Karyotype evolution in monitor lizards: cross-species chromosome mapping of cDNA reveals highly conserved synteny and gene order in the Toxicofera clade

Abstract

The water monitor lizard (Varanus salvator macromaculatus (VSA), Platynota) has a chromosome number of 2n = 40: its karyotype consists of 16 macrochromosomes and 24 microchromosomes. To delineate the process of karyotype evolution in V. salvator macromaculatus, we constructed a cytogenetic map with 86 functional genes and compared it with those of the butterfly lizard (Leiolepis reevesii rubritaeniata (LRE); 2n = 36) and Japanese four-striped rat snake (Elaphe quadrivirgata (EQU); 2n = 36), members of the Toxicofera clade. The syntenies and gene orders of macrochromosomes were highly conserved between these species except for several chromosomal rearrangements: eight pairs of VSA macrochromosomes and/or chromosome arms exhibited homology with six pairs of LRE macrochromosomes and eight pairs of EQU macrochromosomes. Furthermore, the genes mapped to microchromosomes of three species were all located on chicken microchromosomes or chromosome 4p. No reciprocal translocations were found in the species, and their karyotypic differences were caused by: low frequencies of interchromosomal rearrangements, such as tandem fusions, or centric fissions/fusions between macrochromosomes and between macro- and microchromosomes; and intrachromosomal rearrangements, such as paracentric inversions or centromere repositioning. The chromosomal rearrangements that occurred in macrochromosomes of the Varanus lineage were also identified through comparative cytogenetic mapping of V. salvator macromaculatus and V. exanthematicus. Morphologic differences in chromosomes 6–8 between the two species could have resulted from pericentric inversion or centromere repositioning.

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Abbreviations

BLAST:

Basic Local Alignment Search Tool

cDNA:

Complementary DNA

EQU:

Elaphe quadrivirgata

FISH:

Fluorescence in situ hybridization

GGA:

Gallus gallus

LRE:

Leiolepis reevesii rubritaeniata

MYA:

Million years ago

rRNA:

Ribosomal RNA

VSA:

Varanus salvator macromaculatus

References

  1. Alföldi J, Di Palma F, Grabherr M et al (2011) The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477:587–591

    PubMed Central  PubMed  Article  Google Scholar 

  2. Amer SAM, Kumazawa Y (2008) Timing of a mtDNA gene rearrangement and intercontinental dispersal of varanid lizards. Gene Genet Syst 83:275–280

    CAS  Article  Google Scholar 

  3. Ast JC (2001) Mitochondrial DNA evidence and evolution in Varanoidea (Squamata). Cladistics 17:211–226

    Article  Google Scholar 

  4. Bennett D, Thakoordyal R (2003) The Savannah Monitor Lizard: the truth about Varanus exanthematicus. Viper Press, UK, pp 1–83

    Google Scholar 

  5. Chaiprasertsri N, Uno Y, Peyachoknagul S et al. (2013) Highly species-specific centromeric repetitive DNA sequences in lizards: molecular cytogenetic characterization of a novel family of satellite DNA sequences isolated from the water monitor lizard (Varanus salvator macromaculatus, Platynota). J Hered 104:798–806

    Google Scholar 

  6. Glor RE, Laport RG (2012) Are subspecies of Anolis lizards that differ in dewlap color and pattern also genetically distinct? A mitochondrial analysis. Mol Phylogenet Evol 64:255–260

    PubMed  Article  Google Scholar 

  7. International Chicken Genome Sequencing Consortium (ICGSC) (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716

    Article  Google Scholar 

  8. King M, King D (1975) Chromosomal evolution in the lizard genus Varanus (Reptilia). Aust J Biol Sci 28:89–108

    CAS  PubMed  Google Scholar 

  9. King M, Mengden GA, King D (1982) A pericentric-inversion polymorphism and a ZZ/ZW sex-chromosome system in Varanus acanthurus Boulenger analyzed by G- and C-banding and Ag staining. Genetica 58:39–45

    Article  Google Scholar 

  10. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163

    CAS  PubMed  Article  Google Scholar 

  11. Kumazawa Y, Endo H (2004) Mitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements. DNA Res 11:115–125

    CAS  PubMed  Article  Google Scholar 

  12. Matsubara K, Tarui H, Toriba M et al (2006) Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes. Proc Natl Acad Sci U S A 103:18190–18195

