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Fig. S1 Effect of the proportion of draft genome sequence subsampling (from 1% to full genome analysis) on the precision and accuracy of the number of loci predicted for a ddRAD protocol using PstI and MspI and 210–260 bp fragment size selection on Anguilla anguilla.

Fig. S2 Alternative ddRAD protocol parameterizations to target 50 000 loci at the A. anguilla genome scale using PstI and MspI enzyme combination with a narrow size selection range (A, 50 pb) and a wide size selection range (B, 70 pb), typically setup using a Pippin Prep system. Light grey histogram represents the fragment size distribution following double digestion and adapter-based fragment selection; the red portion illustrates the size selected fragments. Each subfigure illustrates the graphical output of SimRAD function size.select.

Fig. S3 GBS fragment size distribution obtained by in silico digestion of Bos taurus whole reference genome using different restriction enzymes (ApeKI, PstI or EcoT22I) or combination (EcoT22I & PstI) illustrating digestion in repetitive genomic regions for ApeKI and the double digestion EcoT22I and PstI, as already obtained from real digestion experiment followed by Agilent BioAnalyzer 2100 analysis (see Supplemental Figure S1 in De Donato et al. 2013).

men12273-sup-0002-SupplementaryFile.Rtext/r34KFile S1 R script used to reproduce all results presented in this manuscript.

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