3.2 Chromosome-level genome assembly
We obtained 145.8 Gb raw reads, 124-fold coverage of the genome (Table S3) via Hi-C sequencing at the chromosomal level, which produced 497.8 million total clean read pairs with Q30 of 93.2%, and 380.2 million clean read pairs, accounting for 76.4% of the total clean read pairs, which uniquely mapped the polished C. undulatus genome. After exclusion of the clean read pairs that could not provide interaction information, we obtained 320.6 million clean read pairs (64.4%), which provided valid interaction information for chromosome assembly. With the valid interaction information, the contigs were clustered, ordered, and oriented into chromosomes. Finally, 308 contigs with an N50 length of 3.7 Mb were clustered into 24 scaffolds with an N50 length of 51.5 Mb (Table S3), reliably anchored on the 24 chromosomes, and a final genome size of 1173.2 Mb, representing a 99.98% draft genome. The size of the 24 chromosomes ranges from 27.2 Mb to 59.6 Mb (Fig. 2), providing the chromosomal genome assembly for the humphead wrasse.