3.1 Library construction and sequencing
The genome of an adult male shrimp was sequenced using the Illumina and PacBio Sequel platforms. PacBio sequencing generated 244 Gb of data and Illumina sequencing generated 130 Gb data (Table 1). We estimated the genome size 1.39 Gb based on the Illumina sequenced short reads k-mer distribution. The genome sequencing depths were 175.54× (PacBio) and 92.78× (Illumina). The final assembly of the M. japonicus genome comprised 1.53 Gb, for which the contig N50 length was 229.974 kb( Table 2).
The Hi-C method successfully clustered the sequences into 42 groups (Figure 2). Finally, a chromosome-level assembly of 1.54 Gb, with a scaffold N50 length of 38.27 Mb, was obtained (Table 2).