Size distribution of RESCAN is affected by library construction and genotype. The size of the restriction fragment sequenced in the RESCAN was calculated from the aligned reference genome. A, B, C. Effect of the method used for the construction of the library on the sampling of fragments. In the left graphs, the blue and red datapoints report respectively the number of total restriction fragment ends available in the genome for the indicated size (before fractionation) and the number sampled by one or more RESCAN reads. The blue points represent the same distribution in A, B and C, but zoomed on different Y-axis values. The right graphs report the distribution of number of RESCAN reads by size. All size fractionation in these preliminary experiments was done by gel electrophoresis and extraction of DNA from a selected section of the gel. D. Effect of a divergent genotype on the range of fragments sizes. The sequencing libraries for A. thaliana Col-0, the accession from which the reference genome is derived, and Ler, a divergent accession, were prepared according to protocol in C. The count of each RESCAN read is plotted versus the reference-deduced size of the restriction fragment to which it mapped. Many high coverage RESCAN reads from the Ler genome occur for fragments whose sizes (according to the Col-0 reference sequence) are not in the correct coverage size range. These cases are assumed to correspond to restriction size polymorphisms.
Monson-Miller et al. BMC Genomics 2012 13:72 doi:10.1186/1471-2164-13-72