Marsupial chromosomics: bridging the gap between genomes and chromosomes

References

Andersson, L., and Georges, M. (2004). Domestic-animal genomics: deciphering the genetics of complex traits. Nat. Rev. Genet. 5, 202–212.
| Domestic-animal genomics: deciphering the genetics of complex traits.Crossref | GoogleScholarGoogle Scholar | 14970822PubMed |

Baverstock, P. R., Adams, M., Archer, M., Mckenzie, N. L., and How, R. (1983). An electrophoretic and chromosomal study of the Dasyurid marsupial genus Ningaui Archer. Aust. J. Zool. 31, 381–392.
| An electrophoretic and chromosomal study of the Dasyurid marsupial genus Ningaui Archer.Crossref | GoogleScholarGoogle Scholar |

Bellott, D. W., Hughes, J. F., Skaletsky, H., Brown, L. G., Pyntikova, T., Cho, T.-J., Koutseva, N., Zaghlul, S., Graves, T., Rock, S., et al. (2014). Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 508, 494–499.
| Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators.Crossref | GoogleScholarGoogle Scholar | 24759411PubMed |

Bender, H. S., Murchison, E. P., Pickett, H. A., Deakin, J. E., Strong, M. A., Conlan, C., McMillan, D. A., Neumann, A. A., Greider, C. W., Hannon, G. J., Reddel, R. R., and Graves, J. A. M. (2012). Extreme telomere length dimorphism in the Tasmanian devil and related marsupials suggests parental control of telomere length. PLoS One 7, .
| Extreme telomere length dimorphism in the Tasmanian devil and related marsupials suggests parental control of telomere length.Crossref | GoogleScholarGoogle Scholar | 23049977PubMed |

Brennan, A. J., Sharp, J. A., Digby, M. R., and Nicholas, K. R. (2007). The tammar wallaby: a model to examine endocrine and local control of lactation. IUBMB Life 59, 146–150.
| The tammar wallaby: a model to examine endocrine and local control of lactation.Crossref | GoogleScholarGoogle Scholar | 17487685PubMed |

Brown, J. D., and O’Neill, R. J. (2010). Chromosomes, conflict, and epigenetics: chromosomal speciation revisited. Annu. Rev. Genomics Hum. Genet. 11, 291–316.
| Chromosomes, conflict, and epigenetics: chromosomal speciation revisited.Crossref | GoogleScholarGoogle Scholar | 20438362PubMed |

Capilla, L., Sánchez-Guillén, R. A., Farré, M., Paytuví-Gallart, A., Malinverni, R., Ventura, J., Larkin, D. M., and Ruiz-Herrera, A. (2016). Mammalian comparative genomics reveals genetic and epigenetic features associated with genome reshuffling in rodentia. Genome Biol. Evol. 8, 3703–3717.
| Mammalian comparative genomics reveals genetic and epigenetic features associated with genome reshuffling in rodentia.Crossref | GoogleScholarGoogle Scholar | 28175287PubMed |

Carbone, L., Harris, R. A., Vessere, G. M., Mootnick, A. R., Humphray, S., Rogers, J., Kim, S. K., Wall, J. D., Martin, D., Jurka, J., Milosavljevic, A., and De Jong, P. J. (2009). Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet. 5, .
| Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution.Crossref | GoogleScholarGoogle Scholar | 19557196PubMed |

Charlesworth, B. (2009). Effective population size and patterns of molecular evolution and variation. Nat. Rev. Genet. 10, 195–205.
| Effective population size and patterns of molecular evolution and variation.Crossref | GoogleScholarGoogle Scholar | 19204717PubMed |

Cheng, Y., Polkinghorne, A., Gillett, A., Jones, E. A., O’Meally, D., Timms, P., and Belov, K. (2018). Characterisation of MHC class I genes in the koala. Immunogenetics 70, 125–133.
| Characterisation of MHC class I genes in the koala.Crossref | GoogleScholarGoogle Scholar | 28669101PubMed |

Chiang, C., Scott, A. J., Davis, J. R., Tsang, E. K., Li, X., Kim, Y., Hadzic, T., Damani, F. N., Ganel, L., Montgomery, S. B., Battle, A., Conrad, D. F., and Hall, I. M. (2017). The impact of structural variation on human gene expression. Nat. Genet. 49, 692–699.
| The impact of structural variation on human gene expression.Crossref | GoogleScholarGoogle Scholar | 28369037PubMed |

Claussen, U. (2005). Chromosomics. Cytogenet. Genome Res. 111, 101–106.
| Chromosomics.Crossref | GoogleScholarGoogle Scholar | 16103649PubMed |

Coyne, J. A., and Orr, H. A. (2004). ‘Speciation.’ (Sinauer Associates: Sunderland.)

