2.2 Library construction and sequencing
Three libraries, including Illumina library, SMRTbell library, and Hi-C
library, were combined to construct the high-quality C. japonicagenome information. A high-quality short-insert (300–350 bp) paired-end
(PE) Illumina library was constructed in accordance with the Illumina
standard protocol (Illumina, USA), and the Illumina library was then
sequenced on the Illumina
NovaSeq-6000
platform. A high-quality SMRTbell library with a fragment size of 20 Kb
was prepared using the SMRTBell Template Preparation Kit 1.0 (PacBio,
USA) according to the manufacturer’s protocol to obtain long genomics
reads for promoting genome assembly. The constructed SMRTBell library
was added to one SMRT cell and then transferred to the PacBio Sequel II
sequencing platform for long-read genomic sequencing. A high-quality
Hi-C library was constructed to obtain a chromosome-scale genome
assembly, and the Hi-C library was sequenced using the Illumina
NovaSeq-6000 platform. Additionally, a high-quality 150 bp PE
RNA-sequencing (RNA-seq) library was constructed according to the
Illumina standard protocol (Illumina, USA) and then sequenced on an
Illumina NovaSeq-6000 platform.
Twenty C. japonica individuals (11 females and 9 males) were used
for whole-genome resequencing. High-quality short-insert (300–350 bp)
PE Illumina libraries were constructed in accordance with the Illumina
standard protocol (Illumina, USA) and then sequenced on the Illumina
NovaSeq-6000 platform.