Abstract
BackgroundRecent 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.ResultsWe 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.ConclusionsThe 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.
Highlights
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
DdRAD-seq produces more effective single nucleotide polymorphism (SNP) genotyping compared with restriction-site associated DNA sequencing (RAD-seq), even using a relatively small number of reads generated by a small nextgeneration benchtop sequencer, such as an Ion Torrent Personal Genome Machine (Life Technologies Corporation, Carlsbad, CA, USA), which was launched in early 2011 [9]
These tags from the parents were clustered into 9,634 RAD loci, of which the centroid sequences were used as reference sequences for SNP discovery
Summary
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. DdRAD-seq produces more effective SNP genotyping compared with RAD-seq, even using a relatively small number of reads generated by a small nextgeneration benchtop sequencer, such as an Ion Torrent Personal Genome Machine (Life Technologies Corporation, Carlsbad, CA, USA), which was launched in early 2011 [9]. This platform performs semiconductor sequencing that relies on the detection of pH changes induced by the release of a proton upon the incorporation of a nucleotide during strand synthesis [10] and generates over 500 million reads per run at 4.5 hours. As the sequencing cost (price per base) continues to drop, the platform will soon be applicable for small and medium-size laboratories [11]
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