Damas, J., O’Connor, R., Farré, M., Lenis, V. P. E., Martell, H. J., Mandawala, A., Fowler, K., Joseph, S., Swain, M. T., Griffin, D. K., and Larkin, D. M. (2017). Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Res. 27, 875–884.
| Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.Crossref | GoogleScholarGoogle Scholar | 27903645PubMed |

Davidow, L. S., Breen, M., Duke, S. E., Samollow, P. B., McCarrey, J. R., and Lee, J. T. (2007). The search for a marsupial XIC reveals a break with vertebrate synteny. Chromosome Res. 15, 137–146.
| The search for a marsupial XIC reveals a break with vertebrate synteny.Crossref | GoogleScholarGoogle Scholar | 17333538PubMed |

Daza-Vamenta, R., Glusman, G., Rowen, L., Guthrie, B., and Geraghty, D. E. (2004). Genetic divergence of the rhesus macaque major histocompatibility complex. Genome Res. 14, 1501–1515.
| Genetic divergence of the rhesus macaque major histocompatibility complex.Crossref | GoogleScholarGoogle Scholar | 15289473PubMed |

Deakin, J. E. (2010). Physical and comparative gene maps in marsupials. In ‘Marsupial Genetics and Genomics’. (Eds J. Deakin, P. Waters, and J. Marshall Graves.) pp. 101–115. (Springer: Dordrecht.)

Deakin, J. E., and Kruger-Andrzejewska, M. (2016). Marsupials as models for understanding the role of chromosome rearrangements in evolution and disease. Chromosoma 125, 633–644.
| Marsupials as models for understanding the role of chromosome rearrangements in evolution and disease.Crossref | GoogleScholarGoogle Scholar | 27255308PubMed |

Deakin, J. E., Siddle, H. V., Cross, J. G. R., Belov, K., and Graves, J. A. M. (2007). Class I genes have split from the MHC in the tammar wallaby. Cytogenet. Genome Res. 116, 205–211.
| Class I genes have split from the MHC in the tammar wallaby.Crossref | GoogleScholarGoogle Scholar | 17317961PubMed |

Deakin, J. E., Koina, E., Waters, P. D., Doherty, R., Patel, V. S., Delbridge, M. L., Dobson, B., Fong, J., Hu, Y., Van Den Hurk, C., Pask, A. J., Shaw, G., Smith, C., Thompson, K., Wakefield, M. J., Yu, H., Renfree, M. B., and Marshall Graves, J. A. (2008). Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals. Chromosome Res. 16, 1159–1175.
| Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals.Crossref | GoogleScholarGoogle Scholar | 18987984PubMed |

Deakin, J. E., Bender, H. S., Pearse, A.-M., Rens, W., O’Brien, P. C. M., Ferguson-Smith, M. A., Cheng, Y., Morris, K., Taylor, R., Stuart, A., Belov, K., Amemiya, C. T., Murchison, E. P., Papenfuss, A. T., and Graves, J. A. M. (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.
| Genomic restructuring in the Tasmanian devil facial tumour: chromosome painting and gene mapping provide clues to evolution of a transmissible tumour.Crossref | GoogleScholarGoogle Scholar | 22359511PubMed |

Deakin, J. E., Delbridge, M. L., Koina, E., Harley, N., Alsop, A. E., Wang, C., Patel, V. S., and Graves, J. A. M. (2013). Reconstruction of the ancestral marsupial karyotype from comparative gene maps. BMC Evol. Biol. 13, 258.
| Reconstruction of the ancestral marsupial karyotype from comparative gene maps.Crossref | GoogleScholarGoogle Scholar | 24261750PubMed |

Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. (2002). Capturing chromosome conformation. Science 295, 1306–1311.
| Capturing chromosome conformation.Crossref | GoogleScholarGoogle Scholar | 11847345PubMed |

Dekker, J., Belmont, A. S., Guttman, M., Leshyk, V. O., Lis, J. T., Lomvardas, S., Mirny, L. A., O’Shea, C. C., Park, P. J., Ren, B., Politz, J. C. R., Shendure, J., and Zhong, S. (2017). The 4D nucleome project. Nature 549, 219–226.
| The 4D nucleome project.Crossref | GoogleScholarGoogle Scholar | 28905911PubMed |

Dion-Côté, A. M., Symonová, R., Lamaze, F. C., Šárka, P., Ráb, P., and Bernatchez, L. (2017). Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation. Mol. Ecol. 26, 178–192.
| Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation.Crossref | GoogleScholarGoogle Scholar | 27545583PubMed |

Dostie, J., Richmond, T. A., Arnaout, R. A., Seizer, R. R., Lee, W. L., Honan, T. A., Rubio, T. A., Krumm, A., Lamb, J., Nusbaum, C., Green, R. D., and Dekker, J. (2006). Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 16, 1299–1309.
| Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements.Crossref | GoogleScholarGoogle Scholar | 16954542PubMed |

du Sart, D., Cancilla, M. R., Earle, E., Mao, J. I., Saffery, R., Tainton, K. M., Kalitsis, P., Martyn, J., Barry, A. E., and Andy Choo, K. H. (1997). A functional neo-centromere formed through activation of a latent human centromere and consisting of non-alpha-satellite DNA. Nat. Genet. 16, 144–153.
| A functional neo-centromere formed through activation of a latent human centromere and consisting of non-alpha-satellite DNA.Crossref | GoogleScholarGoogle Scholar | 9171825PubMed |

