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.