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A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication

Wataru Kai1, Kazuharu Nomura2, Atushi Fujiwara1*, Yoji Nakamura1, Motoshige Yasuike1, Nobuhiko Ojima1, Tetsuji Masaoka2, Akiyuki Ozaki2, Yukinori Kazeto2, Koichiro Gen24, Jiro Nagao2, Hideki Tanaka2, Takanori Kobayashi3 and Mitsuru Ototake1

Author Affiliations

1 National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama-shi, Kanagawa 236-8648, Japan

2 National Research Institute of Aquaculture, Fisheries Research Agency, Minami-ise-cho, Mie 516-0193, Japan

3 Fisheries Research Agency, Yokohama-shi, Kanagawa 220-6115, Japan

4 Present address: Seikai National Fisheries Research Institute, Fisheries Research Agency, Nagasaki-shi, Nagasaki 851-2213, Japan

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BMC Genomics 2014, 15:233  doi:10.1186/1471-2164-15-233

Published: 26 March 2014



Recent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication.


We generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication.


The ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel.

Japanese eel; Genetic map; ddRAD-seq; Ion PGM; Synteny; Teleost-specific whole genome duplication