Duke, S. E., Samollow, P. B., Mauceli, E., Lindblad-Toh, K., and Breen, M. (2007). Integrated cytogenetic BAC map of the genome of the gray, short-tailed opossum, Monodelphis domestica. Chromosome Res. 15, 361–370.
| Integrated cytogenetic BAC map of the genome of the gray, short-tailed opossum, Monodelphis domestica.Crossref | GoogleScholarGoogle Scholar | 17406991PubMed |

Duret, L., Chureau, C., Samain, S., Weissanbach, J., and Avner, P. (2006). The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 312, 1653–1655.
| The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene.Crossref | GoogleScholarGoogle Scholar | 16778056PubMed |

Eldridge, M. D. B., and Close, R. L. (1992). Taxonomy of rock wallabies, Petrogale (Marsupialia: Macropodidae). I. A revision of the eastern Petrogale with the description of three new species. Aust. J. Zool. 40, 605–625.
| Taxonomy of rock wallabies, Petrogale (Marsupialia: Macropodidae). I. A revision of the eastern Petrogale with the description of three new species.Crossref | GoogleScholarGoogle Scholar |

Eldridge, M. D. B., and Metcalfe, C. J. (2006). Marsupialia. In ‘Atlas of Mammalian Chromosomes’. (Eds S. J. O’Brien, J. C. Menninger, and W. G. Nash.) pp. 9–62. (John Wiley & Sons: Hoboken.)

English, A. C., Richards, S., Han, Y., Wang, M., Vee, V., Qu, J., Qin, X., Muzny, D. M., Reid, J. G., Worley, K. C., and Gibbs, R. A. (2012). Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One 7, e47768.
| Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology.Crossref | GoogleScholarGoogle Scholar | 23185243PubMed |

Farré, M., Robinson, T. J., and Ruiz-Herrera, A. (2015). An integrative breakage model of genome architecture, reshuffling and evolution: the integrative breakage model of genome evolution, a novel multidisciplinary hypothesis for the study of genome plasticity. BioEssays 37, 479–488.
| An integrative breakage model of genome architecture, reshuffling and evolution: the integrative breakage model of genome evolution, a novel multidisciplinary hypothesis for the study of genome plasticity.Crossref | GoogleScholarGoogle Scholar | 25739389PubMed |

Federico, C., Pappalardo, A. M., Ferrito, V., Tosi, S., and Saccone, S. (2017). Genomic properties of chromosomal bands are linked to evolutionary rearrangements and new centromere formation in primates. Chromosome Res. 25, 261–276.
| Genomic properties of chromosomal bands are linked to evolutionary rearrangements and new centromere formation in primates.Crossref | GoogleScholarGoogle Scholar | 28717965PubMed |

Feigin, C. Y., Newton, A. H., Doronina, L., Schmitz, J., Hipsley, C. A., Mitchell, K. J., Gower, G., Llamas, B., Soubrier, J., Heider, T. N., Menzies, B. R., Cooper, A., Neill, R. J. O., and Pask, A. J. (2018). Into the evolution and demography of an extinct marsupial carnivore. Nat. Ecol. Evol. 2, 182–192.
| Into the evolution and demography of an extinct marsupial carnivore.Crossref | GoogleScholarGoogle Scholar | 29230027PubMed |

Ferguson-Smith, M. A., and Trifonov, V. (2007). Mammalian karyotype evolution. Nat. Rev. Genet. 8, 950–962.
| Mammalian karyotype evolution.Crossref | GoogleScholarGoogle Scholar | 18007651PubMed |

Glas, R., Graves, J. A. M., Toder, R., Ferguson-Smith, M., and O’Brien, P. C. (1999). Cross-species chromosome painting between human and marsupial directly demonstrates the ancient region of the mammalian X. Mamm. Genome 10, 1115–1116.
| Cross-species chromosome painting between human and marsupial directly demonstrates the ancient region of the mammalian X.Crossref | GoogleScholarGoogle Scholar | 10556436PubMed |

Grant, J., Mahadevaiah, S. K., Khil, P., Sangrithi, M. N., Royo, H., Duckworth, J., McCarrey, J. R., VandeBerg, J. L., Renfree, M. B., Taylor, W., Elgar, G., Camerini-Otero, R. D., Gilchrist, M. J., and Turner, J. M. A. (2012). Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation. Nature 487, 254–258.
| Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation.Crossref | GoogleScholarGoogle Scholar | 22722828PubMed |

Graves, J. A. M., Ferguson-Smith, M. A., McLaren, A., Mittwoch, U., Renfree, M. B., and Burgoyne, P. (1995). The evolution of mammalian sex chromosomes and the origin of sex determining genes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 350, 305–312.
| The evolution of mammalian sex chromosomes and the origin of sex determining genes.Crossref | GoogleScholarGoogle Scholar |

Green, B., and Merchant, J. C. (1988). The composition of marsupial milk. In ‘The Developing Marsupial’. (Eds C. H. Tyndale-Biscoe and P. A. Janssens.) pp. 41–54. (Springer-Verlag: New York.)

Hayman, D. (1989). Marsupial cytogenetics. Aust. J. Zool. 37, 331–349.
| Marsupial cytogenetics.Crossref | GoogleScholarGoogle Scholar |

Hayman, D. L., and Martin, P. G. (1974). Mammalia I: Monotremata and Marsupialia. In ‘Animal Cytogenetics Vol. 4: Chordata’. (Ed. B. John.) p. 110. (Gebruder Borntraeger: Berlin.)

