al. 2017. Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Res 27:875–84
    [Google Scholar]
  100. 100. 
    Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B et al. 2014. Gibbon genome and the fast karyotype evolution of small apes. Nature 513:195–201
    [Google Scholar]
  101. 101. 
    Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I et al. 2018. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Res 28:448–59
    [Google Scholar]
  102. 102. 
    Ruiz-Herrera A, Castresana J, Robinson TJ 2006. Is mammalian chromosomal evolution driven by regions of genome fragility. Genome Biol 7:R115
    [Google Scholar]
  103. 103. 
    Kehrer-Sawatzki H, Sandig CA, Goidts V, Hameister H 2005. Breakpoint analysis of the pericentric inversion between chimpanzee chromosome 10 and the homologous chromosome 12 in humans. Cytogenet. Genome Res. 108:91–97
    [Google Scholar]
  104. 104. 
    Nishida C, Ishijima J, Kosaka A, Tanabe H, Habermann FA et al. 2008. Characterization of chromosome structures of Falconinae (Falconidae, Falconiformes, Aves) by chromosome painting and delineation of chromosome rearrangements during their differentiation. Chromosome Res 16:171–81
    [Google Scholar]
  105. 105. 
    Nanda I, Karl E, Griffin DK, Schartl M, Schmid M 2007. Chromosome repatterning in three representative parrots (Psittaciformes) inferred from comparative chromosome painting. Cytogenet. Genome Res. 117:43–53
    [Google Scholar]
  106. 106. 
    de Oliveira EH, Habermann FA, Lacerda O, Sbalqueiro IJ, Wienberg J, Muller S 2005. Chromosome reshuffling in birds of prey: the karyotype of the world's largest eagle (Harpy eagle, Harpia harpyja) compared to that of the chicken (Gallus gallus). Chromosoma 114:338–43
    [Google Scholar]
  107. 107. 
    O'Connor RE, Farré M, Joseph S, Damas J, Kiazim L et al. 2018. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome Biol 19:171
    [Google Scholar]
  108. 108. 
    Wesche PL, Robinson TJ. 2012. Different patterns of Robertsonian fusion pairing in Bovidae and the house mouse: the relationship between chromosome size and nuclear territories. Genet. Res. 94:97–111
    [Google Scholar]
  109. 109. 
    Bovine Genome Seq. Anal. Consort Elsik CG, Tellam RL, Worley KC 2009. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522–28
    [Google Scholar]
  110. 110. 
    Porubsky D, Sanders AD, Höps W, Hsieh P, Sulovari A et al. 2020. Recurrent inversion toggling and great ape genome evolution. Nat. Genet. 52:849–58
    [Google Scholar]
  111. 111. 
    Krefting J, Andrade-Navarro MA, Ibn-Salem J 2018. Evolutionary stability of topologically associating domains is associated with conserved gene regulation. BMC Biol 16:87
    [Google Scholar]
  112. 112. 
    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
    [Google Scholar]
  113. 113. 
    Ruiz-Herrera A, Farré M, Robinson TJ 2012. Molecular cytogenetic and genomic insights into chromosomal evolution. Heredity 108:28–36
    [Google Scholar]
  114. 114. 
    Kim J, Farré M, Auvil L, Capitanu B, Larkin DM et al. 2017. Reconstruction and evolutionary history of eutherian chromosomes. PNAS 114:E5379–E88
    [Google Scholar]
  115. 115. 
    Arai R. 2011. Fish Karyotypes: A Check List Tokyo: Springer
    [Google Scholar]
  116. 116. 
    Wurster DH, Benirschke K. 1970. Indian muntjac, Muntiacus muntjak: a deer with a low diploid chromosome number. Science 168:1364–66
    [Google Scholar]
  117. 117. 
    Deakin JE. 2018. Chromosome evolution in marsupials. Genes 9:72
    [Google Scholar]
  118. 118. 
