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


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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Basic Local Alignment Search Tool


Complementary DNA


Elaphe quadrivirgata


Fluorescence in situ hybridization


Gallus gallus


Leiolepis reevesii rubritaeniata


Million years ago


Ribosomal RNA


Varanus salvator macromaculatus


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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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Corresponding authors

Correspondence to Kornsorn Srikulnath or Yoichi Matsuda.

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Responsible Editor: Fengtang Yang.

Electronic supplementary material

Below is the link to the electronic supplementary material.

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