DOI: 10.5061/dryad.7tb72
title: Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms

description: 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.
description: Table_1Table_1 contains the locus sequences and coded genotypes of each individual used to recreate genomic composition of the Alpine x Baltic cross and their offspring. SNPs that were fixed between parents (following standard genetic mapping procedure) were used in the Structure analysis. Each individual contains two columns per locus with their genotype. Numbers refer to the four different DNA bases: A = 1, C = 2, G = 3, T = 4. 0 = missing data.Table_2Table_2 contains all the locus sequences (sheet 1: ‘Locus sequences’) and SNP information (sheet 2: ‘Genotypes’) that were used for the inference of phylogenetic relationships of Arctic charr and European whitefish.Library1_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library2_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library3_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library4_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library5_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library6_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library7_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library8_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library9_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library10_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library11_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library12_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').Library13_SNPsSequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').RAxML_treefileThe tree file contains three Arctic charr and three European whitefish individuals from different localities in EuropeReplicate_1_genotypes_8xInput file for estimation of the SNP error rate. The R script to analyse this file is provided by Mastretta-Yanes et al. (2014).Replicate_1_genotypes_16xInput file for estimation of the SNP error rate. The R script to analyse this file is provided by Mastretta-Yanes et al. (2014).Replicate_2_genotypes_8xInput file for estimation of the SNP error rate. The R script to analyse this file is provided by Mastretta-Yanes et al. (2014).Replicate_2_genotypes_16xInput file for estimation of the SNP error rate. The R script to analyse this file is provided by Mastretta-Yanes et al. (2014).