    Deakin JE, Bender HS, Pearse AM, Rens W, O'Brien PC et al. 2012. Genomic restructuring in the Tasmanian devil facial tumour: chromosome painting and gene mapping provide clues to evolution of a transmissible tumour. PLOS Genet 8:e1002483
    [Google Scholar]
  119. 119. 
    Nash WG, Menninger JC, Wienberg J, Padilla-Nash HM, O'Brien SJ 2001. The pattern of phylogenomic evolution of the Canidae. Cytogenet. Cell Genet. 95:210–24
    [Google Scholar]
  120. 120. 
    Nash WG, Wienberg J, Ferguson-Smith MA, Menninger JC, O'Brien SJ 1998. Comparative genomics: tracking chromosome evolution in the family Ursidae using reciprocal chromosome painting. Cytogenet. Cell Genet. 83:182–92
    [Google Scholar]
  121. 121. 
    Olmo E. 2008. Trends in the evolution of reptilian chromosomes. Integr. Comp. Biol. 48:486–93
    [Google Scholar]
  122. 122. 
    Ravi V, Venkatesh B. 2008. Rapidly evolving fish genomes and teleost diversity. Curr. Opin. Genet. Dev. 18:544–50
    [Google Scholar]
  123. 123. 
    Burt DW, Bruley C, Dunn IC, Jones CT, Ramage A et al. 1999. The dynamics of chromosome evolution in birds and mammals. Nature 402:411–13
    [Google Scholar]
  124. 124. 
    Lynch M. 2007. The Origins of Genome Architecture Sunderland, MA: Sinauer Assoc.
    [Google Scholar]
  125. 125. 
    McKinley KL, Cheeseman IM. 2016. The molecular basis for centromere identity and function. Nat. Rev. Mol. Cell Biol. 17:16–29
    [Google Scholar]
  126. 126. 
    Black BE, Cleveland DW. 2011. Epigenetic centromere propagation and the nature of CENP-a nucleosomes. Cell 144:471–79
    [Google Scholar]
  127. 127. 
    Blackburn EH, Gall JG. 1978. A tandemly repeated sequence at the termini of the extrachromosomal ribosomal RNA genes in Tetrahymena. J. Mol. Biol 120:33–53
    [Google Scholar]
  128. 128. 
    Blackburn EH. 2000. Telomere states and cell fates. Nature 408:53–56
    [Google Scholar]
  129. 129. 
    Barra V, Fachinetti D. 2018. The dark side of centromeres: types, causes and consequences of structural abnormalities implicating centromeric DNA. Nat. Commun. 9:4340
    [Google Scholar]
  130. 130. 
    Savage SA. 2018. Beginning at the ends: telomeres and human disease. F1000 Res 7:F1000
    [Google Scholar]
  131. 131. 
    Schubert I, Lysak MA. 2011. Interpretation of karyotype evolution should consider chromosome structural constraints. Trends Genet 27:207–16
    [Google Scholar]
  132. 132. 
    Rocchi M, Archidiacono N, Schempp W, Capozzi O, Stanyon R 2012. Centromere repositioning in mammals. Heredity 108:59–67
    [Google Scholar]
  133. 133. 
    Nergadze SG, Piras FM, Gamba R, Corbo M, Cerutti F et al. 2018. Birth, evolution, and transmission of satellite-free mammalian centromeric domains. Genome Res 28:789–99
    [Google Scholar]
  134. 134. 
    White MJD. 1977. Animal Cytology and Evolution Cambridge, UK: Cambridge Univ. Press
    [Google Scholar]
  135. 135. 
    Bolzan AD. 2017. Interstitial telomeric sequences in vertebrate chromosomes: origin, function, instability and evolution. Mutat. Res. 773:51–65
    [Google Scholar]
  136. 136. 
