design: Sus scrofa mtDNAs were PCR-amplified as four overlapping fragments and purified from gel excised band by using QIAquick Gel Extraction Kit. No treatment by CpG methyltransferase M.SssI was carried out for this sample. BS-seq library was constructed from the unmethylated mtDNAs by Zymo Pico Methyl-Seq Library Prep Kit, according to the manufacturers instructions.  Each NGS library was sequenced by Illumina MiSeq instrument using 75 bp paired-end sequencing chemistry.