Genome annotation
From the assembled genome, the repeat sequences were identified in the genome of B. l. tsinlingensis . Repeat sequences accounted for 64.48% of the genome, and the DNA transposons (20.78%) were the most abundant repeat type (Table S12-S13 ). For genome annotation, a total of 55,706 genes were predicted using different annotation methods, and the gene structure was similar to other published genomes of related species (Figure S10 ). The functional annotation results revealed that among these 55,706 protein-coding genes, homologous genes could be found in public databases for 90.14% (50,214) of the genes, which indicated that the gene structure annotation was robust (Table S14 ). The gene density, all types of repeat sequences, and GC density of the assembly are shown in Figure 1B . Owing to the Ss4R event, codon usage in salmonids was uniform (Figure 1C ). In addition, the third position of the synonymous codon of salmonids was more likely to be G or C, which differs from other fishes (Figure 1D ).