Hore, T. A., Koina, E., Wakefield, M. J., and Marshall Graves, J. A. (2007). The region homologous to the X-chromosome inactivation centre has been disrupted in marsupial and monotreme mammals. Chromosome Res. 15, 147–161.
| The region homologous to the X-chromosome inactivation centre has been disrupted in marsupial and monotreme mammals.Crossref | GoogleScholarGoogle Scholar | 17333539PubMed |

Hughes, J. F., and Page, D. C. (2015). The biology and evolution of mammalian Y chromosomes. Annu. Rev. Genet. 49, 507–527.
| The biology and evolution of mammalian Y chromosomes.Crossref | GoogleScholarGoogle Scholar | 26442847PubMed |

Hughes, J. F., Skaletsky, H., Pyntikova, T., Graves, T. A., van Daalen, S. K. M., Minx, P. J., Fulton, R. S., McGrath, S. D., Locke, D. P., Friedman, C., Trask, B. J., Mardis, E. R., Warren, W. C., Repping, S., Rozen, S., Wilson, R. K., and Page, D. C. (2010). Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463, 536–539.
| Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.Crossref | GoogleScholarGoogle Scholar | 20072128PubMed |

Ingles, E. D., and Deakin, J. E. (2015). Global DNA methylation patterns on marsupial and devil facial tumour chromosomes. Mol. Cytogenet. 8, 74.
| Global DNA methylation patterns on marsupial and devil facial tumour chromosomes.Crossref | GoogleScholarGoogle Scholar | 26435750PubMed |

Jain, M., Olsen, H. E., Paten, B., Akeson, M., Branton, D., Daniel, B., Deamer, D., Andre, M., Hagan, B., Benner, S., et al. (2016). The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 17, 239.
| The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.Crossref | GoogleScholarGoogle Scholar | 27887629PubMed |

Jain, M., Olsen, H. E., Turner, D. J., Stoddart, D., Bulazel, D. V., Paten, B., Haussler, D., Willard, H. F., Akeson, M., and Miga, K. H. (2018). Linear assembly of a human centromere on the Y chromosome. Nat. Biotechnol. 36, 321–323.
| Linear assembly of a human centromere on the Y chromosome.Crossref | GoogleScholarGoogle Scholar | 29553574PubMed |

Johnson, R. N., O’Meally, D., Chen, Z., Etherington, G. J., Ho, S. Y. W., Nash, W. J., Grueber, C. E., Cheng, Y., Whittington, C. M., Dennison, S., et al. (2018). Adaptation and conservation insights from the koala genome. Nat. Genet. 50, 1102–1111.
| Adaptation and conservation insights from the koala genome.Crossref | GoogleScholarGoogle Scholar | 29967444PubMed |

Kelley, J., Walter, L., and Trowsdale, J. (2005). Comparative genomics of major histocompatibility complexes. Immunogenetics 56, 683–695.
| Comparative genomics of major histocompatibility complexes.Crossref | GoogleScholarGoogle Scholar | 15605248PubMed |

Kim, J., Farre, M., Auvil, L., Capitanu, B., Larkin, D. M., Ma, J., and Lewin, H. A. (2017). Reconstruction and evolutionary history of eutherian chromosomes. Proc. Natl Acad. Sci. USA 114, E5379–E5388.
| Reconstruction and evolutionary history of eutherian chromosomes.Crossref | GoogleScholarGoogle Scholar | 28630326PubMed |

King, M. (1993). ‘Species Evolution: The Role of Chromosome Change.’ (Cambridge University Press: Cambridge.)

Kirkpatrick, M. (2017). The evolution of genome structure by natural and sexual selection. J. Hered. 108, 3–11.
| The evolution of genome structure by natural and sexual selection.Crossref | GoogleScholarGoogle Scholar | 27388336PubMed |

Koepfli, K.-P., Paten, B., Genome 10K Community of Scientists O’Brien, S. J. (2015). The Genome 10K Project: a way forward. Annu. Rev. Anim. Biosci. 3, 57–111.
| The Genome 10K Project: a way forward.Crossref | GoogleScholarGoogle Scholar | 25689317PubMed |

Kulski, J. K., Shiina, T., Anzai, T., Kohara, S., and Inoko, H. (2002). Comparative genomic analysis of the MHC: The evolution of class I duplication blocks, diversity and complexity from shark to man. Immunol. Rev. 190, 95–122.
| Comparative genomic analysis of the MHC: The evolution of class I duplication blocks, diversity and complexity from shark to man.Crossref | GoogleScholarGoogle Scholar | 12493009PubMed |

Lam, E. T., Hastie, A., Lin, C., Ehrlich, D., Das, S. K., Austin, M. D., Deshpande, P., Cao, H., Nagarajan, N., Xiao, M., and Kwok, P. Y. (2012). Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat. Biotechnol. 30, 771–776.
| Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.Crossref | GoogleScholarGoogle Scholar | 22797562PubMed |

