Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms

Research in evolutionary biology involving nonmodel organisms is rapidly
shifting from using traditional molecular markers such as mtDNA and
microsatellites to higher throughput SNP genotyping methodologies to
address questions in population genetics, phylogenetics and genetic
mapping. Restriction site associated DNA sequencing (RAD sequencing or
RADseq) has become an established method for SNP genotyping on Illumina
sequencing platforms. Here, we developed a protocol and adapters for
double-digest RAD sequencing for Ion Torrent (Life Technologies; Ion
Proton, Ion PGM) semiconductor sequencing. We sequenced thirteen genomic
libraries of three different nonmodel vertebrate species on Ion Proton
with PI chips: Arctic charr Salvelinus alpinus, European whitefish
Coregonus lavaretus and common lizard Zootoca vivipara. This resulted in
~962 million single-end reads overall and a mean of ~74 million reads per
library. We filtered the genomic data using Stacks, a bioinformatic tool
to process RAD sequencing data. On average, we obtained ~11 000
polymorphic loci per library of 6–30 individuals. We validate our new
method by technical and biological replication, by reconstructing
phylogenetic relationships, and using a hybrid genetic cross to track
genomic variants. Finally, we discuss the differences between using the
different sequencing platforms in the context of RAD sequencing, assessing
possible advantages and disadvantages. We show that our protocol can be
used for Ion semiconductor sequencing platforms for the rapid and
cost-effective generation of variable and reproducible genetic markers.