Data from: Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double-digest RADSeq approach (3RAD). We generated libraries using genomic DNA serially extracted from the muscle tissue of 8 individual lake whitefish (Coregonus clupeaformis) following 0-, 12-, 48- and 96-h incubation at room temperature posteuthanasia. This treatment of the tissue resulted in input DNA that ranged in quality from nearly intact to highly sheared. All samples were sequenced as a multiplexed pool on an Illumina MiSeq. Libraries created from low to moderately degraded DNA (12–48 h) performed well. In contrast, the number of RADtags per individual, number of variable sites, and percentage of identical RADtags retained were all dramatically reduced when libraries were made using highly degraded DNA (96-h group). This reduction in performance was largely due to a significant and unexpected loss of raw reads as a result of poor quality scores. Our findings remained consistent after changes in restriction enzymes, modified fold coverage values (2- to 16-fold), and additional read-length trimming. We conclude that starting DNA quality is an important consideration for RADSeq; however, the approach remains robust until genomic DNA is extensively degraded.RadtagCounterPerl script that counts the number of RADtags in each*.matches file within a directorySNPCounterCounts the number of potential variable sites in a .vcf file generated by populations in the stacks programgenotypecounter.plperl script to determine how many genotype calls within the same individual are the same as the 0 hour muscle callcompressposition.plperl script to remove multiple entries for a variable site position and determine the total coverage of each positioncoveragecounter.plperl script to determine if a call in the 12, 48 or 96 file is present in the 0 file and if it is it determines the coverage at that position. The output is the average coverage per snp positionAdapterInfoThis file contains the internal and external adapters for each sample as well as the reverse compliment for the i7 tags.D1FastqFilesFastq files for the first restriction enzyme pair, EcoRI-NheID2FastqFilesFastq files for the second restriction enzyme pair, EcoRI-ClaISamplingInfoFile containing the treatment time, tissue type and restriction enzyme pair of each sampl