Lawton, B. R., Obergfell, C., O’Neill, R. J., and O’Neill, M. J. (2007). Physical mapping of the IGF2 locus in the South American opossum Monodelphis domestica. Cytogenet. Genome Res. 116, 130–131.
| Physical mapping of the IGF2 locus in the South American opossum Monodelphis domestica.Crossref | GoogleScholarGoogle Scholar | 17268191PubMed |

Lefèvre, C. M., Digby, M. R., Whitley, J. C., Strahm, Y., and Nicholas, K. R. (2007). Lactation transcriptomics in the Australian marsupial, Macropus eugenii: transcript sequencing and quantification. BMC Genomics 8, 417.
| Lactation transcriptomics in the Australian marsupial, Macropus eugenii: transcript sequencing and quantification.Crossref | GoogleScholarGoogle Scholar | 17997866PubMed |

Lewin, H. A., Larkin, D. M., Pontius, J., and O’Brien, S. J. (2009). Every genome sequence needs a good map. Genome Res. 19, 1925–1928.
| Every genome sequence needs a good map.Crossref | GoogleScholarGoogle Scholar | 19596977PubMed |

Lieberman-Aiden, E., Van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., Sandstrom, R., Bernstein, B., Bender, M. A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L. A., Lander, E. S., and Dekker, J. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293.
| Comprehensive mapping of long-range interactions reveals folding principles of the human genome.Crossref | GoogleScholarGoogle Scholar | 19815776PubMed |

Loebel, D. A., and Johnston, P. G. (1993). Analysis of DNase 1 sensitivity and methylation of active and inactive X chromosomes of kangaroos (Macropus robustus) by in situ nick translation. Chromosoma 102, 81–87.
| Analysis of DNase 1 sensitivity and methylation of active and inactive X chromosomes of kangaroos (Macropus robustus) by in situ nick translation.Crossref | GoogleScholarGoogle Scholar | 8381740PubMed |

Ma, L., Li, W., and Song, Q. (2017). Chromosome-range whole-genome high-throughput experimental haplotyping by single-chromosome microdissection. Methods Mol. Biol. 1551, 161–169.
| 28138846PubMed |

Mank, J. E., Vicoso, B., Berlin, S., and Charlesworth, B. (2010). Effective population size and the faster-X effect: empirical results and their interpretation. Evolution 64, 663–674.
| Effective population size and the faster-X effect: empirical results and their interpretation.Crossref | GoogleScholarGoogle Scholar | 19796145PubMed |

Marshall, O. J., Chueh, A. C., Wong, L. H., and Choo, K. H. A. (2008). Neocentromeres: new insights into centromere structure, disease development, and karyotype evolution. Am. J. Hum. Genet. 82, 261–282.
| Neocentromeres: new insights into centromere structure, disease development, and karyotype evolution.Crossref | GoogleScholarGoogle Scholar | 18252209PubMed |

Meisel, R. P., and Connallon, T. (2013). The faster-X effect: integrating theory and data. Trends Genet. 29, 537–544.
| The faster-X effect: integrating theory and data.Crossref | GoogleScholarGoogle Scholar | 23790324PubMed |

Mikkelsen, T. S., Wakefield, M. J., Aken, B., Amemiya, C. T., Chang, J. L., Duke, S., Garber, M., Gentles, A. J., Goodstadt, L., Heger, A., et al. (2007). Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447, 167–177.
| Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.Crossref | GoogleScholarGoogle Scholar | 17495919PubMed |

Murchison, E. P., Tovar, C., Hsu, A., Bender, H. S., Kheradpour, P., Rebbeck, C. A., Obendorf, D., Conlan, C., Bahlo, M., Blizzard, C. A., Pyecroft, S., Kreiss, A., Kellis, M., Stark, A., Harkins, T. T., Marshall Graves, J. A., Woods, G. M., Hannon, G. J., and Papenfuss, A. T. (2010). The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science 327, 84–87.
| The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer.Crossref | GoogleScholarGoogle Scholar | 20044575PubMed |

Murchison, E. P., Schulz-Trieglaff, O. B., Ning, Z., Alexandrov, L. B., Bauer, M. J., Fu, B., Hims, M., Ding, Z., Ivakhno, S., Stewart, C., et al. (2012). Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell 148, 780–791.
| Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer.Crossref | GoogleScholarGoogle Scholar | 22341448PubMed |

Murtagh, V. J., O’Meally, D., Sankovic, N., Delbridge, M. L., Kuroki, Y., Boore, J. L., Toyoda, A., Jordan, K. S., Pask, A. J., Renfree, M. B., Fujiyama, A., Marshall Graves, J. A., and Waters, P. D. (2012). Evolutionary history of novel genes on the tammar wallaby Y chromosome: implications for sex chromosome evolution. Genome Res. 22, 498–507.
| Evolutionary history of novel genes on the tammar wallaby Y chromosome: implications for sex chromosome evolution.Crossref | GoogleScholarGoogle Scholar | 22128133PubMed |

O’Connor, R. E., Romanov, M. N., Kiazim, L. G., Barrett, P. M., Farré, M., Damas, J., Ferguson-Smith, M., Valenzuela, N., Larkin, D. M., and Griffin, D. K. (2018). Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nat. Commun. 9, 1883.
| Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs.Crossref | GoogleScholarGoogle Scholar | 29784931PubMed |

