Whole-genome sequencing of native Pekin and Cherry Valley Pekin ducks
Genomic DNA from nine BD and CD individuals was extracted from breast samples using a standard phenol/chloroform extraction procedure. Paired-end sequencing profiles, with an insert size of 380 bp, were constructed according to the manufacturer’s instructions for TureSeq on Illumina Hiseq 4000 platform. Sequencing and base calling were performed according to the standard Illumina protocols. Adapter and low quality reads were removed from the raw data using an in-house perl script. The genomic reads were aligned to the duck reference genome (Anas_platyrhynchos.BGI_duck_1.0) using Burrows-Wheeler algorithm. The alignment outputs (BAM files) were sorted and the PCR duplicates generated during library construction were removed using SAMtools. Genomic variants including SNPs and indels were called using genome analysis toolkit. The genomic variants were annotated, with as much detail as possible, using Python HTseq and an in-house Python script.