Genomic DNA was sheared using a DNA shearing system (Covaris, Cat. #S220) prior to library preparation. Genomic DNA (200 ng) from six Japanese Black cattle (one wild/wild homozygote and five CNVR_221/CNVR_221 homozygotes) was used to generate sequence libraries, which were prepared using TruSeq Nano DNA library prep kit (Illumina, Cat. #20015964) and IDT for Illumina TruSeq DNA UD Indexes (Illumina, Cat. # 20020590) according to the manufacturer’s instructions. The sequence data were generated as 2 × 101 bp reads using the NovaSeq 6000 SP Reagent Kit (Illumina, Cat. # 20027465) and Novaseq6000, and processing and base calling were performed using Illumina Real-Time Analysis 3.
The sequence reads (fastq file) for each animal were aligned to ARS-UCD1.2 genome assembly [42 ] using bwa-0.7.17 [45 (link)]. The bam files were created using Samtools [46 (link), 47 (link)], and duplicate reads were removed using Picard [48 ]. The realignment around indels and recalibration were performed using GATK-4.0.12.0 [49 ]. SNPs and indels were called using Haplotype caller by GATK. The data from the WGS were deposited in the Wagyu genome database (WGDB) of the Japan Livestock Technology Association (Yushima, Bunyouku, Tokyo 113–0034, Japan) and were managed by the WGDB consortium.
The sequence reads (fastq file) for each animal were aligned to ARS-UCD1.2 genome assembly [42 ] using bwa-0.7.17 [45 (link)]. The bam files were created using Samtools [46 (link), 47 (link)], and duplicate reads were removed using Picard [48 ]. The realignment around indels and recalibration were performed using GATK-4.0.12.0 [49 ]. SNPs and indels were called using Haplotype caller by GATK. The data from the WGS were deposited in the Wagyu genome database (WGDB) of the Japan Livestock Technology Association (Yushima, Bunyouku, Tokyo 113–0034, Japan) and were managed by the WGDB consortium.