O’Neill, R. J., O’Neill, M. J., and Graves, J. A. (1998). Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 393, 68–72.
| Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid.Crossref | GoogleScholarGoogle Scholar | 9590690PubMed |

O’Neill, R. J., Eldridge, M. D. B., and Metcalfe, C. J. (2004). Centromere dynamics and chromosome evolution in marsupials. J. Hered. 95, 375–381.
| Centromere dynamics and chromosome evolution in marsupials.Crossref | GoogleScholarGoogle Scholar | 15388765PubMed |

Pearse, A.-M., and Swift, K. (2006). Allograft theory: transmission of devil facial-tumour disease. Nature 439, 549.
| Allograft theory: transmission of devil facial-tumour disease.Crossref | GoogleScholarGoogle Scholar | 16452970PubMed |

Potter, S., Moritz, C., and Eldridge, M. D. B. (2015). Gene flow despite complex Robertsonian fusions among rock-wallaby (Petrogale) species. Biol. Lett. 11, .
| Gene flow despite complex Robertsonian fusions among rock-wallaby (Petrogale) species.Crossref | GoogleScholarGoogle Scholar | 26445985PubMed |

Potter, S., Bragg, J. G., Blom, M. P., Deakin, J. E., Kirkpatrick, M., Eldridge, M. D., and Moritz, C. (2017). Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies. Front. Genet. 8, 10.
| Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies.Crossref | GoogleScholarGoogle Scholar | 28265284PubMed |

Proskuryakova, A. A., Kulemzina, A. I., Perelman, P. L., Makunin, A. I., Larkin, D. M., Farré, M., Kukekova, A. V., Lynn Johnson, J., Lemskaya, N. A., Beklemisheva, V. R., Roelke-Parker, M. E., Bellizzi, J., Ryder, O. A., O’Brien, S. J., and Graphodatsky, A. S. (2017). X chromosome evolution in cetartiodactyla. Genes (Basel) 8, 216.
| X chromosome evolution in cetartiodactyla.Crossref | GoogleScholarGoogle Scholar |

Putnam, N. H., Connell, B. O., Stites, J. C., Rice, B. J., Hartley, P. D., Sugnet, C. W., Haussler, D., and Rokhsar, D. S. (2016). Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 26, 342–350.
| Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.Crossref | GoogleScholarGoogle Scholar | 26848124PubMed |

Pye, R. J., Pemberton, D., Tovar, C., Tubio, J. M. C., Dun, K. A., Fox, S., Darby, J., Hayes, D., Knowles, G. W., Kreiss, A., Siddle, H. V. T., Swift, K., Lyons, B., Murchison, E. P., and Woods, G. M. (2016). A second transmissible cancer in Tasmanian devils. Proc. Natl Acad. Sci. USA 113, 374–379.
| A second transmissible cancer in Tasmanian devils.Crossref | GoogleScholarGoogle Scholar | 26711993PubMed |

Rebollo, R., Horard, B., Hubert, B., and Vieira, C. (2010). Jumping genes and epigenetics: towards new species. Gene 454, 1–7.
| Jumping genes and epigenetics: towards new species.Crossref | GoogleScholarGoogle Scholar | 20102733PubMed |

Reig, O. A., Gardner, A. L., Bianchi, N. O., and Patton, J. L. (1977). The chromosomes of the Didelphidae (Marsupialia) and their evolutionary significance. Biol. J. Linn. Soc. Lond. 9, 191–216.
| The chromosomes of the Didelphidae (Marsupialia) and their evolutionary significance.Crossref | GoogleScholarGoogle Scholar |

Renfree, M. B., Papenfuss, A. T., Deakin, J. E., Lindsay, J., Heider, T., Belov, K., Rens, W., Waters, P. D., Pharo, E. A., Shaw, G., et al. (2011). Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol. 12, R81.
| Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.Crossref | GoogleScholarGoogle Scholar | 21854559PubMed |

Rens, W., O’Brien, P. C. M., Fairclough, H., Harman, L., Graves, J. A. M., and Ferguson-Smith, M. A. (2003). Reversal and convergence in marsupial chromosome evolution. Cytogenet. Genome Res. 102, 282–290.
| Reversal and convergence in marsupial chromosome evolution.Crossref | GoogleScholarGoogle Scholar | 14970718PubMed |

Rens, W., Wallduck, M. S., Lovell, F. L., Ferguson-Smith, M. A., and Ferguson-Smith, A. C. (2010). Epigenetic modifications on X chromosomes in marsupial and monotreme mammals and implications for evolution of dosage compensation. Proc. Natl Acad. Sci. USA 107, 17657–17662.
| Epigenetic modifications on X chromosomes in marsupial and monotreme mammals and implications for evolution of dosage compensation.Crossref | GoogleScholarGoogle Scholar | 20861449PubMed |

Rhoads, A., and Au, K. F. (2015). PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 13, 278–289.
| PacBio sequencing and its applications.Crossref | GoogleScholarGoogle Scholar | 26542840PubMed |

