Chromosome Research

, Volume 14, Issue 2, pp 187–202 | Cite as

cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids

  • Shigehiro Kuraku
  • Junko Ishijima
  • Chizuko Nishida-Umehara
  • Kiyokazu Agata
  • Shigeru Kuratani
  • Yoichi Matsuda


Mammalian and avian genomes comprise several classes of chromosomal segments that vary dramatically in GC-content. Especially in chicken, microchromosomes exhibit a higher GC-content and a higher gene density than macrochromosomes. To understand the evolutionary history of the intra-genome GC heterogeneity in amniotes, it is necessary to examine the equivalence of this GC heterogeneity at the nucleotide level between these animals including reptiles, from which birds diverged. We isolated cDNAs for 39 protein-coding genes from the Chinese soft-shelled turtle, Pelodiscus sinensis, and performed chromosome mapping of 31 genes. The GC-content of exonic third positions (GC3) of P. sinensis genes showed a heterogeneous distribution, and exhibited a significant positive correlation with that of chicken and human orthologs, indicating that the last common ancestor of extant amniotes had already established a GC-compartmentalized genomic structure. Furthermore, chromosome mapping in P. sinensis revealed that microchromosomes tend to contain more GC-rich genes than GC-poor genes, as in chicken. These results illustrate two modes of genome evolution in amniotes: mammals elaborated the genomic configuration in which GC-rich and GC-poor regions coexist in individual chromosomes, whereas sauropsids (reptiles and birds) refined the chromosomal size-dependent GC compartmentalization in which GC-rich genomic fractions tend to be confined to microchromosomes.

Key words

GC-content microchromosome sauropsida turtle 


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Copyright information

© Springer 2006

Authors and Affiliations

  • Shigehiro Kuraku
    • 1
  • Junko Ishijima
    • 2
  • Chizuko Nishida-Umehara
    • 2
    • 3
  • Kiyokazu Agata
    • 4
    • 5
  • Shigeru Kuratani
    • 1
  • Yoichi Matsuda
    • 2
    • 3
  1. 1.Laboratory for Evolutionary MorphologyRIKEN Center for Developmental BiologyChuo-kuJapan
  2. 2.Laboratory of Animal Cytogenetics, Division of Genome Dynamics, Creative Research Initiative “Sousei”Hokkaido UniversityKita-kuJapan
  3. 3.Division of Biological Sciences, Graduate School of ScienceHokkaido UniversitySapporoJapan
  4. 4.Laboratory for Evolutionary Regeneration BiologyRIKEN Center for Developmental BiologyChuo-kuJapan
  5. 5.Laboratory for Molecular Developmental Biology, Department of Biophysics, Graduate School of ScienceKyoto UniversityKyotoJapan

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