    Ventura M, Weigl S, Carbone L, Cardone MF, Misceo D et al. 2004. Recurrent sites for new centromere seeding. Genome Res 14:1696–703
    [Google Scholar]
  137. 137. 
    Meaburn KJ, Misteli T. 2007. Cell biology: chromosome territories. Nature 445:379–81
    [Google Scholar]
  138. 138. 
    Bonev B, Cavalli G. 2016. Organization and function of the 3D genome. Nat. Rev. Genet. 17:661–78
    [Google Scholar]
  139. 139. 
    Rowley MJ, Corces VG. 2018. Organizational principles of 3D genome architecture. Nat. Rev. Genet. 19:789–800
    [Google Scholar]
  140. 140. 
    Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID et al. 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159:1665–80
    [Google Scholar]
  141. 141. 
    Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–93
    [Google Scholar]
  142. 142. 
    Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ et al. 2015. CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell 163:1611–27
    [Google Scholar]
  143. 143. 
    Parada LA, McQueen PG, Misteli T 2004. Tissue-specific spatial organization of genomes. Genome Biol 5:R44
    [Google Scholar]
  144. 144. 
    Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA 1999. Differences in the localization and morphology of chromosomes in the human nucleus. J. Cell Biol. 145:1119–31
    [Google Scholar]
  145. 145. 
    Dixon JR, Selvaraj S, Yue F, Kim A, Li Y et al. 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485:376–80
    [Google Scholar]
  146. 146. 
    Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I et al. 2012. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485:381–85
    [Google Scholar]
  147. 147. 
    Vietri Rudan M, Barrington C, Henderson S, Ernst C, Odom DT et al. 2015. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Rep 10:1297–309
    [Google Scholar]
  148. 148. 
    Lazar NH, Nevonen KA, O'Connell B, McCann C, O'Neill RJ et al. 2018. Epigenetic maintenance of topological domains in the highly rearranged gibbon genome. Genome Res 28:983–97
    [Google Scholar]
  149. 149. 
    Fudenberg G, Pollard KS. 2019. Chromatin features constrain structural variation across evolutionary timescales. PNAS 116:2175–80
    [Google Scholar]
  150. 150. 
    Shanta O, Noor A, Hum. Genome Struct. Var. Consort., Sebat J 2020. The effects of common structural variants on 3D chromatin structure.. BMC Genom 21:95
    [Google Scholar]
  151. 151. 
    Yang Y, Zhang Y, Ren B, Dixon JR, Ma J 2019. Comparing 3D genome organization in multiple species using Phylo-HMRF. Cell Syst 8:494–505.e14
    [Google Scholar]
  152. 152. 
    O'Connor RE, Romanov MN, Kiazim LG, Barrett PM, Farré M et al. 2018. Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nat. Commun. 9:1883
    [Google Scholar]
  153. 153. 
    Sacerdot C, Louis A, Bon C, Berthelot C, Roest Crollius H 2018. Chromosome evolution at the origin of the ancestral vertebrate genome. Genome Biol 19:166
    [Google Scholar]
  154. 154. 
    Deakin JE, Ezaz T. 2014. Tracing the evolution of amniote chromosomes. Chromosoma 123:201–16
    [Google Scholar]
  155. 155. 
    IJdo JW, Baldini A, Ward DC, Reeders ST, Wells RA 1991. Origin of human chromosome 2: an ancestral telomere-telomere fusion. PNAS 88:9051–55
    [Google Scholar]
  156. 156. 
    Richard F, Lombard M, Dutrillaux B 2003. Reconstruction of the ancestral karyotype of eutherian mammals. Chromosome Res 11:605–18
    [Google Scholar]
  157. 157. 
    Murphy WJ, Bourque G, Tesler G, Pevzner P, O'Brien SJ 2003. Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Hum. Genom. 1:30–40
    [Google Scholar]
  158. 158. 
