Chromosome Research

, Volume 16, Issue 8, pp 1159–1175 | Cite as

Physical map of two tammar wallaby chromosomes: A strategy for mapping in non-model mammals

  • Janine E. Deakin
  • Edda Koina
  • Paul D. Waters
  • Ruth Doherty
  • Vidushi S. Patel
  • Margaret L. Delbridge
  • Bianca Dobson
  • James Fong
  • Yanqiu Hu
  • Cecilia van den Hurk
  • Andrew J. Pask
  • Geoff Shaw
  • Carly Smith
  • Katherine Thompson
  • Matthew J. Wakefield
  • Hongshi Yu
  • Marilyn B. Renfree
  • Jennifer A. Marshall Graves


Marsupials are especially valuable for comparative genomic studies of mammals. Two distantly related model marsupials have been sequenced: the South American opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii), which last shared a common ancestor about 70 Mya. The six-fold opossum genome sequence has been assembled and assigned to chromosomes with the help of a cytogenetic map. A good cytogenetic map will be even more essential for assembly and anchoring of the two-fold wallaby genome. As a start to generating a physical map of gene locations on wallaby chromosomes, we focused on two chromosomes sharing homology with the human X, wallaby chromosomes X and 5. We devised an efficient strategy for mapping large conserved synteny blocks in non-model mammals, and applied this to generate dense maps of the X and ‘neo-X’ regions and to determine the arrangement of large conserved synteny blocks on chromosome 5. Comparisons between the wallaby and opossum chromosome maps revealed many rearrangements, highlighting the need for comparative gene mapping between South American and Australian marsupials. Frequent rearrangement of the X, along with the absence of a marsupial XIST gene, suggests that inactivation of the marsupial X chromosome does not depend on a whole-chromosome repression by a control locus.

Key words

comparative mapping genomics marsupial X chromosome evolution 



bacterial artificial chromosome


basic local alignment search tool nucleotide


base pair(s)


charge-coupled device


complementary DNA


4′,6-diamidino-2-phenylindole dihydrochloride


2′-deoxyuridine 5′-triphosphate


fluorescence in-situ hybridization


Gallus gallus


Homo sapiens


kilo base pairs


Luria broth


mega base pairs


Monodelphis domestica


major histocompatibility complex


million years ago


olfactory receptor


polymerase chain reaction


radioactive in-situ hybridization


standard sodium citrate


X added region


X chromosome inactivation


X conserved region


X inactivation centre

Supplementary material

10577_2008_1266_MOESM1_ESM.doc (146 kb)
(DOC 146 KB)
10577_2008_1266_MOESM2_ESM.xls (250 kb)
(XLS 249 KB)


