RRBS data of different fragment sizes in pigs

Reduced representation bisulfite sequencing (RRBS) has been used to profile the genome-scale DNA methylation and thereby contribute to understanding the association between cell-specific epigenetic modifications and gene expression in mammalian genomes. For each species, it is important to select the suitable DNA segment sizes for the RRBS. Here, we implemented RRBS on the MspI-digested fragment sizes of 40-110 bp, 110-220 bp and 40-220 bp to evaluate RRBS capacity to characterize the porcine genome. The number and the distribution of CpG sites covered by these three fragment sizes were predicted in silico by bioinformatics and libraries of these three fragment sizes were built and sequenced to assess the real RRBS efficiency. We found that the repetitive sequences appeared to reduce the unique mapping alignment. Under 50 million reads, the number of detected CpG sites with = 10 covered reads in the fragment size of 110-220 bp was similar to the number in the fragment size of 40-220 bp, but sequencing depth was higher than for this fragment size. Our results help to select the optimal fragment size for use of RRBS to investigate the genome-wide DNA methylation in tissue from pigs.