Open Access Research article

Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC3 profiling in snake

Kazumi Matsubara17*, Shigehiro Kuraku23, Hiroshi Tarui38, Osamu Nishimura34, Chizuko Nishida5, Kiyokazu Agata4, Yoshinori Kumazawa1 and Yoichi Matsuda6

Author Affiliations

1 Department of Information and Biological Sciences, Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan

2 Department of Biology, University of Konstanz, Universitaetsstrasse 10, Konstanz, 78457, Germany

3 Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650–0047, Japan

4 Laboratory for Molecular Developmental Biology, Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Kyoto, 606-8502, Japan

5 Department of Natural History Sciences, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan

6 Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan

7 Present address: Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia

8 Present address: Omics Science Center, Yokohama Institute RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

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BMC Genomics 2012, 13:604  doi:10.1186/1471-2164-13-604

Published: 9 November 2012

Additional files

Additional file 1:

FISH mapping of cDNA clones in Elaphe quadrivirgata. FISH mapping of six cDNA clones in Elaphe quadrivirgata.

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Additional file 2:

IDs and GC3 of 184 orthologous gene sets. IDs and GC3 of 184 orthologous gene sets.

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Additional file 3:

IDs and GC-content of the python contigs that include the orthologs of the rat snake ESTs. IDs and GC-content of the python contigs that include the orthologs of the rat snake ESTs.

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Additional file 4:

GC3 distribution of the orthologs in other vertebrates. GC3 distribution of the orthologs in other vertebrates.

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Additional file 5:

R-banded karyotype of Elaphe quadrivirgata. R-banded karyotype of Elaphe quadrivirgata.

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Additional file 6:

Table S1. Functional categories over-represented in either gene group, chicken macrochromosomal genes or microchromosomal genes. Table S2. Chicken macrochromosomal and microchromosomal genes assoted into GO:0051234 and their chromosome locations and GC-contents. Table S3. Chicken macrochromosomal and microchromosomal genes assoted into GO:0006810 and their chromosome locations and GC-contents. Table S4. Chicken macrochromosomal and microchromosomal genes assoted into GO:0005215 and their chromosome locations and GC-contents. Table S5. Chicken macrochromosomal and microchromosomal genes assoted into GO:0003774 and their chromosome locations and GC-contents. Table S6. Chicken macrochromosomal and microchromosomal genes assoted into GO:0004871 and their chromosome locations and GC-contents. Table S7. Chicken macrochromosomal and microchromosomal genes assorted into GO:0015075 and their chromosome locations and GC-contents. Table S8. Chicken macrochromosomal and microchromosomal genes assorted into GO:0042611 and their chromosome locations and GC-contents. Table S9. Chicken macrochromosomal and microchromosomal genes assorted into GO:0044427 and their chromosome locations and GC-contents. Table S10. Chicken macrochromosomal and microchromosomal genes assorted into GO:0044430 and their chromosome locations and GC-contents. Table S11. Chicken macrochromosomal and microchromosomal genes assorted into GO:0000785 and their chromosome locations and GC-contents. Table S12. Chicken macrochromosomal and microchromosomal genes assorted into GO:0000786 and their chromosome locations and GC-contents. Table S13. Chicken macrochromosomal and microchromosomal genes assorted into IPR003461 and their chromosome locations and GC-contents. Table S14. Chicken macrochromosomal and microchromosomal genes assorted into IPR003597 and their chromosome locations and GC-contents. Table S15. Chicken macrochromosomal and microchromosomal genes assorted into IPR007110 and their chromosome locations and GC-contents. Table S16. The number of genes and mean of GC-content of macro- and microchromosomal genes assorted into each over-represented functional category. The detailed tables for statistically over-represented categories of Gene Ontology or InterPro between the chicken macrochromosomal and microchromosomal genes.

Format: XLSX Size: 164KB Download file

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