Rodríguez Delgado, C. L., Waters, P. D., Gilbert, C., Robinson, T. J., and Graves, J. A. M. (2009). Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years. Chromosome Res. 17, 917–926.
| Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years.Crossref | GoogleScholarGoogle Scholar |

Rofe, R., and Hayman, D. (1985). G-banding evidence for a conserved complement in Marsupialia. Cytogenet. Cell Genet. 39, 40–50.
| G-banding evidence for a conserved complement in Marsupialia.Crossref | GoogleScholarGoogle Scholar | 3979118PubMed |

Sankovic, N., Delbridge, M. L., Grützner, F., Ferguson-Smith, M. A., O’Brien, P. C. M., and Marshall Graves, J. A. (2006). Construction of a highly enriched marsupial Y chromosome-specific BAC sub-library using isolated Y chromosomes. Chromosome Res. 14, 657–664.
| Construction of a highly enriched marsupial Y chromosome-specific BAC sub-library using isolated Y chromosomes.Crossref | GoogleScholarGoogle Scholar | 16964572PubMed |

Sati, S., and Cavalli, G. (2017). Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma 126, 33–44.
| Chromosome conformation capture technologies and their impact in understanding genome function.Crossref | GoogleScholarGoogle Scholar | 27130552PubMed |

Seehausen, O., Butlin, R. K., Keller, I., Wagner, C. E., Boughman, J. W., Hohenlohe, P. A., Peichel, C. L., Saetre, G. P., Bank, C., Brännström, Å., et al. (2014). Genomics and the origin of species. Nat. Rev. Genet. 15, 176–192.
| Genomics and the origin of species.Crossref | GoogleScholarGoogle Scholar | 24535286PubMed |

Sharman, G. B. (1973). Chromosomes of non-Eutherian Mammals. In ‘Cytotaxonomy and Vertebrate Evolution’. (Eds A. N. Chiarelli and E. Capanna.) pp. 485–530. (Academic Press: New York.)

Sharman, G. B. (1974). Marsupial phylogeny and taxonomy. Aust. Mammal. 1, 137–154.

Sharp, J. A., Digby, M., Lefevre, C., Mailer, S., Khalil, E., Topcic, D., Auguste, A., Kwek, J., Brennan, A. J., Familari, M., and Nicholas, K. R. (2008). The comparative genomics of tammar wallaby and cape fur seal lactation models to examine function of milk proteins. In ‘Milk Proteins’. (Eds A. Thompson, M. Boland and H. Singh) pp. 55–79. (Academic Press: San Diego.)

Shevchenko, A. I., Zakharova, I. S., Elisaphenko, E. A., Kolesnikov, N. N., Whitehead, S., Bird, C., Ross, M., Weidman, J. R., Jirtle, R. L., Karamysheva, T. V., Rubtsov, N. B., VandeBerg, J. L., Mazurok, N. A., Nesterova, T. B., Brockdorff, N., and Zakian, S. M. (2007). Genes flanking Xist in mouse and human are separated on the X chromosome in American marsupials. Chromosome Res. 15, 127–136.
| Genes flanking Xist in mouse and human are separated on the X chromosome in American marsupials.Crossref | GoogleScholarGoogle Scholar | 17333537PubMed |

Siddle, H. V., Deakin, J. E., Coggill, P., Hart, E., Cheng, Y., Wong, E. S. W., Harrow, J., Beck, S., and Belov, K. (2009). MHC-linked and un-linked class I genes in the wallaby. BMC Genomics 10, .
| MHC-linked and un-linked class I genes in the wallaby.Crossref | GoogleScholarGoogle Scholar | 19602235PubMed |

Siddle, H. V., Deakin, J. E., Coggill, P., Whilming, L., Harrow, J., Kaufman, J., Beck, S., and Belov, K. (2011). The tammar wallaby major histocompatibility complex shows evidence of past genomic instability. BMC Genomics 12, 421.
| The tammar wallaby major histocompatibility complex shows evidence of past genomic instability.Crossref | GoogleScholarGoogle Scholar | 21854592PubMed |

Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., and de Laat, W. (2006). Nuclear organisation of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38, 1348–1354.
| Nuclear organisation of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).Crossref | GoogleScholarGoogle Scholar | 17033623PubMed |

Stammnitz, M. R., Coorens, T. H. H., Gori, K. C., Hayes, D., Fu, B., Wang, J., Martin-Herranz, D. E., Alexandrov, L. B., Baez-Ortega, A., Barthorpe, S., et al. (2018). The origins and vulnerabilities of two transmissible cancers in Tasmanian devils. Cancer Cell 33, 607–619.e15.
| The origins and vulnerabilities of two transmissible cancers in Tasmanian devils.Crossref | GoogleScholarGoogle Scholar | 29634948PubMed |

Svartman, M., and Vianna-Morgante, A. M. (1998). Kartyotype evolution of marsupials: from higher to lower diploid numbers. Cytogenet. Cell Genet. 82, 263–266.
| Kartyotype evolution of marsupials: from higher to lower diploid numbers.Crossref | GoogleScholarGoogle Scholar | 9858831PubMed |

