Comparative genomics of chromosome rearrangement in vertebrates based on medaka genome information

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Evolution of the genome size in vertebrates is often affected by changes in the noncoding sequences, for which insertions and deletions (indels) of small nucleotide sequences and amplification of repetitive elements are considered responsible. In this project, we especially compared the genomic DNA sequences of two kinds of fish, medaka (Oryzias latipes) and fugu (Takifugu rubripes), which show two-fold difference in the genome size (800 Mb vs. 400 Mb). We determined a contiguous DNA sequence of 790 kb from the medaka chromosome LG22 (linkage group 22). The sequence was aligned common between two fishes, and were found abundant in various repetitive elements including many types of unclassified low copy repeats, all of which accounted for more than a half (54%) of the genome size difference. These results strongly indicated that amplification of repetitive elements and compilation of indels are major driving forces to facilitate changes in the genome size.