    Kulemzina AI, Yang F, Trifonov VA, Ryder OA, Ferguson-Smith MA, Graphodatsky AS 2011. Chromosome painting in Tragulidae facilitates the reconstruction of Ruminantia ancestral karyotype. Chromosome Res 19:531–39
    [Google Scholar]
  159. 159. 
    Beklemisheva VR, Perelman PL, Lemskaya NA, Kulemzina AI, Proskuryakova AA et al. 2016. The ancestral carnivore karyotype as substantiated by comparative chromosome painting of three pinnipeds, the walrus, the Steller sea lion and the Baikal seal (Pinnipedia, Carnivora). PLOS ONE 11:e0147647
    [Google Scholar]
  160. 160. 
    Robinson TJ, Ruiz-Herrera A. 2008. Defining the ancestral eutherian karyotype: a cladistic interpretation of chromosome painting and genome sequence assembly data. Chromosome Res 16:1133–41
    [Google Scholar]
  161. 161. 
    Nakatani Y, Takeda H, Kohara Y, Morishita S 2007. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates Genome Res 17:1254–65
    [Google Scholar]
  162. 162. 
    Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G 2005. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res 15:98–110
    [Google Scholar]
  163. 163. 
    Lewin HA, Larkin DM, Pontius J, O'Brien SJ 2009. Every genome sequence needs a good map. Genome Res 19:1925–28
    [Google Scholar]
  164. 164. 
    Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC et al. 2006. Reconstructing contiguous regions of an ancestral genome. Genome Res 16:1557–65
    [Google Scholar]
  165. 165. 
    Jones BR, Rajaraman A, Tannier E, Chauve C 2012. ANGES: reconstructing ANcestral GEnomeS maps. Bioinformatics 28:2388–90
    [Google Scholar]
  166. 166. 
    Bourque G, Pevzner PA. 2002. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res 12:26–36
    [Google Scholar]
  167. 167. 
    Avdeyev P, Jiang S, Aganezov S, Hu F, Alekseyev MA 2016. Reconstruction of ancestral genomes in presence of gene gain and loss. J. Comput. Biol. 23:150–64
    [Google Scholar]
  168. 168. 
    Zheng C, Sankoff D. 2011. On the PATHGROUPS approach to rapid small phylogeny. BMC Bioinform 12:Suppl. 1S4
    [Google Scholar]
  169. 169. 
    Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D 2011. Cactus: algorithms for genome multiple sequence alignment. Genome Res 21:1512–28
    [Google Scholar]
  170. 170. 
    Armstrong J, Hickey G, Diekhans M, Deran A, Fang Q et al. 2019. Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era. bioRxiv 730531 https://doi.org/10.1101/730531
    [Crossref]
  171. 171. 
    Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S et al. 2014. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Res 24:2077–89
    [Google Scholar]
  172. 172. 
    Armstrong J, Fiddes IT, Diekhans M, Paten B 2019. Whole-genome alignment and comparative annotation. Annu. Rev. Anim. Biosci. 7:41–64
    [Google Scholar]
  173. 173. 
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ 1990. Basic local alignment search tool. J. Mol. Biol. 215:403–10
    [Google Scholar]
  174. 174. 
    Kent WJ. 2002. BLAT—the BLAST-like alignment tool. Genome Res 12:656–64
    [Google Scholar]
  175. 175. 
    Harris RS. 2007. Improved pairwise alignment of genomic DNA PhD Diss., Coll. Eng., Pa. State Univ State College, PA:
    [Google Scholar]
  176. 176. 
    Jain C, Koren S, Dilthey A, Phillippy AM, Aluru S 2018. A fast adaptive algorithm for computing whole-genome homology maps. Bioinformatics 34:i748–i56
    [Google Scholar]
  177. 177. 
    Marcais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A 2018. MUMmer4: a fast and versatile genome alignment system. PLOS Comput. Biol. 14:e1005944
    [Google Scholar]
  178. 178. 
    Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D 2003. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. PNAS 100:11484–89
    [Google Scholar]
  179. 179. 
    Ghiurcuta CG, Moret BM. 2014. Evaluating synteny for improved comparative studies. Bioinformatics 30:i9–18
    [Google Scholar]
  180. 180. 
    Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF et al. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14:708–15
    [Google Scholar]
  181. 181. 
    Frazer KA, Elnitski L, Church DM, Dubchak I, Hardison RC 2003. Cross-species sequence comparisons: a review of methods and available resources. Genome Res 13:1–12
    [Google Scholar]
  182. 182. 
    Nguyen NTT, Vincens P, Crollius HR, Louis A 2018. Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing. Nucleic Acids Res 46:1D816–22
    [Google Scholar]
  183. 183. 
    Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R et al. 2009. Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–45
    [Google Scholar]
  184. 184. 
    Hao Z, Lv D, Ge Y, Shi J, Weijers D et al. 2020. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Comput. Sci. 6:e251
    [Google Scholar]
  185. 185. 
    Bryan C, Guterman G, Ma KL, Lewin H, Larkin D et al. 2017. Synteny Explorer: an interactive visualization application for teaching genome evolution. IEEE Trans. Vis. Comput. Graph. 23:711–20
    [Google Scholar]
  186. 186. 
    Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G et al. 2020. Towards complete and error-free genome assemblies of all vertebrate species. bioRxiv 2020.05.22.110833 https://doi.org/10.1101/2020.05.22.110833
    [Crossref]
  187. 187. 
    Genereux D, Serres A, Armstrong J, Johnson J, Marinescu V et al. 2020. A comparative genomics multitool for scientific discovery and conservation. Nature 23:71063–68
    [Google Scholar]
  188. 188. 
    Benson KF, Chada K. 2002. Molecular characterization of the mouse In(10)17Rk inversion and identification of a novel muscle-specific gene at the proximal breakpoint. Genetics 160:279–87
    [Google Scholar]
  189. 189. 
    Holland LZ, Ocampo Daza D 2018. A new look at an old question: When did the second whole genome duplication occur in vertebrate evolution. Genome Biol 19:209
    [Google Scholar]
  190. 190. 
    Foley NM, Springer MS, Teeling EC 2016. Mammal madness: Is the mammal tree of life not yet resolved. Philos. Trans. R. Soc. Lond. B 371:169920150140
    [Google Scholar]
  191. 191. 
    Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K et al. 2007. Eukaryotic genome size databases. Nucleic Acids Res 35:D332–38
    [Google Scholar]
  192. 192. 
    O'Brien SJ, Menninger JC, Nash WG 2006. Atlas of Mammalian Chromosomes Hoboken, NJ: John Wiley & Sons
    [Google Scholar]
  193. 193. 
    Uno Y, Nishida C, Tarui H, Ishishita S, Takagi C et al. 2012. Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping. PLOS ONE 7:e53027
    [Google Scholar]
  194. 194. 
    Capel B. 2017. Vertebrate sex determination: evolutionary plasticity of a fundamental switch. Nat. Rev. Genet. 18:675–89
    [Google Scholar]
  195. 195. 
    Ferguson-Smith MA, Trifonov V. 2007. Mammalian karyotype evolution. Nat. Rev. Genet. 8:950–62
    [Google Scholar]
  196. 196. 
    Froenicke L, Caldés MG, Graphodatsky A, Müller S, Lyons LA et al. 2006. Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes. Genome Res 16:306–10
    [Google Scholar]
  197. 197. 
    Stanyon R, Rocchi M, Capozzi O, Roberto R, Misceo D et al. 2008. Primate chromosome evolution: ancestral karyotypes, marker order and neocentromeres. Chromosome Res 16:17–39
    [Google Scholar]
/content/journals/10.1146/annurev-animal-020518-114924
Loading
/content/journals/10.1146/annurev-animal-020518-114924
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error