Data from: Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology

Massively parallel sequencing a small proportion of the whole genome at
high coverage enables answering a wide range of questions from molecular
evolution and evolutionary biology to animal and plant breeding and
forensics. In this study, we describe the development of restriction-site
associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our
protocol results in extreme genome complexity reduction using two
rare-cutting restriction enzymes and strict size selection of the library
allowing sequencing of a relatively small number of genomic fragments with
high sequencing depth. We applied this approach to a common freshwater
fish species, the Eurasian perch (Perca fluviatilis L.), and generated
over 2.2 MB of novel sequence data consisting of ~17 000 contigs,
identified 1259 single nucleotide polymorphisms (SNPs). We also estimated
genetic differentiation between the DNA pools from freshwater (Lake
Peipus) and brackish water (the Baltic Sea) populations and identified
SNPs with the strongest signal of differentiation that could be used for
robust individual assignment in the future. This work represents an
important step towards developing genomic resources and genetic tools for
the Eurasian perch. We expect that our ddRAD sequencing protocol for
semiconductor sequencing technology will be useful alternative for
currently available RAD protocols.