Sequencing of the medaka genome was started at the Academia Sequencing Center of the National Institute of Genetics (NIG) in mid 2002. The project was supported by group grant Genome Science (Grant-in-Aid for Scientific Research on Priority Areas supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan).
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The sequencing was conducted by the whole-genome shotgun strategy using southern inbred strain, Hd-rR. The genome was assembled from 13.8 million reads, obtained from the whole genome shotgun plasmid, fosmid, and bacterial artificial chromosome (BAC) libraries. The total size of the assembled contigs was 700.4 megabases (Mb). 50% of nucleotides are covered in scaffolds (or contigs) of length 1.41Mb (9.8 kilobases) that are called N50 values. This contiguity is sufficient to characterize the genomic structures of genes.
Four versions of the medaka genome sequence data named 200406, 200506, version 0.9, and version 1.0 have been released to the public to provide users with timely information. The former two versions had shorter scaffolds that were not anchored on the medaka chromosomes because they were built in 2004 and 2005, before genetics markers were available. Versions 0.9 and 1.0 created in 2006, when comprehensive genetic markers were available, so that about 90% of their scaffolds and ultracontigs were located on the twenty-four medaka chromosomes. Versions 0.9 and 1.0 were built from the identical contigs and scaffolds, but the assembly of version 1.0 is longer than that of version 0.9 because more genetic markers could be used to generate version 1.0. Version 0.9 is left open to the public because most of the data analysis in the medaka genome paper published in Nature (2007) was based on version 0.9.