  1. Alsop AE, Miethke P, Rofe R et al. (2005) Characterizing the chromosomes of the Australian model marsupial Macropus eugenii (tammar wallaby). Chromosome Res 13: 627–636.PubMedCrossRefGoogle Scholar
  2. Bininda-Emonds OR, Cardillo M, Jones KE et al. (2007) The delayed rise of present-day mammals. Nature 446: 507–512.PubMedCrossRefGoogle Scholar
  3. Brown CJ, Lafreniere RG, Powers VE et al. (1991) Localization of the X inactivation centre on the human X chromosome in Xq13. Nature 349: 82–84.PubMedCrossRefGoogle Scholar
  4. Carrel L, Willard HF (2005) X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434: 400–404.PubMedCrossRefGoogle Scholar
  5. Cooper DW, Johnston PG, Graves JAM (1993) X-inactivation in marsupials and monotremes. Semin Dev Biol 4: 117–128.CrossRefGoogle Scholar
  6. Davidow LS, Breen M, Duke SE et al. (2007) The search for a marsupial XIC reveals a break with vertebrate synteny. Chromosome Res 15: 137–146.PubMedCrossRefGoogle Scholar
  7. Deakin JE, Siddle HV, Cross JG, Belov K, Graves JAM (2007) Class I genes have split from the MHC in the tammar wallaby. Cytogenet Genome Res 116: 205–211.PubMedCrossRefGoogle Scholar
  8. Delbridge ML, Graves JAM (2004) Assignment of the eukaryotic translation initiation factor (EIF2S3) to tammar wallaby chromosome 5p by in situ hybridization. Cytogenet Genome Res 107: 139.PubMedCrossRefGoogle Scholar
  9. Delbridge ML, McMillan DA, Doherty RJ, Deakin JE, Graves JAM (2008) Origin and evolution of candidate mental retardation genes on the human X chromosome (MRX). BMC Genomics 9: 65.PubMedCrossRefGoogle Scholar
  10. Duke SE, Samollow PB, Mauceli E, Lindblad-Toh K, Breen M (2007) Integrated cytogenetic BAC map of the genome of the gray, short-tailed opossum, Monodelphis domestica. Chromosome Res 15: 361–370.PubMedGoogle Scholar
  11. Duret L, Chureau C, Samain S, Weissenbach J, Avner P (2006) The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 312: 1653–1655.PubMedCrossRefGoogle Scholar
  12. Edwards CA, Rens W, Clarke O et al. (2007) The evolution of imprinting: chromosomal mapping of orthologues of mammalian imprinted domains in monotreme and marsupial mammals—art. no. 157. BMC Evol Biol 7: 157.PubMedCrossRefGoogle Scholar
  13. Fitzgerald J, Wilcox SA, Graves JAM, Dahl HH (1993) A eutherian X-linked gene, PDHA1, is autosomal in marsupials: a model for the evolution of a second, testis-specific variant in eutherian mammals. Genomics 18: 636–642.PubMedCrossRefGoogle Scholar
  14. Foster JW, Graves JAM (1994) An SRY-related sequence on the marsupial X chromosome: implications for the evolution of the mammalian testis-determining gene. Proc Natl Acad Sci U S A 91: 1927–1931.PubMedCrossRefGoogle Scholar
  15. Gartler SM, Dyer KA, Graves JAM, Rocchi M (1985) A two step model for mammalian X-chromosome inactivation. Prog Clin Biol Res 198: 223–235.PubMedGoogle Scholar
  16. Glas R, De Leo AA, Delbridge ML et al. (1999) Chromosome painting in marsupials: genome conservation in the kangaroo family. Chromosome Res 7: 167–176.PubMedCrossRefGoogle Scholar
  17. Graves JAM (1995) The origin and function of the mammalian Y chromosome and Y-borne genes—an evolving understanding. Bioessays 17: 311–320.PubMedCrossRefGoogle Scholar
  18. Graves JAM, Gartler SM (1986) Mammalian X chromosome inactivation: testing the hypothesis of transcriptional control. Somat Cell Mol Genet 12: 275–280.PubMedCrossRefGoogle Scholar
  19. Graves JAM, Chew GK, Cooper DW, Johnston PG (1979) Marsupial–mouse cell hybrids containing fragments of the marsupial X chromosome. Somatic Cell Genet 5: 481–489.PubMedCrossRefGoogle Scholar
  20. Heard E, Disteche CM (2006) Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev 20: 1848–1867.PubMedCrossRefGoogle Scholar
  21. Hore TA, Koina E, Graves JAM (2007) The region homologous to the X-chromosome inactivation centre has been disrupted in marsupial and monotreme mammals. Chromosome Res 15: 147–161.PubMedCrossRefGoogle Scholar
