design: Sus scrofa mtDNAs were PCR-amplified as four overlapping fragments and purified from gel excised band by using QIAquick Gel Extraction Kit. The purified mtDNA fragments were treated with CpG methyltransferase M.SssI then purified by using QIAquick PCR Purification Kit. BS-seq library was constructed from the methylated 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.