Chromosome Research

, Volume 21, Issue 4, pp 361–374 | Cite as

Molecular cytogenetic map of the central bearded dragon, Pogona vitticeps (Squamata: Agamidae)

  • M. J. Young
  • D. O’Meally
  • S. D. Sarre
  • A. Georges
  • T. Ezaz


Reptiles, as the sister group to birds and mammals, are particularly valuable for comparative genomic studies among amniotes. The Australian central bearded dragon (Pogona vitticeps) is being developed as a reptilian model for such comparisons, with whole-genome sequencing near completion. The karyotype consists of 6 pairs of macrochromosomes and 10 pairs microchromosomes (2n = 32), including a female heterogametic ZW sex microchromosome pair. Here, we present a molecular cytogenetic map for P. vitticeps comprising 87 anchor bacterial artificial chromosome clones that together span each macro- and microchromosome. It is the first comprehensive cytogenetic map for any non-avian reptile. We identified an active nucleolus organizer region (NOR) on the sub-telomeric region of 2q by mapping 18S rDNA and Ag-NOR staining. We identified interstitial telomeric sequences in two microchromosome pairs and the W chromosome, indicating that microchromosome fusion has been a mechanism of karyotypic evolution in Australian agamids within the last 21 to 19 million years. Orthology searches against the chicken genome revealed an intrachromosomal rearrangement of P. vitticeps 1q, identified regions orthologous to chicken Z on P. vitticeps 2q, snake Z on P. vitticeps 6q and the autosomal microchromosome pair in P. vitticeps orthologous to turtle Pelodiscus sinensis ZW and lizard Anolis carolinensis XY. This cytogenetic map will be a valuable reference tool for future gene mapping studies and will provide the framework for the work currently underway to physically anchor genome sequences to chromosomes for this model Australian squamate.


Reptile Karyotype Microchromosome FISH Sex chromosome 





ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle


Bacterial artificial chromosome


B cell CLL/lymphoma 6


Basic Local Alignment Search Tool


BLAST-like alignment tool


Carbonic anhydrase X


Chromodomain helicase DNA-binding protein 1


C-terminal binding protein 2


Catenin (cadherin-associated protein), beta 1, 88 kDa




DEAD (Asp-Glu-Ala-Asp) box polypeptide 58


Doublesex and mab-3-related transcription factor 1


2′-Deoxyuridine 5′-triphosphate


Eukaryotic translation initiation factor 3, subunit H


Family with sequence similarity 83, member B


Fibrosin-like 1


Fluorescence in situ hybridization


Growth hormone receptor


GDP-mannose pyrophosphorylase A


Hypocretin (orexin) receptor 2


3-Hydroxymethyl-3-methylglutaryl-CoA lyase-like 1


Integrin-binding sialoprotein


Importin 7


IQ motif and Sec7 domain 3


K(lysine) acetyltransferase 2B


K(lysine) acetyltransferase 7


Kruppel-like factor 6


Neuron navigator 2


Nucleolus organizer region


Nitrogen permease regulator-like 3


Proteasome (prosome, macropain) subunit, alpha type, 2


RAB5A, member RAS oncogene family


Ribosomal DNA


Ribonucleotide reductase M1


Sex-determining region Y


Tax1 (human T-cell leukemia virus type I) binding protein 1


Transmembrane protein 41B


Tumor necrosis factor receptor superfamily, member 11b




WW domain-containing adaptor with coiled coil


Zinc finger protein 143



This work was funded by an ARC DP awarded to SD, AG and Scott Edwards, as was the purchase of the P. vitticeps BAC Library. This work was undertaken by MY as a Bachelor of Applied Science Honours with the Institute of Applied Ecology at the University of Canberra. We would like to thank Jacqui Richardson and Alistair Zealey for their care of captive animals and Juliet Ward for laboratory assistance.

Supplementary material

10577_2013_9362_MOESM1_ESM.doc (117 kb)
ESM 1(DOC 117 kb)


