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

• Main Authors: Recknagel, Hans, Jacobs, Arne, Herzyk, Pawel, Elmer, Kathryn R.
• Format: Dataset
• Language: English
• Published: Dryad 2015
• Subjects: Genomics/Proteomics; Natural Selection and Contemporary Evolution; Arctic; Arctic charr; Salvelinus alpinus
• Online Access: https://dx.doi.org/10.5061/dryad.7tb72; https://datadryad.org/stash/dataset/doi:10.5061/dryad.7tb72

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. ... : 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 ...