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  13. Matsubara K, Kuraku S, Tarui H et al (2012) Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC3 profiling in snake. BMC Genomics 13:604

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  14. Matsuda Y, Chapman VM (1995) Application of fluorescence in situ hybridization in genome analysis of the mouse. Electrophoresis 16:261–272

    CAS  PubMed  Article  Google Scholar 

  15. Matsuda Y, Nishida-Umehara C, Tarui H et al (2005) Highly conserved linkage homology between birds and turtles: bird and turtle chromosomes are precise counterparts of each other. Chromosome Res 13:601–615

    CAS  PubMed  Article  Google Scholar 

  16. Nishida-Umehara C, Tsuda Y, Ishijima J, Ando J, Fujiwara A, Matsuda Y, Griffin DK (2007) The molecular basis of chromosome orthologies and sex chromosomal differentiation in palaeognathous birds. Chromosome Res 15:721–734

    CAS  PubMed  Article  Google Scholar 

  17. Olmo E, Signorino G (2005) Chromorep: a reptile chromosomes database. Internet references. Available from http://chromorep.univpm.it. Accessed 06/04/2013

  18. Shedlock AM, Edwards SV (2009) Amniota. In: Kumar S, Hedges SB (eds) The timetree of life. Oxford University Press, New York, pp 375–379

    Google Scholar 

  19. Srikulnath K, Matsubara K, Uno Y et al (2009a) Karyological characterization of the butterfly lizard (Leiolepis reevesii rubritaeniata, Agamidae, Squamata) by molecular cytogenetic approach. Cytogenet Genome Res 125:213–223

    CAS  PubMed  Article  Google Scholar 

  20. Srikulnath K, Nishida C, Matsubara K et al (2009b) 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 17:975–986

    CAS  PubMed  Article  Google Scholar 

  21. Srikulnath K, Matsubara K, Uno Y et al (2010) Genetic relationship of three butterfly lizard species (Leiolepis reveesii rubritaeniata, Leiolepis belliana belliana, Leiolepis boehmei, Agamidae Squamata) inferred from nuclear gene sequence analysis. Kasetsart J (Nat Sci) 44:424–435

    CAS  Google Scholar 

  22. Townsend TM, Larson A, Louis E, Macey JR (2004) Molecular phylogenetics of Squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree. Syst Biol 53:735–757

    PubMed  Article  Google Scholar 

  23. Uetz P (2013) The TIGR reptile database. The EMBL reptile database. Available from http://www.reptile-database.org/5/4/2013

  24. Uno Y, Nishida C, Tarui H 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

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  25. Vidal N, Hedges SB (2005) The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes. C R Soc Biol 328:1000–1008

    CAS  Article  Google Scholar 

  26. Wiens JJ, Hutter CR, Mulcahy DG et al (2012) Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biol Lett 8:1043–1046

    PubMed Central  PubMed  Article  Google Scholar 

  27. Young MJ, O’Meally D, Sarre SD, Georges A, Ezaz T (2013) Molecular cytogenetic map of the central bearded dragon, Pogona vitticeps (Squamata: Agamidae). Chromosome Res 21:361–374

    CAS  PubMed  Article  Google Scholar 

Download references

Acknowledgments

This work was financially supported by Grants-in-Aid for Scientific Research on Innovative Areas (no. 23113004) and Scientific Research (B) (no. 22370081) from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

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Correspondence to Kornsorn Srikulnath or Yoichi Matsuda.

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Responsible Editor: Fengtang Yang.

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Supplementary Table 1

Species and their accession numbers of the mitochondrial ND2 gene fragments used for molecular identification of V. exanthematicus(XLS 20 kb)

Supplementary Table 2

The cDNA fragments of L. reevesii rubritaeniata (LRE), G. hokouensis (GHO), L. agilis (LAG), and E. quadrivirgata (EQU) homologues of chicken genes, and nucleotide sequence identities between chicken and these squamate reptile cDNA fragments(XLS 39.5 kb)

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Srikulnath, K., Uno, Y., Nishida, C. et al. Karyotype evolution in monitor lizards: cross-species chromosome mapping of cDNA reveals highly conserved synteny and gene order in the Toxicofera clade. Chromosome Res 21, 805–819 (2013). https://doi.org/10.1007/s10577-013-9398-0

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Keywords

  • Monitor lizard
  • Toxicofera
  • Squamata
  • Synteny and gene order
  • Karyotype evolution
  • Cytogenetic map