Next-generation sequencing platforms permit for the cost-effective sequencing of whole or partial genomes in a relatively short time, which is greatly accelerating genomic research in non-model organisms. In particular, single nucleotide polymorphism (SNP) genotyping by restriction-site associated DNA sequencing (RAD-seq) is a powerful approach for developing a large number of genetic markers, for constructing a high-density genetic map and for studying the genetic architecture of complex traits
[1–6]. This approach sequences short targets that immediately flank sites for a particular restriction enzyme throughout a genome; this produces a reduced representation of the genome, allowing oversequencing of the nucleotides next to the restriction sites and detection of SNPs. This approach can rapidly and cost-effectively discover SNPs compared with whole-genome sequencing (reviewed in
); nevertheless, a massive amount of sequence data is required to increase the read depth for more accurate SNP calling. Therefore, in previous studies, RAD-seq has generally been performed using Illumina sequencing platforms, such as the Genome Analyzer IIx (GAIIx) and HiSeq series
[1–6]. Recently, double-digest RAD-seq (ddRAD-seq) has been developed as a simple and robust method
. Unlike the RAD-seq, this approach uses two restriction enzyme comprising a rare-cutting one and frequently-cutting one and avoids random shearing of the DNA. Such precise and repeatable size selection allows stable shared region recovery across samples (or individuals). Thus, ddRAD-seq produces more effective SNP genotyping compared with RAD-seq, even using a relatively small number of reads generated by a small next-generation benchtop sequencer, such as an Ion Torrent Personal Genome Machine (Life Technologies Corporation, Carlsbad, CA, USA), which was launched in early 2011
. This platform performs semiconductor sequencing that relies on the detection of pH changes induced by the release of a proton upon the incorporation of a nucleotide during strand synthesis
 and generates over 500 million reads per run at 4.5 hours. The Ion PGM is a relatively new technology; therefore, its output, including quality and downstream application, has not yet fully matured
. However, as the sequencing cost (price per base) continues to drop, the platform will soon be applicable for small and medium-size laboratories
The Japanese eel (Anguilla japonica) is one of the most widely cultivated fish species in East Asian countries; however, the farming of this species has been completely dependent on seeds from nature, and broodstock domestication on a commercial scale has yet to be fully developed. Aiming for stable production of this species, the first techniques for artificial breeding were established in 1970s
[12, 13]. Thereafter, research has improved these techniques
, and recently we succeeded in obtaining an F2 generation of this species (unpublished results). Although further improvements are required for large-scale commercial production, the broodstock domestication and selective breeding, including a DNA marker-assisted selection based on quantitative trait loci (QTLs), is now within reach. A key step in such a genetic improvement scheme is an accumulation of genomic resources such as a draft genome sequence, transcriptome sequences and a genetic map. Recently, the draft genome of the Japanese eel was sequenced using Illumina platforms, yielding an assembly comprising 323,776 scaffolds and covering 1.15 Gb of the genome; gene prediction and annotation for this assembly are ongoing
. In addition, we constructed the first genetic linkage map of this species
. Integration of a genetic map and assembled sequences enable us to identify a chromosomal order of scaffolds in a draft assembly and provides a valuable resource for fine mapping and positional cloning of QTLs associated with economically important traits
[17, 18]. However, in the Japanese eel, because of the low resolution of the genetic map, the chromosomal order of scaffolds in the current assembly is unknown, which has limited the use of the genomic sequences.
In addition to assisting in genetic studies, a genome map integrating a genetic map and assembled sequences is also a powerful tool for investigating comparative genomics
[19, 20]. Eel species are one of the most distantly related groups to other teleost species and has diverged from the other teleosts in the basal lineage of the teleosts
[21, 22]. Therefore, comparing the genome of the Japanese eel with those of other fishes would provide an opportunity to understand the genomic architecture of ancestral teleosts and chromosomal rearrangement events that occurred during teleost genome evolution. Teleost genomes have experienced a teleost-specific whole genome duplication event (TGD)
[23, 24], which is thought to have triggered an acceleration of chromosomal rearrangements
[4, 25, 26]. Indeed, Kasahara et al.
 inferred that eight major chromosomal rearrangements occurred in the ancestral lineage of zebrafish (Danio rerio) and medaka (Oryzias latipes) after the TGD. In addition, the genome of the spotted gar (Lepisosteus oculatus), whose lineage diverged from the teleost lineage before the TGD, showed that the extent of conserved synteny between the gar and human (Homo sapiens) was higher than that between the gar and zebrafish, and the gar and the stickleback (Gasterosteus aculeatus), suggesting that the TGD accelerated the loss of ancestral syntenies
. Given the phylogenic position among these fishes, the TGD and subsequent chromosomal rearrangements are presumed to have occurred over a relatively short period
. The eel lineage diverged from other teleost lineage within this period
[21, 22]. Therefore, comparative genomics between the Japanese eel and model fishes provides new insights into the genome evolution soon after the TGD.
Here, we generated a ddRAD-based genetic map of the Japanese eel using an Ion PGM sequencer. The map comprised 19 linkage groups with a total of 2,672 SNP markers and 115 Simple Sequence Repeat (SSR) markers and was integrated with the current genome assembly to identify the chromosomal order of the scaffolds. In the current assembly, 151 Mb of the scaffolds has been anchored on the 19 linkage groups, and 70 Mb of them have been ordered on the linkage groups. Comparisons of the genomes between the Japanese eel and model fishes showed a highly conserved synteny among teleosts and revealed the history of genome evolution in the basal lineage of the teleosts.