  22. Kirsch JAW, Lapointe FJ, Springer MS (1997) DNA-hybridisation studies of marsupials and their implications for metatherian classification. Aust J Zool 45: 211–280.CrossRefGoogle Scholar
  23. Kohn M, Kehrer-Sawatzki H, Vogel W, Graves JAM, Hameister H (2004) Wide genome comparisons reveal the origins of the human X chromosome. Trends Genet 20: 598–603.PubMedCrossRefGoogle Scholar
  24. Koina E, Graves JAM (2005) Assignment of the glucose-6-phosphate dehydrogenase (G6PD) gene to tammar wallaby chromosome Xq by fluorescence in situ hybridization with a BAC clone. Cytogenet Genome Res 108: 362.PubMedCrossRefGoogle Scholar
  25. Koina E, Graves JAM (2006) Assignment of the proteolipid protein 1 gene (PLP1) to tammar wallaby chromosome Xq by fluorescence in situ hybridization with a BAC clone. Cytogenet Genome Res 114: 94F.PubMedCrossRefGoogle Scholar
  26. Koina E, Wakefield MJ, Walcher C et al. (2005) Isolation, X location and activity of the marsupial homologue of SLC16A2, an XIST-flanking gene in eutherian mammals. Chromosome Res 13: 687–698.PubMedCrossRefGoogle Scholar
  27. Mikkelsen TS, Wakefield MJ, Aken B et al. (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167–177.PubMedCrossRefGoogle Scholar
  28. National Human Genome Research Institute (2008) Internet references. Retrieved from 1/9/2008.
  29. Ohno S (1967) Sex Chromosomes and Sex Linked Genes. Berlin: Springer.Google Scholar
  30. Pask A, Toder R, Wilcox SA, Camerino G, Graves JAM (1997) The candidate sex-reversing DAX1 gene is autosomal in marsupials: implications for the evolution of sex determination in mammals. Genomics 41: 422–426.PubMedCrossRefGoogle Scholar
  31. Pask A, Renfree MB, Graves JAM (2000) The human sex-reversing ATRX gene has a homologue on the marsupial Y chromosome, ATRY: implications for the evolution of mammalian sex determination. Proc Natl Acad Sci U S A 97: 13198–13202.PubMedCrossRefGoogle Scholar
  32. Rapkins RW, Hore T, Smithwick M et al. (2006) Recent assembly of an imprinted domain from non-imprinted components. PLoS Genet 2: e182.PubMedCrossRefGoogle Scholar
  33. Rens W, O’Brien PC, Fairclough H et al. (2003) Reversal and convergence in marsupial chromosome evolution. Cytogenet Genome Res 102: 282–290.PubMedCrossRefGoogle Scholar
  34. Rofe R, Hayman D (1985) G-banding evidence for a conserved complement in the Marsupialia. Cytogenet Cell Genet 39: 40–50.PubMedCrossRefGoogle Scholar
  35. Samollow PB (2006) Status and applications of genomic resources for the gray, short-tailed opossum, Monodelphis domestica, an American marsupial model for comparative biology. Aust J Zool 54: 173–196.CrossRefGoogle Scholar
  36. Sharman GB (1971) Late DNA replication in the paternally derived X chromosome of female kangaroos. Nature 230: 231–232.PubMedCrossRefGoogle Scholar
  37. Shetty S, Griffin DK, Graves JAM (1999) Comparative painting reveals strong chromosome homology over 80 million years of bird evolution. Chromosome Res 7: 289–295.PubMedCrossRefGoogle Scholar
  38. Shevchenko AI, Zakharova IS, Elisaphenko EA et al. (2007) Genes flanking Xist in mouse and human are separated on the X chromosome in American marsupials. Chromosome Res 15: 127–136.PubMedCrossRefGoogle Scholar
  39. Sinclair AH, Foster JW, Spencer JA et al. (1988) Sequences homologous to ZFY, a candidate human sex-determining gene, are autosomal in marsupials. Nature 336: 780–783.PubMedCrossRefGoogle Scholar
  40. Spencer JA, Sinclair AH, Watson JM, Graves JAM (1991a) Genes on the short arm of the human X chromosome are not shared with the marsupial X. Genomics 11: 339–345.PubMedCrossRefGoogle Scholar
  41. Spencer JA, Watson JM, Graves JAM (1991b) The X chromosome of marsupials shares a highly conserved region with eutherians. Genomics 9: 598–604.PubMedCrossRefGoogle Scholar
