WGS of Humulus lupulus
DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Valencia, CA) following the manufacturers instructions, and stored at 80 for further analysis. The quantity and quality of extracted DNA were determined using a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientic, Waltham, MA, USA) and agarose gel electrophoresis, respectively. A total amount of 0.5 g DNA was used for the DNA sequencing library preparation with TruSeq Nano DNA HT Sample Prep Kit (Illumina, CA, USA) following manufacturers protocol. Briefly, genomic DNA sample was fragmented by sonication to a size of 350 bp. Then, DNA fragments were endpolished, A-tailed, and ligated with the full-length adapter for Illumina sequencing, followed by further PCR amplification. After that, the library was analyzed for size distribution with Agilent 2100 Bioanalyzer (Agilent Technologiesis, CA, USA) and quantified by real-time PCR. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using HiSeq X PE Cluster Kit V2.5 (Illumina, CA, USA) according to the manufacturers instructions. After cluster generation, amplicons were pooled in equal amounts, and paired-end 2-150 bp sequencing was performed using the Illlumina HiSeq X Ten platform at Xuan Chen Biological Technology Co., Ltd. (Shaanxi, China).