Library preparation and genome sequencing
For WGS, PacBio Sequel System (Pacific Bioscience, California, USA) and
Illumina HiSeq (Illumina, California, USA) were employed. For PacBio, a
20-kb library was prepared and four SMRT cells were used for sequencing;
3,267,255 subreads were finally obtained. Illumina paired-end and
mate-pair libraries were prepared using Illumina PCR-Free library prep
kit, Nextera Mate Pair library prep kit, and Kapa Hyper prep kit.
Paired-end libraries were constructed from DNA fragmented with Covaris
S2 and separated with an agarose gel at 200–250-bp (male ZZ) and with
Sage-ELF at 310-530 bp (female ZO). Mate-pair libraries were separated
with CHEF-electrophoresis after tagmentation and DNA recovered from gel
slices 3-kbp to approximately 40-kbp were used for the subsequent
process. All the libraries had different index and mixed to be sequenced
in the same lane. In total, 511,569,649 reads were obtained by Illumina
v4 sequencing of 2 lanes. Table S1 and Table S2 summarize information on
the results of WGS, e.g. read length, read count and total bases.