A new resource of single nucleotide polymorphisms in the Japanese eel Anguilla japonica derived from restriction site-associated DNA
2016
Sekino, M. (National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa (Japan). Research Center for Bioinformatics and Biosciences) | Nakamichi, R. | Iwasaki, Y. | Tanabe, A.S. | Fujiwara, A. | Yasuike, M. | Shiraishi, M. | Saitoh, K.
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 (Fsub(ST) = 0.0015, P = 0.073), although a small portion of loci (0.8 %) exhibited an elevated level of genetic differentiation (Fsub(ST) >= 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.
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