Skip to main content

Molecular structures of centromeric heterochromatin and karyotypic evolution in the Siamese crocodile (Crocodylus siamensis) (Crocodylidae, Crocodylia)


Crocodilians have several unique karyotypic features, such as small diploid chromosome numbers (30–42) and the absence of dot-shaped microchromosomes. Of the extant crocodilian species, the Siamese crocodile (Crocodylus siamensis) has no more than 2n = 30, comprising mostly bi-armed chromosomes with large centromeric heterochromatin blocks. To investigate the molecular structures of C-heterochromatin and genomic compartmentalization in the karyotype, characterized by the disappearance of tiny microchromosomes and reduced chromosome number, we performed molecular cloning of centromeric repetitive sequences and chromosome mapping of the 18S-28S rDNA and telomeric (TTAGGG) n sequences. The centromeric heterochromatin was composed mainly of two repetitive sequence families whose characteristics were quite different. Two types of GC-rich CSI-HindIII family sequences, the 305 bp CSI-HindIII-S (G+C content, 61.3%) and 424 bp CSI-HindIII-M (63.1%), were localized to the intensely PI-stained centric regions of all chromosomes, except for chromosome 2 with PI-negative heterochromatin. The 94 bp CSI-DraI (G+C content, 48.9%) was tandem-arrayed satellite DNA and localized to chromosome 2 and four pairs of small-sized chromosomes. The chromosomal size-dependent genomic compartmentalization that is supposedly unique to the Archosauromorpha was probably lost in the crocodilian lineage with the disappearance of microchromosomes followed by the homogenization of centromeric repetitive sequences between chromosomes, except for chromosome 2.

This is a preview of subscription content, access via your institution.

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9



Alligator mississippiesis


Alligator sinensis


Boa constrictor




barium hydroxide/saline/Giemsa


charge-coupled device


Caiman crocodilus


Caiman latirostris


Crocodylus niloticus


Crocodylus siamensis


orange-fluorescing cyanine


DNA Data Bank of Japan




Elaphe quadrivirgata


fluorescence in-situ hybridization


fluorescein isothiocyanate


Gavialis gangeticus


Gekko hokouensis


million years ago


fundamental number


polymerase chain reaction


propidium iodide


Protobothrops flavoviridis


Python molurus bivittatus


Pelodiscus sinensis


ribosomal DNA (RNA)


sodium dodecyl sulfate


saline sodium citrate


Tomistoma schlegelii




  • Andreozzi L, Federico C, Motta S et al. (2001) Compositional mapping of chicken chromosomes and identification of the gene-richest regions. Chromosome Res 9: 521–532.

    PubMed  Article  CAS  Google Scholar 

  • Baldini A, Miller DA, Miller OJ, Ryder OA, Mitchell AR (1991) A chimpanzee-derived chromosome-specific alpha satellite DNA sequence conserved between chimpanzee and human. Chromosoma 100: 156–161.

    PubMed  Article  CAS  Google Scholar 

  • Belle EMS, Smith N, Eyre-Walker A (2002) Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis. J Mol Evol 55: 356–363.

    PubMed  Article  CAS  Google Scholar 

  • Belterman RHR, de Boer LEM (1984) A karyological study of 55 species of birds, including karyotypes of 39 species new to cytology. Genetica 65: 39–82.

    Article  Google Scholar 

  • Burt DW (2002) Origin and evolution of avian microchromosomes. Cytogenet Genome Res 96: 97–112.

    PubMed  Article  CAS  Google Scholar 

  • Chavananikul V, Suwattana D, Wattanodorn S, Koykul W (1998) Karyotypes and NORs banding patterns in Crocodylus siamensis and Crocodylus porosus. Proc 6th World Congress on Genetics Applied to Livestock Production 25: 319–322.

    Google Scholar 

  • Cohen MM, Gans C (1970) The chromosomes of the order Crocodilia. Cytogenetics 9: 81–105.

    PubMed  Article  CAS  Google Scholar 

  • Cracraft J (2001) Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event. Proc R Soc Lond B 268: 459–469.

    Article  CAS  Google Scholar 

  • Ferguson MWJ, Joanen T (1982) Temperature of egg incubation determines sex in Alligator mississippiensis. Nature 296: 850–853.

    PubMed  Article  CAS  Google Scholar 

  • Gatesy J, Amato G, Norell M, DeSalle R, Hayashi C (2003) Combined support for wholesale taxic atavism in gavialine crocodylians. Syst Biol 52: 403–422.

    PubMed  Article  Google Scholar 

  • Hamada K, Horiike T, Kanaya S et al. (2002) Changes in body temperature pattern in vertebrates do not influence the codon usages of α-globin genes. Genes Genet Syst 77: 197–207.

