Figure 3

Methylation and expression of BGIMBGA003527 as well as SNPs in its upstream 2 kb region. (A) Comparison of MethylC-Seq data of the BGIMBGA003527 DMC cluster with the 454 sequencing data of traditional bisulfite PCR (BS-PCR). Methylation level of the DMCs were examined by MethylC-seq in the three domesticated silkworms Dazao, Js, C108 (Dome_MethylC-Seq) and in the four wild silkworms Wsh, Wyn, CW, XW (Wild_MethylC-Seq) and validated in the same sample sets (Dome_BS and Wild_BS). Validation and test for fixation of methylation differences in more new domesticated (L10_BS, HY_BS, 872_BS, ZZ_BS) and wild silkworms (Wgs_BS, Wzj_BS, Wjs_BS) listed in Additional file 2: Table S1, were conducted using 454 sequencing of BS-PCR amplicons. For MethylC-Seq and validation data, methylation level was calculated by dividing the total reads from each sample set covering mCG by the total reads from that sample set covering that cytosine. For fixation test, methylation level was calculated similarly except that the reads are from each individual. (B) Location of DMCs in genic regions. The gene model is at the bottom, where red blocks indicate exons and the black lines between each two blocks indicate introns. The 4 CG sites in the black ellipse are those validated and tested for fixation. Dome, domesticated silkworms, Wild, wild silkworms. (C) BGIBMGA003527 expression level changes in silk glands of each domesticated individual against wild silkworms, estimated by quantitative real-time PCR. Relative expression ratios of each domesticated to wild silkworms are normalized by logarithmic transformation. Plots shows the average relative expression ratios and error bars shows the standard errors. (D) Nucleotide frequency of the SNPs upstream 2 kb of BGIMBGA003527 surveyed from the published data (http://silkworm.swu.edu.cn/silkdb/resequencing.html) and validated for domesticated and wild silkworms listed in Additional file 2: Table S1 by Sanger sequencing.