  1. Ahl E (1926) Neue Eidechsen und Amphibien. Zoologischer Anzeiger 67:186–192Google Scholar
  2. Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD (2011) The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477:587–591PubMedCrossRefGoogle Scholar
  3. Chinwalla AT, Cook LL, Delehaunty KD, Fewell GA, Fulton LA, Fulton RS, Graves TA, Hillier LDW, Mardis ER, McPherson JD (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562PubMedCrossRefGoogle Scholar
  4. Crawford NG, Faircloth BC, McCormack JE, Brumfield RT, Winker K, Glenn TC (2012) More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biol Lett 8:783–786PubMedCrossRefGoogle Scholar
  5. Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Bouffard P, Burt DW, Crasta O, Crooijmans RPMA, Cooper K (2010) Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biology 8:e1000475PubMedCrossRefGoogle Scholar
  6. Dolezel J, Bartos J, Voglmayr H, Greilhuber J (2003) Nuclear DNA content and genome size of trout and human. Cytometry Part A: The Journal of the International Society for Analytical Cytology 51:127Google Scholar
  7. Ezaz T, Moritz B, Waters P, Marshall Graves JA, Georges A, Sarre SD (2009a) The ZW sex microchromosomes of an Australian dragon lizard share no homology with those of other reptiles or birds. Chromosome Res 17:965–973PubMedCrossRefGoogle Scholar
  8. Ezaz T, Quinn AE, Miura I, Sarre SD, Georges A, Graves JAM (2005) The dragon lizard Pogona vitticeps has ZZ/ZW micro-sex chromosomes. Chromosome Res 13:763–776PubMedCrossRefGoogle Scholar
  9. Ezaz T, Quinn AE, Sarre SD, O’Meally D, Georges A, Marshall Graves JA (2009b) Molecular marker suggests rapid changes of sex-determining mechanisms in Australian dragon lizards. Chromosome Res 17:91–98PubMedCrossRefGoogle Scholar
  10. Fujita MK, Edwards SV, Ponting CP (2011) The Anolis lizard genome: an amniote genome without isochores. Genome Biol Evol 3:974PubMedCrossRefGoogle Scholar
  11. Hedges SB, Dudley J, Kumar S (2006) TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22:2971–2972PubMedCrossRefGoogle Scholar
  12. Hillier LDW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MAM, Delany ME (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716CrossRefGoogle Scholar
  13. Howell WM, Black DA (1980) Controlled silver-staining of nucleolus organizer regions with a protective colloidal developer: a 1-step method. Experientia 36:1014–1015PubMedCrossRefGoogle Scholar
  14. Hugall AF, Foster R, Hutchinson M, Lee MSY (2008) Phylogeny of Australasian agamid lizards based on nuclear and mitochondrial genes: implications for morphological evolution and biogeography. Biol J Linn Soc 93:343–358CrossRefGoogle Scholar
  15. Kasai F, O’Brien PCM, Ferguson-Smith MA (2012) Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken. Biol Lett 8:631–635PubMedCrossRefGoogle Scholar
  16. Kawagoshi T, Uno Y, Matsubara K, Matsuda Y, Nishida C (2009) The ZW micro-sex chromosomes of the Chinese soft-shelled turtle (Pelodiscus sinensis, Trionychidae, Testudines) have the same origin as chicken chromosome 15. Cytogenet Genome Res 125:125–131PubMedCrossRefGoogle Scholar
  17. Kawai A, Nishida-Umehara C, Ishijima J, Tsuda Y, Ota H, Matsuda Y (2007) Different origins of bird and reptile sex chromosomes inferred from comparative mapping of chicken Z-linked genes. Cytogenet Genome Res 117:92–102PubMedCrossRefGoogle Scholar
  18. Kohn M, Högel J, Vogel W, Minich P, Kehrer-Sawatzki H, Graves JAM, Hameister H (2006) Reconstruction of a 450-My-old ancestral vertebrate protokaryotype. Trends Genet 22:203–210PubMedCrossRefGoogle Scholar
  19. Kuraku S, Ishijima J, Nishida-Umehara C, Agata K, Kuratani S, Matsuda Y (2006) cDNA-based gene mapping and GC 3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids. Chromosome Res 14:187–202PubMedCrossRefGoogle Scholar
  20. MacCulloch RD, Upton DE, Murphy RW (1996) Trends in nuclear DNA content among amphibians and reptiles. Comp Biochem Physiol B Biochem Mol Biol 113:601–605CrossRefGoogle Scholar
  21. Martinez PA, Ezaz T, Valenzuela N, Georges A, Marshall Graves JA (2008) An XX/XY heteromorphic sex chromosome system in the Australian chelid turtle Emydura macquarii: a new piece in the puzzle of sex chromosome evolution in turtles. Chromosome Res 16:815–825PubMedCrossRefGoogle Scholar
  22. Matsubara K, Kuraku S, Tarui H, Nishimura O, Nishida C, Agata K, Kumazawa Y, Matsuda Y (2012) Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC3 profiling in snake. BMC Genomics 13:604PubMedCrossRefGoogle Scholar
  23. Matsuda Y, Nishida-Umehara C, Tarui H, Kuroiwa A, Yamada K, Isobe T, Ando J, Fujiwara A, Hirao Y, Nishimura O (2005) Highly conserved linkage homology between birds and turtles: bird and turtle chromosomes are precise counterparts of each other. Chromosome Res 13:601–615PubMedCrossRefGoogle Scholar
