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

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Abstract

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.

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Author notes

  1. Kiyokazu Agata

    Present address: Laboratory for Molecular Developmental Biology, Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan

Authors and Affiliations

  1. Laboratory for Evolutionary Morphology, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan

    Shigehiro Kuraku & Shigeru Kuratani

  2. Laboratory of Animal Cytogenetics, Division of Genome Dynamics, Creative Research Initiative “Sousei”, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, 060-0810, Japan

    Junko Ishijima, Chizuko Nishida-Umehara & Yoichi Matsuda

  3. Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan

    Chizuko Nishida-Umehara & Yoichi Matsuda

  4. Laboratory for Evolutionary Regeneration Biology, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan

    Kiyokazu Agata

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  1. Shigehiro Kuraku
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  2. Junko Ishijima
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Correspondence to Shigehiro Kuraku.

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Kuraku, S., Ishijima, J., Nishida-Umehara, C. et al. 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 (2006). https://doi.org/10.1007/s10577-006-1035-8

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  • DOI: https://doi.org/10.1007/s10577-006-1035-8

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