A new resource of single nucleotide polymorphisms in the Japanese eel Anguilla japonica derived from restriction site-associated DNA

Masashi Sekino, Reiichiro Nakamichi, Yuki Iwasaki, Akifumi S. Tanabe, Atushi Fujiwara, Motoshige Yasuike, Manabu Shiraishi, Kenji Saitoh

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

We present a new resource of single nucleotide polymorphisms (SNPs) in the Japanese eel Anguilla japonica, a catadromous eel species distributed along the west Pacific margin. We used the restriction site-associated DNA (RAD) sequencing for the detection of SNPs. On the basis of glass eel samples collected from two Japanese coastal areas, 33,976 SNP sites that occurred among 18,353 RAD loci were identified. Using the RAD loci, we preliminarily tested genetic differentiation between the two geographical samples. No evidence of genetic population heterogeneity was obtained (FST = 0.0015, P = 0.073), although a small portion of loci (0.8 %) exhibited an elevated level of genetic differentiation (FST ≥ 0.100). A catalogue of SNPs constructed in the present study, in which we provide the positions of SNP sites within RAD loci and the scaffolds in the reference genome, and, if available, the position of RAD loci on genetic linkage groups, will be of great use for advancing ecological and breeding studies in A. japonica.

Original languageEnglish
Pages (from-to)496-504
Number of pages9
JournalIchthyological Research
Volume63
Issue number4
DOIs
Publication statusPublished - 2016 Nov 1
Externally publishedYes

Keywords

  • Genome-wide scan
  • Genotyping by sequencing
  • Natural selection
  • Next-generation sequencing

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics

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