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A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel
Authors:J. M. Pujolar  M. W. Jacobsen  J. Frydenberg  T. D. Als  P. F. Larsen  G. E. Maes  L. Zane  J. B. Jian  L. Cheng  M. M. Hansen
Affiliation:1. Department of Bioscience, Aarhus University, , DK‐8000 Aarhus C, Denmark;2. National Institute of Aquatic Resources, Technical University of Denmark, , DK‐8600 Silkeborg, Denmark;3. Kopenhagen 4. Fur, , DK‐2600 Glostrup, Denmark;5. Laboratory of Biodiversity and Evolutionary Genomics, Deberiotstraat 32, University of Leuven (KU Leuven), , B‐3000 Leuven, Belgium;6. Centre for Sustainable Tropical Fisheries and Aquaculture, School of Marine and Tropical Biology, James Cook University, , Qld 4811 Australia;7. Department of Biology, University of Padova, , I‐35131 Padova, Italy;8. BGI‐Shenzhen, Main Building, Beishan Industrial Zone, , 518083 Shenzhen, China;9. BGI‐Europe, Copenhagen Bio Science Park, , DK‐2200 Copenhagen, Denmark
Abstract:Reduced representation genome sequencing such as restriction‐site‐associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single‐nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the European eel using the RAD sequencing approach that was simultaneously identified and scored in a genome‐wide scan of 30 individuals. Whereas genomic resources are increasingly becoming available for this species, including the recent release of a draft genome, no genome‐wide set of SNP markers was available until now. The generated SNPs were widely distributed across the eel genome, aligning to 4779 different contigs and 19 703 different scaffolds. Significant variation was identified, with an average nucleotide diversity of 0.00529 across individuals. Results varied widely across the genome, ranging from 0.00048 to 0.00737 per locus. Based on the average nucleotide diversity across all loci, long‐term effective population size was estimated to range between 132 000 and 1 320 000, which is much higher than previous estimates based on microsatellite loci. The generated SNP resource consisting of 82 425 loci and 376 918 associated SNPs provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome.
Keywords:effective population size  population genomics  RAD sequencing  SNP discovery
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