    PubMed  Article  CAS  Google Scholar 

  • Hamada K, Horiike T, Ota H, Mizuno K, Shinozawa T (2003) Presence of isochore structures in reptile genomes suggested by the relationship between GC contents of intron regions and those of coding regions. Genes Genet Syst 78: 195–198.

    PubMed  Article  CAS  Google Scholar 

  • Harshman J, Huddleston CJ, Bollback JP, Parsons TJ, Braun MJ (2003) True and false gharials: a nuclear gene phylogeny of Crocodylia. Syst Biol 52: 386–402.

    PubMed  Article  Google Scholar 

  • Head G, May RM, Pendleton L (1987) Environmental determination of sex in the reptiles. Nature 329: 198–199.

    Article  Google Scholar 

  • Hilton-Taylor C (2000) 2000 IUCN Red List of Threatened Species. Gland and Cambridge: IUCN.

    Google Scholar 

  • Hughes S, Zelus D, Mouchiroud D (1999) Warm-blooded isochore structure in Nile crocodile and turtle. Mol Biol Evol 16: 1521–1527.

    PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Iwabe N, Hara Y, Kumazawa Y et al. (2005) Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins. Mol Biol Evol 22: 810–813.

    PubMed  Article  CAS  Google Scholar 

  • Janke A, Arnason U (1997) The complete mitochondrial genome of Alligator mississippiensis and the separation between recent Archosauria (birds and crocodiles). Mol Biol Evol 14: 1266–1272.

    PubMed  CAS  Google Scholar 

  • Janke A, Erpenbeck D, Nilsson M, Arnason U (2001) The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus) implications for amniote phylogeny. Proc R Soc Lond B 268: 623–631.

    Article  CAS  Google Scholar 

  • King M (1983) The Gehyra australis species complex (Sauria: Gekkonidae). Amphibia-Reptilia 4: 147–169.

    Article  Google Scholar 

  • Kumar S, Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392: 917–920.

    PubMed  Article  CAS  Google Scholar 

  • Kumazawa Y (2007) Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations. Gene 388: 19–26.

    PubMed  Article  CAS  Google Scholar 

  • Kumazawa Y, Nishida M (1999) Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: statistical evidence for Archosaurian affinity of turtles. Mol Biol Evol 16: 784–792.

    PubMed  CAS  Google Scholar 

  • Kuraku S, Ishijima J, Nishida-Umehara C, Agata K, Kuratani S, Matsuda Y (2006) cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids. Chromosome Res 14: 187–202.

    PubMed  Article  CAS  Google Scholar 

  • Lang JW, Andrews HV (1994) Temperature-dependent sex determination in crocodilians. J Exp Zool 270: 28–44.

    Article  Google Scholar 

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

    PubMed  Article  CAS  Google Scholar 

  • 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.

    PubMed  Article  CAS  Google Scholar 

  • Matzke MA, Varga F, Berger H et al. (1990) A 41–42 bp tandemly repeated sequence isolated from nuclear envelopes of chicken erythrocytes is located predominantly on microchromosomes. Chromosoma 99: 131–137.

    PubMed  Article  CAS  Google Scholar 

  • Matzke AJM, Varga F, Gruendler P et al. (1992) Characterization of a new repetitive sequence that is enriched on microchromosomes of turkey. Chromosoma 102: 9–14.

    PubMed  Article  CAS  Google Scholar 

  • McQueen HA, Fantes J, Cross SH, Clark VH, Archibald AL, Bird AP (1996) CpG islands of chicken are concentrated on microchromosomes. Nature Genet 12: 321–324.

    PubMed  Article  CAS  Google Scholar 

  • McQueen HA, Siriaco G, Bird AP (1998) Chicken microchromosomes are hyperacetylated, early replicating, and gene rich. Genome Res 8: 621–630.

    PubMed  CAS  Google Scholar 

  • Nishida-Umehara C, Tsuda Y, Ishijima J et al. (2007) The molecular basis of chromosome orthologies and sex chromosomal differentiation in palaeognathous birds. Chromosome Res 15: 721–734.

    PubMed  Article  CAS  Google Scholar 

  • Olmo E, Signorino G (2005) Chromorep: a reptile chromosomes database. Internet references. Retrieved from:

  • Ota H, Chen SL, Shang G (1998) Japalura luei, a new agamid lizard from Taiwan. Copeia 1998: 649–656.

    Article  Google Scholar 

  • Primmer CR, Raudsepp T, Chowdhary BP, Møller AP, Ellegren H (1997) Low frequency of microsatellites in the avian genome. Genome Res 7: 471–482.

    PubMed  CAS  Google Scholar 

  • Polet G, Murphy DJ, Phan Viet Lam, Tran Van Mui (2002) Crocodile conservation at work in Vietnam, re-establishing Crocodylus siamensis in Cat Tien National Park. In Crocodiles: Proceedings of the 16th Working Meeting of the Crocodile Specialist Group of the Species Survival Commission of IUCN-The World Conservation Union. Gland and Cambridge: IUCN, pp. 86–95.

