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.