  42. Spencer JA, Watson JM, Lubahn DB et al. (1991c) The androgen receptor gene is located on a highly conserved region of the X chromosomes of marsupial and monotreme as well as eutherian mammals. J Hered 82: 134–139.PubMedGoogle Scholar
  43. Svartman M, Vianna-Morgante AM (1998) Karyotype evolution of marsupials: from higher to lower diploid numbers. Cytogenet Cell Genet 82: 263–266.PubMedCrossRefGoogle Scholar
  44. Toder R, Graves JAM (1998) CSF2RA, ANT3, and STS are autosomal in marsupials: implications for the origin of the pseudoautosomal region of mammalian sex chromosomes. Mamm Genome 9: 373–376.PubMedCrossRefGoogle Scholar
  45. Tyndale-Biscoe H (2005) Life of Marsupials. Collingwood: CSIRO Publishing.Google Scholar
  46. Tyndale-Biscoe CH, Renfree MB. 1987. Reproductive Physiology of Marsupials. Cambridge: Cambridge University Press.Google Scholar
  47. Veyrunes F, Waters PD, Miethke P et al. (2008) Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Genome Res 18: 965–973.PubMedCrossRefGoogle Scholar
  48. Wakefield MJ, Graves JAM (2003) The kangaroo genome. Leaps and bounds in comparative genomics. EMBO Rep 4: 143–147.PubMedCrossRefGoogle Scholar
  49. Wakefield MJ, Anderson M, Chang E et al. (2008) Cone visual pigments of monotremes: filling the phylogenetic gap. Vis Neurosci 25: 257–264.PubMedCrossRefGoogle Scholar
  50. Warren WC, Hillier LW, Graves JAM et al. (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 453: 175–183.PubMedCrossRefGoogle Scholar
  51. Washington University Genome Sequencing Center (2008) Internet references. Retrieved from 1/9/2008.
  52. Waters PD, Kirby PJ, Graves JAM (2001) Assignment of the SMARCF1 gene to tammar wallaby chromosome 5q by fluorescence in-situ hybridization. Cytogenet Cell Genet 93: 315–316.PubMedCrossRefGoogle Scholar
  53. Waters PD, Sankovic N, Kirby PJ, Delbridge ML, Graves JAM (2003) Assignment of the thymosin beta 4 X/Y chromosome (TMSB4X/Y) gene to tammar wallaby chromosome 5p by fluorescence in-situ hybridization. Cytogenet Genome Res 103: 203F.PubMedCrossRefGoogle Scholar
  54. Watson JM, Spencer JA, Graves JAM, Snead ML, Lau EC (1992) Autosomal localization of the amelogenin gene in monotremes and marsupials: implications for mammalian sex chromosome evolution. Genomics 14: 785–789.PubMedCrossRefGoogle Scholar
  55. Wilcox SA, Watson JM, Spencer JA, Graves JAM (1996) Comparative mapping identifies the fusion point of an ancient mammalian X-autosomal rearrangement. Genomics 35: 66–70.PubMedCrossRefGoogle Scholar
  56. Woodburne MO, Rich TH, Springer MS (2003) The evolution of tribospheny and the antiquity of mammalian clades. Mol Phylogenet Evol 28: 360–385.PubMedCrossRefGoogle Scholar
  57. Yu H, Pask AJ, Shaw G, Renfree MB (2006) Differential expression of WNT4 in testicular and ovarian development in a marsupial. BMC Dev Biol 6: 44.PubMedCrossRefGoogle Scholar
  58. Yue Y, Haaf T (2006) 7E olfactory receptor gene clusters and evolutionary chromosome rearrangements. Cytogenet Genome Res 112: 6–10.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Janine E. Deakin
    • 1
  • Edda Koina
    • 1
  • Paul D. Waters
    • 1
  • Ruth Doherty
    • 1
  • Vidushi S. Patel
    • 1
  • Margaret L. Delbridge
    • 1
  • Bianca Dobson
    • 1
  • James Fong
    • 1
  • Yanqiu Hu
    • 2
  • Cecilia van den Hurk
    • 1
  • Andrew J. Pask
    • 2
  • Geoff Shaw
    • 2
  • Carly Smith
    • 1
  • Katherine Thompson
    • 1
  • Matthew J. Wakefield
    • 3
  • Hongshi Yu
    • 2
  • Marilyn B. Renfree
    • 2
  • Jennifer A. Marshall Graves
    • 1
  1. 1.ARC Centre of Excellence for Kangaroo Genomics, Research School of Biological SciencesThe Australian National UniversityCanberraAustralia
  2. 2.ARC Centre of Excellence for Kangaroo Genomics, Department of ZoologyUniversity of MelbourneVictoriaAustralia
  3. 3.The Walter and Eliza Hall InstituteVictoriaAustralia

Personalised recommendations