title: 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.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.forename: Wataru
authors.initials: W
authors.lastname: Kai
authors.forename: Kazuharu
authors.initials: K
authors.lastname: Nomura
authors.affiliation: National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama-shi, Kanagawa 236-8648, Japan. jiwara@affrc.go.jp.
authors.forename: Atushi
authors.initials: A
authors.lastname: Fujiwara
authors.forename: Yoji
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Motoshige
authors.initials: M
authors.lastname: Yasuike
authors.forename: Nobuhiko
authors.initials: N
authors.lastname: Ojima
authors.forename: Tetsuji
authors.initials: T
authors.lastname: Masaoka
authors.forename: Akiyuki
authors.initials: A
authors.lastname: Ozaki
authors.forename: Yukinori
authors.initials: Y
authors.lastname: Kazeto
authors.forename: Koichiro
authors.initials: K
authors.lastname: Gen
authors.forename: Jiro
authors.initials: J
authors.lastname: Nagao
authors.forename: Hideki
authors.initials: H
authors.lastname: Tanaka
authors.forename: Takanori
authors.initials: T
authors.lastname: Kobayashi
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Ototake
mesh_terms: D000811:Anguilla / Q000235:genetics*; D000818:Animals; D005075:Biological Evolution; D002874:Chromosome Mapping; D005260:Female; D020440:Gene Duplication; D015723:Gene Library; D008040:Genetic Linkage; D016678:Genome; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D007564:Japan; D008297:Male; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA