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.