    Google Scholar 

  • Rest JS, Ast JC, Austin CC et al. (2003) Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Mol Phylogent Evol 29: 289–297.

    Article  CAS  Google Scholar 

  • Ross CA, Magnusson WE (1989) Living crocodilians. In Ross CA, ed. Crocodiles and Alligators. New York: Facts On File, pp. 58–73.

    Google Scholar 

  • Shibusawa M, Nishibori M, Nishida-Umehara C et al. (2004) Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny. Cytogenet Genome Res 106: 111–119.

    PubMed  Article  CAS  Google Scholar 

  • Sibley CG, Ahlquist JE (1990) Phylogeny and Classification of Birds: A Study in Molecular Evolution. New Haven: Yale University Press.

    Google Scholar 

  • Smith J, Burt DW (1998) Parameters of the chicken genome (Gallus gallus). Anim Genet 29: 290–294.

    PubMed  Article  CAS  Google Scholar 

  • Smith J, Bruley CK, Paton IR et al. (2000) Differences in gene density on chicken macrochromosomes and microchromosomes. Anim Genet 31: 96–103.

    PubMed  Article  CAS  Google Scholar 

  • Sumner AT (1972) A simple technique for demonstrating centromeric heterochromatin. Exp Cell Res 75: 304–306.

    PubMed  Article  CAS  Google Scholar 

  • Suzuki T, Kurosaki, T, Agata K et al. (1999) Cytogenetic assignment of 29 functional genes to chicken microchromosomes by FISH. Cytogenet Cell Genet 87: 233–237.

    PubMed  Article  CAS  Google Scholar 

  • Takagi N, Sasaki M (1974) A phylogenetic study of bird karyotypes. Chromosoma 46: 91–120.

    PubMed  Article  CAS  Google Scholar 

  • Tanaka K, Suzuki T, Nojiri T, Yamagata T, Namikawa T, Matsuda Y (2000) Characterization and chromosomal distribution of a novel satellite DNA sequence of Japanese quail (Coturnix coturnix japonica). J Hered 91: 412–415.

    PubMed  Article  CAS  Google Scholar 

  • Tsuda Y, Nishida-Umehara C, Ishijima J, Yamada Y, Matsuda Y (2007) Comparison of the Z and W sex chromosomal architectures in elegant crested tinamou (Eudromia elegans) and ostrich (Struthio camelus) and the process of sex chromosome differentiation in palaeognathous birds. Chromosoma 116: 159–173.

    PubMed  Article  Google Scholar 

  • Valenzuela N, Lance V, eds. (2004) Temperature-Dependent Sex Determination in Vertebrates. Smithonian Books, Washington.

    Google Scholar 

  • van Tuinen M, Hedges SB (2001) Calibration of avian molecular clocks. Mol Biol Evol 18: 206–213.

    PubMed  Google Scholar 

  • Waye JS, Willard HF (1989) Concerted evolution of alpha satellite DNA: Evidence for species specificity and a general lack of sequence conservation among alphoid sequences of higher primates. Chromosoma 98: 273–279.

    PubMed  Article  CAS  Google Scholar 

  • Yamada K, Nishida-Umehara C, Matsuda Y (2002a) Characterization and chromosomal distribution of novel satellite DNA sequences of the lesser rhea (Pterocnemia pennata) and the greater rhea (Rhea americana). Chromosome Res 10: 513–523.

    PubMed  Article  CAS  Google Scholar 

  • Yamada K, Shibusawa M, Tsudzuki M, Matsuda Y (2002b) Molecular cloning and characterization of novel centromeric repetitive DNA sequences in the blue-breasted quail (Coturnix chinensis, Galliformes). Cytogenet Genome Res 98: 255–261.

    PubMed  Article  CAS  Google Scholar 

  • Yamada K, Nishida-Umehara C, Matsuda Y (2005) Molecular and cytogenetic characterization of site-specific repetitive DNA sequences in the Chinese soft-shelled turtle (Pelodiscus sinensis, Trionychidae). Chromosome Res 13: 33–46.

    PubMed  Article  CAS  Google Scholar 

Download references


This work was supported by Grants-in-Aid for Scientific Research (nos. 15370001 and 16086201) from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Yoichi Matsuda.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kawagoshi, T., Nishida, C., Ota, H. et al. Molecular structures of centromeric heterochromatin and karyotypic evolution in the Siamese crocodile (Crocodylus siamensis) (Crocodylidae, Crocodylia). Chromosome Res 16, 1119–1132 (2008).

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Key words

  • Archosauromorpha
  • crocodilian
  • genomic compartmentalization
  • heterochromatin
  • karyotype evolution
  • microchromosome
  • repetitive sequence