Taylor, R. L., Zhang, Y., Schöning, J. P., and Deakin, J. E. (2017). Identification of candidate genes for devil facial tumour disease tumourigenesis. Sci. Rep. 7, 8761.
| Identification of candidate genes for devil facial tumour disease tumourigenesis.Crossref | GoogleScholarGoogle Scholar | 28821767PubMed |

Teague, B., Waterman, M. S., Goldstein, S., Potamousis, K., Zhou, S., Reslewic, S., Sarkar, D., Valouev, A., Churas, C., Kidd, J. M., Kohn, S., Runnheim, R., Lamers, C., Forrest, D., Newtown, M. A., Eichler, E. E., Kent-First, M., Surti, U., Livny, M., and Schwartz, D. C. (2010). High-resolution human genome structure by single-molecule analysis. Proc. Natl Acad. Sci. USA 107, 10848–10853.
| High-resolution human genome structure by single-molecule analysis.Crossref | GoogleScholarGoogle Scholar | 20534489PubMed |

Toder, R., Wakefield, M. J., and Graves, J. A. (2000). The minimal mammalian Y chromosome – the marsupial Y as a model system. Cytogenet. Cell Genet. 91, 285–292.
| The minimal mammalian Y chromosome – the marsupial Y as a model system.Crossref | GoogleScholarGoogle Scholar | 11173870PubMed |

Tomaszkiewicz, M., Rangavittal, S., Cechova, M., Sanchez, C., Fescemyer, H. W., Harris, R., Ye, D., Brien, C. M. O., Chikhi, R., Ryder, O. A., Ferguson-Smith, M. A., Medvedev, P., and Makova, K. D. (2016). A time- and cost-effective strategy to sequence mammalian Y chromosomes: an application to the de novo assembly of gorilla Y. Genome Res. 26, 530–540.
| A time- and cost-effective strategy to sequence mammalian Y chromosomes: an application to the de novo assembly of gorilla Y.Crossref | GoogleScholarGoogle Scholar | 26934921PubMed |

Tomaszkiewicz, M., Medvedev, P., and Makova, K. D. (2017). Y and W chromosome assemblies: approaches and discoveries. Trends Genet. 33, 266–282.
| Y and W chromosome assemblies: approaches and discoveries.Crossref | GoogleScholarGoogle Scholar | 28236503PubMed |

Trowsdale, J. (2002). The gentle art of gene arrangement: the meaning of gene clusters. Genome Biol. 3, comment2002.1.
| The gentle art of gene arrangement: the meaning of gene clusters.Crossref | GoogleScholarGoogle Scholar | 11897017PubMed |

Ullastres, A., Farré, M., Capilla, L., and Ruiz-Herrera, A. (2014). Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions. BMC Genomics 15, 530.
| Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions.Crossref | GoogleScholarGoogle Scholar | 24969235PubMed |

Ventura, M., Weigl, S., Carbone, L., Cardone, M. F., Misceo, D., Teti, M., D’Addabbo, P., Wandall, A., Björck, E., de Jong, P. J., She, X., Eichler, E. E., Archidiacono, N., and Rocchi, M. (2004). Recurrent sites for new centromere seeding. Genome Res. 14, 1696–1703.
| Recurrent sites for new centromere seeding.Crossref | GoogleScholarGoogle Scholar | 15342555PubMed |

Vijay, N., Weissensteiner, M., Burri, R., Kawakami, T., Ellegren, H., and Wolf, J. B. W. (2017). Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa. Mol. Ecol. 26, 4284–4295.
| Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa.Crossref | GoogleScholarGoogle Scholar | 28570015PubMed |

Wang, C., Deakin, J. E., Rens, W., Zenger, K. R., Belov, K., Marshall Graves, J. A., and Nicholas, F. W. (2011a). A first-generation integrated tammar wallaby map and its use in creating a tammar wallaby first-generation virtual genome map. BMC Genomics 12, 422.
| A first-generation integrated tammar wallaby map and its use in creating a tammar wallaby first-generation virtual genome map.Crossref | GoogleScholarGoogle Scholar | 21854555PubMed |

Wang, C., Webley, L., Wei, K.-J., Wakefield, M. J., Patel, H. R., Deakin, J. E., Alsop, A., Marshall Graves, J. A., Cooper, D. W., Nicholas, F. W., and Zenger, K. R. (2011b). A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii). BMC Genet. 12, 72.
| A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii).Crossref | GoogleScholarGoogle Scholar | 21854616PubMed |

Westerman, M., and Woolley, P. A. (1990). Cytogenetics of some New Guinean dasyurids and genome evolution in the Dasyuridae (Marsupialia). Aust. J. Zool. 37, 521–531.
| Cytogenetics of some New Guinean dasyurids and genome evolution in the Dasyuridae (Marsupialia).Crossref | GoogleScholarGoogle Scholar |

Westerman, M., and Woolley, P. A. (1993). Chromosomes and the evolution of dasyurid marsupials: an overview. Sci. New Guinea 19, 123–130.

Young, G. J., Graves, J. A. M., Barbieri, I., Woolley, P. A., Cooper, D. W., and Westerman, M. (1982). The chromosomes of dasyurids (Masupialia). In ‘Carnivorous Marsupials’. (Ed. M. Archer.) pp. 783–795. (Royal Zoological Society of New South Wales: Sydney.)