2.3 Library construction and sequencing
For Illumina sequencing, a short-insert paired-end DNA library with an
insert size of 350 bp was constructed using Illumina’s DNA library
preparation kits following standard protocols, and then sequenced on the
Illumina HiSeq X Ten platform (Illumina Inc., San Diego, CA, USA). Reads
containing more than 20% low-quality bases (Q-value ≤ 5), the reads
containing more than 10% ambiguous bases, as well as the reads with
adapter contamination, were all removed. For PacBio sequencing, the
high-quality gDNA was sheared into approximately 20 kb fragments using a
g-TURE device. Sheared DNA was purified and concentrated using AMPure XP
Beads, and then were used to construct the single-molecule real-time
(SMRT) bell libraries. Two 20 kb SMRT bell libraries were prepared and
sequenced on the PacBio RS II sequencing platform (Pacific Biosciences,
Menlo Park, CA, USA. Hi-C technology was further used to obtain the
chromosome-level genome assembly. A Hi-C library was constructed
according to the standard protocol described previously (Belton et al.,
2012) and sequenced on the Illumina Hiseq X Ten platform to generate
150-bp paired-end reads. For long-read RNA sequencing (Iso-Seq), RNA
samples from seven tissues were mixed at an equal molarity and sequenced
on the PacBio Sequel platform. For Illumina RNA sequencing, the
libraries for seven tissues were constructed using the NEBNext mRNA
Library Prep Master Mix Set following the manufacturer’s instructions
(NEB, Ipswich, MA, USA). All libraries were subjected to paired‑end 150
bp sequencing on the Illumina Hiseq X Ten.