  24. Meyne J, Baker RJ, Hobart HH, Hsu T, Ryder OA, Ward OG, Wiley JE, Wurster-Hill DH, Yates TL, Moyzis RK (1990) Distribution of non-telomeric sites of the (TTAGGG)n telomeric sequence in vertebrate chromosomes. Chromosoma 99:3–10PubMedCrossRefGoogle Scholar
  25. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447:167–177PubMedCrossRefGoogle Scholar
  26. Nakatani Y, Takeda H, Kohara Y, Morishita S (2007) Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res 17:1254–1265PubMedCrossRefGoogle Scholar
  27. O’Meally D, Miller H, Patel H, Marshall Graves JA, Ezaz T (2009) The first cytogenetic map of the tuatara, Sphenodon punctatus. Cytogenet genome res 127:213–223PubMedCrossRefGoogle Scholar
  28. O’Meally D, Ezaz T, Georges A, Sarre SD, Graves JA (2012) Are some chromosomes particularly good at sex? Insights from amniotes. Chromosome Res 20:7–19Google Scholar
  29. Olmo E, Signorino G (2005) Chromorep: a reptile chromosomes database. Accessed 7 May 2013
  30. Organ CL, Janes DE (2008) Evolution of sex chromosomes in Sauropsida. Integr Comp Biol 48:512–519PubMedCrossRefGoogle Scholar
  31. Patel VS, Ezaz T, Deakin JE, Marshall Graves JA (2010) Globin gene structure in a reptile supports the transpositional model for amniote α- and β-globin gene evolution. Chromosome Res 18:897–907PubMedCrossRefGoogle Scholar
  32. Paull D, Williams EE, Hall WP (1976) Lizard karyotypes from the Galapagos Islands: chromosomes in phylogeny and evolution. Breviora 441:1–31Google Scholar
  33. Pokorná M, Giovannotti M, Kratochvíl L, Caputo V, Olmo E, Ferguson-Smith MA, Rens W (2012) Conservation of chromosomes syntenic with avian autosomes in squamate reptiles revealed by comparative chromosome painting. Chromosoma 121:409–418Google Scholar
  34. Pokorná M, Giovannotti M, Kratochvíl L, Kasai F, Trifonov VA, O’Brien PCM, Caputo V, Olmo E, Ferguson-Smith MA, Rens W (2011) Strong conservation of the bird Z chromosome in reptilian genomes is revealed by comparative painting despite 275 million years divergence. Chromosoma 120:455–468PubMedCrossRefGoogle Scholar
  35. Porter CA, Hamilton MJ, Sites Jr JW, Baker RJ (1991) Location of ribosomal DNA in chromosomes of squamate reptiles: systematic and evolutionary implications. Herpetologica 47:271–280Google Scholar
  36. Quinn AE, Georges A, Sarre SD, Guarino F, Ezaz T, Graves JAM (2007) Temperature sex reversal implies sex gene dosage in a reptile. Science 316:411–411PubMedCrossRefGoogle Scholar
  37. Ruiz-Herrera A, Nergadze S, Santagostino M, Giulotto E (2008) Telomeric repeats far from the ends: mechanisms of origin and role in evolution. Cytogenet Genome Res 122:219–228PubMedCrossRefGoogle Scholar
  38. Sarre SD, Ezaz T, Georges A (2011) Transitions between sex-determining systems in reptiles and amphibians. Annu Rev Genom Hum Genet 12:391–406CrossRefGoogle Scholar
  39. Sarre SD, Georges A, Quinn A (2004) The ends of a continuum: genetic and temperature-dependent sex determination in reptiles. BioEssays 26:639–645PubMedCrossRefGoogle Scholar
  40. Shedlock AM, Edwards SV (2009) Amniotes (amniota). In: Hedges SB, Kumar S (eds) The timetree of life. Oxford University Press, New York, pp 375–379Google Scholar
  41. Srikulnath K, Nishida C, Matsubara K, Uno Y, Thongpan A, Suputtitada S, Apisitwanich S, Matsuda Y (2009) Karyotypic evolution in squamate reptiles: comparative gene mapping revealed highly conserved linkage homology between the butterfly lizard (Leiolepis reevesii rubritaeniata, Agamidae, Lacertilia) and the Japanese four-striped rat snake (Elaphe quadrivirgata, Colubridae, Serpentes). Chromosome Res 17:975–986PubMedCrossRefGoogle Scholar
  42. Uno Y, Nishida C, Tarui H, Ishishita S, Takagi C, Nishimura O, Ishijima J, Ota H, Kosaka A, Matsubara K (2012) Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping. PLoS One 7:e53027PubMedCrossRefGoogle Scholar
  43. Wakefield MJ, Graves JAM (2003) The kangaroo genome. EMBO Rep 4:143–147PubMedCrossRefGoogle Scholar
  44. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LDW, Künstner A, Searle S, White S, Vilella AJ, Fairley S (2010) The genome of a songbird. Nature 464:757–762PubMedCrossRefGoogle Scholar
  45. Warren WC, Hillier LDW, Graves JAM, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 453:175–183PubMedCrossRefGoogle Scholar
  46. Witten G (1983) Some karyotypes of Australian agamids (Reptilia: Lacertilia). Aust J Zool 31:533–540CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • M. J. Young
    • 1
  • D. O’Meally
    • 1
  • S. D. Sarre
    • 1
  • A. Georges
    • 1
  • T. Ezaz
    • 1
  1. 1.Institute for Applied EcologyUniversity of CanberraCanberraAustralia

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